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Conserved domains on  [gi|15236426|ref|NP_192559|]
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P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
65-127 4.50e-38

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


The actual alignment was detected with superfamily member PLN03110:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 216  Bit Score: 127.74  E-value: 4.50e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426   65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:PLN03110 101 DNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQalaEKEGLSFLETSALEATNVEKAF 166
 
Name Accession Description Interval E-value
PLN03110 PLN03110
Rab GTPase; Provisional
65-127 4.50e-38

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 127.74  E-value: 4.50e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426   65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:PLN03110 101 DNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQalaEKEGLSFLETSALEATNVEKAF 166
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
65-127 2.39e-30

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


Pssm-ID: 206660 [Multi-domain]  Cd Length: 165  Bit Score: 106.49  E-value: 2.39e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHK---TESLSFLETSALEATNVEKAF 127
Cdd:cd01868  92 ENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAfaeKNGLSFIETSALDGTNVEEAF 157
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
65-127 1.07e-24

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 92.19  E-value: 1.07e-24
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426     65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:smart00175  89 ENLENWLKELREYASPNVVIMLVGNKSDLEEQRQVSREEAEafaEEHGLPFFETSAKTNTNVEEAF 154
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
65-127 1.04e-20

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: 81.79  E-value: 1.04e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426    65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDG---HKTESLSFLETSALEATNVEKAF 127
Cdd:pfam00071  88 ENVKKWVEEILRHADENVPIVLVGNKCDLEDQRVVSTEEGealAKELGLPFMETSAKTNENVEEAF 153
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
63-127 2.14e-08

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: 49.68  E-value: 2.14e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15236426    63 MKERLQRWLRELRDHADSNIVIMMAGNKADLNHlRSVAEEDGHKTESLSFL---ETSALEATNVEKAF 127
Cdd:TIGR00231  91 VEEILEKQTKEIIHHADSGVPIILVGNKIDLKD-ADLKTHVASEFAKLNGEpiiPLSAETGKNIDSAF 157
 
Name Accession Description Interval E-value
PLN03110 PLN03110
Rab GTPase; Provisional
65-127 4.50e-38

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 127.74  E-value: 4.50e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426   65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:PLN03110 101 DNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQalaEKEGLSFLETSALEATNVEKAF 166
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
65-127 2.39e-30

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


Pssm-ID: 206660 [Multi-domain]  Cd Length: 165  Bit Score: 106.49  E-value: 2.39e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHK---TESLSFLETSALEATNVEKAF 127
Cdd:cd01868  92 ENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAfaeKNGLSFIETSALDGTNVEEAF 157
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
65-127 1.07e-24

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 92.19  E-value: 1.07e-24
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426     65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:smart00175  89 ENLENWLKELREYASPNVVIMLVGNKSDLEEQRQVSREEAEafaEEHGLPFFETSAKTNTNVEEAF 154
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
65-127 1.04e-20

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: 81.79  E-value: 1.04e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426    65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDG---HKTESLSFLETSALEATNVEKAF 127
Cdd:pfam00071  88 ENVKKWVEEILRHADENVPIVLVGNKCDLEDQRVVSTEEGealAKELGLPFMETSAKTNENVEEAF 153
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
65-127 9.33e-20

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: 79.13  E-value: 9.33e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd01860  90 EKAKSWVKELQEHGPPNIVIALAGNKADLESKRQVSTEEAQeyaDENGLLFMETSAKTGENVNELF 155
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
65-127 9.99e-19

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: 76.34  E-value: 9.99e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd00154  89 ENLDKWLNELKEYAPPNIPIILVGNKSDLEDERQVSTEEAQqfaKENGLLFFETSAKTGENVDEAF 154
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
65-127 1.22e-17

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


Pssm-ID: 206658 [Multi-domain]  Cd Length: 168  Bit Score: 74.00  E-value: 1.22e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd01866  93 NHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYEEGEafaREHGLIFMETSAKTASNVEEAF 158
PLN03108 PLN03108
Rab family protein; Provisional
67-127 4.70e-16

