NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|665505975|ref|NP_001287815|]
View 

rho-related GTP-binding protein RhoD isoform 2 [Homo sapiens]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 16-144 9.14e-69

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 cd04132:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 197  Bit Score: 206.04  E-value: 9.14e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSLLMVFADGAFPE--------------------------------------------------- 44
Cdd:cd04132    2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEeyvptvfenyvttlqvpngkiielalwdtagqedydrlrplsypdvdvili 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ----------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSAR 108
Cdd:cd04132   82 cysvdnptsldnvedkWYPEVNHFCPGTPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAK 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 665505975 109 LHDNVHAVFQEAAEVALSSRGRNFWRRITQGFCVVT 144
Cdd:cd04132  162 LMENVDEVFDAAINVALSKSGRAARKKKKKKKCVIL 197
 
Name Accession Description Interval E-value
Rho4_like cd04132
Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a ...
 16-144 9.14e-69

Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. 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.


Pssm-ID: 206704 [Multi-domain]  Cd Length: 197  Bit Score: 206.04  E-value: 9.14e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSLLMVFADGAFPE--------------------------------------------------- 44
Cdd:cd04132    2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEeyvptvfenyvttlqvpngkiielalwdtagqedydrlrplsypdvdvili 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ----------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSAR 108
Cdd:cd04132   82 cysvdnptsldnvedkWYPEVNHFCPGTPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAK 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 665505975 109 LHDNVHAVFQEAAEVALSSRGRNFWRRITQGFCVVT 144
Cdd:cd04132  162 LMENVDEVFDAAINVALSKSGRAARKKKKKKKCVIL 197
RHO smart00174
Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like ...
 20-126 9.91e-51

Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.


Pssm-ID: 197554 [Multi-domain]  Cd Length: 174  Bit Score: 159.32  E-value: 9.91e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    20 VVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------- 44
Cdd:smart00174   1 LVVVGDGAVGKTCLLIVYTTNAFPEdyvptvfenysadvevdgkpvelglwdtagqedydrlrplsypdtdvflicfsvd 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    45 -----------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNV 113
Cdd:smart00174  81 spasfenvkekWYPEVKHFCPNVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGV 160

                          170
                   ....*....|...
gi 665505975   114 HAVFQEAAEVALS 126
Cdd:smart00174 161 REVFEEAIRAALN 173
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 19-125 4.41e-23

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: 88.34  E-value: 4.41e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEeyiptigvdfytktievdgktvklqiwdtagqerfralrplyyrgadgfllvyd 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   45 ------------WYPEVNHFC-KKVPIIVVGCKTDLRKDKslvnklrrnglePVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:pfam00071  81 itsrdsfenvkkWVEEILRHAdENVPIVLVGNKCDLEDQR------------VVSTEEGEALAKELG-LPFMETSAKTNE 147

                         170
                  ....*....|....
gi 665505975  112 NVHAVFQEAAEVAL 125
Cdd:pfam00071 148 NVEEAFEELAREIL 161
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
16-126 5.98e-05

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 40.73  E-value: 5.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSL-------------------------------------------------------------- 33
Cdd:COG1100    2 GEKKIVVVGTGGVGKTSLvnrlvgdifslekylstngvtidkkelkldgldvdlviwdtpgqdefretrqfyarqltgas 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  34 LMVF-ADG-------AFPEWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRrngLEpvtyhrgqEMARSVGAVAYLEC 105
Cdd:COG1100   82 LYLFvVDGtreetlqSLYELLESLRRLGKKSPIILVLNKIDLYDEEEIEDEER---LK--------EALSEDNIVEVVAT 150

                        170       180
                 ....*....|....*....|.
gi 665505975 106 SARLHDNVHAVFQEAAEVALS 126
Cdd:COG1100  151 SAKTGEGVEELFAALAEILRG 171
PTZ00369 PTZ00369
Ras-like protein; Provisional
 55-119 2.34e-04

Ras-like protein; Provisional


Pssm-ID: 240385 [Multi-domain]  Cd Length: 189  Bit Score: 39.46  E-value: 2.34e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665505975  55 KVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHDNVHAVFQE 119
Cdd:PTZ00369 110 RVPMILVGNKCDLDSERQ------------VSTGEGQELAKSFG-IPFLETSAKQRVNVDEAFYE 161
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 31-77 1.79e-03

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: 36.58  E-value: 1.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665505975   31 TSLLMVFaDGAFP---------EWYPEVNHFCKK-VPIIVVGCKTDLR------KDKSLVNKL 77
Cdd:TIGR00231  76 ERSLRVF-DIVILvldveeileKQTKEIIHHADSgVPIILVGNKIDLKdadlktHVASEFAKL 137
 
Name Accession Description Interval E-value
Rho4_like cd04132
Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a ...
 16-144 9.14e-69

Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like; Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. 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.


