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Conserved domains on  [gi|755524411|ref|XP_011240344|]
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ras-related protein Rab-20 isoform X1 [Mus musculus]

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 ...
 11-185 4.63e-89

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 cd04126:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 220  Bit Score: 260.22  E-value: 4.63e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKEGpasgkvG 90
Cdd:cd04126   53 GREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQEKDA------G 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 SCVSTKVPKQVQPEDAVALYKKILKYKMLDEREMPAAEQMCFETSAKTGYNVDLLFETLFDLVVPMIMRQRAEESDqTVD 170
Cdd:cd04126  127 DRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGYNVDELFEYLFNLVLPLILAQRAEANR-TQG 205

                        170
                 ....*....|....*
gi 755524411 171 IASCKTPKQTRSGCC 185
Cdd:cd04126  206 TVNLPNPKRSKSKCC 220
 
Name Accession Description Interval E-value
Rab20 cd04126
Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be ...
 11-185 4.63e-89

Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. 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: 133326 [Multi-domain]  Cd Length: 220  Bit Score: 260.22  E-value: 4.63e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKEGpasgkvG 90
Cdd:cd04126   53 GREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQEKDA------G 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 SCVSTKVPKQVQPEDAVALYKKILKYKMLDEREMPAAEQMCFETSAKTGYNVDLLFETLFDLVVPMIMRQRAEESDqTVD 170
Cdd:cd04126  127 DRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGYNVDELFEYLFNLVLPLILAQRAEANR-TQG 205

                        170
                 ....*....|....*
gi 755524411 171 IASCKTPKQTRSGCC 185
Cdd:cd04126  206 TVNLPNPKRSKSKCC 220
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 11-149 2.01e-19

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: 80.25  E-value: 2.01e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411   11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:pfam00071  57 GQERFRALRPLYYRGADGFLLVYDITSRDSFENVKKWVEEILRHADENVPIVLVGNKCDLEDQR---------------- 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411   91 scvstkvpkQVQPEDAVALYKKI-LKYkmlderempaaeqmcFETSAKTGYNVDLLFETL 149
Cdd:pfam00071 121 ---------VVSTEEGEALAKELgLPF---------------METSAKTNENVEEAFEEL 156
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 11-149 7.31e-17

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 73.70  E-value: 7.31e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411    11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:smart00175  58 GQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQR---------------- 121

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411    91 scvstkvpkQVQPEDAVALYKkilKYKMlderempaaeqMCFETSAKTGYNVDLLFETL 149
Cdd:smart00175 122 ---------QVSREEAEAFAE---EHGL-----------PFFETSAKTNTNVEEAFEEL 157
PLN03118 PLN03118
Rab family protein; Provisional
 11-186 4.78e-13

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 64.69  E-value: 4.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTE--TANNDCLFAIVGNKVDLTSERDteggekegpasgk 88
Cdd:PLN03118  71 GQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVElySTNQDCVKMLVGNKVDRESERD------------- 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  89 vgscvstkvpkqVQPEDAVALykkilkykmlderempAAEQMC--FETSAKTGYNVDLLFETLFDLV--VPMIMrqraEE 164
Cdd:PLN03118 138 ------------VSREEGMAL----------------AKEHGClfLECSAKTRENVEQCFEELALKImeVPSLL----EE 185

                        170       180
                 ....*....|....*....|....*.
gi 755524411 165 SDQTV--DIASCKTPKQ--TRSGCCA 186
Cdd:PLN03118 186 GSTAVkrNILKQKPEHQppPNGGCCS 211
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
11-166 5.41e-08

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 50.36  E-value: 5.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCR---GAAAIILTYDVNHPQSLFELEDrFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKEgpasg 87
Cdd:COG1100   62 GQDEFRETRQFYARqltGASLYLFVVDGTREETLQSLYE-LLESLRRLGKKSPIILVLNKIDLYDEEEIEDEERL----- 135

