NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|56181887|gb|AAV83924|]
View 

RAR-like GTPase variant [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
9-262 4.95e-114

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd04121:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 189  Bit Score: 325.35  E-value: 4.95e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   9 KSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQ 88
Cdd:cd04121   1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEIDE-------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04121  81 GIILVYDITNRWSFDGIDRWIKEIDEhapgvpkilvgnrlhlafkRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFT 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887 150 ELSRIVLMRHGmekiwrpnrvfslqdlccraivsctpvhlidklplpvtikshlksfsmangmnavmmhgrsyslasgag 229
Cdd:cd04121 161 ELARIVLMRHG--------------------------------------------------------------------- 171
                       250       260       270
                ....*....|....*....|....*....|...
gi 56181887 230 gggskgnslkrsksiRPPQSPPQNCSRSNCKIS 262
Cdd:cd04121 172 ---------------RPPQSPPQNCSRNSCKIS 189
SOCS_Rab40 cd03742
SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab ...
168-210 6.66e-24

SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


:

Pssm-ID: 239711  Cd Length: 43  Bit Score: 90.70  E-value: 6.66e-24
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 56181887 168 NRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMAN 210
Cdd:cd03742   1 NKVLSLQDLCCRAIVSCTPVYLIDKLPLPVSIKSHLKSFAMAN 43
 
Name Accession Description Interval E-value
Rab40 cd04121
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ...
9-262 4.95e-114

Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133321 [Multi-domain]  Cd Length: 189  Bit Score: 325.35  E-value: 4.95e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   9 KSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQ 88
Cdd:cd04121   1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEIDE-------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04121  81 GIILVYDITNRWSFDGIDRWIKEIDEhapgvpkilvgnrlhlafkRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFT 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887 150 ELSRIVLMRHGmekiwrpnrvfslqdlccraivsctpvhlidklplpvtikshlksfsmangmnavmmhgrsyslasgag 229
Cdd:cd04121 161 ELARIVLMRHG--------------------------------------------------------------------- 171
                       250       260       270
                ....*....|....*....|....*....|...
gi 56181887 230 gggskgnslkrsksiRPPQSPPQNCSRSNCKIS 262
Cdd:cd04121 172 ---------------RPPQSPPQNCSRNSCKIS 189
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
15-158 1.67e-67

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 206.20  E-value: 1.67e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     95 DITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRI 154
Cdd:smart00175  81 DITNRESFENLENWLKELREyaspnvvimlvgnksdleeqRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELARE 160

                   ....
gi 56181887    155 VLMR 158
Cdd:smart00175 161 ILKR 164
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
16-156 7.14e-45

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 148.43  E-value: 7.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGADGFLLVYD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    96 ITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRIV 155
Cdd:pfam00071  81 ITSRDSFENVKKWVEEIlrhadenvpivlvgnkcdleDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREI 160

                  .
gi 56181887   156 L 156
Cdd:pfam00071 161 L 161
PLN03118 PLN03118
Rab family protein; Provisional
1-152 1.04e-34

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 124.01  E-value: 1.04e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    1 MGSQGSPVKSYDYLLKFLLVGDSDVGKGEILESLQDGAAESpYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIF 80
Cdd:PLN03118   1 MGSSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSSVED-LAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTLT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   81 RSYSRGAQGILLVYDITNRWSFDGI-DRWIKEID---------------------ERQVPTEQARAYAEKNCMTFFEVSP 138
Cdd:PLN03118  80 SSYYRNAQGIILVYDVTRRETFTNLsDVWGKEVElystnqdcvkmlvgnkvdresERDVSREEGMALAKEHGCLFLECSA 159
                        170
                 ....*....|....
gi 56181887  139 LCNFNVIESFTELS 152
Cdd:PLN03118 160 KTRENVEQCFEELA 173
SOCS_Rab40 cd03742
SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab ...
168-210 6.66e-24

SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239711  Cd Length: 43  Bit Score: 90.70  E-value: 6.66e-24
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 56181887 168 NRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMAN 210
Cdd:cd03742   1 NKVLSLQDLCCRAIVSCTPVYLIDKLPLPVSIKSHLKSFAMAN 43
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
13-154 8.92e-14

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 67.70  E-value: 8.92e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  13 YLLKFLLVGDSDVGKGEILESLQDGA-AESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSR---GAQ 88
Cdd:COG1100   2 GEKKIVVVGTGGVGKTSLVNRLVGDIfSLEKYLSTNGVTIDKKELKLDGLDVDLVIWDTPGQDEFRETRQFYARqltGAS 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIES 147
Cdd:COG1100  82 LYLFVVDGTREETLQSLYELLESLrrlgkkspiilvlnkidlydeEEIEDEERLKEALSEDNIVEVVATSAKTGEGVEEL 161

                ....*..
gi 56181887 148 FTELSRI 154
Cdd:COG1100 162 FAALAEI 168
SOCS smart00253
suppressors of cytokine signalling; suppressors of cytokine signalling
165-206 5.30e-13

suppressors of cytokine signalling; suppressors of cytokine signalling


Pssm-ID: 128549  Cd Length: 43  Bit Score: 61.93  E-value: 5.30e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 56181887    165 WRPNRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSF 206
Cdd:smart00253   2 PRPSNVPSLQHLCRFTIRRCTRTDQIKTLPLPPKLKDYLSYY 43
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
16-120 2.04e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 60.85  E-value: 2.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    16 KFLLVGDSDVGKGEILESL-QDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:TIGR00231   3 KIVIVGHPNVGKSTLLNSLlGNKGSITEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVF 82
                          90       100
                  ....*....|....*....|....*...
gi 56181887    95 DITNRW-SF-DGIDRWIKEIdERQVPTE 120
Cdd:TIGR00231  83 DIVILVlDVeEILEKQTKEI-IHHADSG 109
SOCS_box pfam07525
SOCS box; The SOCS box acts as a bridge between specific substrate- binding domains and more ...
170-204 7.81e-06

SOCS box; The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.


Pssm-ID: 462192  Cd Length: 39  Bit Score: 41.77  E-value: 7.81e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 56181887   170 VFSLQDLCCRAIVSCT---PVHLIDKLPLPVTIKSHLK 204
Cdd:pfam07525   2 PRSLQHLCRLAIRRALgkrRLGAIDKLPLPPLLKDYLL 39
 
Name Accession Description Interval E-value
Rab40 cd04121
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ...
9-262 4.95e-114

Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133321 [Multi-domain]  Cd Length: 189  Bit Score: 325.35  E-value: 4.95e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   9 KSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQ 88
Cdd:cd04121   1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEIDE-------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04121  81 GIILVYDITNRWSFDGIDRWIKEIDEhapgvpkilvgnrlhlafkRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFT 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887 150 ELSRIVLMRHGmekiwrpnrvfslqdlccraivsctpvhlidklplpvtikshlksfsmangmnavmmhgrsyslasgag 229
Cdd:cd04121 161 ELARIVLMRHG--------------------------------------------------------------------- 171
                       250       260       270
                ....*....|....*....|....*....|...
gi 56181887 230 gggskgnslkrsksiRPPQSPPQNCSRSNCKIS 262
Cdd:cd04121 172 ---------------RPPQSPPQNCSRNSCKIS 189
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
15-158 1.67e-67

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 206.20  E-value: 1.67e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     95 DITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRI 154
Cdd:smart00175  81 DITNRESFENLENWLKELREyaspnvvimlvgnksdleeqRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELARE 160

                   ....
gi 56181887    155 VLMR 158
Cdd:smart00175 161 ILKR 164
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
15-153 2.14e-54

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 172.64  E-value: 2.14e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd00154   1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVY 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56181887  95 DITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd00154  81 DVTNRESFENLDKWLNELkeyappnipiilvgnksdleDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
12-158 5.34e-49

Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 159.36  E-value: 5.34e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  12 DYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGIL 91
Cdd:cd01867   1 DYLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTITTSYYRGAMGII 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  92 LVYDITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTEL 151
Cdd:cd01867  81 LVYDITDEKSFENIKNWMRNIDEhasedvermlvgnkcdmeekRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTL 160

                ....*..
gi 56181887 152 SRIVLMR 158
Cdd:cd01867 161 AKDILKK 167
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
15-153 6.88e-45