Pssm-ID: 206704 [Multi-domain]  Cd Length: 197  Bit Score: 206.04  E-value: 9.14e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSLLMVFADGAFPE--------------------------------------------------- 44
Cdd:cd04132    2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEeyvptvfenyvttlqvpngkiielalwdtagqedydrlrplsypdvdvili 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ----------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSAR 108
Cdd:cd04132   82 cysvdnptsldnvedkWYPEVNHFCPGTPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAK 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 665505975 109 LHDNVHAVFQEAAEVALSSRGRNFWRRITQGFCVVT 144
Cdd:cd04132  162 LMENVDEVFDAAINVALSKSGRAARKKKKKKKCVIL 197
RHO smart00174
Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like ...
 20-126 9.91e-51

Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.


Pssm-ID: 197554 [Multi-domain]  Cd Length: 174  Bit Score: 159.32  E-value: 9.91e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    20 VVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------- 44
Cdd:smart00174   1 LVVVGDGAVGKTCLLIVYTTNAFPEdyvptvfenysadvevdgkpvelglwdtagqedydrlrplsypdtdvflicfsvd 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    45 -----------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNV 113
Cdd:smart00174  81 spasfenvkekWYPEVKHFCPNVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGV 160

                          170
                   ....*....|...
gi 665505975   114 HAVFQEAAEVALS 126
Cdd:smart00174 161 REVFEEAIRAALN 173
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
 18-123 2.75e-39

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: 129.97  E-value: 2.75e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------------------------------------------------- 44
Cdd:cd00157    1 IKIVVVGDGAVGKTCLLISYTTNKFPTeyvptvfdnysanvtvdgkqvnlglwdtagqeeydrlrplsypqtdvfllcfs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 -------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNgLEPVTYHRGQEMARSVGAVAYLECSARLHD 111
Cdd:cd00157   81 vdspssfenvktkWYPEIKHYCPNVPIILVGTKIDLRDDGNTLKKLEKK-QKPITPEEGEKLAKEIGAVKYMECSALTQE 159

                        170
                 ....*....|..
gi 665505975 112 NVHAVFQEAAEV 123
Cdd:cd00157  160 GLKEVFDEAIRA 171
RhoA_like cd01870
Ras homology family A (RhoA)-like includes RhoA, RhoB and RhoC; The RhoA subfamily consists of ...
 19-125 1.86e-33

Ras homology family A (RhoA)-like includes RhoA, RhoB and RhoC; The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. 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. RhoA and RhoC are observed only in geranylgeranylated forms; however, RhoB can be present in palmitoylated, farnesylated, and geranylgeranylated forms. RhoA and RhoC are highly relevant for tumor progression and invasiveness; however, RhoB has recently been suggested to be a tumor suppressor. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206662 [Multi-domain]  Cd Length: 175  Bit Score: 115.60  E-value: 1.86e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd01870    3 KLVIVGDGACGKTCLLIVFSKDQFPEvyvptvfenyvadievdgkqvelalwdtagqedydrlrplsypdtdvilmcfsi 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDN 112
Cdd:cd01870   83 dspdslenipekWTPEVKHFCPNVPIILVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEG 162

                        170
                 ....*....|...
gi 665505975 113 VHAVFQEAAEVAL 125
Cdd:cd01870  163 VREVFEMATRAAL 175
RhoG cd01875
Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a ...
 15-125 4.13e-30

Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases); RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. 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.


Pssm-ID: 133277 [Multi-domain]  Cd Length: 191  Bit Score: 107.40  E-value: 4.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  15 VRSVKVVLVGDGGCGKTSLLMVFADGAFPE-------------------------------------------------- 44
Cdd:cd01875    1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKeyiptvfdnysaqtavdgrtvslnlwdtagqeeydrlrtlsypqtnvfii 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ----------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSAR 108
Cdd:cd01875   81 cfsiaspssyenvrhkWHPEVCHHCPNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSAL 160

                        170
                 ....*....|....*..
gi 665505975 109 LHDNVHAVFQEAAEVAL 125
Cdd:cd01875  161 NQDGVKEVFAEAVRAVL 177
Rac1_like cd01871
Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)-like ...
 17-120 1.42e-27

Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)-like consists of Rac1, Rac2 and Rac3; The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleotide association and is more efficiently activated by the RacGEF Tiam1. Both Rac1 and Rac3 have been implicated in the regulation of cell migration and invasion in human metastatic breast cancer. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206663 [Multi-domain]  Cd Length: 174  Bit Score: 100.27  E-value: 1.42e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  17 SVKVVLVGDGGCGKTSLLMVFADGAFP----------------------------------------------------- 43
Cdd:cd01871    1 AIKCVVVGDGAVGKTCLLISYTTNAFPgeyiptvfdnysanvmvdgkpvnlglwdtagqedydrlrplsypqtdvflicf 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  44 -------------EWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLH 110
Cdd:cd01871   81 slvspasfenvraKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQ 160

                        170
                 ....*....|
gi 665505975 111 DNVHAVFQEA 120
Cdd:cd01871  161 RGLKTVFDEA 170
Rnd cd04131
Rho family GTPase subfamily Rnd includes Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8; The Rnd ...
 19-125 8.53e-27

Rho family GTPase subfamily Rnd includes Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8; The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206703 [Multi-domain]  Cd Length: 176  Bit Score: 98.27  E-value: 8.53e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd04131    3 KIVLVGDSQCGKTALLQVFAKDSFPEnyvptvfenytasfevdkqrielslwdtsgspyydnvrplsypdsdavlicfdi 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDN 112
Cdd:cd04131   83 srpetldsvlkkWKGEVREFCPNTPVLLVGCKSDLRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSEN 162

                        170
                 ....*....|....
gi 665505975 113 -VHAVFQEAAEVAL 125
Cdd:cd04131  163 sVRDVFEMATLACL 176
Rho2 cd04129
Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal ...
 19-128 2.85e-23

Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. 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 proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).