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411  88 kvgscvstkvpKQVQPEDAVALYkkilkykmlderempaaeqmcFETSAKTGYNVDLLFETLFDlvvpmIMRQRAEESD 166
Cdd:COG1100  136 -----------KEALSEDNIVEV---------------------VATSAKTGEGVEELFAALAE-----ILRGEGDSLD 177
 
Name Accession Description Interval E-value
Rab20 cd04126
Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be ...
 11-185 4.63e-89

Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. 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: 133326 [Multi-domain]  Cd Length: 220  Bit Score: 260.22  E-value: 4.63e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKEGpasgkvG 90
Cdd:cd04126   53 GREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQEKDA------G 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 SCVSTKVPKQVQPEDAVALYKKILKYKMLDEREMPAAEQMCFETSAKTGYNVDLLFETLFDLVVPMIMRQRAEESDqTVD 170
Cdd:cd04126  127 DRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGYNVDELFEYLFNLVLPLILAQRAEANR-TQG 205

                        170
                 ....*....|....*
gi 755524411 171 IASCKTPKQTRSGCC 185
Cdd:cd04126  206 TVNLPNPKRSKSKCC 220
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 11-151 3.36e-22

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: 87.51  E-value: 3.36e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd00154   58 GQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDER---------------- 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  91 scvstkvpkQVQPEDAVALYKkilKYKMLderempaaeqmCFETSAKTGYNVDLLFETLFD 151
Cdd:cd00154  122 ---------QVSTEEAQQFAK---ENGLL-----------FFETSAKTGENVDEAFESLAR 159
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 11-149 2.01e-19

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: 80.25  E-value: 2.01e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411   11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:pfam00071  57 GQERFRALRPLYYRGADGFLLVYDITSRDSFENVKKWVEEILRHADENVPIVLVGNKCDLEDQR---------------- 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411   91 scvstkvpkQVQPEDAVALYKKI-LKYkmlderempaaeqmcFETSAKTGYNVDLLFETL 149
Cdd:pfam00071 121 ---------VVSTEEGEALAKELgLPF---------------METSAKTNENVEEAFEEL 156
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 11-149 7.31e-17

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 73.70  E-value: 7.31e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411    11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:smart00175  58 GQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQR---------------- 121

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411    91 scvstkvpkQVQPEDAVALYKkilKYKMlderempaaeqMCFETSAKTGYNVDLLFETL 149
Cdd:smart00175 122 ---------QVSREEAEAFAE---EHGL-----------PFFETSAKTNTNVEEAFEEL 157
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
 11-149 2.88e-16

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: 72.20  E-value: 2.88e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd01860   59 GQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLESKR---------------- 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  91 scvstkvpkQVQPEDAVALykkilkykmlderempAAEQMC--FETSAKTGYNVDLLFETL 149
Cdd:cd01860  123 ---------QVSTEEAQEY----------------ADENGLlfMETSAKTGENVNELFTEI 158
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
 11-154 7.99e-15

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: 68.40  E-value: 7.99e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd04123   58 GQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQR---------------- 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755524411  91 scvstkvpkQVQPEDAVALYKKI-LKYkmlderempaaeqmcFETSAKTGYNVDLLFETLFDLVV 154
Cdd:cd04123  122 ---------VVSKSEAEEYAKSVgAKH---------------FETSAKTGKGIEELFLSLAKRMI 162
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 11-149 7.45e-14

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: 65.80  E-value: 7.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGL-TETANNDCLFAIVGNKVDltserdteggekegpasgkv 89
Cdd:cd01863   58 GQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELdTYSTNPDAVKMLVGNKID-------------------- 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  90 gscvstKVPKQVQPEDAVALYKkilKYKMLderempaaeqmcF-ETSAKTGYNVDLLFETL 149
Cdd:cd01863  118 ------KENREVTREEGQKFAR---KHNML------------FiETSAKTRIGVQQAFEEL 157
Rab7 cd01862
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ...
 11-149 8.50e-14