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 148.61  E-value: 6.88e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd01863   1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVY 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56181887  95 DITNRWSFDGIDRWIKEID--------------------ERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd01863  81 DVTRRDTFDNLDTWLNELDtystnpdavkmlvgnkidkeNREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVE 159
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
16-156 7.14e-45

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 148.43  E-value: 7.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGADGFLLVYD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    96 ITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRIV 155
Cdd:pfam00071  81 ITSRDSFENVKKWVEEIlrhadenvpivlvgnkcdleDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREI 160

                  .
gi 56181887   156 L 156
Cdd:pfam00071 161 L 161
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
13-153 3.61e-42

Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 141.70  E-value: 3.61e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  13 YLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd01869   1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQERFRTITSSYYRGAHGIII 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  93 VYDITNRWSFDGIDRWIKEID--------------------ERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:cd01869  81 VYDVTDQESFNNVKQWLQEIDryasenvnkllvgnkcdltdKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMA 160

                .
gi 56181887 153 R 153
Cdd:cd01869 161 R 161
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
9-159 2.53e-40

Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 138.06  E-value: 2.53e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   9 KSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQ 88
Cdd:cd04110   1 RDYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTITSTYYRGTH 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEI-------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04110  81 GVIVVYDVTNGESFVNVKRWLQEIeqncddvckvlvgnknddpERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFN 160
                       170
                ....*....|
gi 56181887 150 ELSRIVLMRH 159
Cdd:cd04110 161 CITELVLRAK 170
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
12-151 5.45e-40

Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206660 [Multi-domain]  Cd Length: 165  Bit Score: 136.15  E-value: 5.45e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  12 DYLLKFLLVGDSDVGKGEIL------ESLQDGAAespyaySNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSR 85
Cdd:cd01868   1 DYLFKIVLIGDSGVGKSNLLsrftrnEFNLDSKS------TIGVEFATRTIQIDGKTIKAQIWDTAGQERYRAITSAYYR 74
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  86 GAQGILLVYDITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVI 145
Cdd:cd01868  75 GAVGALLVYDITKKSTFENVERWLKELRDhadsnivimlvgnksdlrhlRAVPTEEAKAFAEKNGLSFIETSALDGTNVE 154

                ....*.
gi 56181887 146 ESFTEL 151
Cdd:cd01868 155 EAFKQL 160
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
15-157 2.47e-37

Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206698 [Multi-domain]  Cd Length: 164  Bit Score: 129.33  E-value: 2.47e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04117   1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERYQTITKQYYRRAQGIFLVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRI 154
Cdd:cd04117  81 DISSERSYQHIMKWVSDVDEyapegvqkilignkadeeqkRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTEL 160

                ...
gi 56181887 155 VLM 157
Cdd:cd04117 161 VLQ 163
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
12-155 3.14e-35

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 123.70  E-value: 3.14e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  12 DYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGIL 91
Cdd:cd01864   1 DFLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQERFRTITQSYYRSANGAI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  92 LVYDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTF-FEVSPLCNFNVIESFTE 150
Cdd:cd01864  81 IAYDITRRSSFESVPHWIEEVekygasnvvlllignkcdleEQREVLFEEACTLAEHYGILAvLETSAKESSNVEEAFLL 160

                ....*
gi 56181887 151 LSRIV 155
Cdd:cd01864 161 MATEL 165
PLN03118 PLN03118
Rab family protein; Provisional
1-152 1.04e-34

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 124.01  E-value: 1.04e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    1 MGSQGSPVKSYDYLLKFLLVGDSDVGKGEILESLQDGAAESpYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIF 80
Cdd:PLN03118   1 MGSSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSSVED-LAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTLT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   81 RSYSRGAQGILLVYDITNRWSFDGI-DRWIKEID---------------------ERQVPTEQARAYAEKNCMTFFEVSP 138
Cdd:PLN03118  80 SSYYRNAQGIILVYDVTRRETFTNLsDVWGKEVElystnqdcvkmlvgnkvdresERDVSREEGMALAKEHGCLFLECSA 159
                        170
                 ....*....|....
gi 56181887  139 LCNFNVIESFTELS 152
Cdd:PLN03118 160 KTRENVEQCFEELA 173
PLN03110 PLN03110
Rab GTPase; Provisional
11-154 5.73e-34

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 122.34  E-value: 5.73e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   11 YDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGI 90
Cdd:PLN03110   9 YDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGA 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   91 LLVYDITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESF-T 149
Cdd:PLN03110  89 LLVYDITKRQTFDNVQRWLRELRDhadsnivimmagnksdlnhlRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFqT 168

                 ....*
gi 56181887  150 ELSRI 154
Cdd:PLN03110 169 ILLEI 173
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
16-152 4.03e-32

Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 115.80  E-value: 4.03e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:cd01861   2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYD 81
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56181887  96 ITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:cd01861  82 ITNRQSFDNTDKWIDDVrdergndviivlvgnktdlsDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIA 158
Rab4 cd04113
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ...
15-155 8.18e-32

Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206696 [Multi-domain]  Cd Length: 161  Bit Score: 114.84  E-value: 8.18e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04113   1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSVTRSYYRGAAGALLVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRI 154
Cdd:cd04113  81 DITSRESFNALTNWLTDArtlaspdiviilvgnkkdleDDREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARS 160

                .
gi 56181887 155 V 155
Cdd:cd04113 161 I 161
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
11-156 1.09e-31

Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206658 [Multi-domain]  Cd Length: 168  Bit Score: 114.83  E-value: 1.09e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  11 YDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGI 90
Cdd:cd01866   1 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  91 LLVYDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTE 150
Cdd:cd01866  81 LLVYDITRRETFNHLTSWLEDArqhsnsnmtimlignkcdleSRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFIN 160

                ....*.
gi 56181887 151 LSRIVL 156
Cdd:cd01866 161 TAKEIY 166
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
14-155 1.85e-31

Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 114.24  E-value: 1.85e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  14 LLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd01865   1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILM 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  94 YDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd01865  81 YDITNEESFNAVQDWSTQIktyswdnaqvilvgnkcdmeDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVD 160

                ..
gi 56181887 154 IV 155
Cdd:cd01865 161 II 162
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
13-153 3.69e-31

Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 114.86  E-value: 3.69e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  13 YLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTI-LLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGIL 91
Cdd:cd04111   1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIeIEPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  92 LVYDITNRWSFDGIDRWIKE---------------------IDERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTE 150
Cdd:cd04111  81 LVFDITNRESFEHVHDWLEEarshiqphrpvfilvghkcdlESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFEL 160

                ...
gi 56181887 151 LSR 153
Cdd:cd04111 161 LTQ 163
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
16-156 1.01e-30

Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206653 [Multi-domain]  Cd Length: 163  Bit Score: 111.87  E-value: 1.01e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGK---------GEILESLQD--GAAespyaysngidYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYS 84
Cdd:cd01860   3 KLVLLGDSSVGKssivlrfvkNEFSENQEStiGAA-----------FLTQTVNLDDTTVKFEIWDTAGQERYRSLAPMYY 71
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  85 RGAQGILLVYDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNV 144
Cdd:cd01860  72 RGAAAAIVVYDITSEESFEKAKSWVKELqehgppnivialagnkadleSKRQVSTEEAQEYADENGLLFMETSAKTGENV 151
                       170
                ....*....|..
gi 56181887 145 IESFTELSRIVL 156
Cdd:cd01860 152 NELFTEIARKLP 163
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
13-155 6.78e-30

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 109.93  E-value: 6.78e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  13 YLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd04122   1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYYRGAAGALM 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  93 VYDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:cd04122  81 VYDITRRSTYNHLSSWLTDArnltnpntviflignkadleAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETA 160

                ...
gi 56181887 153 RIV 155
Cdd:cd04122 161 KKI 163
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
8-152 2.56e-29

Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133314 [Multi-domain]  Cd Length: 169  Bit Score: 108.83  E-value: 2.56e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   8 VKSYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGA 87
Cdd:cd04114   1 MEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERFRSITQSYYRSA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  88 QGILLVYDITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIES 147
Cdd:cd04114  81 NALILTYDITCEESFRCLPEWLREIeqyannkvitilvgnkidlaERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKL 160

                ....*
gi 56181887 148 FTELS 152
Cdd:cd04114 161 FLDLA 165
PLN03108 PLN03108
Rab family protein; Provisional
10-150 3.56e-29

