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Conserved domains on  [gi|1622869786|ref|XP_028690420|]
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rab-like protein 6 isoform X1 [Macaca mulatta]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 67-245 2.87e-14

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 cd00154:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 159  Bit Score: 70.95  E-value: 2.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPT--QEIQVTSIHWSYKTtddiVKVEVWDVVdkGKckkrgdglkmendpq 144
Cdd:cd00154     1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTigVDFKSKTIEVDGKK----VKLQIWDTA--GQ--------------- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 eaESDMALDAEFldvYKSCNGVVMMFDITKQWTFNYI---LRELPK-VPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDN 220
Cdd:cd00154    60 --ERFRSITSSY---YRGAHGAILVYDVTNRESFENLdkwLNELKEyAPPNIPIILVGNKSDLEDERQVSTEEAQQFAKE 134

                         170       180
                  ....*....|....*....|....*
gi 1622869786 221 LDsrppgssyFRYAESSMKNSFGLK 245
Cdd:cd00154   135 NG--------LLFFETSAKTGENVD 151
PRK07764 super family cl35613
DNA polymerase III subunits gamma and tau; Validated
 469-664 4.89e-06

DNA polymerase III subunits gamma and tau; Validated


The actual alignment was detected with superfamily member PRK07764:

Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 469 ATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQnitlsseeeaevVDPPKGPAP 548
Cdd:PRK07764  616 AAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAG------------GAAPAAPPP 683

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 549 APQQC------SEPETKWSSTPASKPRRGTAPTRAAAPPRPGGASVRTGPEKHSSTRPPAEIEPGKGEQASSSESDPEGP 622
Cdd:PRK07764  684 APAPAapaapaGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPA 763

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1622869786 623 IAAQmlsfvmDDPDFESEASDTQRrvDEFPVRDDPSDVTDED 664
Cdd:PRK07764  764 PAPA------AAPAAAPPPSPPSE--EEEMAEDDAPSMDDED 797
Fe-S_biosyn super family cl00400
Iron-sulphur cluster biosynthesis; This family is involved in iron-sulphur cluster ...
 1-27 3.69e-05

Iron-sulphur cluster biosynthesis; This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.


The actual alignment was detected with superfamily member TIGR00049:

Pssm-ID: 444888 [Multi-domain]  Cd Length: 105  Bit Score: 43.34  E-value: 3.69e-05
                          10        20
                  ....*....|....*....|....*..
gi 1622869786   1 MDYVEDKLSIVFVFSNPSIKGTCGWGE 27
Cdd:TIGR00049  75 IDYVEELLGSGFTFTNPNAKGTCGCGK 101
 
Name Accession Description Interval E-value
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 67-245 2.87e-14

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: 70.95  E-value: 2.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPT--QEIQVTSIHWSYKTtddiVKVEVWDVVdkGKckkrgdglkmendpq 144
Cdd:cd00154     1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTigVDFKSKTIEVDGKK----VKLQIWDTA--GQ--------------- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 eaESDMALDAEFldvYKSCNGVVMMFDITKQWTFNYI---LRELPK-VPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDN 220
Cdd:cd00154    60 --ERFRSITSSY---YRGAHGAILVYDVTNRESFENLdkwLNELKEyAPPNIPIILVGNKSDLEDERQVSTEEAQQFAKE 134

                         170       180
                  ....*....|....*....|....*
gi 1622869786 221 LDsrppgssyFRYAESSMKNSFGLK 245
Cdd:cd00154   135 NG--------LLFFETSAKTGENVD 151
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 68-245 1.91e-11

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: 62.92  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRL-QGRpFVEEYIPTQEI--QVTSIhwsykTTDDI-VKVEVWDVVdkgkckkrgdGlkmendp 143
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFtQNK-FPEEYIPTIGVdfYTKTI-----EVDGKtVKLQIWDTA----------G------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 144 QEaesdmaldaEFLDV----YKSCNGVVMMFDITKQWTFNYI---LRELPKV-PTHVPVCVLGNYRDMGEHRVILPDDVR 215
Cdd:pfam00071  58 QE---------RFRALrplyYRGADGFLLVYDITSRDSFENVkkwVEEILRHaDENVPIVLVGNKCDLEDQRVVSTEEGE 128

