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Conserved domains on  [gi|67188550|ref|NP_430255|]
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RNA polymerase II subunit A C-terminal domain phosphatase isoform 2 [Homo sapiens]

Protein Classification

HAD_FCP1-like and BRCT_CTDP1 domain-containing protein( domain architecture ID 13089361)

protein containing domains Biotinyl_lipoyl_domains, HAD_FCP1-like, BRCT_CTDP1, and FCP1_C

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 177-323 1.37e-70

FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031.


:

Pssm-ID: 131304  Cd Length: 156  Bit Score: 229.47  E-value: 1.37e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   177 LHRNRKLVLMVDLDQTLIHTTEQHCQQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156
FCP1_C super family cl07811
FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy ...
 716-806 7.57e-50

FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.


The actual alignment was detected with superfamily member pfam09309:

Pssm-ID: 462751  Cd Length: 254  Bit Score: 176.16  E-value: 7.57e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   716 ERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGP-PAPSS 794
Cdd:pfam09309   1 ERWDRVEEQLFPLKDDYTKTQRENSPAAFPDRQGALPTALFHPTPIHPKAQPGPEVRIYDPNTGKLIRKGPQGSsPGPPG 80

                          90
                  ....*....|..
gi 67188550   795 SLPIRQEPSSFR 806
Cdd:pfam09309  81 SLPVHGEHSSFR 92
BRCT_CTDP1 cd17729
BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar ...
 621-723 4.35e-45

BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar proteins; CTDP1 (EC 3.1.3.16), also termed TFIIF-associating CTD phosphatase, or TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1), promotes the activity of RNA polymerase II through processively dephosphorylating 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. It plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation.


:

Pssm-ID: 349361 [Multi-domain]  Cd Length: 97  Bit Score: 156.92  E-value: 4.35e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 621 DIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVlspdapDRATHLIAARAGTEKVLQAQEC 700
Cdd:cd17729   1 DVKDILPELRSKVLKGCVIVFSGVIPTGIDPERSRLWKLAESLGAKVVTDLS------PRTTHLVAAKLGTEKVKQALKM 74

                        90       100
                ....*....|....*....|...
gi 67188550 701 GHLHVVNPDWLWSCLERWDKVEE 723
Cdd:cd17729  75 PGIHVVHPDWLWACAERWERVDE 97
Biotinyl_lipoyl_domains super family cl11404
Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the ...
 21-111 3.50e-06

Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue.


The actual alignment was detected with superfamily member cd06850:

Pssm-ID: 448245 [Multi-domain]  Cd Length: 67  Bit Score: 45.10  E-value: 3.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  21 EVRCPGPAplRLLEWRVAAGAAVRIGSVLAVFEaaasaqssgasqsrvasggcvrpA-RPERRLRSERAGVVRELCAQPG 99
Cdd:cd06850   1 EVTAPMPG--TVVKVLVKEGDKVEAGQPLAVLE-----------------------AmKMENEVTAPVAGVVKEILVKEG 55

                        90
                ....*....|..
gi 67188550 100 QVVAPGAVLVRL 111
Cdd:cd06850  56 DQVEAGQLLVVI 67
PRK07764 super family cl35613
DNA polymerase III subunits gamma and tau; Validated
 331-539 4.64e-05

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: 47.29  E-value: 4.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  331 APPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPA 410
Cdd:PRK07764 591 APGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWP 670

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  411 QAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTdldfDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAA 490
Cdd:PRK07764 671 AKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT----PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPD 746

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 67188550  491 PEGAGALAQGSSLEPGRPAAPSlPGEAEPGAHAPDKEPELGGQEEGERD 539
Cdd:PRK07764 747 DPPDPAGAPAQPPPPPAPAPAA-APAAAPPPSPPSEEEEMAEDDAPSMD 794
 
Name Accession Description Interval E-value
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 177-323 1.37e-70

FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031.


Pssm-ID: 131304  Cd Length: 156  Bit Score: 229.47  E-value: 1.37e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   177 LHRNRKLVLMVDLDQTLIHTTEQHCQQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156
CPDc smart00577
catalytic domain of ctd-like phosphatases;
181-327 3.86e-54

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 184.35  E-value: 3.86e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550    181 RKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPML-HTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGF 259
Cdd:smart00577   1 KKKTLVLDLDETLVHSTHRSFKEWTNRDFIVPVLIDGHPHGvYVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 67188550    260 LDPeKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYFQGTG 327
Cdd:smart00577  81 LDP-KKYFGYRRLFRDECVFVKGKYVKDLSLLNRDLSKVIIIDDSPDSWPFHPeNLIPIKPWFGDPDDT 148
FCP1_C pfam09309
FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy ...
 716-806 7.57e-50

FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.


Pssm-ID: 462751  Cd Length: 254  Bit Score: 176.16  E-value: 7.57e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   716 ERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGP-PAPSS 794
Cdd:pfam09309   1 ERWDRVEEQLFPLKDDYTKTQRENSPAAFPDRQGALPTALFHPTPIHPKAQPGPEVRIYDPNTGKLIRKGPQGSsPGPPG 80

                          90
                  ....*....|..
gi 67188550   795 SLPIRQEPSSFR 806
Cdd:pfam09309  81 SLPVHGEHSSFR 92
BRCT_CTDP1 cd17729
BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar ...
 621-723 4.35e-45

BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar proteins; CTDP1 (EC 3.1.3.16), also termed TFIIF-associating CTD phosphatase, or TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1), promotes the activity of RNA polymerase II through processively dephosphorylating 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. It plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation.


Pssm-ID: 349361 [Multi-domain]  Cd Length: 97  Bit Score: 156.92  E-value: 4.35e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 621 DIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVlspdapDRATHLIAARAGTEKVLQAQEC 700
Cdd:cd17729   1 DVKDILPELRSKVLKGCVIVFSGVIPTGIDPERSRLWKLAESLGAKVVTDLS------PRTTHLVAAKLGTEKVKQALKM 74

                        90       100
                ....*....|....*....|...
gi 67188550 701 GHLHVVNPDWLWSCLERWDKVEE 723
Cdd:cd17729  75 PGIHVVHPDWLWACAERWERVDE 97
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 182-317 5.18e-44

human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily; Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319823  Cd Length: 134  Bit Score: 155.45  E-value: 5.18e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 182 KLVLMVDLDQTLIHTTEQHCQQMSNKgiFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:cd07521   1 KLTLVLDLDETLVHSTWKPVLSEDFK--IPVLPDGREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLD 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67188550 262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLFPCgDSMVCIIDD-REDVWKFAPNLITV 317
Cdd:cd07521  79 PNGLFIDRR-LFRDSCVYVDGNyVKDLSKLFRD-LSKVVIIDDsPGSYWLQPENAIPI 134
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 183-320 1.86e-26

NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.


Pssm-ID: 397254  Cd Length: 160  Bit Score: 106.17  E-value: 1.86e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   183 LVLmvDLDQTLIHTTEQhcqqMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLDP 262
Cdd:pfam03031   3 LVL--DLDETLVHSSFE----PPLKSDFILPVPGETHGGYVKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILDP 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 67188550   263 EKKLFSHRiLSRDECID---PFSKtgNLRNLFPcgD-SMVCIIDDREDVWKFAP-NLITVKKY 320
Cdd:pfam03031  77 NGKLFSHR-LYRESCKFedgVYVK--DLSLLGR--DlSRVVIVDNSPDSFLLQPdNGIPIPPF 134
BRCT smart00292
breast cancer carboxy-terminal domain;
631-715 6.68e-07

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 47.76  E-value: 6.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550    631 SKVLADVAIIFSGlhptNFPIEKTREHYH-ATALGAKILTRLVlspdaPDRATHLIAARAGTEKV--LQAQECGhLHVVN 707
Cdd:smart00292   1 PKLFKGKTFYITG----SFDKEERDELKElIEALGGKVTSSLS-----SKTTTHVIVGSPEGGKLelLKAIALG-IPIVK 70


                   ....*...
gi 67188550    708 PDWLWSCL 715
Cdd:smart00292  71 EEWLLDCL 78
biotinyl_domain cd06850
The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all ...
 21-111 3.50e-06

The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.


Pssm-ID: 133459 [Multi-domain]  Cd Length: 67  Bit Score: 45.10  E-value: 3.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  21 EVRCPGPAplRLLEWRVAAGAAVRIGSVLAVFEaaasaqssgasqsrvasggcvrpA-RPERRLRSERAGVVRELCAQPG 99
Cdd:cd06850   1 EVTAPMPG--TVVKVLVKEGDKVEAGQPLAVLE-----------------------AmKMENEVTAPVAGVVKEILVKEG 55

                        90
                ....*....|..
gi 67188550 100 QVVAPGAVLVRL 111
Cdd:cd06850  56 DQVEAGQLLVVI 67
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 630-715 6.73e-06

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 44.59  E-value: 6.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   630 KSKVLADVAIIFSGLhptnfpIEKTREHYH--ATALGAKIltrlvlSPDAPDRATHLIAArAGTEKVLQAQECGhLHVVN 707
Cdd:pfam00533   2 KEKLFSGKTFVITGL------DGLERDELKelIEKLGGKV------TDSLSKKTTHVIVE-ARTKKYLKAKELG-IPIVT 67


                  ....*...
gi 67188550   708 PDWLWSCL 715
Cdd:pfam00533  68 EEWLLDCI 75
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 331-539 4.64e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.29  E-value: 4.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  331 APPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPA 410
Cdd:PRK07764 591 APGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWP 670

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  411 QAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTdldfDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAA 490
Cdd:PRK07764 671 AKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT----PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPD 746

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 67188550  491 PEGAGALAQGSSLEPGRPAAPSlPGEAEPGAHAPDKEPELGGQEEGERD 539
Cdd:PRK07764 747 DPPDPAGAPAQPPPPPAPAPAA-APAAAPPPSPPSEEEEMAEDDAPSMD 794
AceF COG0508
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component ...
 32-111 3.02e-03

Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component [Energy production and conversion]; Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440274 [Multi-domain]  Cd Length: 77  Bit Score: 37.35  E-value: 3.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  32 LLEWRVAAGAAVRIGSVL-------AVFEaaasaqssgasqsrvasggcvrparperrLRSERAGVVRELCAQPGQVVAP 104
Cdd:COG0508  19 IVEWLVKEGDTVKEGDPLaevetdkATME-----------------------------VPAPAAGVLLEILVKEGDTVPV 69


                ....*..
gi 67188550 105 GAVLVRL 111
Cdd:COG0508  70 GAVIAVI 76
 
Name Accession Description Interval E-value
FCP1_euk TIGR02250
FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the ...
 177-323 1.37e-70

FCP1-like phosphatase, phosphatase domain; This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031.


Pssm-ID: 131304  Cd Length: 156  Bit Score: 229.47  E-value: 1.37e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   177 LHRNRKLVLMVDLDQTLIHTTEQHCQQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156
CPDc smart00577
catalytic domain of ctd-like phosphatases;
181-327 3.86e-54

catalytic domain of ctd-like phosphatases;


Pssm-ID: 214729  Cd Length: 148  Bit Score: 184.35  E-value: 3.86e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550    181 RKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPML-HTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGF 259
Cdd:smart00577   1 KKKTLVLDLDETLVHSTHRSFKEWTNRDFIVPVLIDGHPHGvYVKKRPGVDEFLKRASELFELVVFTAGLRMYADPVLDL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 67188550    260 LDPeKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYFQGTG 327
Cdd:smart00577  81 LDP-KKYFGYRRLFRDECVFVKGKYVKDLSLLNRDLSKVIIIDDSPDSWPFHPeNLIPIKPWFGDPDDT 148
FCP1_C pfam09309
FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy ...
 716-806 7.57e-50

FCP1, C-terminal; The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains.


Pssm-ID: 462751  Cd Length: 254  Bit Score: 176.16  E-value: 7.57e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   716 ERWDKVEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGKLIRTGARGP-PAPSS 794
Cdd:pfam09309   1 ERWDRVEEQLFPLKDDYTKTQRENSPAAFPDRQGALPTALFHPTPIHPKAQPGPEVRIYDPNTGKLIRKGPQGSsPGPPG 80

                          90
                  ....*....|..
gi 67188550   795 SLPIRQEPSSFR 806
Cdd:pfam09309  81 SLPVHGEHSSFR 92
BRCT_CTDP1 cd17729
BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar ...
 621-723 4.35e-45

BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar proteins; CTDP1 (EC 3.1.3.16), also termed TFIIF-associating CTD phosphatase, or TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1), promotes the activity of RNA polymerase II through processively dephosphorylating 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. It plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation.


Pssm-ID: 349361 [Multi-domain]  Cd Length: 97  Bit Score: 156.92  E-value: 4.35e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 621 DIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHATALGAKILTRLVlspdapDRATHLIAARAGTEKVLQAQEC 700
Cdd:cd17729   1 DVKDILPELRSKVLKGCVIVFSGVIPTGIDPERSRLWKLAESLGAKVVTDLS------PRTTHLVAAKLGTEKVKQALKM 74

                        90       100
                ....*....|....*....|...
gi 67188550 701 GHLHVVNPDWLWSCLERWDKVEE 723
Cdd:cd17729  75 PGIHVVHPDWLWACAERWERVDE 97
HAD_FCP1-like cd07521
human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid ...
 182-317 5.18e-44

human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily; Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319823  Cd Length: 134  Bit Score: 155.45  E-value: 5.18e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 182 KLVLMVDLDQTLIHTTEQHCQQMSNKgiFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:cd07521   1 KLTLVLDLDETLVHSTWKPVLSEDFK--IPVLPDGREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLD 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67188550 262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLFPCgDSMVCIIDD-REDVWKFAPNLITV 317
Cdd:cd07521  79 PNGLFIDRR-LFRDSCVYVDGNyVKDLSKLFRD-LSKVVIIDDsPGSYWLQPENAIPI 134
NIF pfam03031
NLI interacting factor-like phosphatase; This family contains a number of NLI interacting ...
 183-320 1.86e-26

NLI interacting factor-like phosphatase; This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain.


Pssm-ID: 397254  Cd Length: 160  Bit Score: 106.17  E-value: 1.86e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   183 LVLmvDLDQTLIHTTEQhcqqMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLDP 262
Cdd:pfam03031   3 LVL--DLDETLVHSSFE----PPLKSDFILPVPGETHGGYVKKRPGLDEFLKELSKYYEIVIFTASSKEYADPVLDILDP 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 67188550   263 EKKLFSHRiLSRDECID---PFSKtgNLRNLFPcgD-SMVCIIDDREDVWKFAP-NLITVKKY 320
Cdd:pfam03031  77 NGKLFSHR-LYRESCKFedgVYVK--DLSLLGR--DlSRVVIVDNSPDSFLLQPdNGIPIPPF 134
HIF-SF_euk TIGR02251
Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a ...
 182-322 4.76e-19

Dullard-like phosphatase domain; This model represents the putative phosphatase domain of a family of eukaryotic proteins including "Dullard", and the NLI interacting factor (NIF)-like phosphatases. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDNxPxxa) and aparrently lacking the last aspartate. This domain is classified as a "Class III" HAD, since there is no large "cap" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in FCP1-like phosphatases (TIGR02250), and together both are detected by the pfam03031.


Pssm-ID: 274055  Cd Length: 162  Bit Score: 85.04  E-value: 4.76e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   182 KLVLMVDLDQTLIHTTEQHCQQMSNKgIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:TIGR02251   1 KKTLVLDLDETLVHSTFKMPKVDADF-KVPVLIDGKIIQVYVFKRPHVDEFLERVSKWYELVIFTASLEEYADPVLDILD 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 67188550   262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLfpCGD-SMVCIIDDREDVWKFAP-NLITVKKYVY 322
Cdd:TIGR02251  80 RGGKVISRR-LYRESCVFTNGKyVKDLSLV--GKDlSKVIIIDNSPYSYSLQPdNAIPIKSWFS 140
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 639-714 1.25e-08

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


Pssm-ID: 349339 [Multi-domain]  Cd Length: 68  Bit Score: 52.36  E-value: 1.25e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 67188550 639 IIFSGLhptnFPIEKTREHYHATALGAKIltrlvlSPDAPDRATHLIAARAGTEKVLQAQECGHLHVVNPDWLWSC 714
Cdd:cd00027   3 ICFSGL----DDEEREELKKLIEALGGKV------SESLSSKVTHLIAKSPSGEKYYLAALAWGIPIVSPEWLLDC 68
BRCT_TopBP1_rpt2_like cd17731
second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; ...
 682-718 8.39e-08

second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the second BRCT domain.