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 109.65  E-value: 3.56e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   10 SYDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQG 89
Cdd:PLN03108   2 SYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSITRSYYRGAAG 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   90 ILLVYDITNRWSFDGIDRWIKEIDE--------------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:PLN03108  82 ALLVYDITRRETFNHLASWLEDARQhananmtimlignkcdlahrRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFI 161

                 .
gi 56181887  150 E 150
Cdd:PLN03108 162 K 162
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
15-174 4.86e-29

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 108.95  E-value: 4.86e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04120   1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSITSAYYRSAKGIILVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEID--------------------ERQVPTEQARAYAEK-NCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd04120  81 DITKKETFDDLPKWMKMIDkyasedaelllvgnkldcetDREITRQQGEKFAQQiTGMRFCEASAKDNFNVDEIFLKLVD 160
                       170       180
                ....*....|....*....|...
gi 56181887 154 IVLMRHGMEKIWR--PNRVFSLQ 174
Cdd:cd04120 161 DILKKMPLDILRNelSNSILSLQ 183
Rab7 cd01862
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ...
15-159 1.03e-27

Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206655 [Multi-domain]  Cd Length: 172  Bit Score: 104.67  E-value: 1.03e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd01862   1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSLGVAFYRGADCCVLVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKE---------------------ID---ERQVPTEQARAYAE-KNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd01862  81 DVTNPKSFESLDSWRDEfliqasprdpenfpfvvlgnkIDleeKRQVSTKKAQQWCKsKGNIPYFETSAKEAINVDQAFE 160
                       170
                ....*....|
gi 56181887 150 ELSRIVLMRH 159
Cdd:cd01862 161 TIARLALEQE 170
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
11-158 2.32e-26

Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206700 [Multi-domain]  Cd Length: 180  Bit Score: 101.42  E-value: 2.32e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  11 YDYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLD----------GRRVKLELWDTSGQGRFCTIF 80
Cdd:cd04127   1 YDYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNsqgpdgtsgkAFRVHLQLWDTAGQERFRSLT 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  81 RSYSRGAQGILLVYDITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPL 139
Cdd:cd04127  81 TAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLqahaycenpdivlignkadlpDQREVSERQARELADKYGIPYFETSAA 160
                       170
                ....*....|....*....
gi 56181887 140 CNFNVIESFTELSRIVLMR 158
Cdd:cd04127 161 TGQNVEKAVETLLDLIMKR 179
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
16-153 1.14e-25

Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206695 [Multi-domain]  Cd Length: 191  Bit Score: 99.94  E-value: 1.14e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGA-AESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04112   2 KVMLVGDSGVGKTCLLVRFKDGAfLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLY 81
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56181887  95 DITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd04112  82 DVTNKSSFDNIRAWLTEIleyaqsdvvimllgnkadmsGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAK 160
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
54-153 1.77e-24

Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206642 [Multi-domain]  Cd Length: 160  Bit Score: 95.67  E-value: 1.77e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  54 TTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEI--------------------- 112
Cdd:cd00876  38 KQIVVDGETYTLDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQIlrvkdkedvpivlvgnkcdle 117
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 56181887 113 DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd00876 118 NERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVR 158
SOCS_Rab40 cd03742
SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab ...
168-210 6.66e-24

SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239711  Cd Length: 43  Bit Score: 90.70  E-value: 6.66e-24
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 56181887 168 NRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSFSMAN 210
Cdd:cd03742   1 NKVLSLQDLCCRAIVSCTPVYLIDKLPLPVSIKSHLKSFAMAN 43
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
16-115 3.32e-22

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 88.33  E-value: 3.32e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILL---DGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTFDPKYKSTIGVDFKTKTVLEnddNGKKIKLNIWDTAGQERFRSLHPFYYRGAAAALL 80
                          90       100
                  ....*....|....*....|...
gi 56181887    93 VYDITnrwSFDGIDRWIKEIDER 115
Cdd:pfam08477  81 VYDSR---TFSNLKYWLRELKKY 100
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
16-137 3.22e-21

Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133315 [Multi-domain]  Cd Length: 170  Bit Score: 87.49  E-value: 3.22e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRF-CTIFRSYSRGAQGILLVY 94
Cdd:cd04115   4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFrKSMVQHYYRNVHAVVFVY 83
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56181887  95 DITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVS 137
Cdd:cd04115  84 DVTNMASFHSLPSWIEECeqhslpnevprilvgnkcdlrEQIQVPTDLAQRFADAHSMPLFETS 147
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
16-156 1.21e-20

Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133323 [Multi-domain]  Cd Length: 162  Bit Score: 85.74  E-value: 1.21e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:cd04123   2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYYRDADGAILVYD 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  96 ITNRWSFDGIDRWIKEI--------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSRIV 155
Cdd:cd04123  82 ITDADSFQKVKKWIKELkqmrgnnislvivgnkidleRQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161

                .
gi 56181887 156 L 156
Cdd:cd04123 162 I 162
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
15-156 2.79e-20

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 84.71  E-value: 2.79e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04119   1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKE----------------------IDE---RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04119  81 DVTDRQSFEALDSWLKEmkqeggphgnmenivvvvcankIDLtkhRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQ 160

                ....*..
gi 56181887 150 ELSRIVL 156
Cdd:cd04119 161 TLFSSIV 167
Rab9 cd04116
Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate ...
14-155 4.77e-20

Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206697 [Multi-domain]  Cd Length: 170  Bit Score: 84.15  E-value: 4.77e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  14 LLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04116   5 LLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQERFRSLRTPFYRGSDCCLLT 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  94 YDITNRWSFDGIDRWIKE-----------------------IDERQVPTEQARAYAEKN-CMTFFEVSPLCNFNVIESFT 149
Cdd:cd04116  85 FSVDDSQSFQNLSNWKKEfiyyadvkepesfpfvilgnkidIPERQVSTEEAQAWCRDNgDYPYFETSAKDATNVAAAFE 164

                ....*.
gi 56181887 150 ELSRIV 155
Cdd:cd04116 165 EAVRRV 170
RAS smart00173
Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. ...
16-155 9.70e-18

Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades


Pssm-ID: 214541 [Multi-domain]  Cd Length: 164  Bit Score: 77.98  E-value: 9.70e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     16 KFLLVGDSDVGKGEIleSLQDGAAESPYAYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:smart00173   2 KLVVLGSGGVGKSAL--TIQFIQGHFVDDYDPTIeDSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVY 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     95 DITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:smart00173  80 SITDRQSFEEIKKFREQIlrvkdrddvpivlvgnkcdleSERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVR 159

                   ..
gi 56181887    154 IV 155
Cdd:smart00173 160 EI 161
RabL2 cd04124
Rab GTPase-like family 2 (Rab-like2); RabL2 (Rab-like2) subfamily. RabL2s are novel Rab ...
15-150 2.24e-17

Rab GTPase-like family 2 (Rab-like2); RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share > 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133324 [Multi-domain]  Cd Length: 161  Bit Score: 76.82  E-value: 2.24e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILES-LQDGAAE---SPYAYSNgidYKTTTILlDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGI 90
Cdd:cd04124   1 VKIILLGDSAVGKSKLVERfLMDGYEPqqlSTYALTL---YKHNAKF-EGKTILVDFWDTAGQERFQTMHASYYHKAHAC 76
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56181887  91 LLVYDITNRWSFDGIDRWIKEIDE--RQVP--------------TEQARAYAEKNCMTFFEVSPLCNFNVIESFTE 150
Cdd:cd04124  77 ILVFDVTRKITYKNLSKWYEELREyrPEIPcivvankidldpsvTQKKFNFAEKHNLPLYYVSAADGTNVVKLFQD 152
Rab23_like cd04106
Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family ...
15-152 2.80e-17

Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133306 [Multi-domain]  Cd Length: 162  Bit Score: 76.71  E-value: 2.80e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRR--VKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd04106   1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDedVRLMLWDTAGQEEFDAITKAYYRGAQACIL 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56181887  93 VYDITNRWSFDGIDRW-------------------IKEIDERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:cd04106  81 VFSTTDRESFEAIESWkekveaecgdipmvlvqtkIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLA 159
small_GTPase smart00010
Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small ...
50-155 2.82e-17

Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily.