                         170       180       190
                  ....*....|....*....|....*....|
gi 1622869786 216 DFIDNLDsrppgssyFRYAESSMKNSFGLK 245
Cdd:pfam00071 129 ALAKELG--------LPFMETSAKTNENVE 150
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 67-217 1.97e-09

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 57.13  E-value: 1.97e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786   67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPT--QEIQVTSIHWSYKTtddiVKVEVWDVVdkGkckkrgdglkmendpQ 144
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTigVDFKTKTIEVDGKR----VKLQIWDTA--G---------------Q 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  145 EaesdmaldaEFLDV----YKSCNGVVMMFDITKQWTFNYILRELPKVPTH----VPVCVLGNYRDMGEHRVILPDDVRD 216
Cdd:smart00175  60 E---------RFRSItssyYRGAVGALLVYDITNRESFENLENWLKELREYaspnVVIMLVGNKSDLEEQRQVSREEAEA 130


                   .
gi 1622869786  217 F 217
Cdd:smart00175 131 F 131
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 469-664 4.89e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 469 ATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQnitlsseeeaevVDPPKGPAP 548
Cdd:PRK07764  616 AAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAG------------GAAPAAPPP 683

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 549 APQQC------SEPETKWSSTPASKPRRGTAPTRAAAPPRPGGASVRTGPEKHSSTRPPAEIEPGKGEQASSSESDPEGP 622
Cdd:PRK07764  684 APAPAapaapaGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPA 763

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1622869786 623 IAAQmlsfvmDDPDFESEASDTQRrvDEFPVRDDPSDVTDED 664
Cdd:PRK07764  764 PAPA------AAPAAAPPPSPPSE--EEEMAEDDAPSMDDED 797
TIGR00049 TIGR00049
Iron-sulfur cluster assembly accessory protein; Proteins in this subfamily appear to be ...
 1-27 3.69e-05

Iron-sulfur cluster assembly accessory protein; Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 272875 [Multi-domain]  Cd Length: 105  Bit Score: 43.34  E-value: 3.69e-05
                          10        20
                  ....*....|....*....|....*..
gi 1622869786   1 MDYVEDKLSIVFVFSNPSIKGTCGWGE 27
Cdd:TIGR00049  75 IDYVEELLGSGFTFTNPNAKGTCGCGK 101
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
66-225 1.46e-04

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 43.43  E-value: 1.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  66 SVKIVIRGDRNTGKTALWHRLQGRPF-VEEYIPTQEIQVTSIHWSYKTTDdiVKVEVWDVvdkgkckkrgDGLkmenDPQ 144
Cdd:COG1100     3 EKKIVVVGTGGVGKTSLVNRLVGDIFsLEKYLSTNGVTIDKKELKLDGLD--VDLVIWDT----------PGQ----DEF 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 EAESdmaldAEFLDVYKSCNGVVMMFDITKQWTF---NYILRELPKVPTHVPVCVLGNYRD-MGEHRVILPDDVRDFIDN 220
Cdd:COG1100    67 RETR-----QFYARQLTGASLYLFVVDGTREETLqslYELLESLRRLGKKSPIILVLNKIDlYDEEEIEDEERLKEALSE 141


                  ....*
gi 1622869786 221 LDSRP 225
Cdd:COG1100   142 DNIVE 146
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 505-647 2.50e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 43.99  E-value: 2.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 505 DDV--DLEDQPRGSSPPPAGPVPSQNITLSSEEEAEVVDPPKGPAPAPQQCSEPETKWSSTPASKPRRGTAPTRAAAPPR 582
Cdd:NF040712  181 DDEarWLIDPDFGRPLRPLATVPRLAREPADARPEEVEPAPAAEGAPATDSDPAEAGTPDDLASARRRRAGVEQPEDEPV 260

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622869786 583 PGGASVRTGP--EKHSSTRPPAEIEPGKGEQASSSESDPEGPIAAQMLSFVMDDPDFESEASDTQRR 647
Cdd:NF040712  261 GPGAAPAAEPdeATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPEAEEPARPEPPPAPKPKRR 327
IscA COG0316
Fe-S cluster assembly iron-binding protein IscA [Posttranslational modification, protein ...
 1-27 7.51e-04

Fe-S cluster assembly iron-binding protein IscA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440085 [Multi-domain]  Cd Length: 107  Bit Score: 39.75  E-value: 7.51e-04
                          10        20
                  ....*....|....*....|....*..
gi 1622869786   1 MDYVEDKLSIVFVFSNPSIKGTCGWGE 27
Cdd:COG0316    77 IDYVEELLGSGFKFNNPNAKSSCGCGE 103
DamX COG3266
Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell ...
 453-630 9.41e-03

Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442497 [Multi-domain]  Cd Length: 455  Bit Score: 39.45  E-value: 9.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 453 EDFVPDDRLDRSFLEDATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQNITLS 532
Cdd:COG3266   202 ADALALLLLLLASALGEAVAAAAELAALALLAAGAAEVLTARLVLLLLIIGSALKAPSQASSASAPATTSLGEQQEVSLP 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 533 SEEEAEvvdPPKGPAPAPQQCSEPETKWSSTPASKPRRGTAPTRAAAPP--RPGGASVRTGPEKHSSTRPPA--EIEPGK 608
Cdd:COG3266   282 PAVAAQ---PAAAAAAQPSAVALPAAPAAAAAAAAPAEAAAPQPTAAKPvvTETAAPAAPAPEAAAAAAAPAapAVAKKL 358

                         170       180
                  ....*....|....*....|..
gi 1622869786 609 GEQASSSESDPEGPIAAQMLSF 630
Cdd:COG3266   359 AADEQWLASQPASHYTLQLLGA 380
 
Name Accession Description Interval E-value
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 67-245 2.87e-14

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: 70.95  E-value: 2.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPT--QEIQVTSIHWSYKTtddiVKVEVWDVVdkGKckkrgdglkmendpq 144
Cdd:cd00154     1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTigVDFKSKTIEVDGKK----VKLQIWDTA--GQ--------------- 59

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 eaESDMALDAEFldvYKSCNGVVMMFDITKQWTFNYI---LRELPK-VPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDN 220
Cdd:cd00154    60 --ERFRSITSSY---YRGAHGAILVYDVTNRESFENLdkwLNELKEyAPPNIPIILVGNKSDLEDERQVSTEEAQQFAKE 134

                         170       180
                  ....*....|....*....|....*
gi 1622869786 221 LDsrppgssyFRYAESSMKNSFGLK 245
Cdd:cd00154   135 NG--------LLFFETSAKTGENVD 151
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 68-245 1.91e-11

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: 62.92  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRL-QGRpFVEEYIPTQEI--QVTSIhwsykTTDDI-VKVEVWDVVdkgkckkrgdGlkmendp 143
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFtQNK-FPEEYIPTIGVdfYTKTI-----EVDGKtVKLQIWDTA----------G------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 144 QEaesdmaldaEFLDV----YKSCNGVVMMFDITKQWTFNYI---LRELPKV-PTHVPVCVLGNYRDMGEHRVILPDDVR 215
Cdd:pfam00071  58 QE---------RFRALrplyYRGADGFLLVYDITSRDSFENVkkwVEEILRHaDENVPIVLVGNKCDLEDQRVVSTEEGE 128

                         170       180       190
                  ....*....|....*....|....*....|
gi 1622869786 216 DFIDNLDsrppgssyFRYAESSMKNSFGLK 245
Cdd:pfam00071 129 ALAKELG--------LPFMETSAKTNENVE 150
Ras cd00876
Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the ...
 68-217 1.94e-10

Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases); The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206642 [Multi-domain]  Cd Length: 160  Bit Score: 59.85  E-value: 1.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRL-QGRpFVEEYIPTqeiqvtsIHWSYKTT----DDIVKVEVWDVVdkGkckkrgdglkmend 142
Cdd:cd00876     1 KLVVLGAGGVGKSALTIRFvSGE-FVEEYDPT-------IEDSYRKQivvdGETYTLDILDTA--G-------------- 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 143 pQEAESDMAldaeflDVY-KSCNGVVMMFDITKQWTF-------NYILRELPKvpTHVPVCVLGNYRDMGEHRVILPDDV 214
Cdd:cd00876    57 -QEEFSAMR------DQYiRNGDGFILVYSITSRESFeeiknirEQILRVKDK--EDVPIVLVGNKCDLENERQVSTEEG 127