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: 65.76  E-value: 8.50e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELE---DRFLGLTETANNDCL-FAIVGNKVDLTSERDteggekegpas 86
Cdd:cd01862   58 GQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDswrDEFLIQASPRDPENFpFVVLGNKIDLEEKRQ----------- 126

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  87 gkvgscVSTKvpkqvqpedavalykkilkykmlderempAAEQMC--------FETSAKTGYNVDLLFETL 149
Cdd:cd01862  127 ------VSTK-----------------------------KAQQWCkskgnipyFETSAKEAINVDQAFETI 162
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
 11-113 2.34e-13

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: 64.57  E-value: 2.34e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERD--TEGGEKEGPASGK 88
Cdd:cd01861   58 GQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQvsTEEGEKKAKENNA 137

                         90       100
                 ....*....|....*....|....*
gi 755524411  89 VGSCVSTKVPKQVQPedavaLYKKI 113
Cdd:cd01861  138 MFIETSAKAGHNVKQ-----LFKKI 157
PLN03118 PLN03118
Rab family protein; Provisional
 11-186 4.78e-13

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 64.69  E-value: 4.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTE--TANNDCLFAIVGNKVDLTSERDteggekegpasgk 88
Cdd:PLN03118  71 GQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVElySTNQDCVKMLVGNKVDRESERD------------- 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  89 vgscvstkvpkqVQPEDAVALykkilkykmlderempAAEQMC--FETSAKTGYNVDLLFETLFDLV--VPMIMrqraEE 164
Cdd:PLN03118 138 ------------VSREEGMAL----------------AKEHGClfLECSAKTRENVEQCFEELALKImeVPSLL----EE 185

                        170       180
                 ....*....|....*....|....*.
gi 755524411 165 SDQTV--DIASCKTPKQ--TRSGCCA 186
Cdd:PLN03118 186 GSTAVkrNILKQKPEHQppPNGGCCS 211
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
 11-149 2.44e-11

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: 59.08  E-value: 2.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELE---DRFLGLTETANNDCLfaIVGNKVDLTSERdteggekegpasg 87
Cdd:cd00876   56 GQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKnirEQILRVKDKEDVPIV--LVGNKCDLENER------------- 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755524411  88 kvgscvstkvpkQVQPEDAVALykkilkykmlderempAAEQMC--FETSAKTGYNVDLLFETL 149
Cdd:cd00876  121 ------------QVSTEEGEAL----------------AEEWGCpfLETSAKTNINIDELFNTL 156
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
 11-150 3.23e-10

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: 56.03  E-value: 3.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSlFELEDRFLG-LTETANNDCLFAIVGNKVDLTSERdteggekegpasgkv 89
Cdd:cd01868   61 GQERYRAITSAYYRGAVGALLVYDITKKST-FENVERWLKeLRDHADSNIVIMLVGNKSDLRHLR--------------- 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755524411  90 gscvstkvpkQVQPEDAVALYKKilkykmlderempaaEQMCF-ETSAKTGYNVDLLFETLF 150
Cdd:cd01868  125 ----------AVPTEEAKAFAEK---------------NGLSFiETSALDGTNVEEAFKQLL 161
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
 11-149 1.22e-09

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: 54.52  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDteggekegpasgkvg 90
Cdd:cd04114   65 GQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAERRE--------------- 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 scvstkVPKQVQpedavalykkilkykmldeREMPAAEQMCF-ETSAKTGYNVDLLFETL 149
Cdd:cd04114  130 ------VSQQRA-------------------EEFSDAQDMYYlETSAKESDNVEKLFLDL 164
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
 11-149 2.35e-09

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: 53.81  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd01867   61 GQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDMEEKR---------------- 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 scvstkvpkQVQPEDAVALYKKI-LKYkmlderempaaeqmcFETSAKTGYNVDLLFETL 149
Cdd:cd01867  125 ---------VVSKEEGEALAREYgIKF---------------LETSAKANINVEEAFLTL 160
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
 11-149 2.39e-09