Pssm-ID: 197466 [Multi-domain]  Cd Length: 166  Bit Score: 76.83  E-value: 2.82e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     50 DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEI----------------- 112
Cdd:smart00010  37 DSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQIlrvkdrddvpivlvgnk 116
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 56181887    113 ----DERQVPTEQARAYAEK-NCMtFFEVSPLCNFNVIESFTELSRIV 155
Cdd:smart00010 117 cdleNERVVSTEEGKELARQwGCP-FLETSAKERINVDEAFYDLVREI 163
M_R_Ras_like cd04145
R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, ...
15-155 9.50e-17

R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133345 [Multi-domain]  Cd Length: 164  Bit Score: 75.14  E-value: 9.50e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEI-LESLQ-------DGAAESPYAysngidyKTTTIllDGRRVKLELWDTSGQGRFCTIFRSYSRG 86
Cdd:cd04145   3 YKLVVVGGGGVGKSALtIQFIQsyfvtdyDPTIEDSYT-------KQCEI--DGQWARLDILDTAGQEEFSAMREQYMRT 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  87 AQGILLVYDITNRWSFDGIDRW------IKEIDE---------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVI 145
Cdd:cd04145  74 GEGFLLVFSVTDRGSFEEVDKFhtqilrVKDRDEfpmilvgnkadlehqRQVSREEGQELARQLKIPYIETSAKDRVNVD 153
                       170
                ....*....|
gi 56181887 146 ESFTELSRIV 155
Cdd:cd04145 154 KAFHDLVRVI 163
PTZ00099 PTZ00099
rab6; Provisional
40-152 3.01e-16

rab6; Provisional


Pssm-ID: 185444 [Multi-domain]  Cd Length: 176  Bit Score: 74.40  E-value: 3.01e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   40 ESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEI------- 112
Cdd:PTZ00099   6 DNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDIlnergkd 85
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 56181887  113 -------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:PTZ00099  86 viialvgnktdlgDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKIA 138
Rab32_Rab38 cd04107
Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are ...
15-156 1.01e-15

Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206692 [Multi-domain]  Cd Length: 201  Bit Score: 73.50  E-value: 1.01e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLD-GRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04107   1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDpNTVVRLQLWDIAGQERFGGMTRVYYKGAVGAIIV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  94 YDITNRWSFDGIDRWIKEIDER-------------------------QVPTEQARAYAEKNCMT-FFEVSPLCNFNVIES 147
Cdd:cd04107  81 FDVTRPSTFEAVLKWKADLDSKvtlpngepipalllankcdlkkerlAKDPEQMDQFCKENGFIgWFETSAKENINIEEA 160

                ....*....
gi 56181887 148 FTELSRIVL 156
Cdd:cd04107 161 MRFLVKNIL 169
SOCS_SOCS_like cd03717
SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of ...
168-206 1.02e-15

SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to cytokines. Identified as negative regulators of the cytokine-JAK-STAT pathway, they seem to play a role in many immunological and pathological processes. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. Related SOCS boxes are also present in Rab40-like proteins and insect proteins of unknown function that also contain a NEUZ (domain in neuralized proteins) domain.


Pssm-ID: 239687  Cd Length: 39  Bit Score: 68.78  E-value: 1.02e-15
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 56181887 168 NRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSF 206
Cdd:cd03717   1 TSVRSLQHLCRFVIRQCTRRDLIDQLPLPRRLKDYLKEY 39
RabL4 cd04101
Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ...
15-153 3.24e-15

Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.


Pssm-ID: 206688 [Multi-domain]  Cd Length: 167  Bit Score: 71.40  E-value: 3.24e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESP--YAYSNGIDY--KTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGI 90
Cdd:cd04101   1 AQCAVVGDPAVGKSALVQMFHSDGATFQknYTMTTGCDLvvKTVPVPDTSDSVELFIFDSAGQELFSDMVENVWEQPAVV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  91 LLVYDITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFT 149
Cdd:cd04101  81 CVVYDVTNEVSFNNCSRWINRVrthshglhtpgvlvgnkcdltDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFL 160

                ....
gi 56181887 150 ELSR 153
Cdd:cd04101 161 SLAR 164
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
13-154 8.92e-14

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 67.70  E-value: 8.92e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  13 YLLKFLLVGDSDVGKGEILESLQDGA-AESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSR---GAQ 88
Cdd:COG1100   2 GEKKIVVVGTGGVGKTSLVNRLVGDIfSLEKYLSTNGVTIDKKELKLDGLDVDLVIWDTPGQDEFRETRQFYARqltGAS 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIES 147
Cdd:COG1100  82 LYLFVVDGTREETLQSLYELLESLrrlgkkspiilvlnkidlydeEEIEDEERLKEALSEDNIVEVVATSAKTGEGVEEL 161

                ....*..
gi 56181887 148 FTELSRI 154
Cdd:COG1100 162 FAALAEI 168
Rab24 cd04118
Rab GTPase family 24 (Rab24); Rab24 is distinct from other Rabs in several ways. It exists ...
15-148 2.22e-13

Rab GTPase family 24 (Rab24); Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133318 [Multi-domain]  Cd Length: 193  Bit Score: 66.81  E-value: 2.22e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILES-LQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04118   1 VKVVMLGKESVGKTSLVERyVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSERYEAMSRIYYRGAKAAIVC 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56181887  94 YDITNRWSFDGIDRWIKEI-----------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESF 148
Cdd:cd04118  81 YDLTDSSSFERAKFWVKELqnleehckiylcgtksdlieqdrSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELF 158
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
15-154 2.34e-13

Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy.


Pssm-ID: 206641 [Multi-domain]  Cd Length: 171  Bit Score: 66.41  E-value: 2.34e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPY---AYSNgidYkTTTILLDGRRVKLELWDTSGQGRFCTIFR-SYSrGAQGI 90
Cdd:cd00157   1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYvptVFDN---Y-SANVTVDGKQVNLGLWDTAGQEEYDRLRPlSYP-QTDVF 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  91 LLVYDITNRWSFDGI-DRWIKEI----------------DER--------------QVPTEQARAYAEK-NCMTFFEVSP 138
Cdd:cd00157  76 LLCFSVDSPSSFENVkTKWYPEIkhycpnvpiilvgtkiDLRddgntlkklekkqkPITPEEGEKLAKEiGAVKYMECSA 155
                       170
                ....*....|....*.
gi 56181887 139 LCNFNVIESFTELSRI 154
Cdd:cd00157 156 LTQEGLKEVFDEAIRA 171
RHO smart00174
Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like ...
19-157 2.64e-13

Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.


Pssm-ID: 197554 [Multi-domain]  Cd Length: 174  Bit Score: 66.10  E-value: 2.64e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     19 LVGDSDVGKGEILESLQDGA---AESPYAYSNgidYkTTTILLDGRRVKLELWDTSGQGRFCTIfR--SYSrGAQGILLV 93
Cdd:smart00174   3 VVGDGAVGKTCLLIVYTTNAfpeDYVPTVFEN---Y-SADVEVDGKPVELGLWDTAGQEDYDRL-RplSYP-DTDVFLIC 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     94 YDITNRWSFDGI-DRWIKEI-----------------------------DERQVP--TEQARAYAEK-NCMTFFEVSPLC 140
Cdd:smart00174  77 FSVDSPASFENVkEKWYPEVkhfcpnvpiilvgtkldlrndkstleelsKKKQEPvtYEQGQALAKRiGAVKYLECSALT 156
                          170
                   ....*....|....*..
gi 56181887    141 NFNVIESFTELSRIVLM 157
Cdd:smart00174 157 QEGVREVFEEAIRAALN 173
SOCS smart00253
suppressors of cytokine signalling; suppressors of cytokine signalling
165-206 5.30e-13

suppressors of cytokine signalling; suppressors of cytokine signalling


Pssm-ID: 128549  Cd Length: 43  Bit Score: 61.93  E-value: 5.30e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 56181887    165 WRPNRVFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSF 206
Cdd:smart00253   2 PRPSNVPSLQHLCRFTIRRCTRTDQIKTLPLPPKLKDYLSYY 43
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
16-171 1.03e-11

Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus.


