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Conserved domains on  [gi|29826299|ref|NP_816931|]
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ADP-ribosylation factor-like protein 6 isoform 1 [Homo sapiens]

Protein Classification

ADP-ribosylation factor-like protein 6( domain architecture ID 10134977)

ADP-ribosylation factor-like protein 6 (Arl6), a member of the Arf family of small GTPases, may play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation; at least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 19-180 2.51e-117

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


:

Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 329.39  E-value: 2.51e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD 98
Cdd:cd04157   1 NILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  99 RLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 178
Cdd:cd04157  81 RLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQ 160


                ..
gi 29826299 179 DQ 180
Cdd:cd04157 161 AQ 162
 
Name Accession Description Interval E-value
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 19-180 2.51e-117

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 329.39  E-value: 2.51e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD 98
Cdd:cd04157   1 NILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  99 RLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 178
Cdd:cd04157  81 RLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQ 160


                ..
gi 29826299 179 DQ 180
Cdd:cd04157 161 AQ 162
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 18-181 8.22e-62

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 188.59  E-value: 8.22e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    18 VHVLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSS 97
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLG--EIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    98 DRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 177
Cdd:pfam00025  79 DRDRIEEAKEELHALLNEEEL--ADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWL 156


                  ....
gi 29826299   178 QDQI 181
Cdd:pfam00025 157 SNYI 160
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 7-183 2.20e-52

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: 165.48  E-value: 2.20e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299      7 LSVLLGlkKKEVHVLCLGLDNSGKTTIINKLKPsnAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKE 86
Cdd:smart00177   5 FSKLFG--NKEMRILMVGLDAAGKTTILYKLKL--GESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     87 GQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIK 166
Cdd:smart00177  81 TQGLIFVVDSNDRDRIDEAREELHRMLNEDEL--RDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATS 158

                          170
                   ....*....|....*..
gi 29826299    167 GEGLQEGVDWLQDQIQT 183
Cdd:smart00177 159 GDGLYEGLTWLSNNLKN 175
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 1-183 9.79e-49

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 156.28  E-value: 9.79e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    1 MGLLDRLSVLLGLKKKEVHVLCLGLDNSGKTTIINKLKPSNAQSQniLPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLW 80
Cdd:PLN00223   1 MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTT--IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLW 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   81 EHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHIC 160
Cdd:PLN00223  79 RHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDEL--RDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQ 156

                        170       180
                 ....*....|....*....|...
gi 29826299  161 ASDAIKGEGLQEGVDWLQDQIQT 183
Cdd:PLN00223 157 STCATSGEGLYEGLDWLSNNIAN 179
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 17-143 2.63e-13

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: 64.32  E-value: 2.63e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    17 EVHVLCLGLDNSGKTTIINKL---KPSNAQSQnilPTIGFSIEK----FKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQA 89
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLlgnKGSITEYY---PGTTRNYVTtvieEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVER 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826299    90 IIFVIDSSDRLRMVVAKEELDTllnhPDIKHRR---IPILFFANKMDLRDAVTSVKV 143
Cdd:TIGR00231  78 SLRVFDIVILVLDVEEILEKQT----KEIIHHAdsgVPIILVGNKIDLKDADLKTHV 130
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-172 3.61e-10

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 56.14  E-value: 3.61e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  15 KKEVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFK----SSSLSFTVFDMSGQGRYRNLWEHYYKEGQ-- 88
Cdd:COG1100   1 MGEKKIVVVGTGGVGKTSLVNRLVGDIFSLEKYLSTNGVTIDKKElkldGLDVDLVIWDTPGQDEFRETRQFYARQLTga 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  89 -AIIFVIDSSDRLRMVVAKEELDTLLNHpdikHRRIPILFFANKMDLRDAVtsVKVSQLLCLENIKDK-PWHICASDAIK 166
Cdd:COG1100  81 sLYLFVVDGTREETLQSLYELLESLRRL----GKKSPIILVLNKIDLYDEE--EIEDEERLKEALSEDnIVEVVATSAKT 154


                ....*.
gi 29826299 167 GEGLQE 172
Cdd:COG1100 155 GEGVEE 160
 
Name Accession Description Interval E-value
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 19-180 2.51e-117

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 329.39  E-value: 2.51e-117
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD 98
Cdd:cd04157   1 NILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  99 RLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 178
Cdd:cd04157  81 RLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQ 160


                ..
gi 29826299 179 DQ 180
Cdd:cd04157 161 AQ 162
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 19-180 3.60e-76

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: 225.15  E-value: 3.60e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD 98
Cdd:cd00878   1 RILMLGLDGAGKTTILYKLKLG--EVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSD 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  99 RLRMVVAKEELDTLLNHPdiKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 178
Cdd:cd00878  79 RERIEEAKNELHKLLNEE--ELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLI 156