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: 53.87  E-value: 2.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDV-------NHPQSLFELeDRFlgltetANNDCLFAIVGNKVDLTSERDteggekeg 83
Cdd:cd01869   60 GQERFRTITSSYYRGAHGIIIVYDVtdqesfnNVKQWLQEI-DRY------ASENVNKLLVGNKCDLTDKKV-------- 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755524411  84 pasgkvgscVSTKVPKqvqpedavalykkilkyKMLDEREMPAaeqmcFETSAKTGYNVDLLFETL 149
Cdd:cd01869  125 ---------VDYTEAK-----------------EFADELGIPF-----LETSAKNATNVEEAFMTM 159
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
11-166 5.41e-08

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 50.36  E-value: 5.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCR---GAAAIILTYDVNHPQSLFELEDrFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKEgpasg 87
Cdd:COG1100   62 GQDEFRETRQFYARqltGASLYLFVVDGTREETLQSLYE-LLESLRRLGKKSPIILVLNKIDLYDEEEIEDEERL----- 135

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411  88 kvgscvstkvpKQVQPEDAVALYkkilkykmlderempaaeqmcFETSAKTGYNVDLLFETLFDlvvpmIMRQRAEESD 166
Cdd:COG1100  136 -----------KEALSEDNIVEV---------------------VATSAKTGEGVEELFAALAE-----ILRGEGDSLD 177
PLN03108 PLN03108
Rab family protein; Provisional
 11-113 1.81e-07

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 49.17  E-value: 1.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSER--DTEGGEKEGPASGK 88
Cdd:PLN03108  64 GQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRavSTEEGEQFAKEHGL 143

                         90       100
                 ....*....|....*....|....*...
gi 755524411  89 VGSCVSTKVPKQVQP---EDAVALYKKI 113
Cdd:PLN03108 144 IFMEASAKTAQNVEEafiKTAAKIYKKI 171
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
 11-185 2.59e-07

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: 48.71  E-value: 2.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd04112   59 GQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSGER---------------- 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  91 scvstkvpkQVQPEDAVALYKkilkykmldEREMPAaeqmcFETSAKTGYNVDLLFetlfdLVVPMIMRQRAEE--SDQT 168
Cdd:cd04112  123 ---------VVKREDGERLAK---------EYGVPF-----METSAKTGLNVELAF-----TAVAKELKHRSVEqpDEPK 174

                        170
                 ....*....|....*..
gi 755524411 169 VDIASCKTPKQTRSGCC 185
Cdd:cd04112  175 FKIQDYVEKQKKSSGCC 191
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
 11-81 3.10e-07

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: 48.47  E-value: 3.10e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDT--EGGEK 81
Cdd:cd04120   58 GQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREItrQQGEK 130
PLN03110 PLN03110
Rab GTPase; Provisional
 11-186 7.74e-07

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 47.62  E-value: 7.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSlFELEDRFL-GLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkv 89
Cdd:PLN03110  70 GQERYRAITSAYYRGAVGALLVYDITKRQT-FDNVQRWLrELRDHADSNIVIMMAGNKSDLNHLR--------------- 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  90 gscvstkvpkQVQPEDAvalykkilkyKMLDEREmpaaEQMCFETSAKTGYNVDLLFETLFDLVVPMIMRQR--AEES-- 165
Cdd:PLN03110 134 ----------SVAEEDG----------QALAEKE----GLSFLETSALEATNVEKAFQTILLEIYHIISKKAlaAQEAaa 189

                        170       180
                 ....*....|....*....|....*.
gi 755524411 166 -----DQTVDIASCKTPKQTRSGCCA 186
Cdd:PLN03110 190 nsglpGQGTTINVADTSGNNKRGCCS 215
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 11-69 1.10e-06

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: 45.58  E-value: 1.10e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755524411   11 GREQFHGLGSLYCRGAAAIILTYDVNHPQS----LFELEDRflgltetANNDCLFaIVGNKVD 69
Cdd:pfam08477  60 GQERFRSLHPFYYRGAAAALLVYDSRTFSNlkywLRELKKY-------AGNSPVI-LVGNKID 114
RSR1 cd04177
RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that ...
 11-158 1.19e-06

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: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFEL-EDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkv 89
Cdd:cd04177   58 GTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELgELREQVLRIKDSDNVPMVLVGNKADLEDDR--------------- 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411  90 gscvstkvpkQVQPEDAVALYKKILKYKMlderempaaeqmcFETSAKTGYNVDLLFETLFDLVVPMIM 158
Cdd:cd04177  123 ----------QVSREDGVSLSQQWGNVPF-------------YETSARKRTNVDEVFIDLVRQIICVIM 168
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
 11-157 2.03e-06

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: 45.95  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETA---NNDCLfaIVGNKVDLTSERdteggekegpasg 87
Cdd:cd04127   72 GQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAyceNPDIV--LIGNKADLPDQR------------- 136

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  88 kvgscvstkvpkQVQPEDAVALYKKI-LKYkmlderempaaeqmcFETSAKTGYNVDLLFETLFDLVVPMI 157
Cdd:cd04127  137 ------------EVSERQARELADKYgIPY---------------FETSAATGQNVEKAVETLLDLIMKRM 180
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 21-151 2.86e-06

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: 45.14  E-value: 2.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  21 LYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLfaIVGNKVDLtserdteggekegpasgkvgscvstkvpkq 100
Cdd:cd00882   71 LLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPII--LVGNKIDL------------------------------ 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 755524411 101 VQPEDAVALYKKILKYKMLDERempaaeqmCFETSAKTGYNVDLLFETLFD 151
Cdd:cd00882  119 LEEREVEELLRLEELAKILGVP--------VFEVSAKTGEGVDELFEKLIE 161
small_GTPase smart00010
Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small ...
 10-150 5.66e-06

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: 44.47  E-value: 5.66e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411    10 TGREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCL-FAIVGNKVDLTSERdteggekegpasgk 88
Cdd:smart00010  58 AGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVpIVLVGNKCDLENER-------------- 123

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755524411    89 vgscvstkvpkQVQPEDAVALykkilkykmlderempAAEQMC--FETSAKTGYNVDLLFETLF 150
Cdd:smart00010 124 -----------VVSTEEGKEL----------------ARQWGCpfLETSAKERINVDEAFYDLV 160
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
 11-153 1.40e-05

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: 43.36  E-value: 1.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd01865   59 GQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDER---------------- 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755524411  91 sCVSTKVPKQVqpedavalykkilkykmlderempaAEQM---CFETSAKTGYNVDLLFETLFDLV 153
Cdd:cd01865  123 -VVSAERGRQL-------------------------ADQLgfeFFEASAKENINVKQVFERLVDII 162
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
 11-82 1.93e-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: 42.94  E-value: 1.93e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFE----LEDrflGLTETANNDCLFAIVGNKVDLTSERDTEGGEKE 82
Cdd:cd04108   58 GQERFKCIASTYYRGAQAIIIVFDLTDVASLEHtrqwLED---ALKENDPSSVLLFLVGTKKDLSSPAQYALMEQD 130
Rab28 cd04109
Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown ...
 22-74 2.74e-05

Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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: 206694 [Multi-domain]  Cd Length: 213  Bit Score: 42.86  E-value: 2.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 755524411  22 YCRGAAAIILTYDVNHPQSLFELEDRF---LGLTETANNDCLFAIVGNKVDLTSER 74
Cdd:cd04109   70 YIYGAQAVCLVYDITNSQSFENLEDWLsvvKKVNEESETKPKMVLVGNKTDLEHNR 125
Rab4 cd04113
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ...
 11-77 2.99e-05