Pssm-ID: 206643 [Multi-domain]  Cd Length: 166  Bit Score: 61.55  E-value: 1.03e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:cd00877   2 KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFD 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  96 ITNRWSFDGIDRWIKE------------------IDERQVPTEQARAYAEKNCMtFFEVSPLCNFNVIESFTELSRIVLm 157
Cdd:cd00877  82 VTSRVTYKNVPNWHRDlvrvcenipivlcgnkvdIKDRKVKPKQITFHRKKNLQ-YYEISAKSNYNFEKPFLWLARKLL- 159
                       170
                ....*....|....
gi 56181887 158 rhgmekiWRPNRVF 171
Cdd:cd00877 160 -------GNPNLEF 166
Rab28 cd04109
Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown ...
15-113 1.03e-11

Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206694 [Multi-domain]  Cd Length: 213  Bit Score: 62.51  E-value: 1.03e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGR-RVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04109   1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSlNVTLQVWDIGGQQIGGKMLDKYIYGAQAVCLV 80
                        90       100
                ....*....|....*....|
gi 56181887  94 YDITNRWSFDGIDRWIKEID 113
Cdd:cd04109  81 YDITNSQSFENLEDWLSVVK 100
RERG_RasL11_like cd04146
Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like ...
58-155 1.81e-11

Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like families; RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tumor suppressor activity.


Pssm-ID: 206713 [Multi-domain]  Cd Length: 166  Bit Score: 60.75  E-value: 1.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  58 LDGRRVKLELWDTSGQ-GRFCTIFR-SYSRGAQGILLVYDITNRWSFDGIDRWIKEIDE--------------------- 114
Cdd:cd04146  42 IDGEQVSLEIQDTPGQqQNEDPESLeRSLRWADGFVLVYSITDRSSFDVVSQLLQLIREikkrdgeipvilvgnkadllh 121
                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 56181887 115 -RQVPTEQARAYAEKNCMTFFEVSPLCNFN-VIESFTELSRIV 155
Cdd:cd04146 122 sRQVSTEEGQKLALELGCLFFEVSAAENYLeVQNVFHELCREV 164
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
16-120 2.04e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 60.85  E-value: 2.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    16 KFLLVGDSDVGKGEILESL-QDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:TIGR00231   3 KIVIVGHPNVGKSTLLNSLlGNKGSITEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVF 82
                          90       100
                  ....*....|....*....|....*...
gi 56181887    95 DITNRW-SF-DGIDRWIKEIdERQVPTE 120
Cdd:TIGR00231  83 DIVILVlDVeEILEKQTKEI-IHHADSG 109
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
16-111 3.52e-11

Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206693 [Multi-domain]  Cd Length: 170  Bit Score: 60.28  E-value: 3.52e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:cd04108   2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTYYRGAQAIIIVFD 81
                        90
                ....*....|....*.
gi 56181887  96 ITNRWSFDGIDRWIKE 111
Cdd:cd04108  82 LTDVASLEHTRQWLED 97
Ras2 cd04144
Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases); The Ras2 subfamily, ...
16-153 5.54e-11

Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases); The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133344 [Multi-domain]  Cd Length: 190  Bit Score: 60.25  E-value: 5.54e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEIleSLQDGAAESPYAYSNGID--YKTTTILlDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04144   1 KLVVLGDGGVGKTAL--TIQLCLNHFVETYDPTIEdsYRKQVVV-DGQPCMLEVLDTAGQEEYTALRDQWIREGEGFILV 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  94 YDITNRWSFDGIDRWIKEI-----------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTE 150
Cdd:cd04144  78 YSITSRSTFERVERFREQIqrvkdesaadvpimivgnkcdkvYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYT 157

                ...
gi 56181887 151 LSR 153
Cdd:cd04144 158 LVR 160
RalA_RalB cd04139
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ...
16-153 1.06e-10

Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206710 [Multi-domain]  Cd Length: 163  Bit Score: 58.59  E-value: 1.06e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEI-LESLQDGAAEspyaysngiDYKTT-------TILLDGRRVKLELWDTSGQGRFCTIFRSYSRGA 87
Cdd:cd04139   2 KVIMVGSGGVGKSALtLQFMYDEFVE---------DYEPTkadsyrkKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSG 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  88 QGILLVYDITNRWSFDGI----DRWIKEIDE-----------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIE 146
Cdd:cd04139  73 EGFLLVFSITDMESFTALaefrEQILRVKEDdnvplllvgnkcdledkRQVSVEEAANLAEQWGVNYVETSAKTRANVDK 152

                ....*..
gi 56181887 147 SFTELSR 153
Cdd:cd04139 153 VFFDLVR 159
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
16-153 1.30e-10

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 59.32  E-value: 1.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYD 95
Cdd:PTZ00132  11 KLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFD 90
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56181887   96 ITNRWSFDGIDRWIKEI------------------DERQVPTEQARAYAEKNcMTFFEVSPLCNFNVIESFTELSR 153
Cdd:PTZ00132  91 VTSRITYKNVPNWHRDIvrvcenipivlvgnkvdvKDRQVKARQITFHRKKN-LQYYDISAKSNYNFEKPFLWLAR 165
RSR1 cd04177
RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that ...
16-156 2.39e-10

RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133377 [Multi-domain]  Cd Length: 168  Bit Score: 57.88  E-value: 2.39e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEI-LESLQDGAAESpyaYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLV 93
Cdd:cd04177   3 KIVVLGAGGVGKSALtVQFVQNVFIES---YDPTIeDSYRKQVEIDGRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLV 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  94 YDITNRWSFD-------GIDRwIKE---------------IDERQVPTEQARAYAEK-NCMTFFEVSPLCNFNVIESFTE 150
Cdd:cd04177  80 YSVTSEASLNelgelreQVLR-IKDsdnvpmvlvgnkadlEDDRQVSREDGVSLSQQwGNVPFYETSARKRTNVDEVFID 158

                ....*.
gi 56181887 151 LSRIVL 156
Cdd:cd04177 159 LVRQII 164
Spg1 cd04128
Septum-promoting GTPase (Spg1); Spg1p. Spg1p (septum-promoting GTPase) was first identified in ...
15-134 3.23e-10

Septum-promoting GTPase (Spg1); Spg1p. Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 206701 [Multi-domain]  Cd Length: 182  Bit Score: 57.79  E-value: 3.23e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04128   1 LKIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFINMLPLVCKDAVAILFMF 80
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56181887  95 DITNRWSFDGIDRWIKE------------------------IDERQVPTEQARAYAEK-NCMTFF 134
Cdd:cd04128  81 DLTRKSTLNSIKEWYRQargfnktaipilvgtkydlfadlpPEEQEEITKQARKYAKAmKAPLIF 145
Rap_like cd04136
Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, ...
50-153 3.50e-10

Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206708 [Multi-domain]  Cd Length: 164  Bit Score: 57.18  E-value: 3.50e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  50 DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEI----------------- 112
Cdd:cd04136  36 DSYRKQIEVDCQQCMLEILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQIlrvkdtedvpmilvgnk 115
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 56181887 113 ----DERQVPTEQARAYAEKNC-MTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd04136 116 cdleDERVVSKEEGQNLARQWGnCPFLETSAKSKINVDEIFYDLVR 161
RheB cd04137
Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) ...
53-151 3.60e-10

Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that leads to cell growth and cell-cycle progression. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 206709 [Multi-domain]  Cd Length: 180  Bit Score: 57.64  E-value: 3.60e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  53 TTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIdRWIKEI-------------------- 112
Cdd:cd04137  39 SKIITYKGQEYHLEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVV-KVIYDKildmlgkesvpivlvgnksd 117
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 56181887 113 --DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTEL 151
Cdd:cd04137 118 lhMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELL 158
Rap1 cd04175
Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap ...
58-153 4.18e-10

Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines; interestingly, in the SCCs, the active GTP-bound form localized to the nucleus, while the inactive GDP-bound form localized to the cytoplasm. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap1a, which is stimulated by T-cell receptor (TCR) activation, is a positive regulator of T cells by directing integrin activation and augmenting lymphocyte responses. In murine hippocampal neurons, Rap1b determines which neurite will become the axon and directs the recruitment of Cdc42, which is required for formation of dendrites and axons. In murine platelets, Rap1b is required for normal homeostasis in vivo and is involved in integrin activation. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133375 [Multi-domain]  Cd Length: 164  Bit Score: 57.14  E-value: 4.18e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  58 LDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIKEI---------------------DERQ 116
Cdd:cd04175  44 VDGQQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQIlrvkdtedvpmilvgnkcdleDERV 123
                        90       100       110
                ....*....|....*....|....*....|....*..
gi 56181887 117 VPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd04175 124 VGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVR 160
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
20-167 6.39e-10

