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Conserved domains on  [gi|117938759|ref|NP_536350|]
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protein GNAS isoform XLas [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
 684-1031 1.01e-180

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


:

Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 527.87  E-value: 1.01e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  684 HRLLLLGAGESGKSTIVKQMRILHVNGFNGEggeedpqaarsnsdgEKATKVQDIKNNLKEAIETIVAAMSNLVPPveLA 763
Cdd:cd00066     1 VKLLLLGAGESGKSTILKQMKILHGNGFSDE---------------ERREFRPVIYSNILQSMKALLRAMETLNIP--YG 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  764 NPENQFRVDYILSVMN-VPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQADYVPSDQDLLR 842
Cdd:cd00066    64 DPENEKDAKKILSLAPrAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAKYFLDNLDRISDPDYIPTEQDILR 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  843 CRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNN 922
Cdd:cd00066   144 SRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNS 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  923 RWLRTISVILFLNKQDLLAEKVLagKSKIEDYFPEFaryttpedatpePGEDPRVTRAKYFIRDEFLRISTasgDGRHYC 1002
Cdd:cd00066   224 RWFANTSIILFLNKKDLFEEKIK--KSPLTDYFPDY------------TGPPNDYEEAAKYIKKKFLDLNR---NPNKEI 286

                         330       340
                  ....*....|....*....|....*....
gi 117938759 1003 YPHFTCAVDTENIRRVFNDCRDIIQRMHL 1031
Cdd:cd00066   287 YPHFTCATDTENIRFVFDAVKDIILQNNL 315
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
84-300 3.10e-04

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK12323:

Pssm-ID: 481241 [Multi-domain]  Cd Length: 700  Bit Score: 44.87  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   84 AFREAGAHGSYSPPPEEAMPFEAEQPSLGGFWPTLEQPGFPSGVHAGLEAFGPALMEPGAFSGARPglggyspPPEEAMP 163
Cdd:PRK12323  362 AFRPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRS-------PAPEALA 434

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  164 FEFDQPAQRGCSQLLLQ-------VPDLAPGGPGAAGVPGAPPEEPQALRPAKAGSRGGYSPPPEETMPFELDGEGFGDD 236
Cdd:PRK12323  435 AARQASARGPGGAPAPApapaaapAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQP 514

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 117938759  237 SPPPGLSRVIAQVDGSSQFAAVAASSAVRLTPAANAPPLWVPG----AIGSPSQEAVRPPSNFTGSSP 300
Cdd:PRK12323  515 DAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATepvvAPRPPRASASGLPDMFDGDWP 582
UDM1_RNF168_RNF169-like cd22249
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ...
 642-676 7.05e-03

UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets.


:

Pssm-ID: 409016 [Multi-domain]  Cd Length: 66  Bit Score: 36.09  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 117938759  642 AEKRRQMRKEALEKRAQKRAEKKRSKLIDKQLQDE 676
Cdd:cd22249     9 EEYEAQLKKLEEERRKEREEEEKASEELIRKLQEE 43
 
Name Accession Description Interval E-value
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
 684-1031 1.01e-180

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


Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 527.87  E-value: 1.01e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  684 HRLLLLGAGESGKSTIVKQMRILHVNGFNGEggeedpqaarsnsdgEKATKVQDIKNNLKEAIETIVAAMSNLVPPveLA 763
Cdd:cd00066     1 VKLLLLGAGESGKSTILKQMKILHGNGFSDE---------------ERREFRPVIYSNILQSMKALLRAMETLNIP--YG 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  764 NPENQFRVDYILSVMN-VPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQADYVPSDQDLLR 842
Cdd:cd00066    64 DPENEKDAKKILSLAPrAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAKYFLDNLDRISDPDYIPTEQDILR 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  843 CRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNN 922
Cdd:cd00066   144 SRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNS 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  923 RWLRTISVILFLNKQDLLAEKVLagKSKIEDYFPEFaryttpedatpePGEDPRVTRAKYFIRDEFLRISTasgDGRHYC 1002
Cdd:cd00066   224 RWFANTSIILFLNKKDLFEEKIK--KSPLTDYFPDY------------TGPPNDYEEAAKYIKKKFLDLNR---NPNKEI 286

                         330       340
                  ....*....|....*....|....*....
gi 117938759 1003 YPHFTCAVDTENIRRVFNDCRDIIQRMHL 1031
Cdd:cd00066   287 YPHFTCATDTENIRFVFDAVKDIILQNNL 315
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 663-1034 7.55e-167

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


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 493.25  E-value: 7.55e-167
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    663 KKRSKLIDKQLQDEKMGYMCTHRLLLLGAGESGKSTIVKQMRILHVNGFNGEggeedpqaarsnsdgEKATKVQDIKNNL 742
Cdd:smart00275    1 IRRNKEIEKQLEEERKKKKREVKLLLLGAGESGKSTILKQMRILHGDGFSQE---------------ERREYRPLIYSNI 65

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    743 KEAIETIVAAMSNLVPPVElaNPENQFRVDYILSVMNVPD---FDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQ 819
Cdd:smart00275   66 LESMKALVDAMEELNIPFE--DPESILDIRIITEQFNKTDeteNVLPKEIAKAIKALWKDEGIQECYRRRNEFQLNDSAS 143

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    820 YFLDKIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMV 899
Cdd:smart00275  144 YFLDNIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQV 223

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    900 IREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLagKSKIEDYFPEFaryttpedatpepGEDPRVTR 979
Cdd:smart00275  224 LEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLFEEKIK--KVPLVDYFPDY-------------KGPNDYEA 288

                           330       340       350       360       370
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 117938759    980 AKYFIRDEFLRISTasGDGRHYCYPHFTCAVDTENIRRVFNDCRDIIQRMHLRQY 1034
Cdd:smart00275  289 AAKFIKQKFLRLNR--NSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKDA 341
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 683-1026 5.07e-140

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


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 422.77  E-value: 5.07e-140
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   683 THRLLLLGAGESGKSTIVKQMRILHVNGFngeggeedpqaarsnSDGEKATKVQDIKNNLKEAIETIVAAMSNLvpPVEL 762
Cdd:pfam00503    5 EVKLLLLGAGESGKSTILKQMKIIHGGGF---------------SEEERKQYRPVIYSNILRSLKTLIEAMERL--GIEL 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   763 ANPENQFRVDYILSVMNVP--DFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQADYVPSDQDL 840
Cdd:pfam00503   68 SNPENKERLDDLLSLDSSLknETEFTPELAEDIKRLWNDPGIQECYERRNEFQLPDSAEYFLDNLDRIASPDYVPTDQDI 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   841 LRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIW 920
Cdd:pfam00503  148 LRARVKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRMEESLKLFEEIC 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   921 NNRWLRTISVILFLNKQDLLAEKVlaGKSKIEDYFPEFAryttpedatpepGEDPRVTRAKYFIRDEFLRISTasgDGRH 1000
Cdd:pfam00503  228 NSPWFKNTPIILFLNKKDLFEEKL--KKSPLSDYFPDYT------------GNPNDYEEALKYIRNKFLDLNK---NPNR 290

                          330       340
                   ....*....|....*....|....*.
gi 117938759  1001 YCYPHFTCAVDTENIRRVFNDCRDII 1026
Cdd:pfam00503  291 KIYTHFTCATDTENIRFVFDAVKDII 316
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
850-957 2.50e-06

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 48.82  E-value: 2.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  850 IFETKFQVD--KVNFHMFDVGGQ---RDERRKWIQCFNDVTAIIFVVASSsynmviREDNqTNRLQEALNLFKSIwnnrw 924
Cdd:COG1100    41 IDKKELKLDglDVDLVIWDTPGQdefRETRQFYARQLTGASLYLFVVDGT------REET-LQSLYELLESLRRL----- 108

                          90       100       110
                  ....*....|....*....|....*....|...
gi 117938759  925 LRTISVILFLNKQDLLAEKVLAGKSKIEDYFPE 957
Cdd:COG1100   109 GKKSPIILVLNKIDLYDEEEIEDEERLKEALSE 141
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 860-939 4.68e-06

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 48.04  E-value: 4.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  860 VNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASssynmviredNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDL 939
Cdd:PLN00223   61 ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS----------NDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDL 130
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
84-300 3.10e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.87  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   84 AFREAGAHGSYSPPPEEAMPFEAEQPSLGGFWPTLEQPGFPSGVHAGLEAFGPALMEPGAFSGARPglggyspPPEEAMP 163
Cdd:PRK12323  362 AFRPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRS-------PAPEALA 434

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  164 FEFDQPAQRGCSQLLLQ-------VPDLAPGGPGAAGVPGAPPEEPQALRPAKAGSRGGYSPPPEETMPFELDGEGFGDD 236
Cdd:PRK12323  435 AARQASARGPGGAPAPApapaaapAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQP 514

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 117938759  237 SPPPGLSRVIAQVDGSSQFAAVAASSAVRLTPAANAPPLWVPG----AIGSPSQEAVRPPSNFTGSSP 300
Cdd:PRK12323  515 DAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATepvvAPRPPRASASGLPDMFDGDWP 582
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 852-960 1.06e-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: 40.82  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   852 ETKFQVD--KVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYnmVIR-EDNQTNRLQEALNLFKSiwnnrwlrTI 928
Cdd:TIGR00231   41 TTVIEEDgkTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFDIVIL--VLDvEEILEKQTKEIIHHADS--------GV 110

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 117938759   929 SVILFLNKQDLLAEKV------LAGKSKIEDYFPEFAR 960
Cdd:TIGR00231  111 PIILVGNKIDLKDADLkthvasEFAKLNGEPIIPLSAE 148
UDM1_RNF168_RNF169-like cd22249
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ...
 642-676 7.05e-03

UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets.


Pssm-ID: 409016 [Multi-domain]  Cd Length: 66  Bit Score: 36.09  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 117938759  642 AEKRRQMRKEALEKRAQKRAEKKRSKLIDKQLQDE 676
Cdd:cd22249     9 EEYEAQLKKLEEERRKEREEEEKASEELIRKLQEE 43
 
Name Accession Description Interval E-value
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
 684-1031 1.01e-180

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


Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 527.87  E-value: 1.01e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  684 HRLLLLGAGESGKSTIVKQMRILHVNGFNGEggeedpqaarsnsdgEKATKVQDIKNNLKEAIETIVAAMSNLVPPveLA 763
Cdd:cd00066     1 VKLLLLGAGESGKSTILKQMKILHGNGFSDE---------------ERREFRPVIYSNILQSMKALLRAMETLNIP--YG 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  764 NPENQFRVDYILSVMN-VPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQADYVPSDQDLLR 842
Cdd:cd00066    64 DPENEKDAKKILSLAPrAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAKYFLDNLDRISDPDYIPTEQDILR 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  843 CRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNN 922
Cdd:cd00066   144 SRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNS 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  923 RWLRTISVILFLNKQDLLAEKVLagKSKIEDYFPEFaryttpedatpePGEDPRVTRAKYFIRDEFLRISTasgDGRHYC 1002
Cdd:cd00066   224 RWFANTSIILFLNKKDLFEEKIK--KSPLTDYFPDY------------TGPPNDYEEAAKYIKKKFLDLNR---NPNKEI 286

                         330       340
                  ....*....|....*....|....*....
gi 117938759 1003 YPHFTCAVDTENIRRVFNDCRDIIQRMHL 1031
Cdd:cd00066   287 YPHFTCATDTENIRFVFDAVKDIILQNNL 315
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 663-1034 7.55e-167

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


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 493.25  E-value: 7.55e-167
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    663 KKRSKLIDKQLQDEKMGYMCTHRLLLLGAGESGKSTIVKQMRILHVNGFNGEggeedpqaarsnsdgEKATKVQDIKNNL 742
Cdd:smart00275    1 IRRNKEIEKQLEEERKKKKREVKLLLLGAGESGKSTILKQMRILHGDGFSQE---------------ERREYRPLIYSNI 65

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    743 KEAIETIVAAMSNLVPPVElaNPENQFRVDYILSVMNVPD---FDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQ 819
Cdd:smart00275   66 LESMKALVDAMEELNIPFE--DPESILDIRIITEQFNKTDeteNVLPKEIAKAIKALWKDEGIQECYRRRNEFQLNDSAS 143

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    820 YFLDKIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMV 899
Cdd:smart00275  144 YFLDNIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQV 223

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    900 IREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLagKSKIEDYFPEFaryttpedatpepGEDPRVTR 979
Cdd:smart00275  224 LEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLFEEKIK--KVPLVDYFPDY-------------KGPNDYEA 288

                           330       340       350       360       370
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 117938759    980 AKYFIRDEFLRISTasGDGRHYCYPHFTCAVDTENIRRVFNDCRDIIQRMHLRQY 1034
Cdd:smart00275  289 AAKFIKQKFLRLNR--NSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKDA 341
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 683-1026 5.07e-140

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


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 422.77  E-value: 5.07e-140
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   683 THRLLLLGAGESGKSTIVKQMRILHVNGFngeggeedpqaarsnSDGEKATKVQDIKNNLKEAIETIVAAMSNLvpPVEL 762
Cdd:pfam00503    5 EVKLLLLGAGESGKSTILKQMKIIHGGGF---------------SEEERKQYRPVIYSNILRSLKTLIEAMERL--GIEL 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   763 ANPENQFRVDYILSVMNVP--DFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLDKIDVIKQADYVPSDQDL 840
Cdd:pfam00503   68 SNPENKERLDDLLSLDSSLknETEFTPELAEDIKRLWNDPGIQECYERRNEFQLPDSAEYFLDNLDRIASPDYVPTDQDI 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   841 LRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIW 920
Cdd:pfam00503  148 LRARVKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRMEESLKLFEEIC 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   921 NNRWLRTISVILFLNKQDLLAEKVlaGKSKIEDYFPEFAryttpedatpepGEDPRVTRAKYFIRDEFLRISTasgDGRH 1000
Cdd:pfam00503  228 NSPWFKNTPIILFLNKKDLFEEKL--KKSPLSDYFPDYT------------GNPNDYEEALKYIRNKFLDLNK---NPNR 290

                          330       340
                   ....*....|....*....|....*.
gi 117938759  1001 YCYPHFTCAVDTENIRRVFNDCRDII 1026
Cdd:pfam00503  291 KIYTHFTCATDTENIRFVFDAVKDII 316
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 847-941 1.21e-12

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 66.83  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  847 TSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmviREdnqtnRLQEALNLFKSIWNNRWLR 926
Cdd:cd00878    30 TIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSD-----RE-----RIEEAKNELHKLLNEEELK 99

                          90
                  ....*....|....*
gi 117938759  927 TISVILFLNKQDLLA 941
Cdd:cd00878   100 GAPLLILANKQDLPG 114
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 856-939 2.81e-11

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 63.01  E-value: 2.81e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   856 QVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmvirednqTNRLQEALNLFKSIWNNRWLRTISVILFLN 935
Cdd:pfam00025   40 TYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSAD----------RDRIEEAKEELHALLNEEELADAPLLILAN 109


                   ....
gi 117938759   936 KQDL 939
Cdd:pfam00025  110 KQDL 113
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 856-939 3.28e-08

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


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 54.27  E-value: 3.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  856 QVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSsynmviREDnqtnRLQEALNLFKSIWNNRWLRTISVILFLN 935
Cdd:cd04160    47 EVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDST------DRE----RFNESKSAFEKVINNEALEGVPLLVLAN 116


                  ....
gi 117938759  936 KQDL 939
Cdd:cd04160   117 KQDL 120
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 860-939 5.38e-08

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 53.62  E-value: 5.38e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  860 VNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYnmvirednqtNRLQEALNLFKSIWNNRWLRTISVILFLNKQDL 939
Cdd:cd04149    53 VKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADR----------DRIDEARQELHRIINDREMRDALLLVFANKQDL 122
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 855-939 1.02e-07

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


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 52.41  E-value: 1.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  855 FQVDKV-----NFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASssynmviredNQTNRLQEALNLFKSIWNNRWLRTIS 929
Cdd:cd04150    34 FNVETVeykniSFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS----------NDRERIGEAREELQRMLNEDELRDAV 103