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: 42.42  E-value: 2.99e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEdRFLGLTET-ANNDCLFAIVGNKVDLTSERDTE 77
Cdd:cd04113   58 GQERFRSVTRSYYRGAAGALLVYDITSRESFNALT-NWLTDARTlASPDIVIILVGNKKDLEDDREVT 124
PTZ00099 PTZ00099
rab6; Provisional
 11-149 3.71e-05

rab6; Provisional


Pssm-ID: 185444 [Multi-domain]  Cd Length: 176  Bit Score: 42.42  E-value: 3.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:PTZ00099  38 GQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLR---------------- 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755524411  91 scvstkvpkqvqpedavalykkilkyKMLDEREMPAAEQ---MCFETSAKTGYNVDLLFETL 149
Cdd:PTZ00099 102 --------------------------KVTYEEGMQKAQEyntMFHETSAKAGHNIKVLFKKI 137
Rab24 cd04118
Rab GTPase family 24 (Rab24); Rab24 is distinct from other Rabs in several ways. It exists ...
 11-185 9.60e-05

Rab GTPase family 24 (Rab24); Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. 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: 133318 [Multi-domain]  Cd Length: 193  Bit Score: 41.39  E-value: 9.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSlFElEDRFLgLTETANND--CLFAIVGNKVDL-TSERDTeggekegpasg 87
Cdd:cd04118   59 GSERYEAMSRIYYRGAKAAIVCYDLTDSSS-FE-RAKFW-VKELQNLEehCKIYLCGTKSDLiEQDRSL----------- 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  88 kvgscvstkvpKQVQPEDAVALYKKIlkykmlderempaaEQMCFETSAKTGYNVDLLFETLFDLVVPMIMRQRAEEsdQ 167
Cdd:cd04118  125 -----------RQVDFHDVQDFADEI--------------KAQHFETSSKTGQNVDELFQKVAEDFVSRANNQMNTE--K 177

                        170
                 ....*....|....*...
gi 755524411 168 TVDIASCKTPKqtRSGCC 185
Cdd:cd04118  178 GVDLGQKKNSY--FYSCC 193
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
 11-82 1.86e-04

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: 40.10  E-value: 1.86e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERDTEGGEKE 82
Cdd:cd01866   62 GQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYEEGE 133
Rab32_Rab38 cd04107
Rab GTPase families 18 (Rab18) and 32 (Rab32); Rab38/Rab32 subfamily. Rab32 and Rab38 are ...
 11-185 2.05e-04

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: 40.37  E-value: 2.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPqSLFE--------LEDRFLGltetANNDCLFAI-VGNKVDLTSERDteggek 81
Cdd:cd04107   59 GQERFGGMTRVYYKGAVGAIIVFDVTRP-STFEavlkwkadLDSKVTL----PNGEPIPALlLANKCDLKKERL------ 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  82 egpasgkvgscvstkvpkQVQPEDAVALYKkilkykmldEREMPAaeqmCFETSAKTGYNVDLLFETLFDLVVP-MIMRQ 160
Cdd:cd04107  128 ------------------AKDPEQMDQFCK---------ENGFIG----WFETSAKENINIEEAMRFLVKNILKnDKGLQ 176

                        170       180
                 ....*....|....*....|....*
gi 755524411 161 RAEESDQTVDIASCKTPKQTRSGCC 185
Cdd:cd04107  177 SPEPDEDNVIDLKQETTTSKSKSCC 201
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
 11-75 3.25e-04

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: 39.43  E-value: 3.25e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERD 75
Cdd:cd04122   60 GQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRD 124
Rap_like cd04136
Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, ...
 11-92 3.54e-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: 39.47  E-value: 3.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQS---LFELEDRFLGLTETanNDCLFAIVGNKVDLTSERdtEGGEKEGPA-S 86
Cdd:cd04136   58 GTEQFTAMRDLYIKNGQGFALVYSITAQQSfndLQDLREQILRVKDT--EDVPMILVGNKCDLEDER--VVSKEEGQNlA 133