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 57.33  E-value: 6.39e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     20 VGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDITNR 99
Cdd:smart00176   1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTAR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887    100 WSFDGIDRWIK------------------EIDERQVPTEQARAYAEKNcMTFFEVSPLCNFNVIESFTELSRIVLMRHGM 161
Cdd:smart00176  81 VTYKNVPNWHRdlvrvcenipivlcgnkvDVKDRKVKAKSITFHRKKN-LQYYDISAKSNYNFEKPFLWLARKLIGDPNL 159

                   ....*.
gi 56181887    162 EKIWRP 167
Cdd:smart00176 160 EFVAMP 165
SOCS cd03587
SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region ...
169-206 1.69e-09

SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239641  Cd Length: 41  Bit Score: 52.09  E-value: 1.69e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 56181887 169 RVFSLQDLCCRAIVSCT---PVHLIDKLPLPVTIKSHLKSF 206
Cdd:cd03587   1 NPRSLQHLCRLAIRRCLgkrRLDLIDKLPLPPRLKDYLLYK 41
H_N_K_Ras_like cd04138
Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B; H-Ras/N-Ras/K-Ras subfamily. H-Ras, ...
15-153 3.02e-09

Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B; H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133338 [Multi-domain]  Cd Length: 162  Bit Score: 54.73  E-value: 3.02e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEI-LESLQDGAAESpyaYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd04138   2 YKLVVVGAGGVGKSALtIQLIQNHFVDE---YDPTIeDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLC 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  93 VYDITNRWSFDGIDRW------IKEIDE--------------RQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELS 152
Cdd:cd04138  79 VFAINSRKSFEDIHTYreqikrVKDSDDvpmvlvgnkcdlaaRTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLV 158

                .
gi 56181887 153 R 153
Cdd:cd04138 159 R 159
PLN03071 PLN03071
GTP-binding nuclear protein Ran; Provisional
15-153 3.78e-09

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 178620 [Multi-domain]  Cd Length: 219  Bit Score: 55.53  E-value: 3.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:PLN03071  14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMF 93
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56181887   95 DITNRWSFDGIDRWIK------------------EIDERQVPTEQArAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:PLN03071  94 DVTARLTYKNVPTWHRdlcrvcenipivlcgnkvDVKNRQVKAKQV-TFHRKKNLQYYEISAKSNYNFEKPFLYLAR 169
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
18-118 5.17e-09

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 54.00  E-value: 5.17e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  18 LLVGDSDVGKGEILESL-QDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRF-----CTIFRSYSRGAQGIL 91
Cdd:cd00882   1 VVVGRGGVGKSSLLNALlGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFgglgrEELARLLLRGADLIL 80
                        90       100
                ....*....|....*....|....*...
gi 56181887  92 LVYDITNRWSFDGIDR-WIKEIDERQVP 118
Cdd:cd00882  81 LVVDSTDRESEEDAKLlILRRLRKEGIP 108
Rho4_like cd04132
Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a ...
12-112 5.27e-09

Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.


Pssm-ID: 206704 [Multi-domain]  Cd Length: 197  Bit Score: 54.65  E-value: 5.27e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  12 DYLLKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFR-SYSrGAQGI 90
Cdd:cd04132   1 DLKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQEDYDRLRPlSYP-DVDVI 79
                        90       100
                ....*....|....*....|...
gi 56181887  91 LLVYDITNRWSFDGI-DRWIKEI 112
Cdd:cd04132  80 LICYSVDNPTSLDNVeDKWYPEV 102
Rit_Rin_Ric cd04141
Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related ...
16-153 5.31e-09

Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related protein which interacts with calmodulin (Ric); Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to signal in parallel with the Ras pathway or stimulate the Ras pathway at some upstream point, and binding of calmodulin to Ric may negatively regulate Ric activity.


Pssm-ID: 206712 [Multi-domain]  Cd Length: 172  Bit Score: 54.09  E-value: 5.31e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEIleSLQDGAAESPYAYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04141   4 KIVMLGAGGVGKSAV--TMQFISHSFPDYHDPTIeDAYKTQARIDNEPALLDILDTAGQAEFTAMRDQYMRCGEGFIICY 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIESFTELSR 153
Cdd:cd04141  82 SVTDRHSFQEASEFKELItrvrltediplvlvgnkvdleQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVR 161
Wrch_1 cd04130
Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42; Wrch-1 (Wnt-1 ...
15-148 9.72e-09

Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42; Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133330 [Multi-domain]  Cd Length: 173  Bit Score: 53.56  E-value: 9.72e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTiFRS--YSrGAQGILL 92
Cdd:cd04130   1 LKCVLVGDGAVGKTSLIVSYTTNGYPTEYV-PTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDK-LRPlcYP-DTDVFLL 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  93 VYDITNRWSFDGI-DRWIKEI-------------------------------DERQVPTEQARAYAEK-NCMTFFEVSPL 139
Cdd:cd04130  78 CFSVVNPSSFQNIsEKWIPEIrkhnpkapiilvgtqadlrtdvnvliqlaryGEKPVSQSRAKALAEKiGACEYIECSAL 157

                ....*....
gi 56181887 140 CNFNVIESF 148
Cdd:cd04130 158 TQKNLKEVF 166
PTZ00369 PTZ00369
Ras-like protein; Provisional
16-155 2.34e-08

Ras-like protein; Provisional


Pssm-ID: 240385 [Multi-domain]  Cd Length: 189  Bit Score: 52.56  E-value: 2.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   16 KFLLVGDSDVGKGEI-LESLQ-------DGAAESPYAYSNGIDYKTTtiLLDgrrvkleLWDTSGQGRFCTIFRSYSRGA 87
Cdd:PTZ00369   7 KLVVVGGGGVGKSALtIQFIQnhfideyDPTIEDSYRKQCVIDEETC--LLD-------ILDTAGQEEYSAMRDQYMRTG 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   88 QGILLVYDITNRWSFDGIDRWIKEI---------------------DERQVPTEQARAYAEKNCMTFFEVSPLCNFNVIE 146
Cdd:PTZ00369  78 QGFLCVYSITSRSSFEEIASFREQIlrvkdkdrvpmilvgnkcdldSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDE 157

                 ....*....
gi 56181887  147 SFTELSRIV 155
Cdd:PTZ00369 158 AFYELVREI 166
Rnd cd04131
Rho family GTPase subfamily Rnd includes Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8; The Rnd ...
16-114 1.34e-07

Rho family GTPase subfamily Rnd includes Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8; The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206703 [Multi-domain]  Cd Length: 176  Bit Score: 50.12  E-value: 1.34e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESL-QDGAAES--PYAYSNgidyKTTTILLDGRRVKLELWDTSGQGRFCTIfR--SYSRgAQGI 90
Cdd:cd04131   3 KIVLVGDSQCGKTALLQVFaKDSFPENyvPTVFEN----YTASFEVDKQRIELSLWDTSGSPYYDNV-RplSYPD-SDAV 76
                        90       100
                ....*....|....*....|....*
gi 56181887  91 LLVYDITNRWSFDGI-DRWIKEIDE 114
Cdd:cd04131  77 LICFDISRPETLDSVlKKWKGEVRE 101
Rnd1_Rho6 cd04174
Rnd1/Rho6 GTPases; Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2 ...
16-112 1.45e-07

Rnd1/Rho6 GTPases; Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206737 [Multi-domain]  Cd Length: 232  Bit Score: 50.83  E-value: 1.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESL-QDGAAES--PYAYSNgidyKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd04174  15 KLVLVGDVQCGKTAMLQVLaKDCYPETyvPTVFEN----YTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLL 90
                        90       100
                ....*....|....*....|.
gi 56181887  93 VYDITNRWSFD-GIDRWIKEI 112
Cdd:cd04174  91 CFDISRPEIFDsALKKWRAEI 111
Rnd3_RhoE_Rho8 cd04172
Rnd3/RhoE/Rho8 GTPases; Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho ...
10-114 1.34e-06

Rnd3/RhoE/Rho8 GTPases; Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight junction formation. Rnd3/RhoE is underexpressed in prostate cancer cells both in vitro and in vivo; re-expression of Rnd3/RhoE suppresses cell cycle progression and increases apoptosis, suggesting it may play a role in tumor suppression. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206735 [Multi-domain]  Cd Length: 182  Bit Score: 47.36  E-value: 1.34e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  10 SYDYLLKFLLVGDSDVGKGEILESL-QDGAAES--PYAYSNgidyKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRG 86
Cdd:cd04172   1 NQNVKCKIVVVGDSQCGKTALLHVFaKDCFPENyvPTVFEN----YTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPD 76
                        90       100
                ....*....|....*....|....*....
gi 56181887  87 AQGILLVYDITNRWSFDGI-DRWIKEIDE 114
Cdd:cd04172  77 SDAVLICFDISRPETLDSVlKKWKGEIQE 105
RabL3 cd04102
Rab GTPase-like family 3 (Rab-like3); RabL3 (Rab-like3) subfamily. RabL3s are novel proteins ...
15-115 1.78e-06

Rab GTPase-like family 3 (Rab-like3); RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown.