Pssm-ID: 349363 [Multi-domain]  Cd Length: 77  Bit Score: 50.23  E-value: 8.39e-08
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 67188550 682 THLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERW 718
Cdd:cd17731  41 THLIAGSPSGQKYEFARKWNSIHIVTPEWLYDSIEAG 77
BRCT smart00292
breast cancer carboxy-terminal domain;
631-715 6.68e-07

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 47.76  E-value: 6.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550    631 SKVLADVAIIFSGlhptNFPIEKTREHYH-ATALGAKILTRLVlspdaPDRATHLIAARAGTEKV--LQAQECGhLHVVN 707
Cdd:smart00292   1 PKLFKGKTFYITG----SFDKEERDELKElIEALGGKVTSSLS-----SKTTTHVIVGSPEGGKLelLKAIALG-IPIVK 70


                   ....*...
gi 67188550    708 PDWLWSCL 715
Cdd:smart00292  71 EEWLLDCL 78
biotinyl_domain cd06850
The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all ...
 21-111 3.50e-06

The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.


Pssm-ID: 133459 [Multi-domain]  Cd Length: 67  Bit Score: 45.10  E-value: 3.50e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  21 EVRCPGPAplRLLEWRVAAGAAVRIGSVLAVFEaaasaqssgasqsrvasggcvrpA-RPERRLRSERAGVVRELCAQPG 99
Cdd:cd06850   1 EVTAPMPG--TVVKVLVKEGDKVEAGQPLAVLE-----------------------AmKMENEVTAPVAGVVKEILVKEG 55

                        90
                ....*....|..
gi 67188550 100 QVVAPGAVLVRL 111
Cdd:cd06850  56 DQVEAGQLLVVI 67
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 630-715 6.73e-06

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 44.59  E-value: 6.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   630 KSKVLADVAIIFSGLhptnfpIEKTREHYH--ATALGAKIltrlvlSPDAPDRATHLIAArAGTEKVLQAQECGhLHVVN 707
Cdd:pfam00533   2 KEKLFSGKTFVITGL------DGLERDELKelIEKLGGKV------TDSLSKKTTHVIVE-ARTKKYLKAKELG-IPIVT 67


                  ....*...
gi 67188550   708 PDWLWSCL 715
Cdd:pfam00533  68 EEWLLDCI 75
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 331-539 4.64e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.29  E-value: 4.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  331 APPGSRESQTRKKVNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPA 410
Cdd:PRK07764 591 APGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWP 670

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  411 QAPTSSQELAGAPEPQGSCAQGGRVAPGQRPAQGATGTdldfDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAA 490
Cdd:PRK07764 671 AKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT----PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPD 746

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 67188550  491 PEGAGALAQGSSLEPGRPAAPSlPGEAEPGAHAPDKEPELGGQEEGERD 539
Cdd:PRK07764 747 DPPDPAGAPAQPPPPPAPAPAA-APAAAPPPSPPSEEEEMAEDDAPSMD 794
BRCT_Rad4_rpt2 cd17746
second BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and ...
 647-728 1.59e-04

second BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins; Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system which couples S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the second one.


Pssm-ID: 349377 [Multi-domain]  Cd Length: 91  Bit Score: 41.45  E-value: 1.59e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 647 TNFPI-EKTREHYHATALGAKiltrlvLSPDAPDRATHLIAARAGTEKVLQAQECGhLHVVNPDWLWSCLERWDKVEEQL 725
Cdd:cd17746  15 TNIGQpERSRIENYVLKHGGT------FCPDLTRDVTHLIAGTSSGRKYEYALKWK-INVVCVEWLWQSIQRNAVLEPQY 87


                ...
gi 67188550 726 FPL 728
Cdd:cd17746  88 FQL 90
BRCT_XRCC1_rpt1 cd17725
First (central) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar ...
 660-714 2.29e-04

First (central) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar proteins; XRCC1 is a DNA repair protein that corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. It forms homodimers and interacts with polynucleotide kinase (PNK), DNA polymerase-beta (POLB), DNA ligase III (LIG3), APTX, APLF, and APEX1. XRCC1 contains an N-terminal XRCC1-specific domain and two BRCT domains. This family corresponds to the first one.