                  ...
gi 1622869786 215 RDF 217
Cdd:cd00876   128 EAL 130
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 67-217 1.97e-09

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


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 57.13  E-value: 1.97e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786   67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPT--QEIQVTSIHWSYKTtddiVKVEVWDVVdkGkckkrgdglkmendpQ 144
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTigVDFKTKTIEVDGKR----VKLQIWDTA--G---------------Q 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  145 EaesdmaldaEFLDV----YKSCNGVVMMFDITKQWTFNYILRELPKVPTH----VPVCVLGNYRDMGEHRVILPDDVRD 216
Cdd:smart00175  60 E---------RFRSItssyYRGAVGALLVYDITNRESFENLENWLKELREYaspnVVIMLVGNKSDLEEQRQVSREEAEA 130


                   .
gi 1622869786  217 F 217
Cdd:smart00175 131 F 131
RERG_RasL11_like cd04146
Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like ...
 68-213 5.38e-09

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: 56.13  E-value: 5.38e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRLQGRPFVEEYIPTQEiqvtSIHWSYKTTD-DIVKVEVWDVVdkgkckkrgdglkmenDPQEA 146
Cdd:cd04146     1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLE----SLYSRQVTIDgEQVSLEIQDTP----------------GQQQN 60

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622869786 147 ESDMALDAEFldvyKSCNGVVMMFDITKQWTFN------YILRELPKVPTHVPVCVLGNYRDMGEHRVILPDD 213
Cdd:cd04146    61 EDPESLERSL----RWADGFVLVYSITDRSSFDvvsqllQLIREIKKRDGEIPVILVGNKADLLHSRQVSTEE 129
Ran cd00877
Ras-related nuclear proteins (Ran)/TC4 family of small GTPases; Ran GTPase is involved in ...
 68-260 4.45e-08

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: 53.46  E-value: 4.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHR-LQGRpFVEEYIPTQEIQVTSIHwsYKTTDDIVKVEVWDVVdkGKCKKrgDGLKmendpqea 146
Cdd:cd00877     2 KLVLVGDGGTGKTTFVKRhLTGE-FEKKYVATLGVEVHPLD--FHTNRGKIRFNVWDTA--GQEKF--GGLR-------- 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 147 esdmalDAEFLDVykscNGVVMMFDITKQWTFNYI---LRELPKVPTHVPVCVLGNYRDMGEHRVilPDDVRDFIdnlds 223
Cdd:cd00877    67 ------DGYYIQG----QCAIIMFDVTSRVTYKNVpnwHRDLVRVCENIPIVLCGNKVDIKDRKV--KPKQITFH----- 129

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1622869786 224 RPPGSSYFryaESSMKNSFGlkylhkfFNIPFLQLQR 260
Cdd:cd00877   130 RKKNLQYY---EISAKSNYN-------FEKPFLWLAR 156
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 68-202 2.34e-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: 47.12  E-value: 2.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRLQGRPFVEEYIPTqeIQVTSIHWSYKTTDD---IVKVEVWDVVdkGkckkrgdglkmendpQ 144
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTFDPKYKST--IGVDFKTKTVLENDDngkKIKLNIWDTA--G---------------Q 61

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622869786 145 EAESdmALDAEFldvYKSCNGVVMMFDITKQWTFNYILRELPKVPTHVPVCVLGNYRD 202
Cdd:pfam08477  62 ERFR--SLHPFY---YRGAAAALLVYDSRTFSNLKYWLRELKKYAGNSPVILVGNKID 114
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 469-664 4.89e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 469 ATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQnitlsseeeaevVDPPKGPAP 548
Cdd:PRK07764  616 AAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAG------------GAAPAAPPP 683

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 549 APQQC------SEPETKWSSTPASKPRRGTAPTRAAAPPRPGGASVRTGPEKHSSTRPPAEIEPGKGEQASSSESDPEGP 622
Cdd:PRK07764  684 APAPAapaapaGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPA 763

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1622869786 623 IAAQmlsfvmDDPDFESEASDTQRrvDEFPVRDDPSDVTDED 664
Cdd:PRK07764  764 PAPA------AAPAAAPPPSPPSE--EEEMAEDDAPSMDDED 797
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
 68-245 3.36e-05

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


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 44.90  E-value: 3.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  68 KIVIRGDRNTGKTALWHRLQGRPFVEEYIPTqeiqvTSIHWSYKTT---DDIVKVEVWDVVDKgkckkrgdglkmendpq 144
Cdd:cd01865     3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVST-----VGIDFKVKTVyrnDKRIKLQIWDTAGQ----------------- 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 eaESDMALDAEFldvYKSCNGVVMMFDITKQWTFNYILRELPKVPTH----VPVCVLGNYRDMGEHRVILPDDVRDFIDN 220
Cdd:cd01865    61 --ERYRTITTAY---YRGAMGFILMYDITNEESFNAVQDWSTQIKTYswdnAQVILVGNKCDMEDERVVSAERGRQLADQ 135

                         170       180
                  ....*....|....*....|....*
gi 1622869786 221 LDsrppgssyFRYAESSMKNSFGLK 245
Cdd:cd01865   136 LG--------FEFFEASAKENINVK 152
TIGR00049 TIGR00049
Iron-sulfur cluster assembly accessory protein; Proteins in this subfamily appear to be ...
 1-27 3.69e-05

Iron-sulfur cluster assembly accessory protein; Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 272875 [Multi-domain]  Cd Length: 105  Bit Score: 43.34  E-value: 3.69e-05
                          10        20
                  ....*....|....*....|....*..
gi 1622869786   1 MDYVEDKLSIVFVFSNPSIKGTCGWGE 27
Cdd:TIGR00049  75 IDYVEELLGSGFTFTNPNAKGTCGCGK 101
PRK04654 PRK04654
sec-independent translocase; Provisional
 450-626 1.33e-04

sec-independent translocase; Provisional


Pssm-ID: 135173 [Multi-domain]  Cd Length: 214  Bit Score: 44.03  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 450 QSVEDFVPDDRLDRSfLEDATPARDEKKVGAKAAQQDSDSDAEALgsnplvagfQDDVDLEDQPRGSSPPPAGPVPSQNI 529
Cdd:PRK04654   48 QELERELEAEELKRS-LQDVQASLREAEDQLRNTQQQVEQGARAL---------HDDVSRDIDIRTSATPVATPLELAHA 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 530 TLSSEEEAE---VVDPPKGPAPAPqqcsepetkwssTPASKPRRGTAPTRAAAP-----PRPGGASVRTGPEKHSSTRPP 601
Cdd:PRK04654  118 DLSASAQVDaaaGAEPGAGQAHTP------------VPAPAPVIAQAQPIAPAPhqtlvPAPHDTIVPAPHAAHLPSAPA 185

                         170       180
                  ....*....|....*....|....*
gi 1622869786 602 AEIEPGKGEQASSSESDPEGPIAAQ 626
Cdd:PRK04654  186 TPVSVAPVDAGTSASPTPSEPTKIQ 210
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
66-225 1.46e-04

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 43.43  E-value: 1.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  66 SVKIVIRGDRNTGKTALWHRLQGRPF-VEEYIPTQEIQVTSIHWSYKTTDdiVKVEVWDVvdkgkckkrgDGLkmenDPQ 144
Cdd:COG1100     3 EKKIVVVGTGGVGKTSLVNRLVGDIFsLEKYLSTNGVTIDKKELKLDGLD--VDLVIWDT----------PGQ----DEF 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 EAESdmaldAEFLDVYKSCNGVVMMFDITKQWTF---NYILRELPKVPTHVPVCVLGNYRD-MGEHRVILPDDVRDFIDN 220
Cdd:COG1100    67 RETR-----QFYARQLTGASLYLFVVDGTREETLqslYELLESLRRLGKKSPIILVLNKIDlYDEEEIEDEERLKEALSE 141


                  ....*
gi 1622869786 221 LDSRP 225
Cdd:COG1100   142 DNIVE 146
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 491-628 1.68e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 491 AEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQNITLSSEEEAEVVDPPKGPAPAPQQcsEPETKWSSTPASKPRR 570
Cdd:PRK07764  378 LERLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAP--APPSPAGNAPAGGAPS 455

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622869786 571 GTAPTRAAAPPRPGGASvRTGPEKHSSTRPPAEIEPGKGEQASSSESDPEGPIAAQML 628
Cdd:PRK07764  456 PPPAAAPSAQPAPAPAA-APEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATL 512
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
 73-263 1.80e-04

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 43.46  E-value: 1.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786   73 GDRNTGKTALWHRLQGRPFVEEYIPTQEIQVTSIhwSYKTTDDIVKVEVWDVVDKGKCKKRGDGLkmendpqeaesdmal 152
Cdd:smart00176   2 GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPL--VFHTNRGPIRFNVWDTAGQEKFGGLRDGY--------------- 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  153 daefldvYKSCNGVVMMFDITKQWTFNYI---LRELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDFIDNLdsrppgss 229
Cdd:smart00176  65 -------YIQGQCAIIMFDVTARVTYKNVpnwHRDLVRVCENIPIVLCGNKVDVKDRKVKAKSITFHRKKNL-------- 129

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1622869786  230 yfRYAESSMKNSFGlkylhkfFNIPFLQLQRETL 263
Cdd:smart00176 130 --QYYDISAKSNYN-------FEKPFLWLARKLI 154
Rab40 cd04121
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ...
 67-266 2.34e-04

Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. 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: 133321 [Multi-domain]  Cd Length: 189  Bit Score: 43.00  E-value: 2.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPTQEIqvtsihwSYKTTDDI-----VKVEVWDVVDKGKckkrgdglkmen 141
Cdd:cd04121     7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGI-------DYKTTTILldgrrVKLQLWDTSGQGR------------ 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 142 dpqeaesdmaldaeFLDVYKS----CNGVVMMFDITKQWTFNYILRELPKVPTH---VPVCVLGNYRDMGEHRVILPDDV 214
Cdd:cd04121    68 --------------FCTIFRSysrgAQGIILVYDITNRWSFDGIDRWIKEIDEHapgVPKILVGNRLHLAFKRQVATEQA 133

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622869786 215 RDFIDNLdsrppGSSYFRYaeSSMKNsfglkylhkfFNI--PFLQLQRETLLRQ 266
Cdd:cd04121   134 QAYAERN-----GMTFFEV--SPLCN----------FNIteSFTELARIVLMRH 170
SepH NF040712
septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces ...
 505-647 2.50e-04

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.


Pssm-ID: 468676 [Multi-domain]  Cd Length: 346  Bit Score: 43.99  E-value: 2.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 505 DDV--DLEDQPRGSSPPPAGPVPSQNITLSSEEEAEVVDPPKGPAPAPQQCSEPETKWSSTPASKPRRGTAPTRAAAPPR 582
Cdd:NF040712  181 DDEarWLIDPDFGRPLRPLATVPRLAREPADARPEEVEPAPAAEGAPATDSDPAEAGTPDDLASARRRRAGVEQPEDEPV 260

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622869786 583 PGGASVRTGP--EKHSSTRPPAEIEPGKGEQASSSESDPEGPIAAQMLSFVMDDPDFESEASDTQRR 647
Cdd:NF040712  261 GPGAAPAAEPdeATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPEAEEPARPEPPPAPKPKRR 327
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 70-217 4.05e-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: 41.67  E-value: 4.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  70 VIRGDRNTGKTALWHRLQGRPFVE---EYIPTQEIQVTSIHWSYKTtddiVKVEVWDVVDkgkckkrgdglkmendpQEA 146
Cdd:cd00882     1 VVVGRGGVGKSSLLNALLGGEVGEvsdVPGTTRDPDVYVKELDKGK----VKLVLVDTPG-----------------LDE 59

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622869786 147 ESDMALDAEFLDVYKSCNGVVMMFDITKQWTFNYI--LRELPKVPTHVPVCVLGNYRDMGEHRVILPDDVRDF 217
Cdd:cd00882    60 FGGLGREELARLLLRGADLILLVVDSTDRESEEDAklLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEE 132
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 515-607 4.22e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 43.90  E-value: 4.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 515 GSSPPPAGPVPSQNITLSSEEEAEVVDPPKGPAPAPQqcsePETKWSSTPASKPRRGTAPTRAA-------APPRPGGAS 587
Cdd:PRK14959  395 ATIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPS----PRVPWDDAPPAPPRSGIPPRPAPrmpeaspVPGAPDSVA 470

                          90       100
                  ....*....|....*....|.
gi 1622869786 588 VRTG-PEKHSSTRPPAEIEPG 607
Cdd:PRK14959  471 SASDaPPTLGDPSDTAEHTPS 491
IscA COG0316
Fe-S cluster assembly iron-binding protein IscA [Posttranslational modification, protein ...
 1-27 7.51e-04

Fe-S cluster assembly iron-binding protein IscA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440085 [Multi-domain]  Cd Length: 107  Bit Score: 39.75  E-value: 7.51e-04
                          10        20
                  ....*....|....*....|....*..
gi 1622869786   1 MDYVEDKLSIVFVFSNPSIKGTCGWGE 27
Cdd:COG0316    77 IDYVEELLGSGFKFNNPNAKSSCGCGE 103
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 467-625 1.54e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 41.47  E-value: 1.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 467 EDATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPA--GPVPSQNITLSSEEEA---EVVD 541
Cdd:PTZ00436  183 KDRERARREDAAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAkaAAAPAKAAAAPAKAAAppaKAAA 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 542 PPKGPAPAPQQCSEPETKWSSTP----ASKPRRGTAPTRAAAPPrpggASVRTGPEKHSSTRPPAEIEPGKGEQASSSES 617
Cdd:PTZ00436  263 PPAKAAAPPAKAAAPPAKAAAPPakaaAPPAKAAAAPAKAAAAP----AKAAAAPAKAAAPPAKAAAPPAKAATPPAKAA 338


                  ....*...
gi 1622869786 618 DPEGPIAA 625
Cdd:PTZ00436  339 APPAKAAA 346
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
 67-215 2.02e-03

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 39.65  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVEEYIPTQEIQ--VTSIhwsyKTTDDIVKVEVWdvvdkgkckkrgdglkmendpq 144
Cdd:cd04119     1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDygVKKV----SVRNKEVRVNFF---------------------- 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 145 eaesDMALDAEFLDV----YKSCNGVVMMFDITKQWTFNYI---LREL------PKVPTHVPVCVLGNYRDMGEHRVILP 211
Cdd:cd04119    55 ----DLSGHPEYLEVrnefYKDTQGVLLVYDVTDRQSFEALdswLKEMkqeggpHGNMENIVVVVCANKIDLTKHRAVSE 130


                  ....
gi 1622869786 212 DDVR 215
Cdd:cd04119   131 DEGR 134
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 542-652 2.08e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.60  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 542 PPKGPAPA-PQQCSEPETKWSSTPASKPRRGTAPTRAAAPPRPGGASVRTGPEKHSSTRPPaeIEPGKGEQASSSESDPE 620
Cdd:PTZ00449  606 PTRPKSPKlPELLDIPKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPKSPKPP--FDPKFKEKFYDDYLDAA 683

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1622869786 621 GPiAAQMLSFVMDDPDFESEASDTQRRVDEFP 652
Cdd:PTZ00449  684 AK-SKETKTTVVLDESFESILKETLPETPGTP 714
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 545-625 2.15e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.51  E-value: 2.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 545 GPAPAPQQCSEPETKWSSTPASKPRRGTAPTRAAAPPRPGGASVRTGPEKHSSTRPPAEIEPGKGEQASSSESDPEGPIA 624
Cdd:PRK07764  589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668


                  .
gi 1622869786 625 A 625
Cdd:PRK07764  669 W 669
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 488-669 3.33e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 3.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 488 DSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQNITLSSEEEAEVVDPPKGPAPAPQQCSEPETKWSSTPASK 567
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 568 PRRGTAPTRAAAPPRPGGASVR---TGPEKHSSTRPPAeiePGKGEQASSSESDPEGPIAAQmlsfvmddpdfESEASDT 644
Cdd:PRK07764  670 PAKAGGAAPAAPPPAPAPAAPAapaGAAPAQPAPAPAA---TPPAGQADDPAAQPPQAAQGA-----------SAPSPAA 735

                         170       180
                  ....*....|....*....|....*
gi 1622869786 645 QRRVDEFPVRDDPSDVTDEDEALAQ 669
Cdd:PRK07764  736 DDPVPLPPEPDDPPDPAGAPAQPPP 760
PHA03379 PHA03379
EBNA-3A; Provisional
 471-614 3.56e-03

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 40.81  E-value: 3.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 471 PARDEKKVGAKAAQQDSDSDAEALGSNPLvagfQDDVDLEDQPRGSSPPpaGPVPsqNITLSSEEEAEVVDPPKGPAPAP 550
Cdd:PHA03379  428 PQSLETATSHGSAQVPEPPPVHDLEPGPL----HDQHSMAPCPVAQLPP--GPLQ--DLEPGDQLPGVVQDGRPACAPVP 499

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622869786 551 QQCSEPETKWSSTPASKPRRGTAPTR----AAAP-PRPGGAsvrtgPEKHSSTRPPAEIEPGKGEQASS 614
Cdd:PHA03379  500 APAGPIVRPWEASLSQVPGVAFAPVMpqpmPVEPvPVPTVA-----LERPVCPAPPLIAMQGPGETSGI 563
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 67-124 3.57e-03

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 38.74  E-value: 3.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622869786  67 VKIVIRGDRNTGKTALWHRLQGRPFVeEYIPTQEIQVTSIhwSYKTtddiVKVEVWDV 124
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIV-TTIPTIGFNVETV--TYKN----VKFTVWDV 51
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 467-593 4.96e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 40.47  E-value: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 467 EDATPARDEKKVGAKAAQQDSdsdAEALGSNPLVAGfqddvdlEDQPRGSSPPPAGPVPSQnitlSSEEEAEVVDPPKGP 546
Cdd:PRK14951  377 EKKTPARPEAAAPAAAPVAQA---AAAPAPAAAPAA-------AASAPAAPPAAAPPAPVA----APAAAAPAAAPAAAP 442

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622869786 547 APAPQQCSEP--ETKWSSTPASK--PRRGTAPTRAAAPPRPGGASVRTGPE 593
Cdd:PRK14951  443 AAVALAPAPPaqAAPETVAIPVRvaPEPAVASAAPAPAAAPAAARLTPTEE 493
DamX COG3266
Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell ...
 453-630 9.41e-03

Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442497 [Multi-domain]  Cd Length: 455  Bit Score: 39.45  E-value: 9.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 453 EDFVPDDRLDRSFLEDATPARDEKKVGAKAAQQDSDSDAEALGSNPLVAGFQDDVDLEDQPRGSSPPPAGPVPSQNITLS 532
Cdd:COG3266   202 ADALALLLLLLASALGEAVAAAAELAALALLAAGAAEVLTARLVLLLLIIGSALKAPSQASSASAPATTSLGEQQEVSLP 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622869786 533 SEEEAEvvdPPKGPAPAPQQCSEPETKWSSTPASKPRRGTAPTRAAAPP--RPGGASVRTGPEKHSSTRPPA--EIEPGK 608
Cdd:COG3266   282 PAVAAQ---PAAAAAAQPSAVALPAAPAAAAAAAAPAEAAAPQPTAAKPvvTETAAPAAPAPEAAAAAAAPAapAVAKKL 358

                         170       180
                  ....*....|....*....|..
gi 1622869786 609 GEQASSSESDPEGPIAAQMLSF 630
Cdd:COG3266   359 AADEQWLASQPASHYTLQLLGA 380
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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