Pssm-ID: 206689  Cd Length: 204  Bit Score: 47.59  E-value: 1.78e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNG-------IDYKTTTIllDGRRVKLELWDTSGQGRFCTIFRS----- 82
Cdd:cd04102   1 VKVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGcsvdvrhHTYGEGTP--EEKTFYVELWDVGGSVGSAESVKStravf 78
                        90       100       110
                ....*....|....*....|....*....|...
gi 56181887  83 YSRgAQGILLVYDITNRWSFDGIDRWIKEIDER 115
Cdd:cd04102  79 YNQ-INGIIFVHDLTNKKSSQNLYRWSLEALNR 110
SOCS_box smart00969
The SOCS box acts as a bridge between specific substrate- binding domains and more generic ...
171-206 2.33e-06

The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases;


Pssm-ID: 198037  Cd Length: 34  Bit Score: 43.17  E-value: 2.33e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 56181887    171 FSLQDLCCRAIVSCTpvHLIDKLPLPVTIKSHLKSF 206
Cdd:smart00969   1 RSLQHLCRLAIRRSL--GGIDKLPLPPRLKDYLLYY 34
Rab20 cd04126
Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be ...
15-113 2.80e-06

Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133326 [Multi-domain]  Cd Length: 220  Bit Score: 46.82  E-value: 2.80e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYktttiLLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04126   1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFY-----LKQWGPYNISIWDTAGREQFHGLGSMYCRGAAAVILTY 75
                        90       100
                ....*....|....*....|
gi 56181887  95 DITNRWSFDGI-DRWIKEID 113
Cdd:cd04126  76 DVSNVQSLEELeDRFLGLTD 95
SOCS_box pfam07525
SOCS box; The SOCS box acts as a bridge between specific substrate- binding domains and more ...
170-204 7.81e-06

SOCS box; The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.


Pssm-ID: 462192  Cd Length: 39  Bit Score: 41.77  E-value: 7.81e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 56181887   170 VFSLQDLCCRAIVSCT---PVHLIDKLPLPVTIKSHLK 204
Cdd:pfam07525   2 PRSLQHLCRLAIRRALgkrRLGAIDKLPLPPLLKDYLL 39
Rnd2_Rho7 cd04173
Rnd2/Rho7 GTPases; Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1 ...
16-114 1.35e-05

Rnd2/Rho7 GTPases; Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in spermatocytes and early spermatids, with male-germ-cell Rac GTPase-activating protein (MgcRacGAP), where it localizes to the Golgi-derived pro-acrosomal vesicle. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.


Pssm-ID: 206736 [Multi-domain]  Cd Length: 221  Bit Score: 45.02  E-value: 1.35e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESL-QDGAAES--PYAYSNgidyKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILL 92
Cdd:cd04173   3 KIVVVGDTQCGKTALLHVFaKDNYPESyvPTVFEN----YTASFEIDKHRIELNMWDTSGSSYYDNVRPLAYPDSDAVLI 78
                        90       100
                ....*....|....*....|...
gi 56181887  93 VYDITNRWSFDGI-DRWIKEIDE 114
Cdd:cd04173  79 CFDISRPETLDSVlKKWQGETQE 101
Rho2 cd04129
Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal ...
16-158 2.20e-05

Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).


Pssm-ID: 206702 [Multi-domain]  Cd Length: 190  Bit Score: 44.05  E-value: 2.20e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGaaESPYAYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIfR--SYSRgAQGILL 92
Cdd:cd04129   3 KLVIVGDGACGKTSLLYVFTLG--EFPEEYHPTVfENYVTDCRVDGKPVQLALWDTAGQEEYERL-RplSYSK-AHVILI 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  93 VYDITNRWSFDGID-RWIKEI-----------------------------DERQVPTEQA-RAYAEKNCMTFFEVSPLCN 141
Cdd:cd04129  79 GFAIDTPDSLENVRtKWIEEVrrycpnvpvilvglkkdlrqeavakgnyaTDEFVPIQQAkLVARAIGAKKYMECSALTG 158
                       170
                ....*....|....*...
gi 56181887 142 FNVIESFTELSRI-VLMR 158
Cdd:cd04129 159 EGVDDVFEAATRAaLLVR 176
Rop_like cd04133
Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) ...
15-112 3.53e-05

Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example, Rop1, Rop3, and Rop5 are all involved in pollen-tube growth; Rop2 plays a role in response to low-oxygen environments, cell-morphology, and root-hair development; root-hair development is also regulated by Rop4 and Rop6; Rop6 is also responsible for ABA response, and ABA response is also regulated by Rop10. Plants retain some of the regulatory mechanisms that are shared by other members of the Rho family, but have also developed a number of unique modes for regulating Rops. Unique RhoGEFs have been identified that are exclusively active toward Rop proteins, such as those containing the domain PRONE (plant-specific Rop nucleotide exchanger). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206705 [Multi-domain]  Cd Length: 173  Bit Score: 43.30  E-value: 3.53e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04133   2 IKCVTVGDGAVGKTCMLISYTSNTFPTDYV-PTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAF 80
                        90
                ....*....|....*....
gi 56181887  95 DITNRWSFDGI-DRWIKEI 112
Cdd:cd04133  81 SLISKASYENVlKKWIPEL 99
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
18-118 3.74e-05

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 42.95  E-value: 3.74e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  18 LLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTttilLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVYDIT 97
Cdd:cd00878   3 LMLGLDGAGKTTILYKLKLGEVVTTIP-TIGFNVET----VEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSS 77
                        90       100
                ....*....|....*....|....*
gi 56181887  98 NR----WSFDGIDRWIKEIDERQVP 118
Cdd:cd00878  78 DRerieEAKNELHKLLNEEELKGAP 102
RGK cd04148
Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases; RGK subfamily. The RGK (Rem, Rem2, Rad, ...
15-164 5.51e-05

Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases; RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD.


Pssm-ID: 206715 [Multi-domain]  Cd Length: 219  Bit Score: 43.16  E-value: 5.51e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04148   1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQEDGMWLEDSCMQVGDAYVIVY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEIDE---------------------RQVPTEQARAYA-EKNCMtFFEVSPLCNFNVIESFTELS 152
Cdd:cd04148  81 SVTDRSSFEKASELRIQLRRarqaedipiilvgnksdlvrsREVSVQEGRACAvVFDCK-FIETSAALQHNVDELFEGIV 159
                       170
                ....*....|..
gi 56181887 153 RIVLMRHGMEKI 164
Cdd:cd04148 160 RQVRLRRDSKEK 171
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
15-99 6.17e-05

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 42.60  E-value: 6.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887     15 LKFLLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTTTIlldgRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:smart00177  14 MRILMVGLDAAGKTTILYKLKLGESVTTIP-TIGFNVETVTY----KNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVV 88

                   ....*
gi 56181887     95 DITNR 99
Cdd:smart00177  89 DSNDR 93
PLN00023 PLN00023
GTP-binding protein; Provisional
18-114 6.95e-05

GTP-binding protein; Provisional


Pssm-ID: 177661  Cd Length: 334  Bit Score: 43.31  E-value: 6.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887   18 LLVGDSDVGKGEILESLQDGAAESPYAYSNG-------IDYKT-----TTILLDGRR-VKLELWDTSGQGRF--C-TIFr 81
Cdd:PLN00023  25 LVVGDSGVGKSSLVHLIVKGSSIARPPQTIGctvgvkhITYGSpgsssNSIKGDSERdFFVELWDVSGHERYkdCrSLF- 103
                         90       100       110
                 ....*....|....*....|....*....|...
gi 56181887   82 sYSRgAQGILLVYDITNRWSFDGIDRWIKEIDE 114
Cdd:PLN00023 104 -YSQ-INGVIFVHDLSQRRTKTSLQKWASEVAA 134
RhoG cd01875
Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a ...
15-73 1.66e-04

Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.