Pssm-ID: 206702 [Multi-domain]  Cd Length: 190  Bit Score: 89.89  E-value: 2.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd04129    3 KLVIVGDGACGKTSLLYVFTLGEFPEeyhptvfenyvtdcrvdgkpvqlalwdtagqeeyerlrplsyskahviligfai 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKslVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDN 112
Cdd:cd04129   83 dtpdslenvrtkWIEEVRRYCPNVPVILVGLKKDLRQEA--VAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEG 160

                        170
                 ....*....|....*.
gi 665505975 113 VHAVFQEAAEVALSSR 128
Cdd:cd04129  161 VDDVFEAATRAALLVR 176
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 19-125 4.41e-23

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: 88.34  E-value: 4.41e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEeyiptigvdfytktievdgktvklqiwdtagqerfralrplyyrgadgfllvyd 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   45 ------------WYPEVNHFC-KKVPIIVVGCKTDLRKDKslvnklrrnglePVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:pfam00071  81 itsrdsfenvkkWVEEILRHAdENVPIVLVGNKCDLEDQR------------VVSTEEGEALAKELG-LPFMETSAKTNE 147

                         170
                  ....*....|....
gi 665505975  112 NVHAVFQEAAEVAL 125
Cdd:pfam00071 148 NVEEAFEELAREIL 161
Cdc42 cd01874
cell division cycle 42 (Cdc42) is a small GTPase of the Rho family; Cdc42 is an essential ...
 44-125 1.00e-22

cell division cycle 42 (Cdc42) is a small GTPase of the Rho family; Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addition, Cdc42 has been implicated in a number of human diseases through interactions with its regulators and downstream effectors. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206664 [Multi-domain]  Cd Length: 175  Bit Score: 88.01  E-value: 1.00e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  44 EWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEAAEV 123
Cdd:cd01874   94 KWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDEAILA 173


                 ..
gi 665505975 124 AL 125
Cdd:cd01874  174 AL 175
Rnd2_Rho7 cd04173
Rnd2/Rho7 GTPases; Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1 ...
 19-134 2.98e-22

Rnd2/Rho7 GTPases; Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in spermatocytes and early spermatids, with male-germ-cell Rac GTPase-activating protein (MgcRacGAP), where it localizes to the Golgi-derived pro-acrosomal vesicle. 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.


Pssm-ID: 206736 [Multi-domain]  Cd Length: 221  Bit Score: 87.77  E-value: 2.98e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd04173    3 KIVVVGDTQCGKTALLHVFAKDNYPEsyvptvfenytasfeidkhrielnmwdtsgssyydnvrplaypdsdavlicfdi 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARL-HD 111
Cdd:cd04173   83 srpetldsvlkkWQGETQEFCPNAKLVLVGCKLDMRTDLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMsEN 162

                        170       180
                 ....*....|....*....|...
gi 665505975 112 NVHAVFQEAAEVALSSRGRNFWR 134
Cdd:cd04173  163 SVRDVFHVTTLASVRREHPSLKR 185
Wrch_1 cd04130
Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42; Wrch-1 (Wnt-1 ...
 45-120 6.87e-21

Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42; Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133330 [Multi-domain]  Cd Length: 173  Bit Score: 83.22  E-value: 6.87e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 665505975  45 WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEA 120
Cdd:cd04130   94 WIPEIRKHNPKAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVFDTA 169
Rnd1_Rho6 cd04174
Rnd1/Rho6 GTPases; Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2 ...
 11-126 3.47e-20

Rnd1/Rho6 GTPases; Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206737 [Multi-domain]  Cd Length: 232  Bit Score: 82.80  E-value: 3.47e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  11 APPGVRSVKVVLVGDGGCGKTSLLMVFADGAFPE---------------------------------------------- 44
Cdd:cd04174    7 PQPLVVRCKLVLVGDVQCGKTAMLQVLAKDCYPEtyvptvfenytacleteeqrvelslwdtsgspyydnvrplcysdsd 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 --------------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLE 104
Cdd:cd04174   87 avllcfdisrpeifdsalkkWRAEILDYCPSTRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLE 166

                        170       180
                 ....*....|....*....|...
gi 665505975 105 CSARLHD-NVHAVFQEAAEVALS 126
Cdd:cd04174  167 CSAFTSEkSIHSIFRTASLLCIN 189
Rnd3_RhoE_Rho8 cd04172
Rnd3/RhoE/Rho8 GTPases; Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho ...
 19-120 8.26e-20

