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Conserved domains on  [gi|559098403|ref|NP_001273989|]
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rab5 GDP/GTP exchange factor isoform a [Homo sapiens]

Protein Classification

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). ...
 78-178 9.88e-34

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: 118.85  E-value: 9.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559098403   78 KAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKN-EPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRlM 156
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRdESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL-L 81

                          90       100
                  ....*....|....*....|..
gi 559098403  157 TGEDGYYFTNLCCAVAFIEKLD 178
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLD 103
DUF5601 super family cl39530
Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 ...
 9-28 1.84e-04

Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature.


The actual alignment was detected with superfamily member pfam18151:

Pssm-ID: 465668  Cd Length: 65  Bit Score: 39.11  E-value: 1.84e-04
                          10        20
                  ....*....|....*....|
gi 559098403    9 PERVEKIMDQIEKYIMTRLY 28
Cdd:pfam18151  46 DEQLEQLLDGVEKYIMTKLY 65
 
Name Accession Description Interval E-value
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 78-178 9.88e-34

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: 118.85  E-value: 9.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559098403   78 KAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKN-EPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRlM 156
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRdESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL-L 81

                          90       100
                  ....*....|....*....|..
gi 559098403  157 TGEDGYYFTNLCCAVAFIEKLD 178
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLD 103
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 86-191 1.41e-28

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


Pssm-ID: 128469  Cd Length: 117  Bit Score: 106.00  E-value: 1.41e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559098403    86 MDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPsRLMTGEDGYYFT 165
Cdd:smart00167  12 LQLYKSPSDKIKCLLRACKLIYTLLETQSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEYMEEFLEP-SLLTGEGGYYLT 90

                           90       100
                   ....*....|....*....|....*..
gi 559098403   166 NLCCAVAFIEKL-DAQSLNLSQEDFDR 191
Cdd:smart00167  91 SLSAALALIKGLtEAHALPLSPEQELE 117
DUF5601 pfam18151
Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 ...
 9-28 1.84e-04

Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature.


Pssm-ID: 465668  Cd Length: 65  Bit Score: 39.11  E-value: 1.84e-04
                          10        20
                  ....*....|....*....|
gi 559098403    9 PERVEKIMDQIEKYIMTRLY 28
Cdd:pfam18151  46 DEQLEQLLDGVEKYIMTKLY 65
 
Name Accession Description Interval E-value
VPS9 pfam02204
Vacuolar sorting protein 9 (VPS9) domain; This domain acts as a GDP-GTP exchange factor (GEF). ...
 78-178 9.88e-34

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: 118.85  E-value: 9.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559098403   78 KAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKN-EPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRlM 156
Cdd:pfam02204   3 QAQQELKKLNEAKSPREKLKCLLRTCKLITEALSKSNRdESLGADDLLPILIYVLIRANPPNLYSNLQFISEFRDPDL-L 81

                          90       100
                  ....*....|....*....|..
gi 559098403  157 TGEDGYYFTNLCCAVAFIEKLD 178
Cdd:pfam02204  82 SGEEGYYLTTLEAALEFIESLD 103
VPS9 smart00167
Domain present in VPS9; Domain present in yeast vacuolar sorting protein 9 and other proteins.
 86-191 1.41e-28

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


Pssm-ID: 128469  Cd Length: 117  Bit Score: 106.00  E-value: 1.41e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559098403    86 MDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPsRLMTGEDGYYFT 165
Cdd:smart00167  12 LQLYKSPSDKIKCLLRACKLIYTLLETQSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEYMEEFLEP-SLLTGEGGYYLT 90

                           90       100
                   ....*....|....*....|....*..
gi 559098403   166 NLCCAVAFIEKL-DAQSLNLSQEDFDR 191
Cdd:smart00167  91 SLSAALALIKGLtEAHALPLSPEQELE 117
DUF5601 pfam18151
Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 ...
 9-28 1.84e-04

Domain of unknown function (DUF5601); This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature.


Pssm-ID: 465668  Cd Length: 65  Bit Score: 39.11  E-value: 1.84e-04
                          10        20
                  ....*....|....*....|
gi 559098403    9 PERVEKIMDQIEKYIMTRLY 28
Cdd:pfam18151  46 DEQLEQLLDGVEKYIMTKLY 65
 
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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