Pssm-ID: 133277 [Multi-domain]  Cd Length: 191  Bit Score: 41.53  E-value: 1.66e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYKTTTILlDGRRVKLELWDTSGQ 73
Cdd:cd01875   4 IKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAV-DGRTVSLNLWDTAGQ 61
SOCS_SOCS4 cd03738
SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the ...
171-206 1.90e-04

SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239707  Cd Length: 56  Bit Score: 38.43  E-value: 1.90e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 56181887 171 FSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSF 206
Cdd:cd03738   4 FSLQHICRTVICNCTTYDGIDALPIPSSMKLYLKEY 39
RhoA_like cd01870
Ras homology family A (RhoA)-like includes RhoA, RhoB and RhoC; The RhoA subfamily consists of ...
16-156 2.64e-04

Ras homology family A (RhoA)-like includes RhoA, RhoB and RhoC; The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranylgeranylated forms; however, RhoB can be present in palmitoylated, farnesylated, and geranylgeranylated forms. RhoA and RhoC are highly relevant for tumor progression and invasiveness; however, RhoB has recently been suggested to be a tumor suppressor. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206662 [Multi-domain]  Cd Length: 175  Bit Score: 40.49  E-value: 2.64e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESPYAYSNGIDYkTTTILLDGRRVKLELWDTSGQgrfctifRSYSR-------GAQ 88
Cdd:cd01870   3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENY-VADIEVDGKQVELALWDTAGQ-------EDYDRlrplsypDTD 74
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  89 GILLVYDITNRWSFDGI-DRWIKEI----------------DERQ---------------VPTEQARAYAEK-NCMTFFE 135
Cdd:cd01870  75 VILMCFSIDSPDSLENIpEKWTPEVkhfcpnvpiilvgnkkDLRNdehtirelakmkqepVKPEEGRAMAEKiGAFGYLE 154
                       170       180
                ....*....|....*....|.
gi 56181887 136 VSPLCNFNVIESFTELSRIVL 156
Cdd:cd01870 155 CSAKTKEGVREVFEMATRAAL 175
Rac1_like cd01871
Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)-like ...
15-112 2.75e-04

Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)-like consists of Rac1, Rac2 and Rac3; The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleotide association and is more efficiently activated by the RacGEF Tiam1. Both Rac1 and Rac3 have been implicated in the regulation of cell migration and invasion in human metastatic breast cancer. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206663 [Multi-domain]  Cd Length: 174  Bit Score: 40.57  E-value: 2.75e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAYSNgIDYKTTTILLDGRRVKLELWDTSGQGRFcTIFRSYSRGAQGILLV- 93
Cdd:cd01871   2 IKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPVNLGLWDTAGQEDY-DRLRPLSYPQTDVFLIc 79
                        90       100
                ....*....|....*....|
gi 56181887  94 YDITNRWSFDGID-RWIKEI 112
Cdd:cd01871  80 FSLVSPASFENVRaKWYPEV 99
Rhes_like cd04143
Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); ...
16-151 4.07e-04

Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression levels in other tissues. Dexras1 localizes primarily to the cytoplasm, and is a critical regulator of the circadian master clock to photic and nonphotic input. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.


Pssm-ID: 133343 [Multi-domain]  Cd Length: 247  Bit Score: 40.89  E-value: 4.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  16 KFLLVGDSDVGKGEILESLQDGAAESpyAYSNGI-DYKTTTILLDGRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04143   2 RMVVLGASKVGKTAIVSRFLGGRFEE--QYTPTIeDFHRKLYSIRGEVYQLDILDTSGNHPFPAMRRLSILTGDVFILVF 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  95 DITNRWSFDGIDRWIKEIDE-----------------------------RQVPTEQARAY-AEKNCMTFFEVSPLCNFNV 144
Cdd:cd04143  80 SLDNRESFEEVCRLREQILEtksclknktkenvkipmvicgnkadrdfpREVQRDEVEQLvGGDENCAYFEVSAKKNSNL 159

                ....*..
gi 56181887 145 IESFTEL 151
Cdd:cd04143 160 DEMFRAL 166
SOCS_SOCS5 cd03739
SOCS (suppressors of cytokine signaling) box of SOCS5-like proteins. Together with CIS1, the ...
171-206 1.18e-03

SOCS (suppressors of cytokine signaling) box of SOCS5-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS5 inhibits Th2 differentiation by inhibiting IL-4 signaling. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239708  Cd Length: 57  Bit Score: 36.51  E-value: 1.18e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 56181887 171 FSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHLKSF 206
Cdd:cd03739   4 FSLQYICRAVICRCTTYDGIDALPLPSMLQDFLKEY 39
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
15-99 1.54e-03

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 38.22  E-value: 1.54e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTTTIlldgRRVKLELWDTSGQGRFCTIFRSYSRGAQGILLVY 94
Cdd:cd04149  10 MRILMLGLDAAGKTTILYKLKLGQSVTTIP-TVGFNVETVTY----KNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVV 84

                ....*
gi 56181887  95 DITNR 99
Cdd:cd04149  85 DSADR 89
Tc10 cd04135
Rho GTPase TC10 (Tc10); TC10 is a Rho family protein that has been shown to induce microspike ...
15-114 1.77e-03

Rho GTPase TC10 (Tc10); TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interactions with CFTR-associated ligand (CAL). The GTP-bound form of TC10 directs the trafficking of CFTR from the juxtanuclear region to the secretory pathway toward the plasma membrane, away from CAL-mediated DFTR degradation in the lysosome. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206707 [Multi-domain]  Cd Length: 174  Bit Score: 38.07  E-value: 1.77e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56181887  15 LKFLLVGDSDVGKGEILESLQDGAAESPYAySNGIDYKTTTILLDGRRVKLELWDTSGQGRFCTIfRSYSRGAQGILLV- 93
Cdd:cd04135   1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYV-PTVFDHYAVSVTVGGKQYLLGLYDTAGQEDYDRL-RPLSYPMTDVFLIc 78
                        90       100
                ....*....|....*....|..
gi 56181887  94 YDITNRWSFDGI-DRWIKEIDE 114
Cdd:cd04135  79 FSVVNPASFQNVkEEWVPELKE 100
SOCS_ASB_like cd03716
SOCS (suppressors of cytokine signaling) box of ASB (ankyrin repeat and SOCS box) and SSB ...
172-203 2.19e-03

SOCS (suppressors of cytokine signaling) box of ASB (ankyrin repeat and SOCS box) and SSB (SPRY domain-containing SOCS box proteins) protein families. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence of a variable number of repeats. SSB proteins contain a central SPRY domain and a C-terminal SOCS. Recently, it has been shown that all four SSB proteins interact with the MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF), and that SSB-1, SSB-2, and SSB-4 interact with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain.


Pssm-ID: 239686  Cd Length: 42  Bit Score: 35.16  E-value: 2.19e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 56181887 172 SLQDLCCRAIVSC---TPVHLIDKLPLPVTIKSHL 203
Cdd:cd03716   5 SLQHLCRLAIRRClgrRRLELIKKLPLPPRLKDYL 39
SOCS_SOCS6 cd03740
SOCS (suppressors of cytokine signaling) box of SOCS6-like proteins. Together with CIS1, the ...
170-203 2.83e-03

SOCS (suppressors of cytokine signaling) box of SOCS6-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.


Pssm-ID: 239709  Cd Length: 41  Bit Score: 34.70  E-value: 2.83e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 56181887 170 VFSLQDLCCRAIVSCTPVHLIDKLPLPVTIKSHL 203
Cdd:cd03740   3 VRSLQYLCRFVIRQYTRIDLIQKLPLPNKMKGYL 36
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH