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Conserved domains on  [gi|1958642080|ref|XP_038946135|]
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guanine nucleotide exchange factor for Rab-3A isoform X2 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rab11BD_RAB3IP_like super family cl41767
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 ...
 313-469 6.14e-100

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 (RAB3IL1) and similar proteins; The family includes RAB3IP and RAB3IL1, as well as Rab guanine nucleotide exchange factor SEC2 from yeast. RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. SEC2 is a guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. SEC2 binds the Rab GTPase YPT32 but does not have exchange activity on YPT32. The model corresponds to the Rab11a/Rab11b-binding region of family members which lies within the carboxy-terminus, a region distinct from their GEF domain and Rab3a-binding region.


The actual alignment was detected with superfamily member cd21069:

Pssm-ID: 425398  Cd Length: 163  Bit Score: 296.77  E-value: 6.14e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 313 SRQVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----EC 387
Cdd:cd21069     2 GKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavEC 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 388 NNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKLG 467
Cdd:cd21069    82 GGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKLG 161


                  ..
gi 1958642080 468 FF 469
Cdd:cd21069   162 FY 163
Sec2p super family cl05764
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 139-207 8.55e-12

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


The actual alignment was detected with superfamily member pfam06428:

Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 61.05  E-value: 8.55e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958642080 139 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 207
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
 
Name Accession Description Interval E-value
Rab11BD_RAB3IL1 cd21069
Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called ...
 313-469 6.14e-100

Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IL1 lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411033  Cd Length: 163  Bit Score: 296.77  E-value: 6.14e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 313 SRQVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----EC 387
Cdd:cd21069     2 GKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavEC 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 388 NNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKLG 467
Cdd:cd21069    82 GGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKLG 161


                  ..
gi 1958642080 468 FF 469
Cdd:cd21069   162 FY 163
Sec2p pfam06428
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 139-207 8.55e-12

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 61.05  E-value: 8.55e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958642080 139 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 207
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
110-207 4.49e-06

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 48.75  E-value: 4.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 110 SRLRSSSMEIREkgsefLKEELYKAQKELKLKDEECERlckVRAQLEQ---ELEELTASLfEEAHKMVREANMKQAASEK 186
Cdd:COG4372    31 EQLRKALFELDK-----LQEELEQLREELEQAREELEQ---LEEELEQarsELEQLEEEL-EELNEQLQAAQAELAQAQE 101

                          90       100
                  ....*....|....*....|.
gi 1958642080 187 QLKEAWGKIDMLQAEVTALKT 207
Cdd:COG4372   102 ELESLQEEAEELQEELEELQK 122
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 125-206 6.72e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 42.35  E-value: 6.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080  125 EFLKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTA 204
Cdd:TIGR02168  192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEE 271


                   ..
gi 1958642080  205 LK 206
Cdd:TIGR02168  272 LR 273
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 127-206 6.90e-04

polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.


Pssm-ID: 197361 [Multi-domain]  Cd Length: 87  Bit Score: 38.48  E-value: 6.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 127 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELT-----ASLFEEAHKMVREANMKQAASEKQLKEawgKIDMLQAE 201
Cdd:cd09803     6 LAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPvlkaqAEIYKSDFEAERAAREKLHQEKEQLAE---QLEYLQRE 82


                  ....*
gi 1958642080 202 VTALK 206
Cdd:cd09803    83 NQELK 87
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
115-206 2.41e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 2.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 115 SSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvraqlEQELEELTASLFEEAHKMVREANMKQ----AASEKQLKE 190
Cdd:PRK03918  612 KELEREEKELKKLEEELDKAFEELAETEKRLEEL-------RKELEELEKKYSEEEYEELREEYLELsrelAGLRAELEE 684

                          90
                  ....*....|....*.
gi 1958642080 191 AWGKIDMLQAEVTALK 206
Cdd:PRK03918  685 LEKRREEIKKTLEKLK 700
 
Name Accession Description Interval E-value
Rab11BD_RAB3IL1 cd21069
Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called ...
 313-469 6.14e-100

Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IL1 lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411033  Cd Length: 163  Bit Score: 296.77  E-value: 6.14e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 313 SRQVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----EC 387
Cdd:cd21069     2 GKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavEC 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 388 NNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKLG 467
Cdd:cd21069    82 GGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKLG 161


                  ..
gi 1958642080 468 FF 469
Cdd:cd21069   162 FY 163
Rab11BD_RAB3IP cd21068
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP); RAB3IP, also called Rabin-3, or ...
 313-469 1.73e-72

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP); RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IP lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411032  Cd Length: 193  Bit Score: 227.50  E-value: 1.73e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 313 SRQVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLP-----NVEC 387
Cdd:cd21068    29 CKEADLSLYNEFRLWKEEPTMDRTCPFLDRIYQEDIFPCLTFSKSELASAVLEAVENNTLSIEPVGLQPLRfvkasAVEC 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 388 NNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVR-QDAEPMFWEIMRLRKGMSLAKL 466
Cdd:cd21068   109 GGPKKCALSGQTKSCKHRIKLGDSSNYYYISPFCRYRITSVCNFFTYIRYIQQGLVKqQDVDQMFWEVMQLRKEMSLAKL 188


                  ...
gi 1958642080 467 GFF 469
Cdd:cd21068   189 GYY 191
Rab11BD_RAB3IP_like cd21044
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 ...
 316-467 1.34e-53

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 (RAB3IL1) and similar proteins; The family includes RAB3IP and RAB3IL1, as well as Rab guanine nucleotide exchange factor SEC2 from yeast. RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. SEC2 is a guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. SEC2 binds the Rab GTPase YPT32 but does not have exchange activity on YPT32. The model corresponds to the Rab11a/Rab11b-binding region of family members which lies within the carboxy-terminus, a region distinct from their GEF domain and Rab3a-binding region.


Pssm-ID: 411031  Cd Length: 178  Bit Score: 177.94  E-value: 1.34e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 316 VDTTLFAEFQAWRASP-----TLDKNCPFLERVYREDVGPCLDFTVQELSAL----VRTAVEDNTLTIEPVASQTLPNVE 386
Cdd:cd21044     3 VDLVLFEEFQEFLKAPsslslSLLKSSPFLKRILAEDIEPCLRFDPALLNWLlkkrLLAAILENTLEIEPISGSTETSSS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 387 CNNTN-----------TCALSGLART--CHHRIRLGDSDGH-YYISPSSRARITAVCNFFTYVRYIQQGLVRQ-DAEPMF 451
Cdd:cd21044    83 SNNTApvsspppaspkKCALCGESRLdaCLYRLRLSDSDSEwYPICSYCRNRLRAVCDFFAYLRYIRQGLVKSrSIEKLY 162

                         170
                  ....*....|....*.
gi 1958642080 452 WEIMRLRKGMSLAKLG 467
Cdd:cd21044   163 LEILRLRLRMFLARLG 178
Sec2p pfam06428
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 139-207 8.55e-12

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 61.05  E-value: 8.55e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958642080 139 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 207
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
110-207 4.49e-06

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 48.75  E-value: 4.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 110 SRLRSSSMEIREkgsefLKEELYKAQKELKLKDEECERlckVRAQLEQ---ELEELTASLfEEAHKMVREANMKQAASEK 186
Cdd:COG4372    31 EQLRKALFELDK-----LQEELEQLREELEQAREELEQ---LEEELEQarsELEQLEEEL-EELNEQLQAAQAELAQAQE 101

                          90       100
                  ....*....|....*....|.
gi 1958642080 187 QLKEAWGKIDMLQAEVTALKT 207
Cdd:COG4372   102 ELESLQEEAEELQEELEELQK 122
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 127-209 4.44e-05

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 45.53  E-value: 4.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 127 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTALK 206
Cdd:COG4942    25 AEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRI-AALARRIRALEQELAALEAELAELEKEIAELRAELEAQK 103


                  ...
gi 1958642080 207 TLV 209
Cdd:COG4942   104 EEL 106
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
110-221 4.80e-05

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 45.66  E-value: 4.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 110 SRLRSSSMEIREKGSEF--LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASlfeeahkmVREANMKQAASEKQ 187
Cdd:COG4372    80 EELEELNEQLQAAQAELaqAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQ--------IAELQSEIAEREEE 151

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1958642080 188 LKEAWGKIDMLQAEVTALKTLVITSTPASPNREL 221
Cdd:COG4372   152 LKELEEQLESLQEELAALEQELQALSEAEAEQAL 185
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 125-206 6.72e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 42.35  E-value: 6.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080  125 EFLKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTA 204
Cdd:TIGR02168  192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEE 271


                   ..
gi 1958642080  205 LK 206
Cdd:TIGR02168  272 LR 273
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 127-206 6.90e-04

polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.


Pssm-ID: 197361 [Multi-domain]  Cd Length: 87  Bit Score: 38.48  E-value: 6.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 127 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELT-----ASLFEEAHKMVREANMKQAASEKQLKEawgKIDMLQAE 201
Cdd:cd09803     6 LAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPvlkaqAEIYKSDFEAERAAREKLHQEKEQLAE---QLEYLQRE 82


                  ....*
gi 1958642080 202 VTALK 206
Cdd:cd09803    83 NQELK 87
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
127-207 7.01e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 42.06  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 127 LKEELYKAQKELKLKDEECERL---CKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVT 203
Cdd:COG4717   130 LYQELEALEAELAELPERLEELeerLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLA 209


                  ....
gi 1958642080 204 ALKT 207
Cdd:COG4717   210 ELEE 213
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 128-207 9.01e-04

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 39.09  E-value: 9.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 128 KEELYKAQKELKLKDEECERLCKV----RAQLEQELEELTASLFE------EAHKMVREAnMKQAASEKQLKEAWGK-ID 196
Cdd:pfam13863   5 KREMFLVQLALDAKREEIERLEELlkqrEEELEKKEQELKEDLIKfdkflkENDAKRRRA-LKKAEEETKLKKEKEKeIK 83

                          90
                  ....*....|.
gi 1958642080 197 MLQAEVTALKT 207
Cdd:pfam13863  84 KLTAQIEELKS 94
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
115-206 2.41e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 2.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 115 SSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvraqlEQELEELTASLFEEAHKMVREANMKQ----AASEKQLKE 190
Cdd:PRK03918  612 KELEREEKELKKLEEELDKAFEELAETEKRLEEL-------RKELEELEKKYSEEEYEELREEYLELsrelAGLRAELEE 684

                          90
                  ....*....|....*.
gi 1958642080 191 AWGKIDMLQAEVTALK 206
Cdd:PRK03918  685 LEKRREEIKKTLEKLK 700
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 108-206 2.65e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.43  E-value: 2.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080  108 DVSRLRSssmEIREKGSEF--LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASE 185
Cdd:TIGR02168  268 KLEELRL---EVSELEEEIeeLQKELYALANEISRLEQQKQILRERLANLERQLEELEAQL-EELESKLDELAEELAELE 343

                           90       100
                   ....*....|....*....|.
gi 1958642080  186 KQLKEAWGKIDMLQAEVTALK 206
Cdd:TIGR02168  344 EKLEELKEELESLEAELEELE 364
PRK12704 PRK12704
phosphodiesterase; Provisional
 113-185 3.69e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 39.76  E-value: 3.69e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958642080 113 RSSSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvRAQLEQELEE---LTAslfEEAHKMVREaNMKQAASE 185
Cdd:PRK12704  101 KLELLEKREEELEKKEKELEQKQQELEKKEEELEEL---IEEQLQELERisgLTA---EEAKEILLE-KVEEEARH 169
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 117-209 3.83e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 37.16  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 117 MEIREKGSEFLK---------EELYKAQKELKlkdEECERLCKVRAQLEQELeeltaslfEEAHKMVREANMKQAASEKQ 187
Cdd:pfam13863  13 LALDAKREEIERleellkqreEELEKKEQELK---EDLIKFDKFLKENDAKR--------RRALKKAEEETKLKKEKEKE 81

                          90       100
                  ....*....|....*....|..
gi 1958642080 188 LKEAWGKIDMLQAEVTALKTLV 209
Cdd:pfam13863  82 IKKLTAQIEELKSEISKLEEKL 103
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 115-202 7.30e-03

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 39.00  E-value: 7.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080  115 SSMEIREKGSEFLKEELYKAQKELK-----LKDEECE---RLCKVRAQLEQELEELTASL--FEEahkmvrEANMKQAAs 184
Cdd:pfam01576  190 SDLEERLKKEEKGRQELEKAKRKLEgestdLQEQIAElqaQIAELRAQLAKKEEELQAALarLEE------ETAQKNNA- 262

                           90
                   ....*....|....*...
gi 1958642080  185 EKQLKEAWGKIDMLQAEV 202
Cdd:pfam01576  263 LKKIRELEAQISELQEDL 280
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
129-206 7.34e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 38.98  E-value: 7.34e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958642080 129 EELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTALK 206
Cdd:COG4717   149 EELEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELE 226
BAR_SNX cd07596
The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid ...
 109-194 7.92e-03

The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins; BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.


Pssm-ID: 153280 [Multi-domain]  Cd Length: 218  Bit Score: 37.72  E-value: 7.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958642080 109 VSRLRSSSMEIREKGSEfLKEELYKAQKELKlkdEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQL 188
Cdd:cd07596   133 LEKLKAAPGIKPAKVEE-LEEELEEAESALE---EARKRYEEISERLKEELKRFHEERARDLKAALKEFARLQVQYAEKI 208


                  ....*.
gi 1958642080 189 KEAWGK 194
Cdd:cd07596   209 AEAWES 214
 
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.
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