                ..
gi 29826299 179 DQ 180
Cdd:cd00878 157 EQ 158
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 18-181 8.22e-62

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 188.59  E-value: 8.22e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    18 VHVLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSS 97
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLG--EIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    98 DRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 177
Cdd:pfam00025  79 DRDRIEEAKEELHALLNEEEL--ADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWL 156


                  ....
gi 29826299   178 QDQI 181
Cdd:pfam00025 157 SNYI 160
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 7-180 2.63e-53

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 167.57  E-value: 2.63e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   7 LSVLLGLKK---KEVHVLCLGLDNSGKTTIINKLkpSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHY 83
Cdd:cd04155   2 LSILRKLKPssrQEVRILLLGLDNAGKTTILKQL--ASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNY 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  84 YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNhpDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASD 163
Cdd:cd04155  80 FENTDVLIYVIDSADRKRFEEAGQELVELLE--EEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACS 157

                       170
                ....*....|....*..
gi 29826299 164 AIKGEGLQEGVDWLQDQ 180
Cdd:cd04155 158 AKTGEGLQEGMNWVCKN 174
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 7-183 2.20e-52

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: 165.48  E-value: 2.20e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299      7 LSVLLGlkKKEVHVLCLGLDNSGKTTIINKLKPsnAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKE 86
Cdd:smart00177   5 FSKLFG--NKEMRILMVGLDAAGKTTILYKLKL--GESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     87 GQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIK 166
Cdd:smart00177  81 TQGLIFVVDSNDRDRIDEAREELHRMLNEDEL--RDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATS 158

                          170
                   ....*....|....*..
gi 29826299    167 GEGLQEGVDWLQDQIQT 183
Cdd:smart00177 159 GDGLYEGLTWLSNNLKN 175
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 16-177 2.20e-51

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 162.90  E-value: 2.20e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  16 KEVHVLCLGLDNSGKTTIINKLKPSNAQSQNilPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVID 95
Cdd:cd04153  14 KEYKVIIVGLDNAGKTTILYQFLLGEVVHTS--PTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVID 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  96 SSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVD 175
Cdd:cd04153  92 STDRERLPLTKEELYKMLAHEDL--RKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLD 169


                ..
gi 29826299 176 WL 177
Cdd:cd04153 170 WI 171
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 20-180 1.56e-50

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 159.88  E-value: 1.56e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKPSNAQSQniLPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR 99
Cdd:cd04151   2 ILILGLDGAGKTTILYRLQVGEVVTT--IPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDR 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299 100 LRMVVAKEELDTLLNHPDIKhrRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 179
Cdd:cd04151  80 DRLGISKSELHAMLEEEELK--DAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWLVN 157


                .
gi 29826299 180 Q 180
Cdd:cd04151 158 T 158
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 14-179 5.73e-49

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: 156.47  E-value: 5.73e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  14 KKKEVHVLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFV 93
Cdd:cd04149   6 GNKEMRILMLGLDAAGKTTILYKLKLG--QSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFV 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  94 IDSSDRLRMVVAKEELDTLLNhpDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEG 173
Cdd:cd04149  84 VDSADRDRIDEARQELHRIIN--DREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEG 161


                ....*.
gi 29826299 174 VDWLQD 179
Cdd:cd04149 162 LTWLSS 167
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 18-180 7.56e-49

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 155.64  E-value: 7.56e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  18 VHVLCLGLDNSGKTTIINKLKPSNAQSQniLPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSS 97
Cdd:cd04150   1 MRILMVGLDAAGKTTILYKLKLGEIVTT--IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSN 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  98 DRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 177
Cdd:cd04150  79 DRERIGEAREELQRMLNEDEL--RDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWL 156


                ...
gi 29826299 178 QDQ 180
Cdd:cd04150 157 SNN 159
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 1-183 9.79e-49

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 156.28  E-value: 9.79e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    1 MGLLDRLSVLLGLKKKEVHVLCLGLDNSGKTTIINKLKPSNAQSQniLPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLW 80
Cdd:PLN00223   1 MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTT--IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLW 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   81 EHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHIC 160
Cdd:PLN00223  79 RHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDEL--RDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQ 156

                        170       180
                 ....*....|....*....|...
gi 29826299  161 ASDAIKGEGLQEGVDWLQDQIQT 183
Cdd:PLN00223 157 STCATSGEGLYEGLDWLSNNIAN 179
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 1-182 1.35e-47

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 153.46  E-value: 1.35e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    1 MGL-LDRL-SVLLGlkKKEVHVLCLGLDNSGKTTIINKLKPSNAQSQniLPTIGFSIEKFKSSSLSFTVFDMSGQGRYRN 78
Cdd:PTZ00133   1 MGLwLSSAfKSLFG--KKEVRILMVGLDAAGKTTILYKLKLGEVVTT--IPTIGFNVETVEYKNLKFTMWDVGGQDKLRP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   79 LWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWH 158
Cdd:PTZ00133  77 LWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDEL--RDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWY 154

                        170       180
                 ....*....|....*....|....
gi 29826299  159 ICASDAIKGEGLQEGVDWLQDQIQ 182
Cdd:PTZ00133 155 IQGCCATTAQGLYEGLDWLSANIK 178
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 13-177 1.74e-42

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 140.15  E-value: 1.74e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  13 LKKKEVHVLCLGLDNSGKTTIINKLkpSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd04154  10 QKEREMRILMLGLDNAGKTTILKKF--NGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIW 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  93 VIDSSDRLRMVVAKEELDTLLnhpdiKHRRI---PILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEG 169
Cdd:cd04154  88 VVDSSDRARLEDCKRELQKLL-----VEERLagaTLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTGEN 162


                ....*...
gi 29826299 170 LQEGVDWL 177
Cdd:cd04154 163 LLDGIDWL 170
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 18-181 2.95e-37

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 127.22  E-value: 2.95e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  18 VHVLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFK-----SSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd04152   4 LHIVMLGLDSAGKTTVLYRLKFN--EFVNTVPTKGFNTEKIKvslgnAKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVF 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  93 VIDSSDRLRMVVAKEELDTLLNHPDikHRRIPILFFANKMDLRDAVTSVKVSQLLCL-ENIKDKPWHICASDAIKGEGLQ 171
Cdd:cd04152  82 VVDSVDVERMEEAKTELHKITKFSE--NQGVPVLVLANKQDLPNALPVSEVEKLLALhELSSSTPWHVQPACAIIGEGLQ 159

                       170
                ....*....|
gi 29826299 172 EGVDWLQDQI 181
Cdd:cd04152 160 EGLEKLYEMI 169
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 19-173 1.01e-35

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 122.52  E-value: 1.01e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKpsNAQSQNILPTIGFSIEKFKS-SSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSS 97
Cdd:cd04156   1 QVLLLGLDSAGKSTLLYKLK--HAELVTTIPTVGFNVEMLQLeKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSS 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29826299  98 DRLRMVVAKEELDTLLNHPDIKHRriPILFFANKMDLRDAVTSVKVSQLLCLENI-KDKPWHICASDAIKGEGLQEG 173
Cdd:cd04156  79 DEARLDESQKELKHILKNEHIKGV--PVVLLANKQDLPGALTAEEITRRFKLKKYcSDRDWYVQPCSAVTGEGLAEA 153
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 20-181 2.32e-35

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 121.67  E-value: 2.32e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKPSnaQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR 99
Cdd:cd04158   2 VVTLGLDGAGKTTILFKLKQD--EFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHR 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299 100 LRMVVAKEELDTLLNHPDIkhRRIPILFFANKMDLRDAVTSVKVSQLLCLENI-KDKPWHICASDAIKGEGLQEGVDWLQ 178
Cdd:cd04158  80 DRVSEAHSELAKLLTEKEL--RDALLLIFANKQDVAGALSVEEMTELLSLHKLcCGRSWYIQGCDARSGMGLYEGLDWLS 157


                ...
gi 29826299 179 DQI 181
Cdd:cd04158 158 RQL 160
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 11-177 2.78e-34

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 119.69  E-value: 2.78e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  11 LGLKKKEVHVLCLGLDNSGKTTIINKLKpSNAQSQNIlPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAI 90
Cdd:cd00879  13 LGLYKKEAKIVFLGLDNAGKTTLLHMLK-DDRLAQHV-PTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGI 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  91 IFVIDSSDRLRMVVAKEELDTLLNHPDIKHRriPILFFANKMDLRDAVTSVKVSQLLCLEN------------IKDKPWH 158
Cdd:cd00879  91 VFLVDAADPERFQESKEELDSLLNDEELANV--PILILGNKIDKPGAVSEEELREALGLYGtttgkggvslkvSNIRPVE 168

                       170
                ....*....|....*....
gi 29826299 159 ICASDAIKGEGLQEGVDWL 177
Cdd:cd00879 169 VFMCSVVKRQGYGEGFRWL 187
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 20-179 1.57e-32

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 114.36  E-value: 1.57e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLK-------PSNAQSQnILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd04160   2 VLILGLDNAGKTTFLEQTKtkfsknyKGLNPSK-ITPTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  93 VIDSSDRLRMVVAKEELDTLLNHPDIKHrrIPILFFANKMDLRDAVTSVKVSQLLcleniKDKPWHICASD-------AI 165
Cdd:cd04160  81 VIDSTDRERFNESKSAFEKVINNEALEG--VPLLVLANKQDLPDALSVAEIKEVF-----DDCIALIGRRDclvqpvsAL 153

                       170
                ....*....|....
gi 29826299 166 KGEGLQEGVDWLQD 179
Cdd:cd04160 154 EGEGVEEGIEWLVD 167
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 20-177 3.74e-32

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 113.64  E-value: 3.74e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLkpSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR 99
Cdd:cd04161   2 LLTVGLDNAGKTTLVSAL--QGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDD 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299 100 LRMVVAKEELDTLLNHPDIKHRriPILFFANKMDLRDAVTSVKVSQLLCLENIKDK---PWHICASDAIKGEG------L 170
Cdd:cd04161  80 DRVQEVKEILRELLQHPRVSGK--PILVLANKQDKKNALLGADVIEYLSLEKLVNEnksLCHIEPCSAIEGLGkkidpsI 157


                ....*..
gi 29826299 171 QEGVDWL 177
Cdd:cd04161 158 VEGLRWL 164
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 23-177 1.58e-30

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 108.94  E-value: 1.58e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  23 LGLDNSGKTTIINKLKpSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRM 102
Cdd:cd04159   5 VGLQNSGKTTLVNVIA-SGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKL 83

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29826299 103 VVAKEELDTLLNHPDIKHrrIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 177
Cdd:cd04159  84 EVAKNELHDLLEKPSLEG--IPLLVLGNKNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 20-166 2.14e-28

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 103.68  E-value: 2.14e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKpSNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR 99
Cdd:cd04162   2 ILVLGLDGAGKTSLLHSLS-SERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADS 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29826299 100 LRMVVAKEELDTLLNHPDIkhrrIPILFFANKMDLRDAVTSVKVSQLLCLENI-KDKPWHICASDAIK 166
Cdd:cd04162  81 ERLPLARQELHQLLQHPPD----LPLVVLANKQDLPAARSVQEIHKELELEPIaRGRRWILQGTSLDD 144
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 11-181 1.74e-27

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 101.94  E-value: 1.74e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     11 LGLKKKEVHVLCLGLDNSGKTTIINKLKpsNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAI 90
Cdd:smart00178  11 LGLWNKHAKILFLGLDNAGKTTLLHMLK--NDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGI 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     91 IFVIDSSDRLRMVVAKEELDTLLNHPDIKhrRIPILFFANKMDLRDAVTSVKVSQLLCLEN-------IKDKPWHICASD 163
Cdd:smart00178  89 VYLVDAYDKERFAESKRELDALLSDEELA--TVPFLILGNKIDAPYAASEDELRYALGLTNtttgkgkVGVRPVEVFMCS 166

                          170
                   ....*....|....*...
gi 29826299    164 AIKGEGLQEGVDWLQDQI 181
Cdd:smart00178 167 VVRRMGYGEGFKWLSQYI 184
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 23-177 1.38e-16

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: 72.87  E-value: 1.38e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  23 LGLDNSGKTTIINKL--KPSNAQSQNILPTIGFSIEKF--KSSSLSFTVFDMSGQGRYRNLWE-----HYYKEGQAIIFV 93
Cdd:cd00882   3 VGRGGVGKSSLLNALlgGEVGEVSDVPGTTRDPDVYVKelDKGKVKLVLVDTPGLDEFGGLGReelarLLLRGADLILLV 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  94 IDSSDRlrmvvAKEELDTLLNHPDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPwhICASDAIKGEGLQEG 173
Cdd:cd00882  83 VDSTDR-----ESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVP--VFEVSAKTGEGVDEL 155


                ....
gi 29826299 174 VDWL 177
Cdd:cd00882 156 FEKL 159
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 19-147 1.42e-15

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 71.20  E-value: 1.42e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  19 HVLCLGLDNSGKTTIINKLKPSNAQSQ--NILPTIGFSIEKfKSSSLSFTVFDMSGQGRYRN-LWEHYYKEGQAIIFVID 95
Cdd:cd04105   2 TVLLLGPSDSGKTALFTKLTTGKVRSTvtSIEPNVASFYSN-SSKGKKLTLVDVPGHEKLRDkLLEYLKASLKAIVFVVD 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 29826299  96 SSDRLRMV--VAKEELDTLLNHPDIKHrRIPILFFANKMDLRDAVTSVKVSQLL 147
Cdd:cd04105  81 SATFQKNIrdVAEFLYDILTDLEKIKN-KIPILIACNKQDLFTAKPAKKIKELL 133
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 17-143 2.63e-13

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: 64.32  E-value: 2.63e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    17 EVHVLCLGLDNSGKTTIINKL---KPSNAQSQnilPTIGFSIEK----FKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQA 89
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLlgnKGSITEYY---PGTTRNYVTtvieEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVER 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826299    90 IIFVIDSSDRLRMVVAKEELDTllnhPDIKHRR---IPILFFANKMDLRDAVTSVKV 143
Cdd:TIGR00231  78 SLRVFDIVILVLDVEEILEKQT----KEIIHHAdsgVPIILVGNKIDLKDADLKTHV 130
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-172 3.61e-10

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 56.14  E-value: 3.61e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  15 KKEVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFK----SSSLSFTVFDMSGQGRYRNLWEHYYKEGQ-- 88
Cdd:COG1100   1 MGEKKIVVVGTGGVGKTSLVNRLVGDIFSLEKYLSTNGVTIDKKElkldGLDVDLVIWDTPGQDEFRETRQFYARQLTga 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  89 -AIIFVIDSSDRLRMVVAKEELDTLLNHpdikHRRIPILFFANKMDLRDAVtsVKVSQLLCLENIKDK-PWHICASDAIK 166
Cdd:COG1100  81 sLYLFVVDGTREETLQSLYELLESLRRL----GKKSPIILVLNKIDLYDEE--EIEDEERLKEALSEDnIVEVVATSAKT 154


                ....*.
gi 29826299 167 GEGLQE 172
Cdd:COG1100 155 GEGVEE 160
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 20-133 4.11e-10

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: 54.82  E-value: 4.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    20 VLCLGLDNSGKTTIINKLKpSNAQSQNILPTIG-------FSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:pfam08477   2 VVLLGDSGVGKTSLLKRFV-DDTFDPKYKSTIGvdfktktVLENDDNGKKIKLNIWDTAGQERFRSLHPFYYRGAAAALL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 29826299    93 VIDSSDrlrmvvaKEELDTLLNhpDIKHRR--IPILFFANKMD 133
Cdd:pfam08477  81 VYDSRT-------FSNLKYWLR--ELKKYAgnSPVILVGNKID 114
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 48-134 1.10e-09

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 56.06  E-value: 1.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    48 LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD----------RLRMVVAKEELDTLLNHPD 117
Cdd:pfam00503 152 VKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEydqvlyeddsTNRMEESLKLFEEICNSPW 231

                          90
                  ....*....|....*..
gi 29826299   118 IKHRRIpILFFaNKMDL 134
Cdd:pfam00503 232 FKNTPI-ILFL-NKKDL 246
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 29-136 6.56e-08

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: 49.76  E-value: 6.56e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  29 GKTTIINKLKpSNAQSQNILPTIG--FSIE--KFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRlrmvv 104
Cdd:cd00154  12 GKTSLLLRFV-DNKFSENYKSTIGvdFKSKtiEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNR----- 85

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 29826299 105 aK--EELDTLLNhpDIKHR---RIPILFFANKMDLRD 136
Cdd:cd00154  86 -EsfENLDKWLN--ELKEYappNIPIILVGNKSDLED 119
PLN03118 PLN03118
Rab family protein; Provisional
 20-99 1.53e-07

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 49.28  E-value: 1.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   20 VLCLGLDNSGKTTIINKLKPSNAQsqNILPTIG--FSIEKFK--SSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVID 95
Cdd:PLN03118  17 ILLIGDSGVGKSSLLVSFISSSVE--DLAPTIGvdFKIKQLTvgGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYD 94


                 ....
gi 29826299   96 SSDR 99
Cdd:PLN03118  95 VTRR 98
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
 45-134 2.98e-07

Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.


Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 49.06  E-value: 2.98e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  45 QNIL----PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR----------LRMVVAKEELD 110
Cdd:cd00066 139 QDILrsrvKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYdqvlvedesvNRMQESLKLFD 218

                        90       100
                ....*....|....*....|....
gi 29826299 111 TLLNHPDIKHRRIpILFFaNKMDL 134
Cdd:cd00066 219 SICNSRWFANTSI-ILFL-NKKDL 240
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 20-134 1.55e-06

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: 45.76  E-value: 1.55e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKpSNAQSQNILPTIGFSiekFKSSSLS-------FTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd01863   3 ILLIGDSGVGKSSLLLRFT-DDTFDEDLSSTIGVD---FKVKTVTvdgkkvkLAIWDTAGQERFRTLTSSYYRGAQGVIL 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 29826299  93 VIDSSDRLRMVVAK---EELDTLLNHPDIKhrripILFFANKMDL 134
Cdd:cd01863  79 VYDVTRRDTFDNLDtwlNELDTYSTNPDAV-----KMLVGNKIDK 118
Rab32_Rab38 cd04107
Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are ...
 20-151 3.12e-06

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: 45.76  E-value: 3.12e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKpSNAQSQNILPTIG--FS---IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVI 94
Cdd:cd04107   3 VLVIGDLGVGKTSIIKRYV-HGVFSQHYKATIGvdFAlkvIEWDPNTVVRLQLWDIAGQERFGGMTRVYYKGAVGAIIVF 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 29826299  95 DSSDR--LRMVVA-KEELDTLLNHPDikHRRIPILFFANKMDLRDAVTSVKVSQL--LCLEN 151
Cdd:cd04107  82 DVTRPstFEAVLKwKADLDSKVTLPN--GEPIPALLLANKCDLKKERLAKDPEQMdqFCKEN 141
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 45-134 4.87e-06

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 45.65  E-value: 4.87e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     45 QNIL----PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSS--DRL--------RMVVAKEELD 110
Cdd:smart00275 162 QDILrsrvPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSeyDQVleedestnRMQESLNLFE 241

                           90       100
                   ....*....|....*....|....
gi 29826299    111 TLLNHPdiKHRRIPILFFANKMDL 134
Cdd:smart00275 242 SICNSR--WFANTSIILFLNKIDL 263
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
 23-136 1.02e-05

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: 44.23  E-value: 1.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     23 LGLDNSGKTTIInKLKPSNAQSQNILPTIGFSIEKF----KSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSD 98
Cdd:smart00176   1 VGDGGTGKTTFV-KRHLTGEFEKKYVATLGVEVHPLvfhtNRGPIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTA 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 29826299     99 RLrmvvakeeldTLLNHPDIkHR-------RIPILFFANKMDLRD 136
Cdd:smart00176  80 RV----------TYKNVPNW-HRdlvrvceNIPIVLCGNKVDVKD 113
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
 28-137 1.56e-05

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: 43.06  E-value: 1.56e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  28 SGKTTIINKLKPSNAQSQNIlPTIGFSIEKFKSSS----LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLrmv 103
Cdd:cd00877  11 TGKTTFVKRHLTGEFEKKYV-ATLGVEVHPLDFHTnrgkIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRV--- 86

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 29826299 104 vakeeldTLLNHPDIkHRR-------IPILFFANKMDLRDA 137
Cdd:cd00877  87 -------TYKNVPNW-HRDlvrvcenIPIVLCGNKVDIKDR 119
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
 29-117 1.65e-05

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: 43.33  E-value: 1.65e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  29 GKTTIINKLkPSNAQSQNILPTIG--FSIEKFKSSSLSFTV--FDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVV 104
Cdd:cd04108  12 GKTCLINRF-CKDVFDKNYKATIGvdFEMERFEVLGVPFSLqlWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEH 90

                        90
                ....*....|...
gi 29826299 105 AKEELDTLLNHPD 117
Cdd:cd04108  91 TRQWLEDALKEND 103
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 23-181 1.71e-05

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 43.00  E-value: 1.71e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  23 LGLDNSGKTTIINKLkpSNaqsQNILPT----------IGFSIEKFKSSSLSFT----VFDMSGQGRYRN--LWEHyYKE 86
Cdd:cd00880   3 FGRPNVGKSSLLNAL--LG---QNVGIVspipgttrdpVRKEWELLPLGPVVLIdtpgLDEEGGLGRERVeeARQV-ADR 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  87 GQAIIFVIDSSDRLrmvvakEELDTLLNhpDIKHRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPwhICASDAIK 166
Cdd:cd00880  77 ADLVLLVVDSDLTP------VEEEAKLG--LLRERGKPVLLVLNKIDLVPESEEEELLRERKLELLPDLP--VIAVSALP 146

                       170
                ....*....|....*
gi 29826299 167 GEGLQEgvdwLQDQI 181
Cdd:cd00880 147 GEGIDE----LRKKI 157
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 29-136 3.62e-05

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: 42.12  E-value: 3.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    29 GKTTIINKLkpsnaqSQNI-----LPTIGFSiekFKSSSLS-------FTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDS 96
Cdd:pfam00071  11 GKSSLLIRF------TQNKfpeeyIPTIGVD---FYTKTIEvdgktvkLQIWDTAGQERFRALRPLYYRGADGFLLVYDI 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 29826299    97 SDRlrmvvakeelDTLLN----HPDIKH---RRIPILFFANKMDLRD 136
Cdd:pfam00071  82 TSR----------DSFENvkkwVEEILRhadENVPIVLVGNKCDLED 118
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 29-136 3.69e-05

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 42.11  E-value: 3.69e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299     29 GKTTIINKLKpSNAQSQNILPTIGfsIEkFKSSSLSF-------TVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDR-- 99
Cdd:smart00175  12 GKSSLLSRFT-DGKFSEQYKSTIG--VD-FKTKTIEVdgkrvklQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRes 87

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 29826299    100 -LRMVVAKEELDTLLNHPdikhrrIPILFFANKMDLRD 136
Cdd:smart00175  88 fENLENWLKELREYASPN------VVIMLVGNKSDLEE 119
Rab9 cd04116
Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate ...
 14-151 5.77e-05

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: 41.78  E-value: 5.77e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  14 KKKEVHVLCLGLDNSGKTTIINKLKPSNAQSQNiLPTIGFsieKFKSSSL-------SFTVFDMSGQGRYRNLWEHYYKE 86
Cdd:cd04116   2 KSSLLKVILLGDGGVGKSSLMNRYVTNKFDTQL-FHTIGV---EFLNKDLevdghfvTLQIWDTAGQERFRSLRTPFYRG 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29826299  87 GQA--IIFVIDSSDRLR-MVVAKEEldtLLNHPDIKH-RRIPILFFANKMDLRDAVTSVKVSQLLCLEN 151
Cdd:cd04116  78 SDCclLTFSVDDSQSFQnLSNWKKE---FIYYADVKEpESFPFVILGNKIDIPERQVSTEEAQAWCRDN 143
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 20-147 1.27e-04

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 40.89  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    20 VLCLGLDNSGKTTIINKL-----KPSNAqsqNILPTIGFSIEKFKSSslSFTVFDMSGQG--RYRNLWEHYYKEG-QAII 91
Cdd:pfam09439   6 VIIAGLCDSGKTSLFTLLttdsvRPTVT---SQEPSAAYRYMLNKGN--SFTLIDFPGHVklRYKLLETLKDSSSlKGIV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826299    92 FVIDSS-DRLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDAVTSVKVSQLL 147
Cdd:pfam09439  81 FVVDSTiFPKEVTDTAEFLYDILSITELLKNGIDILIACNKQESFTARPPKKIKQAL 137
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
 29-146 2.11e-04

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 40.45  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299   29 GKTTIINKLKPSNAQSQNIlPTIGFSIE--KFKSS--SLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRlrmvv 104
Cdd:PTZ00132  21 GKTTFVKRHLTGEFEKKYI-PTLGVEVHplKFYTNcgPICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSR----- 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 29826299  105 akeelDTLLN----HPDIKH--RRIPILFFANKMDLRDavTSVKVSQL 146
Cdd:PTZ00132  95 -----ITYKNvpnwHRDIVRvcENIPIVLVGNKVDVKD--RQVKARQI 135
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 19-131 2.38e-04

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 39.14  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    19 HVLCLGLDNSGKTTIINKLKPSNAQSQNILP-TIGFSIEKFKSSSLSFTVFDM--------SGQGRYRNLWEHyyKEGQA 89
Cdd:pfam01926   1 RVALVGRPNVGKSTLINALTGAKAIVSDYPGtTRDPNEGRLELKGKQIILVDTpgliegasEGEGLGRAFLAI--IEADL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 29826299    90 IIFVIDSSDRLrmvvaKEELDTLLNHpdIKHRRIPILFFANK 131
Cdd:pfam01926  79 ILFVVDSEEGI-----TPLDEELLEL--LRENKKPIILVLNK 113
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
 20-99 1.01e-03

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: 38.03  E-value: 1.01e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLKPSNAQSQNIlPTIGFSiekFKSSSLS-------FTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd04117   3 LLLIGDSGVGKTCLLCRFTDNEFHSSHI-STIGVD---FKMKTIEvdgikvrIQIWDTAGQERYQTITKQYYRRAQGIFL 78


                ....*...
gi 29826299  93 VID-SSDR 99
Cdd:cd04117  79 VYDiSSER 86
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
 20-97 1.31e-03

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: 37.95  E-value: 1.31e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLCLGLDNSGKTTIINKLkpsnaqSQNILP-----TIG--FSIE--KFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAI 90
Cdd:cd04114  10 IVLIGNAGVGKTCLVRRF------TQGLFPpgqgaTIGvdFMIKtvEIKGEKIKLQIWDTAGQERFRSITQSYYRSANAL 83


                ....*..
gi 29826299  91 IFVIDSS 97
Cdd:cd04114  84 ILTYDIT 90
Obg_like cd01881
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ...
 24-175 1.64e-03

Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.


Pssm-ID: 206668 [Multi-domain]  Cd Length: 167  Bit Score: 37.37  E-value: 1.64e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  24 GLDNSGKTTIINKLKPSNAQSQNI-LPTIGFSIEKFKSSSL-SFTVFDM--------SGQGRYRNLWEHYYkEGQAIIFV 93
Cdd:cd01881   4 GLPNVGKSTLLSALTSAKVEIASYpFTTLEPNVGVFEFGDGvDIQIIDLpglldgasEGRGLGEQILAHLY-RSDLILHV 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  94 IDSSDRLRMVVAkEELDTL---LNHPDIKHRRIPILFFANKMDlrdavtSVKVSQLLCLENIKDKP-WHICASDAIKGEG 169
Cdd:cd01881  83 IDASEDCVGDPL-EDQKTLneeVSGSFLFLKNKPEMIVANKID------MASENNLKRLKLDKLKRgIPVVPTSALTRLG 155


                ....*.
gi 29826299 170 LQEGVD 175
Cdd:cd01881 156 LDRVIR 161
Gtr1_RagA pfam04670
Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a ...
 20-134 1.65e-03

Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologs of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.