Rnd3/RhoE/Rho8 GTPases; Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight junction formation. Rnd3/RhoE is underexpressed in prostate cancer cells both in vitro and in vivo; re-expression of Rnd3/RhoE suppresses cell cycle progression and increases apoptosis, suggesting it may play a role in tumor suppression. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206735 [Multi-domain]  Cd Length: 182  Bit Score: 80.48  E-value: 8.26e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd04172    7 KIVVVGDSQCGKTALLHVFAKDCFPEnyvptvfenytasfeidtqrielslwdtsgspyydnvrplsypdsdavlicfdi 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDN 112
Cdd:cd04172   87 srpetldsvlkkWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSEN 166


                 ....*....
gi 665505975 113 -VHAVFQEA 120
Cdd:cd04172  167 sVRDIFHVA 175
Rho3 cd04134
Ras homology family 3 (Rho3) of small guanosine triphosphatases (GTPases); Rho3 is a member of ...
 19-130 1.59e-18

Ras homology family 3 (Rho3) of small guanosine triphosphatases (GTPases); Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. 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.


Pssm-ID: 206706 [Multi-domain]  Cd Length: 185  Bit Score: 77.21  E-value: 1.59e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd04134    2 KVVVLGDGACGKTSLLNVFTRGYFPQvyeptvfenyihdifvdglavelslwdtagqeefdrlrslsyadthvimlcfsv 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKlrrnGLEPVTYHRGQEMARSVGAVAYLECSARLHDN 112
Cdd:cd04134   82 dnpdslenveskWLAEIRHHCPGVKLVLVALKCDLREPRNERDR----GTHTISYEEGLAVAKRINACRYLECSAKLNRG 157

                        170
                 ....*....|....*...
gi 665505975 113 VHAVFQEAAEVALSSRGR 130
Cdd:cd04134  158 VNEAFTEAARVALNARPP 175
Rop_like cd04133
Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) ...
 44-125 6.43e-18

Rho-related protein from plants (Rop)-like; The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example, Rop1, Rop3, and Rop5 are all involved in pollen-tube growth; Rop2 plays a role in response to low-oxygen environments, cell-morphology, and root-hair development; root-hair development is also regulated by Rop4 and Rop6; Rop6 is also responsible for ABA response, and ABA response is also regulated by Rop10. Plants retain some of the regulatory mechanisms that are shared by other members of the Rho family, but have also developed a number of unique modes for regulating Rops. Unique RhoGEFs have been identified that are exclusively active toward Rop proteins, such as those containing the domain PRONE (plant-specific Rop nucleotide exchanger). 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206705 [Multi-domain]  Cd Length: 173  Bit Score: 75.65  E-value: 6.43e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  44 EWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVnkLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEAAEV 123
Cdd:cd04133   94 KWIPELRHYAPGVPIVLVGTKLDLRDDKQFF--ADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDAAIKV 171


                 ..
gi 665505975 124 AL 125
Cdd:cd04133  172 VL 173
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 18-122 5.66e-16

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: 69.79  E-value: 5.66e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------------------------------------------------- 44
Cdd:cd00154    1 FKIVLIGDSGVGKTSLLLRFVDNKFSEnykstigvdfksktievdgkkvklqiwdtagqerfrsitssyyrgahgailvy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 -------------WYPEVNHFC-KKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAVaYLECSARLH 110
Cdd:cd00154   81 dvtnresfenldkWLNELKEYApPNIPIILVGNKSDLEDERQ------------VSTEEAQQFAKENGLL-FFETSAKTG 147

                        170
                 ....*....|..
gi 665505975 111 DNVHAVFQEAAE 122
Cdd:cd00154  148 ENVDEAFESLAR 159
Tc10 cd04135
Rho GTPase TC10 (Tc10); TC10 is a Rho family protein that has been shown to induce microspike ...
 18-120 2.40e-15

Rho GTPase TC10 (Tc10); TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interactions with CFTR-associated ligand (CAL). The GTP-bound form of TC10 directs the trafficking of CFTR from the juxtanuclear region to the secretory pathway toward the plasma membrane, away from CAL-mediated DFTR degradation in the lysosome. 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. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206707 [Multi-domain]  Cd Length: 174  Bit Score: 68.89  E-value: 2.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------------------------------------------------- 44
Cdd:cd04135    1 LKCVVVGDGAVGKTCLLMSYANDAFPEeyvptvfdhyavsvtvggkqyllglydtagqedydrlrplsypmtdvflicfs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 -------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHD 111
Cdd:cd04135   81 vvnpasfqnvkeeWVPELKEYAPNVPYLLIGTQIDLRDDPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQK 160


                 ....*....
gi 665505975 112 NVHAVFQEA 120
Cdd:cd04135  161 GLKTVFDEA 169
Miro1 cd01893
Mitochondrial Rho family 1 (Miro1), N-terminal; Miro1 subfamily. Miro (mitochondrial Rho) ...
 16-117 1.72e-13

Mitochondrial Rho family 1 (Miro1), N-terminal; Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.