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 70.74  E-value: 4.70e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426   67 LQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:PLN03108  97 LASWLEDARQHANANMTIMLIGNKCDLAHRRAVSTEEGEqfaKEHGLIFMEASAKTAQNVEEAF 160
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
65-127 1.19e-12

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


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 60.91  E-value: 1.19e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDG----HKTESLSFLETSALEATNVEKAF 127
Cdd:cd01864  92 ESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQREVLFEEActlaEHYGILAVLETSAKESSNVEEAF 158
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
65-127 2.14e-12

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


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 60.36  E-value: 2.14e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTES---LSFLETSALEATNVEKAF 127
Cdd:cd01867  92 ENIKNWMRNIDEHASEDVERMLVGNKCDMEEKRVVSKEEGEALAReygIKFLETSAKANINVEEAF 157
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
67-127 5.83e-12

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: 59.14  E-value: 5.83e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426  67 LQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAE---EDGHKTESLSFLETSALEATNVEKAF 127
Cdd:cd04114  98 LPEWLREIEQYANNKVITILVGNKIDLAERREVSQqraEEFSDAQDMYYLETSAKESDNVEKLF 161
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
65-127 8.26e-12

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


Pssm-ID: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 58.40  E-value: 8.26e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd01861  89 DNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGEkkaKENNAMFIETSAKAGHNVKQLF 154
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
60-127 4.57e-10

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


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 54.07  E-value: 4.57e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15236426  60 RSLMKERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHK---TESLSFLETSALEATNVEKAF 127
Cdd:cd04122  86 RRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYEEAKQfadENGLLFLECSAKTGENVEDAF 156
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
65-127 6.89e-10

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


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 53.49  E-value: 6.89e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHK-TESL--SFLETSALEATNVEKAF 127
Cdd:cd01869  91 NNVKQWLQEIDRYASENVNKLLVGNKCDLTDKKVVDYTEAKEfADELgiPFLETSAKNATNVEEAF 156
Rab4 cd04113
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ...
67-127 7.62e-10

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


Pssm-ID: 206696 [Multi-domain]  Cd Length: 161  Bit Score: 53.59  E-value: 7.62e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15236426  67 LQRWLRELRDHADSNIVIMMAGNKADLNHLRSV--------AEEDGhktesLSFLETSALEATNVEKAF 127
Cdd:cd04113  91 LTNWLTDARTLASPDIVIILVGNKKDLEDDREVtfleasrfAQENG-----LLFLETSALTGENVEEAF 154
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
65-127 1.02e-09

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: 52.91  E-value: 1.02e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDhaDSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd00876  90 KNIREQILRVKD--KEDVPIVLVGNKCDLENERQVSTEEGEalaEEWGCPFLETSAKTNINIDELF 153
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
65-127 2.87e-09

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


Pssm-ID: 206695 [Multi-domain]  Cd Length: 191  Bit Score: 52.56  E-value: 2.87e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04112  90 DNIRAWLTEILEYAQSDVVIMLLGNKADMSGERVVKREDGErlaKEYGVPFMETSAKTGLNVELAF 155
Ras2 cd04144
Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases); The Ras2 subfamily, ...
65-127 3.75e-09

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


Pssm-ID: 133344 [Multi-domain]  Cd Length: 190  Bit Score: 52.16  E-value: 3.75e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15236426  65 ERLQRW---LRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04144  87 ERVERFreqIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAalaRRLGCEFIEASAKTNVNVERAF 155
RAS smart00173
Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. ...
71-127 5.80e-09

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


Pssm-ID: 214541 [Multi-domain]  Cd Length: 164  Bit Score: 51.02  E-value: 5.80e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15236426     71 LRE--LRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKAF 127
Cdd:smart00173  93 FREqiLRVKDRDDVPIVLVGNKCDLESERVVSTEEGKELArqwGCPFLETSAKERVNVDEAF 154
small_GTPase smart00010
Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small ...
74-127 9.79e-09

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


Pssm-ID: 197466 [Multi-domain]  Cd Length: 166  Bit Score: 50.64  E-value: 9.79e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426     74 LRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKAF 127
Cdd:smart00010 100 LRVKDRDDVPIVLVGNKCDLENERVVSTEEGKELArqwGCPFLETSAKERINVDEAF 156
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
63-127 2.14e-08

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: 49.68  E-value: 2.14e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15236426    63 MKERLQRWLRELRDHADSNIVIMMAGNKADLNHlRSVAEEDGHKTESLSFL---ETSALEATNVEKAF 127
Cdd:TIGR00231  91 VEEILEKQTKEIIHHADSGVPIILVGNKIDLKD-ADLKTHVASEFAKLNGEpiiPLSAETGKNIDSAF 157
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
58-127 3.70e-08

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


Pssm-ID: 133323 [Multi-domain]  Cd Length: 162  Bit Score: 48.76  E-value: 3.70e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15236426  58 DGRSLMKERLqrWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04123  84 DADSFQKVKK--WIKELKQMRGNNISLVIVGNKIDLERQRVVSKSEAEeyaKSVGAKHFETSAKTGKGIEELF 154
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
65-127 1.21e-07

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


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 48.22  E-value: 1.21e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426  65 ERLQRWLRELRDHAD-SNIVIMMAGNKADLNHLRSVAEEDGHKTES---LSFLETSALEATNVEKAF 127
Cdd:cd04111  92 EHVHDWLEEARSHIQpHRPVFILVGHKCDLESQRQVTREEAEKLAKdlgMKYIETSARTGDNVEEAF 158
RheB cd04137
Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) ...
74-127 2.73e-07

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


Pssm-ID: 206709 [Multi-domain]  Cd Length: 180  Bit Score: 46.86  E-value: 2.73e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426  74 LRDHADSNIVIMMAGNKADLNHLRSVAEEDGHK-TESL--SFLETSALEATNVEKAF 127
Cdd:cd04137  99 LDMLGKESVPIVLVGNKSDLHMERQVSAEEGKKlAESWgaAFLESSAKENENVEEAF 155
RSR1 cd04177
RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that ...
71-127 3.71e-07

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


Pssm-ID: 133377 [Multi-domain]  Cd Length: 168  Bit Score: 46.32  E-value: 3.71e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15236426  71 LRE--LRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTES----LSFLETSALEATNVEKAF 127
Cdd:cd04177  94 LREqvLRIKDSDNVPMVLVGNKADLEDDRQVSREDGVSLSQqwgnVPFYETSARKRTNVDEVF 156
RalA_RalB cd04139
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ...
70-127 7.02e-07

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


Pssm-ID: 206710 [Multi-domain]  Cd Length: 163  Bit Score: 45.49  E-value: 7.02e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15236426  70 WLRELRDHADSNIVIMMAGNKADLNHLRSVA-EEDGHKTES--LSFLETSALEATNVEKAF 127
Cdd:cd04139  94 REQILRVKEDDNVPLLLVGNKCDLEDKRQVSvEEAANLAEQwgVNYVETSAKTRANVDKVF 154
M_R_Ras_like cd04145
R-Ras2/TC21, M-Ras/R-Ras3; The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, ...
84-127 8.30e-07

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


Pssm-ID: 133345 [Multi-domain]  Cd Length: 164  Bit Score: 45.48  E-value: 8.30e-07
                        10        20        30        40
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gi 15236426  84 IMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKAF 127
Cdd:cd04145 110 MILVGNKADLEHQRQVSREEGQELArqlKIPYIETSAKDRVNVDKAF 156
ARHI_like cd04140
A Ras homolog member I (ARHI); ARHI (A Ras homolog member I) is a member of the Ras family ...
71-127 1.49e-06