                 ....*.
gi 755524411  87 GKVGSC 92
Cdd:cd04136  134 RQWGNC 139
Rab9 cd04116
Rab GTPase family 9 (Rab9); Rab9 is found in late endosomes, together with mannose 6-phosphate ...
 11-147 5.12e-04

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: 39.09  E-value: 5.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFEL---EDRFLGLTETANNDCL-FAIVGNKVDLTSERdteggekegpas 86
Cdd:cd04116   63 GQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLsnwKKEFIYYADVKEPESFpFVILGNKIDIPERQ------------ 130

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755524411  87 gkvgscVSTKVPKQVQPEDAVALYkkilkykmlderempaaeqmcFETSAKTGYNVDLLFE 147
Cdd:cd04116  131 ------VSTEEAQAWCRDNGDYPY---------------------FETSAKDATNVAAAFE 164
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
 11-149 7.24e-04

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: 38.57  E-value: 7.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLTSERdteggekegpasgkvg 90
Cdd:cd01864   61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQR---------------- 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 755524411  91 scvstkvpkQVQPEDAVALYKKIlkykmlderEMPAAeqmcFETSAKTGYNVDLLFETL 149
Cdd:cd01864  125 ---------EVLFEEACTLAEHY---------GILAV----LETSAKESSNVEEAFLLM 161
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, ...
 11-153 1.39e-03

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: 37.77  E-value: 1.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNHPQSlFELEDRFLGLTETANNDCLFAI--VGNKVDLTSERdteggekegpasgk 88
Cdd:cd04145   59 GQEEFSAMREQYMRTGEGFLLVFSVTDRGS-FEEVDKFHTQILRVKDRDEFPMilVGNKADLEHQR-------------- 123

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755524411  89 vgscvstkvpkQVQPEDAVALYKKIlkykmlderempaaEQMCFETSAKTGYNVDllfETLFDLV 153
Cdd:cd04145  124 -----------QVSREEGQELARQL--------------KIPYIETSAKDRVNVD---KAFHDLV 160
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
 29-148 1.51e-03

Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho 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 Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy.


Pssm-ID: 206641 [Multi-domain]  Cd Length: 171  Bit Score: 37.52  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755524411  29 IILTYDVNHPQSLFELEDRFLGLTETANNDCLFAIVGNKVDLtseRDtEGGEKEGPASGKvgscvstkvpKQVQPEDAVA 108
Cdd:cd00157   75 FLLCFSVDSPSSFENVKTKWYPEIKHYCPNVPIILVGTKIDL---RD-DGNTLKKLEKKQ----------KPITPEEGEK 140

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 755524411 109 LYKKI--LKYkmlderempaaeqmcFETSAKTGYNVDLLFET 148
Cdd:cd00157  141 LAKEIgaVKY---------------MECSALTQEGLKEVFDE 167
Rap1 cd04175
Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap ...
 11-80 3.65e-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: 3.65e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755524411  11 GREQFHGLGSLYCRGAAAIILTYDVNhPQSLF----ELEDRFLGLTETAnnDCLFAIVGNKVDLTSER--DTEGGE 80
Cdd:cd04175   58 GTEQFTAMRDLYMKNGQGFVLVYSIT-AQSTFndlqDLREQILRVKDTE--DVPMILVGNKCDLEDERvvGKEQGQ 130
Rhes_like cd04143
Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); ...
 120-152 8.05e-03

Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1); This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression levels in other tissues. Dexras1 localizes primarily to the cytoplasm, and is a critical regulator of the circadian master clock to photic and nonphotic input. 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: 133343 [Multi-domain]  Cd Length: 247  Bit Score: 35.88  E-value: 8.05e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 755524411 120 DEREMPAAEQMC---FETSAKTGYNVDLLFETLFDL 152
Cdd:cd04143  134 DEVEQLVGGDENcayFEVSAKKNSNLDEMFRALFSL 169
 
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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