Pssm-ID: 206680 [Multi-domain]  Cd Length: 168  Bit Score: 63.90  E-value: 1.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSLLMVFADGAFPE--------------------------------------------------- 44
Cdd:cd01893    1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPEnvprvlpeitipadvtpervpttivdtssrpqdranlaaeirkanviclvy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 --------------WYPEVNHFCKKVPIIVVGCKTDLRKDKSlvnklrRNGLEpvtyhrgQEMA------RSVgaVAYLE 104
Cdd:cd01893   81 svdrpstlerirtkWLPLIRRLGVKVPIILVGNKSDLRDGSS------QAGLE-------EEMLpimnefREI--ETCVE 145

                        170
                 ....*....|...
gi 665505975 105 CSARLHDNVHAVF 117
Cdd:cd01893  146 CSAKTLINVSEVF 158
RhoBTB cd01873
RhoBTB protein is an atypical member of the Rho family of small GTPases; Members of the RhoBTB ...
 45-124 1.05e-11

RhoBTB protein is an atypical member of the Rho family of small GTPases; Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.


Pssm-ID: 133275 [Multi-domain]  Cd Length: 195  Bit Score: 59.60  E-value: 1.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 WYPEVNHFCKKVPIIVVGCKTDLRK-DKSLVNKLRRNGLEPVTYHR------GQEMARSVGaVAYLECSARLHDNVHAVF 117
Cdd:cd01873  110 WYPEIRHFCPRVPVILVGCKLDLRYaDLDEVNRARRPLARPIKNADilppetGRAVAKELG-IPYYETSVVTQFGVKDVF 188


                 ....*..
gi 665505975 118 QEAAEVA 124
Cdd:cd01873  189 DNAIRAA 195
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
 19-119 4.93e-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: 51.76  E-value: 4.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPEWY-P-------------------------------------------------- 47
Cdd:cd00876    1 KLVVLGAGGVGKSALTIRFVSGEFVEEYdPtiedsyrkqivvdgetytldildtagqeefsamrdqyirngdgfilvysi 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  48 -------EVNHF---------CKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:cd00876   81 tsresfeEIKNIreqilrvkdKEDVPIVLVGNKCDLENERQ------------VSTEEGEALAEEWG-CPFLETSAKTNI 147


                 ....*...
gi 665505975 112 NVHAVFQE 119
Cdd:cd00876  148 NIDELFNT 155
RAS smart00173
Ras subfamily of RAS small GTPases; Similar in fold and function to the bacterial EF-Tu GTPase. ...
 19-119 1.88e-08

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: 50.25  E-value: 1.88e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    19 KVVLVGDGGCGKTSLLMVFADGAFPEWY-P-------------------------------------------------- 47
Cdd:smart00173   2 KLVVLGSGGVGKSALTIQFIQGHFVDDYdPtiedsyrkqieidgevclldildtagqeefsamrdqymrtgegfllvysi 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    48 -------EVNHF---------CKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:smart00173  82 tdrqsfeEIKKFreqilrvkdRDDVPIVLVGNKCDLESERV------------VSTEEGKELARQWG-CPFLETSAKERV 148


                   ....*...
gi 665505975   112 NVHAVFQE 119
Cdd:smart00173 149 NVDEAFYD 156
small_GTPase smart00010
Small GTPase of the Ras superfamily; ill-defined subfamily; SMART predicts Ras-like small ...
 16-119 1.99e-08

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: 50.25  E-value: 1.99e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    16 RSVKVVLVGDGGCGKTSLLMVFADGAFPEWY-P----------------------------------------------- 47
Cdd:smart00010   1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYdPtiedsyrkqieidgevclldildtagqeefsamrdqymrtgegfllv 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    48 ----------EVNHF---------CKKVPIIVVGCKTDLRKDkslvnklRRnglepVTYHRGQEMARSVGaVAYLECSAR 108
Cdd:smart00010  81 ysitdrqsfeEIAKFreqilrvkdRDDVPIVLVGNKCDLENE-------RV-----VSTEEGKELARQWG-CPFLETSAK 147

                          170
                   ....*....|.
gi 665505975   109 LHDNVHAVFQE 119
Cdd:smart00010 148 ERINVDEAFYD 158
RheB cd04137
Ras Homolog Enriched in Brain (RheB) is a small GTPase; Rheb (Ras Homolog Enriched in Brain) ...
 55-117 2.79e-08

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: 49.94  E-value: 2.79e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665505975  55 KVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAvAYLECSARLHDNVHAVF 117
Cdd:cd04137  106 SVPIVLVGNKSDLHMERQ------------VSAEEGKKLAESWGA-AFLESSAKENENVEEAF 155
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 18-125 6.03e-08

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 49.04  E-value: 6.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------------------------------------------------- 44
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEqykstigvdfktktievdgkrvklqiwdtagqerfrsitssyyrgavgallvy 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975    45 -------------WYPEVNHFCK-KVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLH 110
Cdd:smart00175  81 ditnresfenlenWLKELREYASpNVVIMLVGNKSDLEEQRQ------------VSREEAEAFAEEHG-LPFFETSAKTN 147

                          170
                   ....*....|....*
gi 665505975   111 DNVHAVFQEAAEVAL 125
Cdd:smart00175 148 TNVEEAFEELAREIL 162
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 19-65 2.21e-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: 43.65  E-value: 2.21e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 665505975   19 KVVLVGDGGCGKTSLLMVFADGAFPEWYP---EVNHFCKKVPIIVVGCKT 65
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTFDPKYKstiGVDFKTKTVLENDDNGKK 50
Rab28 cd04109
Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown ...
 18-58 5.45e-06

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: 44.02  E-value: 5.45e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPEWYPE---VNHFCKKVPI 58
Cdd:cd04109    1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQtigLDFFSRRITL 44
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, ...
 53-119 8.66e-06

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: 43.17  E-value: 8.66e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 665505975  53 CKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVgAVAYLECSARLHDNVHAVFQE 119
Cdd:cd04145  105 RDEFPMILVGNKADLEHQRQ------------VSREEGQELARQL-KIPYIETSAKDRVNVDKAFHD 158
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 18-122 1.48e-05

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: 42.30  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------------------------------------------------- 44
Cdd:cd01863    1 LKILLIGDSGVGKSSLLLRFTDDTFDEdlsstigvdfkvktvtvdgkkvklaiwdtagqerfrtltssyyrgaqgvilvy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 -------------WYPEVNHFCKK--VPIIVVGCKTDlrkdkslvnKLRRnglePVTYHRGQEMARSVGAVaYLECSARL 109
Cdd:cd01863   81 dvtrrdtfdnldtWLNELDTYSTNpdAVKMLVGNKID---------KENR----EVTREEGQKFARKHNML-FIETSAKT 146

                        170
                 ....*....|...
gi 665505975 110 HDNVHAVFQEAAE 122
Cdd:cd01863  147 RIGVQQAFEELVE 159
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
 19-121 2.82e-05

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: 41.48  E-value: 2.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPE------------------------------------------------------ 44
Cdd:cd01867    5 KLLLIGDSGVGKSCLLLRFSEDSFNPsfistigidfkirtieldgkkiklqiwdtagqerfrtittsyyrgamgiilvyd 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  45 ------------WYPEVN-HFCKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:cd01867   85 itdeksfeniknWMRNIDeHASEDVERMLVGNKCDMEEKRV------------VSKEEGEALAREYG-IKFLETSAKANI 151

                        170
                 ....*....|
gi 665505975 112 NVHAVFQEAA 121
Cdd:cd01867  152 NVEEAFLTLA 161
Rap1 cd04175
Rap1 family GTPase consists of Rap1a and Rap1b isoforms; The Rap1 subgroup is part of the Rap ...
 53-117 3.92e-05

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: 41.35  E-value: 3.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665505975  53 CKKVPIIVVGCKTDLrKDKSLVNKlrrnglepvtyHRGQEMARSVGAvAYLECSARLHDNVHAVF 117
Cdd:cd04175  104 TEDVPMILVGNKCDL-EDERVVGK-----------EQGQNLARQWGC-AFLETSAKAKINVNEIF 155
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
16-126 5.98e-05

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 40.73  E-value: 5.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  16 RSVKVVLVGDGGCGKTSL-------------------------------------------------------------- 33
Cdd:COG1100    2 GEKKIVVVGTGGVGKTSLvnrlvgdifslekylstngvtidkkelkldgldvdlviwdtpgqdefretrqfyarqltgas 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  34 LMVF-ADG-------AFPEWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRrngLEpvtyhrgqEMARSVGAVAYLEC 105
Cdd:COG1100   82 LYLFvVDGtreetlqSLYELLESLRRLGKKSPIILVLNKIDLYDEEEIEDEER---LK--------EALSEDNIVEVVAT 150

                        170       180
                 ....*....|....*....|.
gi 665505975 106 SARLHDNVHAVFQEAAEVALS 126
Cdd:COG1100  151 SAKTGEGVEELFAALAEILRG 171
Rap_like cd04136
Rap-like family consists of Rap1, Rap2 and RSR1; The Rap subfamily consists of the Rap1, Rap2, ...
 55-119 6.73e-05

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: 40.62  E-value: 6.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665505975  55 KVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQE 119
Cdd:cd04136  106 DVPMILVGNKCDLEDERV------------VSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYD 158
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
 18-122 8.01e-05