Pssm-ID: 398377 [Multi-domain]  Cd Length: 231  Bit Score: 37.95  E-value: 1.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299    20 VLCLGLDNSGKTTIInKLKPSNAQSQNIL---PTIGFSIEKFKSSS-LSFTVFDMSGQGRYRNLWEHYYKEG-----QAI 90
Cdd:pfam04670   2 VLLMGLSGSGKSSMR-SVIFSNYSPRDTLrlgATIDVEHSHVRFLGnLVLNLWDCGGQDDFFDNYLTFQKEHifsnvGVL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 29826299    91 IFVIDSSDRLRMvvakEELDTLL--------NHPDIKhrripILFFANKMDL 134
Cdd:pfam04670  81 IYVFDVQSREYE----EDLARLKetiealyqYSPDAK-----VFVLIHKMDL 123
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
 18-99 3.38e-03

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: 36.56  E-value: 3.38e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  18 VHVLCLGLDNSGKTTIINKLKPSNAQSqNILPTIG--FSIEKFKSSSLSFTV--FDMSGQGRYRNLWEHYYKEGQAIIFV 93
Cdd:cd04119   1 IKVISMGNSGVGKSCIIKRYCEGRFVS-KYLPTIGidYGVKKVSVRNKEVRVnfFDLSGHPEYLEVRNEFYKDTQGVLLV 79


                ....*.
gi 29826299  94 IDSSDR 99
Cdd:cd04119  80 YDVTDR 85
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
 20-136 3.53e-03

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: 36.38  E-value: 3.53e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  20 VLcLGLDNSGKTTIINKLKpSNAQSQNILPTIGFSiekFKSSSLS-------FTVFDMSGQGRYRNLWEHYYKEGQAIIF 92
Cdd:cd01860   5 VL-LGDSSVGKSSIVLRFV-KNEFSENQESTIGAA---FLTQTVNlddttvkFEIWDTAGQERYRSLAPMYYRGAAAAIV 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 29826299  93 VIDSSDRLRMVVAKEELDTLLNH--PDIkhrripILFFA-NKMDLRD 136
Cdd:cd01860  80 VYDITSEESFEKAKSWVKELQEHgpPNI------VIALAgNKADLES 120
RabL2 cd04124
Rab GTPase-like family 2 (Rab-like2); RabL2 (Rab-like2) subfamily. RabL2s are novel Rab ...
 18-142 3.79e-03

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: 36.38  E-value: 3.79e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  18 VHVLCLGLDNSGKTTIINKLKPSNAQSQNiLPTIGFSIEK----FKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFV 93
Cdd:cd04124   1 VKIILLGDSAVGKSKLVERFLMDGYEPQQ-LSTYALTLYKhnakFEGKTILVDFWDTAGQERFQTMHASYYHKAHACILV 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 29826299  94 IDSSDRLRMVVAKEELDTLLNHpdikHRRIPILFFANKMDLRDAVTSVK 142
Cdd:cd04124  80 FDVTRKITYKNLSKWYEELREY----RPEIPCIVVANKIDLDPSVTQKK 124
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
 67-138 3.97e-03

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: 36.26  E-value: 3.97e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29826299  67 VFDMSGQGRYR-NLWEHYYKEGQAIIFVID-----SSDRLRMVVaKEELDTLLNHpdikhrRIPILFFANKMDLRDAV 138
Cdd:cd04115  55 LWDTAGQERFRkSMVQHYYRNVHAVVFVYDvtnmaSFHSLPSWI-EECEQHSLPN------EVPRILVGNKCDLREQI 125
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
 64-134 5.94e-03

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: 35.58  E-value: 5.94e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 29826299  64 SFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLnhpDIKHR-RIPILFFANKMDL 134
Cdd:cd00876  48 TLDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQIL---RVKDKeDVPIVLVGNKCDL 116
RabL4 cd04101
Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ...
 29-140 8.94e-03

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: 35.20  E-value: 8.94e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826299  29 GKTTIINKLKPSNAQSQ-NILPTIGFS-IEK-----FKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLR 101
Cdd:cd04101  12 GKSALVQMFHSDGATFQkNYTMTTGCDlVVKtvpvpDTSDSVELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVS 91

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 29826299 102 MVVAKEELDTLLNHPDIKHrrIPILFFANKMDL--RDAVTS 140
Cdd:cd04101  92 FNNCSRWINRVRTHSHGLH--TPGVLVGNKCDLtdRREVDA 130
 
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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