                          90
                  ....*....|
gi 117938759  930 VILFLNKQDL 939
Cdd:cd04150   104 LLVFANKQDL 113
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 859-939 2.57e-07

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


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 51.26  E-value: 2.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  859 KVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYnmvirednqtNRLQEALNLFKSIWNNRWLRTISVILFLNKQD 938
Cdd:cd04156    43 HLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE----------ARLDESQKELKHILKNEHIKGVPVVLLANKQD 112


                  .
gi 117938759  939 L 939
Cdd:cd04156   113 L 113
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 848-940 4.42e-07

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


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 50.86  E-value: 4.42e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  848 SGIFETK-FQVDKVN-----FHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmvirednqTNRLQEALNLFKSIWN 921
Cdd:cd04155    41 SHITPTQgFNIKNVQadgfkLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSAD----------RKRFEEAGQELVELLE 110

                          90
                  ....*....|....*....
gi 117938759  922 NRWLRTISVILFLNKQDLL 940
Cdd:cd04155   111 EEKLAGVPVLVFANKQDLL 129
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 847-957 7.48e-07

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


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 50.08  E-value: 7.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  847 TSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSsynmvireDNQtnRLQEALNLFKSIWNNRWLR 926
Cdd:cd04161    30 TVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSS--------DDD--RVQEVKEILRELLQHPRVS 99

                          90       100       110
                  ....*....|....*....|....*....|.
gi 117938759  927 TISVILFLNKQDLlaEKVLAGKSKIEDYFPE 957
Cdd:cd04161   100 GKPILVLANKQDK--KNALLGADVIEYLSLE 128
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 856-939 1.06e-06

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 49.92  E-value: 1.06e-06
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759    856 QVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASssynmviredNQTNRLQEALNLFKSIWNNRWLRTISVILFLN 935
Cdd:smart00177   53 TYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS----------NDRDRIDEAREELHRMLNEDELRDAVILVFAN 122


                    ....
gi 117938759    936 KQDL 939
Cdd:smart00177  123 KQDL 126
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
850-957 2.50e-06

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 48.82  E-value: 2.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  850 IFETKFQVD--KVNFHMFDVGGQ---RDERRKWIQCFNDVTAIIFVVASSsynmviREDNqTNRLQEALNLFKSIwnnrw 924
Cdd:COG1100    41 IDKKELKLDglDVDLVIWDTPGQdefRETRQFYARQLTGASLYLFVVDGT------REET-LQSLYELLESLRRL----- 108

                          90       100       110
                  ....*....|....*....|....*....|...
gi 117938759  925 LRTISVILFLNKQDLLAEKVLAGKSKIEDYFPE 957
Cdd:COG1100   109 GKKSPIILVLNKIDLYDEEEIEDEERLKEALSE 141
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 860-939 4.68e-06

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 48.04  E-value: 4.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  860 VNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASssynmviredNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDL 939
Cdd:PLN00223   61 ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS----------NDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDL 130
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 845-939 5.26e-06

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


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 47.81  E-value: 5.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  845 VLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASS-SYNMVIREDNQTNRLQEAlnLFKSiwnnr 923
Cdd:cd04157    30 VPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSdRLRMVVAKDELELLLNHP--DIKH----- 102

                          90
                  ....*....|....*.
gi 117938759  924 wlRTISVILFLNKQDL 939
Cdd:cd04157   103 --RRIPILFYANKMDL 116
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 856-944 8.00e-06

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 47.07  E-value: 8.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  856 QVDKVNFHMFDVGGQRDERRKWI-----QCFNDVTAIIFVVASSSYNMvirEDNQTNrlqealnlfkSIWNNRWLRTISV 930
Cdd:cd00882    43 DKGKVKLVLVDTPGLDEFGGLGReelarLLLRGADLILLVVDSTDRES---EEDAKL----------LILRRLRKEGIPI 109

                          90
                  ....*....|....
gi 117938759  931 ILFLNKQDLLAEKV 944
Cdd:cd00882   110 ILVGNKIDLLEERE 123
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 859-939 1.36e-05