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: 40.29  E-value: 8.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPE----------WYPEVNHFCKKV-----------------PI--------IVVG 62
Cdd:cd04123    1 FKVVLLGEGRVGKTSLVLRYVENKFNEkhesttqasfFQKTVNIGGKRIdlaiwdtagqeryhalgPIyyrdadgaILVY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  63 CKTD---LRKDKSLVNKLRR---NGLEP--------------VTYHRGQEMARSVGAvAYLECSARLHDNVHAVFQEAAE 122
Cdd:cd04123   81 DITDadsFQKVKKWIKELKQmrgNNISLvivgnkidlerqrvVSKSEAEEYAKSVGA-KHFETSAKTGKGIEELFLSLAK 159
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
 43-140 8.83e-05

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: 40.51  E-value: 8.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  43 PEWYPE--VNHFCKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHDNVHAVFQEA 120
Cdd:cd04111   95 HDWLEEarSHIQPHRPVFILVGHKCDLESQRQ------------VTREEAEKLAKDLG-MKYIETSARTGDNVEEAFELL 161

                         90       100
                 ....*....|....*....|....*.
gi 665505975 121 AE--VALSSRG----RNFWRRITQGF 140
Cdd:cd04111  162 TQeiYERIKRGelcaLDGWDGVKSGF 187
Rab7 cd01862
Rab GTPase family 7 (Rab7); Rab7 subfamily. Rab7 is a small Rab GTPase that regulates ...
 57-128 1.38e-04

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: 39.57  E-value: 1.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 665505975  57 PIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEAAEVALSSR 128
Cdd:cd01862  111 PFVVLGNKIDLEEKRQ------------VSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQE 170
RSR1 cd04177
RSR1/Bud1p family GTPase; RSR1/Bud1p is a member of the Rap subfamily of the Ras family that ...
 56-120 1.91e-04

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: 39.39  E-value: 1.91e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665505975  56 VPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEA 120
Cdd:cd04177  107 VPMVLVGNKADLEDDRQ------------VSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDL 159
PTZ00369 PTZ00369
Ras-like protein; Provisional
 55-119 2.34e-04

Ras-like protein; Provisional


Pssm-ID: 240385 [Multi-domain]  Cd Length: 189  Bit Score: 39.46  E-value: 2.34e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665505975  55 KVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHDNVHAVFQE 119
Cdd:PTZ00369 110 RVPMILVGNKCDLDSERQ------------VSTGEGQELAKSFG-IPFLETSAKQRVNVDEAFYE 161
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
 17-122 3.93e-04

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: 38.30  E-value: 3.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  17 SVKVVLVGDGGCGKTSLLMVFADGAFPEwYPEVN---HFCKKV-------------------------P---------II 59
Cdd:cd01860    1 QFKLVLLGDSSVGKSSIVLRFVKNEFSE-NQESTigaAFLTQTvnlddttvkfeiwdtagqeryrslaPmyyrgaaaaIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  60 V--VGCKTDLRKDKSLVNKLRRNG--------------LEP---VTYHRGQEMARSVGAVaYLECSARLHDNVHAVFQEA 120
Cdd:cd01860   80 VydITSEESFEKAKSWVKELQEHGppnivialagnkadLESkrqVSTEEAQEYADENGLL-FMETSAKTGENVNELFTEI 158


                 ..
gi 665505975 121 AE 122
Cdd:cd01860  159 AR 160
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
 19-121 4.75e-04

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: 38.08  E-value: 4.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAF-------------------------------------------------------- 42
Cdd:cd01869    4 KLLLIGDSGVGKSCLLLRFADDTYtesyistigvdfkirtieldgktvklqiwdtagqerfrtitssyyrgahgiiivyd 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  43 ----------PEWYPEVNHF-CKKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGaVAYLECSARLHD 111
Cdd:cd01869   84 vtdqesfnnvKQWLQEIDRYaSENVNKLLVGNKCDLTDKKV------------VDYTEAKEFADELG-IPFLETSAKNAT 150

                        170
                 ....*....|
gi 665505975 112 NVHAVFQEAA 121
Cdd:cd01869  151 NVEEAFMTMA 160
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
 42-121 4.99e-04

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: 38.34  E-value: 4.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  42 FPEWYPEVNHFC-KKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSvGAVAYLECSARLHDNVHAVFQEA 120
Cdd:cd04114   98 LPEWLREIEQYAnNKVITILVGNKIDLAERRE------------VSQQRAEEFSDA-QDMYYLETSAKESDNVEKLFLDL 164


                 .
gi 665505975 121 A 121
Cdd:cd04114  165 A 165
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 33-122 7.86e-04

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: 37.44  E-value: 7.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  33 LLMVFADG----AFPEWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKLRRnglepvtyhrgqEMARSVGAVAYLECSAR 108
Cdd:cd00882   80 LLVVDSTDreseEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRL------------EELAKILGVPVFEVSAK 147

                         90
                 ....*....|....
gi 665505975 109 LHDNVHAVFQEAAE 122
Cdd:cd00882  148 TGEGVDELFEKLIE 161
PLN03118 PLN03118
Rab family protein; Provisional
 17-121 8.68e-04