A Ras homolog member I (ARHI); ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. 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: 206711 [Multi-domain]  Cd Length: 165  Bit Score: 44.82  E-value: 1.49e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236426  71 LRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04140  98 ICEIKGNNLEKIPIMLVGNKCDESPSREVSSSEGAalaRTWNCAFMETSAKTNHNVQELF 157
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
65-127 2.02e-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: 44.22  E-value: 2.02e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426  65 ERLQRWLRELRDHADS-NIVIMMAGNKADLNHlRSVAEEDGHK---TESLSFLETSALEATNVEKAF 127
Cdd:cd01863  89 DNLDTWLNELDTYSTNpDAVKMLVGNKIDKEN-REVTREEGQKfarKHNMLFIETSAKTRIGVQQAF 154
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
65-127 5.24e-06

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: 43.11  E-value: 5.24e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15236426  65 ERLQRWLRELRDHADS-----NIVIMMAGNKADLNHLRSVAEEDGHK-TESLSFL--ETSALEATNVEKAF 127
Cdd:cd04119  89 EALDSWLKEMKQEGGPhgnmeNIVVVVCANKIDLTKHRAVSEDEGRLwAESKGFKyfETSACTGEGVNEMF 159
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
67-127 6.10e-06

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


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 42.98  E-value: 6.10e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426  67 LQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKAF 127
Cdd:cd01865  92 VQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVSAERGRQLAdqlGFEFFEASAKENINVKQVF 155
Rab7 cd01862
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ...
65-127 1.18e-05

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


Pssm-ID: 206655 [Multi-domain]  Cd Length: 172  Bit Score: 42.27  E-value: 1.18e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426  65 ERLQRWLRELRDHADSN-------IVImmaGNKADLNHLRSVAEEDGHK----TESLSFLETSALEATNVEKAF 127
Cdd:cd01862  89 ESLDSWRDEFLIQASPRdpenfpfVVL---GNKIDLEEKRQVSTKKAQQwcksKGNIPYFETSAKEAINVDQAF 159
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
70-126 1.86e-05

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


Pssm-ID: 206700 [Multi-domain]  Cd Length: 180  Bit Score: 41.72  E-value: 1.86e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15236426  70 WLRELRDHADS-NIVIMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKA 126
Cdd:cd04127 108 WMSQLQAHAYCeNPDIVLIGNKADLPDQREVSERQARELAdkyGIPYFETSAATGQNVEKA 168
RERG_RasL11_like cd04146
Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like ...
66-127 5.27e-05

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


Pssm-ID: 206713 [Multi-domain]  Cd Length: 166  Bit Score: 40.34  E-value: 5.27e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  66 RLQRWLRELRdHADSNIVIMMAGNKADLNHLRSVAEEDGHKTES---LSFLETSALE-ATNVEKAF 127
Cdd:cd04146  93 QLLQLIREIK-KRDGEIPVILVGNKADLLHSRQVSTEEGQKLALelgCLFFEVSAAEnYLEVQNVF 157
PTZ00369 PTZ00369
Ras-like protein; Provisional
74-127 5.59e-05

Ras-like protein; Provisional


Pssm-ID: 240385 [Multi-domain]  Cd Length: 189  Bit Score: 40.62  E-value: 5.59e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426   74 LRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:PTZ00369 103 LRVKDKDRVPMILVGNKCDLDSERQVSTGEGQelaKSFGIPFLETSAKQRVNVDEAF 159
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
58-92 2.19e-04

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: 37.87  E-value: 2.19e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15236426    58 DGRSlmKERLQRWLRELRDHADsNIVIMMAGNKAD 92
Cdd:pfam08477  83 DSRT--FSNLKYWLRELKKYAG-NSPVILVGNKID 114
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
67-127 2.51e-04

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


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 38.68  E-value: 2.51e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426  67 LQRWLRELRDHADSnIVIMMAGNKADLNHLRSVAEEDGHK---TESLSFLETSALEATNVEKAF 127
Cdd:cd04110  97 VKRWLQEIEQNCDD-VCKVLVGNKNDDPERKVVETEDAYKfagQMGISLFETSAKENINVEEMF 159
PLN03118 PLN03118
Rab family protein; Provisional
70-127 4.03e-04