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


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 46.89  E-value: 1.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  859 KVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYnmvirednqtNRLQEALNLFKSIWNNRWLRTISVILFLNKQD 938
Cdd:cd00879    62 NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADP----------ERFQESKEELDSLLNDEELANVPILILGNKID 131


                  .
gi 117938759  939 L 939
Cdd:cd00879   132 K 132
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 855-939 4.07e-05

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


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 45.42  E-value: 4.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  855 FQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmviREdnqtnRLQEALNLFKSIWNNRWLRTISVILFL 934
Cdd:cd04153    54 IVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTD-----RE-----RLPLTKEELYKMLAHEDLRKAVLLVLA 123


                  ....*
gi 117938759  935 NKQDL 939
Cdd:cd04153   124 NKQDL 128
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 860-939 5.40e-05

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 45.22  E-value: 5.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  860 VNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASssynmviredNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDL 939
Cdd:PTZ00133   61 LKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDS----------NDRERIGDAREELERMLSEDELRDAVLLVFANKQDL 130
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 855-939 8.19e-05

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


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 44.24  E-value: 8.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  855 FQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmvirednqTNRLQEALNLFKSIWNNRWLRTISVILFL 934
Cdd:cd04154    53 LEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSD----------RARLEDCKRELQKLLVEERLAGATLLIFA 122


                  ....*
gi 117938759  935 NKQDL 939
Cdd:cd04154   123 NKQDL 127
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
84-300 3.10e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.87  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   84 AFREAGAHGSYSPPPEEAMPFEAEQPSLGGFWPTLEQPGFPSGVHAGLEAFGPALMEPGAFSGARPglggyspPPEEAMP 163
Cdd:PRK12323  362 AFRPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRS-------PAPEALA 434

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  164 FEFDQPAQRGCSQLLLQ-------VPDLAPGGPGAAGVPGAPPEEPQALRPAKAGSRGGYSPPPEETMPFELDGEGFGDD 236
Cdd:PRK12323  435 AARQASARGPGGAPAPApapaaapAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQP 514

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 117938759  237 SPPPGLSRVIAQVDGSSQFAAVAASSAVRLTPAANAPPLWVPG----AIGSPSQEAVRPPSNFTGSSP 300
Cdd:PRK12323  515 DAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATepvvAPRPPRASASGLPDMFDGDWP 582
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 860-939 5.36e-04

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


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 41.63  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  860 VNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSynmvirednqTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDL 939
Cdd:cd04151    43 LKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTD----------RDRLGISKSELHAMLEEEELKDAVLLVFANKQDM 112
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 852-960 1.06e-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: 40.82  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759   852 ETKFQVD--KVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYnmVIR-EDNQTNRLQEALNLFKSiwnnrwlrTI 928
Cdd:TIGR00231   41 TTVIEEDgkTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFDIVIL--VLDvEEILEKQTKEIIHHADS--------GV 110

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 117938759   929 SVILFLNKQDLLAEKV------LAGKSKIEDYFPEFAR 960
Cdd:TIGR00231  111 PIILVGNKIDLKDADLkthvasEFAKLNGEPIIPLSAE 148
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 838-939 3.21e-03

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


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 39.63  E-value: 3.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117938759  838 QDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSsynmvirednQTNRLQEALNLFK 917
Cdd:cd04158    21 QDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSS----------HRDRVSEAHSELA 90

                          90       100
                  ....*....|....*....|..
gi 117938759  918 SIWNNRWLRTISVILFLNKQDL 939
Cdd:cd04158    91 KLLTEKELRDALLLIFANKQDV 112
UDM1_RNF168_RNF169-like cd22249
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ...
 642-676 7.05e-03

UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets.


Pssm-ID: 409016 [Multi-domain]  Cd Length: 66  Bit Score: 36.09  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 117938759  642 AEKRRQMRKEALEKRAQKRAEKKRSKLIDKQLQDE 676
Cdd:cd22249     9 EEYEAQLKKLEEERRKEREEEEKASEELIRKLQEE 43
 
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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