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 37.73  E-value: 8.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  17 SVKVVLVGDGGCGKTSLLMVFADGAFPEWYPEV----------------------------------NHFCKKVPIIVV- 61
Cdd:PLN03118  14 SFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIgvdfkikqltvggkrlkltiwdtagqerfrtltsSYYRNAQGIILVy 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  62 ---------------GCKTDL---RKD--KSLV-NKLRRNGLEPVTYHRGQEMARSVGAvAYLECSARLHDNVHAVFQEA 120
Cdd:PLN03118  94 dvtrretftnlsdvwGKEVELystNQDcvKMLVgNKVDRESERDVSREEGMALAKEHGC-LFLECSAKTRENVEQCFEEL 172


                 .
gi 665505975 121 A 121
Cdd:PLN03118 173 A 173
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
 19-42 9.27e-04

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: 37.54  E-value: 9.27e-04
                         10        20
                 ....*....|....*....|....
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAF 42
Cdd:cd04112    2 KVMLVGDSGVGKTCLLVRFKDGAF 25
PLN03071 PLN03071
GTP-binding nuclear protein Ran; Provisional
 5-108 9.43e-04

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 178620 [Multi-domain]  Cd Length: 219  Bit Score: 37.81  E-value: 9.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   5 QAAGEEAPPGVRSVKVVLVGDGGCGKTSLLMVFADGAF------------------------------------------ 42
Cdd:PLN03071   1 MALPNQQTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFekkyeptigvevhpldfftncgkirfycwdtagqekfgglrd 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975  43 ------------------------PEWYPEVNHFCKKVPIIVVGCKTDL--RKDKSlvnklrrnglEPVTYHRGQEMars 96
Cdd:PLN03071  81 gyyihgqcaiimfdvtarltyknvPTWHRDLCRVCENIPIVLCGNKVDVknRQVKA----------KQVTFHRKKNL--- 147

                        170
                 ....*....|..
gi 665505975  97 vgavAYLECSAR 108
Cdd:PLN03071 148 ----QYYEISAK 155
RERG_RasL11_like cd04146
Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like ...
 54-120 1.24e-03

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: 36.87  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 665505975  54 KKVPIIVVGCKTDLRKDKSlvnklrrnglepVTYHRGQEMARSVGAvAYLECSARL-HDNVHAVFQEA 120
Cdd:cd04146  106 GEIPVILVGNKADLLHSRQ------------VSTEEGQKLALELGC-LFFEVSAAEnYLEVQNVFHEL 160
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
 7-117 1.46e-03

Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus.


Pssm-ID: 206643 [Multi-domain]  Cd Length: 166  Bit Score: 36.90  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665505975   7 AGEEAPPGVRSVKVVlvgDGGCGktsllMVFADGAF-------PEWYPEVNHFCKKVPIIVVGCKTDLRKDKSLVNKlrr 79
Cdd:cd00877   57 AGQEKFGGLRDGYYI---QGQCA-----IIMFDVTSrvtyknvPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKPKQ--- 125

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 665505975  80 nglepVTYHRGqemarsvGAVAYLECSARLHDNVHAVF 117
Cdd:cd00877  126 -----ITFHRK-------KNLQYYEISAKSNYNFEKPF 151
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 31-77 1.79e-03

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: 36.58  E-value: 1.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665505975   31 TSLLMVFaDGAFP---------EWYPEVNHFCKK-VPIIVVGCKTDLR------KDKSLVNKL 77
Cdd:TIGR00231  76 ERSLRVF-DIVILvldveeileKQTKEIIHHADSgVPIILVGNKIDLKdadlktHVASEFAKL 137
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
 19-46 1.98e-03

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: 36.76  E-value: 1.98e-03
                         10        20
                 ....*....|....*....|....*...
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAFPEWY 46
Cdd:cd04110    8 KLLIIGDSGVGKSSLLLRFADNTFSGSY 35
Rab23_like cd04106
Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family ...
 18-46 3.47e-03

Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. 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: 133306 [Multi-domain]  Cd Length: 162  Bit Score: 35.88  E-value: 3.47e-03
                         10        20
                 ....*....|....*....|....*....
gi 665505975  18 VKVVLVGDGGCGKTSLLMVFADGAFPEWY 46
Cdd:cd04106    1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDY 29
Rit_Rin_Ric cd04141
Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related ...
 16-46 7.29e-03

Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related protein which interacts with calmodulin (Ric); Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to signal in parallel with the Ras pathway or stimulate the Ras pathway at some upstream point, and binding of calmodulin to Ric may negatively regulate Ric activity.


Pssm-ID: 206712 [Multi-domain]  Cd Length: 172  Bit Score: 34.83  E-value: 7.29e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 665505975  16 RSVKVVLVGDGGCGKTSLLMVFADGAFPEWY 46
Cdd:cd04141    1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYH 31
Rab11_like cd01868
Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25; Rab11a, Rab11b, and ...
 19-42 7.66e-03

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: 34.84  E-value: 7.66e-03
                         10        20
                 ....*....|....*....|....
gi 665505975  19 KVVLVGDGGCGKTSLLMVFADGAF 42
Cdd:cd01868    5 KIVLIGDSGVGKSNLLSRFTRNEF 28
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH