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Conserved domains on  [gi|768006510|ref|XP_011524756|]
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ras and Rab interactor-like protein isoform X1 [Homo sapiens]

Protein Classification

VPS9 domain-containing protein; SH2 domain-containing protein( domain architecture ID 10332974)

VPS9 domain-containing protein similar to Homo sapiens VPS9 domain-containing protein 1 that regulates tubular endosome formation through specific activation of Rab22A| SH2 (Src homology 2) domain-containing protein may act as an intracellular signal-transducing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 409-511 4.49e-26

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


:

Pssm-ID: 460489  Cd Length: 104  Bit Score: 102.29  E-value: 4.49e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  409 RIHERLAHLHAACAPRRKVALLLEVCRDVYAGLARGENQDPLGADAFLPALTEELIWSPdIGDTQLDVEFLMELLDPDEL 488
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRAN-PPNLYSNLQFISEFRDPDLL 81

                          90       100
                  ....*....|....*....|...
gi 768006510  489 RGEAGYYLTTWFGALHHIAHYQP 511
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLDP 104
SH2 super family cl15255
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
 40-131 1.06e-06

Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1), Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others.


The actual alignment was detected with superfamily member cd10339:

Pssm-ID: 472789  Cd Length: 101  Bit Score: 47.15  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  40 LTRLQRTWGVWHVPELDTQDAEALVGLWPLGSFLVTGRDPSQALVL----RSGPLPGEVNTYQIQKIPRGVSLESSNLCM 115
Cdd:cd10339    2 LERLLLTRPVWLQLQLNAAEAAHMLQTEPPGTFLVRKSNTRQCQVLcmrlPEASGPAFVSEHYIKESPGGVSLEGSELMF 81

                         90
                 ....*....|....*.
gi 768006510 116 PDLPHLLAFLSASRDV 131
Cdd:cd10339   82 PDLFRLIAFYCHSRDI 97
 
Name Accession Description Interval E-value
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 409-511 4.49e-26

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


Pssm-ID: 460489  Cd Length: 104  Bit Score: 102.29  E-value: 4.49e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  409 RIHERLAHLHAACAPRRKVALLLEVCRDVYAGLARGENQDPLGADAFLPALTEELIWSPdIGDTQLDVEFLMELLDPDEL 488
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRAN-PPNLYSNLQFISEFRDPDLL 81

                          90       100
                  ....*....|....*....|...
gi 768006510  489 RGEAGYYLTTWFGALHHIAHYQP 511
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLDP 104
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 423-506 9.24e-12

Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.


Pssm-ID: 128469  Cd Length: 117  Bit Score: 62.09  E-value: 9.24e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510   423 PRRKVALLLEVCRDVYAGLARGENQDpLGADAFLPALTEELIwSPDIGDTQLDVEFLMELLDPDELRGEAGYYLTTWFGA 502
Cdd:smart00167  18 PSDKIKCLLRACKLIYTLLETQSGEV-AGADDFLPVLIYVII-KCDPRDLLLNAEYMEEFLEPSLLTGEGGYYLTSLSAA 95


                   ....
gi 768006510   503 LHHI 506
Cdd:smart00167  96 LALI 99
SH2_RIN_family cd10339
Src homology 2 (SH2) domain found in Ras and Rab interactor (RIN)-family; The RIN (AKA Ras ...
 40-131 1.06e-06

Src homology 2 (SH2) domain found in Ras and Rab interactor (RIN)-family; The RIN (AKA Ras interaction/interference) family is composed of RIN1, RIN2 and RIN3. These proteins have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs, and RIN3 specifically functions as a Rab31-GEF. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198202  Cd Length: 101  Bit Score: 47.15  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  40 LTRLQRTWGVWHVPELDTQDAEALVGLWPLGSFLVTGRDPSQALVL----RSGPLPGEVNTYQIQKIPRGVSLESSNLCM 115
Cdd:cd10339    2 LERLLLTRPVWLQLQLNAAEAAHMLQTEPPGTFLVRKSNTRQCQVLcmrlPEASGPAFVSEHYIKESPGGVSLEGSELMF 81

                         90
                 ....*....|....*.
gi 768006510 116 PDLPHLLAFLSASRDV 131
Cdd:cd10339   82 PDLFRLIAFYCHSRDI 97
 
Name Accession Description Interval E-value
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 409-511 4.49e-26

Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.


Pssm-ID: 460489  Cd Length: 104  Bit Score: 102.29  E-value: 4.49e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  409 RIHERLAHLHAACAPRRKVALLLEVCRDVYAGLARGENQDPLGADAFLPALTEELIWSPdIGDTQLDVEFLMELLDPDEL 488
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRDESLGADDLLPILIYVLIRAN-PPNLYSNLQFISEFRDPDLL 81

                          90       100
                  ....*....|....*....|...
gi 768006510  489 RGEAGYYLTTWFGALHHIAHYQP 511
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLDP 104
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 423-506 9.24e-12

Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.


Pssm-ID: 128469  Cd Length: 117  Bit Score: 62.09  E-value: 9.24e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510   423 PRRKVALLLEVCRDVYAGLARGENQDpLGADAFLPALTEELIwSPDIGDTQLDVEFLMELLDPDELRGEAGYYLTTWFGA 502
Cdd:smart00167  18 PSDKIKCLLRACKLIYTLLETQSGEV-AGADDFLPVLIYVII-KCDPRDLLLNAEYMEEFLEPSLLTGEGGYYLTSLSAA 95


                   ....
gi 768006510   503 LHHI 506
Cdd:smart00167  96 LALI 99
SH2_RIN_family cd10339
Src homology 2 (SH2) domain found in Ras and Rab interactor (RIN)-family; The RIN (AKA Ras ...
 40-131 1.06e-06

Src homology 2 (SH2) domain found in Ras and Rab interactor (RIN)-family; The RIN (AKA Ras interaction/interference) family is composed of RIN1, RIN2 and RIN3. These proteins have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs, and RIN3 specifically functions as a Rab31-GEF. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198202  Cd Length: 101  Bit Score: 47.15  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  40 LTRLQRTWGVWHVPELDTQDAEALVGLWPLGSFLVTGRDPSQALVL----RSGPLPGEVNTYQIQKIPRGVSLESSNLCM 115
Cdd:cd10339    2 LERLLLTRPVWLQLQLNAAEAAHMLQTEPPGTFLVRKSNTRQCQVLcmrlPEASGPAFVSEHYIKESPGGVSLEGSELMF 81

                         90
                 ....*....|....*.
gi 768006510 116 PDLPHLLAFLSASRDV 131
Cdd:cd10339   82 PDLFRLIAFYCHSRDI 97
SH2_RIN1 cd10393
Src homology 2 (SH2) domain found in Ras and Rab interactor 1 (RIN1)-like proteins; RIN1, a ...
 42-131 1.43e-05

Src homology 2 (SH2) domain found in Ras and Rab interactor 1 (RIN1)-like proteins; RIN1, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. Previous studies showed that RIN1 interacts with EGF receptors via its SH2 domain and regulates trafficking and degradation of EGF receptors via its interaction with STAM, indicating a vital role for RIN1 in regulating endosomal trafficking of receptor tyrosine kinases (RTKs). RIN1 was first identified as a Ras-binding protein that suppresses the activated RAS2 allele in S. cerevisiae. RIN1 binds to the activated Ras through its carboxyl-terminal domain and this Ras-binding domain also binds to 14-3-3 proteins as Raf-1 does. The SH2 domain of RIN1 are thought to interact with the phosphotyrosine-containing proteins, but the physiological partners for this domain are unknown. The proline-rich domain in RIN1 is similar to the consensus SH3 binding regions. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198256  Cd Length: 101  Bit Score: 44.07  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  42 RLQRTWGVWHVPELDTQDAEALVGLWPLGSFLVTGRDPSQALVL------RSGPlpGEVNTYQIQKIPRGVSLESSNLCM 115
Cdd:cd10393    4 RLLLTRPVWLQLRANAAAALHVLRTEPPGTFLVRKSNTRQCQALcvrlpeASGP--SFVSSHYIQESPGGVSLEGSELTF 81

                         90
                 ....*....|....*.
gi 768006510 116 PDLPHLLAFLSASRDV 131
Cdd:cd10393   82 PDLVQLICAYCHTRDI 97
SH2_RIN2 cd10394
Src homology 2 (SH2) domain found in Ras and Rab interactor 2 (RIN2)-like proteins; RIN2, a ...
 40-131 1.42e-04

Src homology 2 (SH2) domain found in Ras and Rab interactor 2 (RIN2)-like proteins; RIN2, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. Ras induces activation of Rab5 through RIN2, which is a direct downstream target of Ras and a direct upstream regulator of Rab5. In other words it is the binding of the GTP-bound form of Ras to the RA domain of RIN2 that enhances the GEF activity toward Rab5. It is thought that the RA domain negatively regulates the Rab5 GEF activity. In steady state, RIN2 is likely to form a closed conformation by an intramolecular interaction between the RA domain and the Vps9p-like (Rab5 GEF) domain, negatively regulating the Rab5 GEF activity. In the active state, the binding of Ras to the RA domain may reduce the intramolecular interaction and stabilize an open conformation of RIN2. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198257  Cd Length: 100  Bit Score: 41.34  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  40 LTRLQRTWGVWHVPELDTQDAEALVGLWPLGSFLVTGRDPSQALVLrSGPLPGE----VNTYQIQKIPRGVSLESSNLCM 115
Cdd:cd10394    2 LDRLLHTHPIWLQLSLSEEEAAEVLQAQPPGIFLVRKSSKMQKKVL-SLRLPCEfgapLKEFAIKESTYTFSLEGSGISF 80

                         90
                 ....*....|....*.
gi 768006510 116 PDLPHLLAFLSASRDV 131
Cdd:cd10394   81 ADLFRLIAFYCISRDV 96
SH2 cd00173
Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they ...
 50-125 2.79e-04

Src homology 2 (SH2) domain; In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1), Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others.


Pssm-ID: 198173 [Multi-domain]  Cd Length: 79  Bit Score: 39.75  E-value: 2.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768006510  50 WHVPELDTQDAEALVGLWPLGSFLV--TGRDPSQ-ALVLRSGplPGEVNTYQIQKIPRGVSL-ESSNLCMPDLPHLLAFL 125
Cdd:cd00173    2 WFHGSISREEAERLLRGKPDGTFLVreSSSEPGDyVLSVRSG--DGKVKHYLIERNEGGYYLlGGSGRTFPSLPELVEHY 79
 
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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