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 38.50  E-value: 4.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15236426   70 WLRELRDHA-DSNIVIMMAGNKADLNHLRSVAEEDG---HKTESLSFLETSALEATNVEKAF 127
Cdd:PLN03118 108 WGKEVELYStNQDCVKMLVGNKVDRESERDVSREEGmalAKEHGCLFLECSAKTRENVEQCF 169
PTZ00099 PTZ00099
rab6; Provisional
65-127 7.59e-04

rab6; Provisional


Pssm-ID: 185444 [Multi-domain]  Cd Length: 176  Bit Score: 37.42  E-value: 7.59e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426   65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTE---SLSFLETSALEATNVEKAF 127
Cdd:PTZ00099  69 ENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAqeyNTMFHETSAKAGHNIKVLF 134
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
65-127 7.95e-04

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: 37.26  E-value: 7.95e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDGHKTESL---SFLETSALEATNVEKAF 127
Cdd:cd04117  89 QHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQGNKLAKEygmDFFETSACTNKNIKESF 154
Rap_like cd04136
Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, ...
71-127 9.11e-04

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


Pssm-ID: 206708 [Multi-domain]  Cd Length: 164  Bit Score: 37.15  E-value: 9.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15236426  71 LRELRDH----ADSNIVIM-MAGNKADLNHLRSVAEEDGHKTES----LSFLETSALEATNVEKAF 127
Cdd:cd04136  91 LQDLREQilrvKDTEDVPMiLVGNKCDLEDERVVSKEEGQNLARqwgnCPFLETSAKSKINVDEIF 156
Rap2 cd04176
Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c; The Rap2 subgroup is part of the Rap ...
81-127 1.32e-03

Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c; The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, including the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. 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: 133376 [Multi-domain]  Cd Length: 163  Bit Score: 36.74  E-value: 1.32e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15236426  81 NIVIMMAGNKADLNHLRSVAEEDGHKTESL---SFLETSALEATNVEKAF 127
Cdd:cd04176 106 KVPIILVGNKVDLESEREVSSAEGRALAEEwgcPFMETSAKSKTMVNELF 155
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
65-127 1.69e-03

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


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 36.53  E-value: 1.69e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15236426  65 ERLQRWLRELRDHADSNIVIMMAGNKADLNHLRSVAEEDG----HKTESLSFLETSALEATNVEKAF 127
Cdd:cd04120  89 DDLPKWMKMIDKYASEDAELLLVGNKLDCETDREITRQQGekfaQQITGMRFCEASAKDNFNVDEIF 155
Rap1 cd04175
Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap ...
71-127 1.72e-03

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


Pssm-ID: 133375 [Multi-domain]  Cd Length: 164  Bit Score: 36.34  E-value: 1.72e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15236426  71 LRE--LRDHADSNIVIMMAGNKADLNHLRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04175  94 LREqiLRVKDTEDVPMILVGNKCDLEDERVVGKEQGQnlaRQWGCAFLETSAKAKINVNEIF 155
RGK cd04148
Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases; RGK subfamily. The RGK (Rem, Rem2, Rad, ...
58-127 2.12e-03

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


Pssm-ID: 206715 [Multi-domain]  Cd Length: 219  Bit Score: 36.23  E-value: 2.12e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236426  58 DGRSLMK-ERLQRWLRELRDHADsnIVIMMAGNKADLNHLRSVAEEDGHKTESL---SFLETSALEATNVEKAF 127
Cdd:cd04148  84 DRSSFEKaSELRIQLRRARQAED--IPIILVGNKSDLVRSREVSVQEGRACAVVfdcKFIETSAALQHNVDELF 155
H_N_K_Ras_like cd04138
Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B; H-Ras/N-Ras/K-Ras subfamily. H-Ras, ...
84-127 7.54e-03

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


Pssm-ID: 133338 [Multi-domain]  Cd Length: 162  Bit Score: 34.32  E-value: 7.54e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15236426  84 IMMAGNKADLNHlRSVAEEDGH---KTESLSFLETSALEATNVEKAF 127
Cdd:cd04138 109 MVLVGNKCDLAA-RTVSTRQGQdlaKSYGIPYIETSAKTRQGVEEAF 154
 
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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