Pssm-ID: 349357 [Multi-domain]  Cd Length: 80  Bit Score: 40.34  E-value: 2.29e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 67188550 660 ATALGAKiltrlvLSPDAPDRATHLIAARAGTEKVLQAQECGHLhVVNPDWLWSC 714
Cdd:cd17725  21 ALEMGAK------YRPDWTADCTHLICAFANTPKYKQVKGAGGI-IVSKEWILDC 68
PTCB-BRCT pfam12738
twin BRCT domain; This is a BRCT domain that appears in duplicate in most member sequences. ...
 661-710 1.42e-03

twin BRCT domain; This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair.


Pssm-ID: 463687 [Multi-domain]  Cd Length: 63  Bit Score: 37.57  E-value: 1.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 67188550   661 TALGAKILTRLVLSpdapdrATHLIAARAGTEKVLQAQECGhLHVVNPDW 710
Cdd:pfam12738  21 EAMGAEYTKDLTKS------VTHLICKSGEGEKYEKAKEWG-IPVVSPLW 63
BRCT_BRC1_like_rpt5 cd17743
fifth BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar ...
 637-717 2.19e-03

fifth BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins; Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. The family also includes Cryptococcus neoformans DNA ligase 4 (LIG4, also known as DNA ligase IV or polydeoxyribonucleotide synthase [ATP] 4), which is involved in dsDNA break repair, and plays a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining. Members in this family contain six BRCT domains. This family corresponds to the fifth one.


Pssm-ID: 349374  Cd Length: 70  Bit Score: 37.61  E-value: 2.19e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550 637 VAIIFSGLHP-TNFPIEKTREhyhataLGAKILtrlvlspDAPDRATHLIAARAG-TEKVLQAQECGHlHVVNPDWLWSC 714
Cdd:cd17743   1 VRLLFTGYKLwTEKEIKKLKK------LGISIV-------EDPDECTHLVAPKIVrTEKFLCALAYAP-VIVTTDWLEAC 66


                ...
gi 67188550 715 LER 717
Cdd:cd17743  67 LKA 69
AceF COG0508
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component ...
 32-111 3.02e-03

Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component [Energy production and conversion]; Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440274 [Multi-domain]  Cd Length: 77  Bit Score: 37.35  E-value: 3.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  32 LLEWRVAAGAAVRIGSVL-------AVFEaaasaqssgasqsrvasggcvrparperrLRSERAGVVRELCAQPGQVVAP 104
Cdd:COG0508  19 IVEWLVKEGDTVKEGDPLaevetdkATME-----------------------------VPAPAAGVLLEILVKEGDTVPV 69


                ....*..
gi 67188550 105 GAVLVRL 111
Cdd:COG0508  70 GAVIAVI 76
dnaA PRK14086
chromosomal replication initiator protein DnaA;
344-538 4.05e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 40.96  E-value: 4.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  344 VNHSRGTEVSEPSPPVRDPEGVTQAPGVEPSNGLEKPaRELNGSEAATPRD---SPRPGKPDERD-----IWPPAQAPTS 415
Cdd:PRK14086  88 VDPSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGP-RADDRPPGLPRQDqlpTARPAYPAYQQrpepgAWPRAADDYG 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550  416 SQ-ELAGAPEPqgscaqggrvAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEGKRGRQKPKAAPeGA 494
Cdd:PRK14086 167 WQqQRLGFPPR----------APYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPEPPP-GA 235

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 67188550  495 GALAQGSSLEPGRPAAPSLPGEAE-PGAHAPDKEPELGGQEEGER 538
Cdd:PRK14086 236 GHVHRGGPGPPERDDAPVVPIRPSaPGPLAAQPAPAPGPGEPTAR 280
BRCT_PAXIP1_rpt2 cd17710
second BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also ...
 682-723 5.11e-03

second BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the second BRCT domain.


Pssm-ID: 349342 [Multi-domain]  Cd Length: 81  Bit Score: 36.83  E-value: 5.11e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 67188550 682 THLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERWDKVEE 723
Cdd:cd17710  40 THLVTGKASGAKYECALKHEGIKIVTPDWVTDCIKAKTLLDE 81
AccB COG0511
Biotin carboxyl carrier protein [Lipid transport and metabolism]; Biotin carboxyl carrier ...
 84-112 5.65e-03

Biotin carboxyl carrier protein [Lipid transport and metabolism]; Biotin carboxyl carrier protein is part of the Pathway/BioSystem: Fatty acid biosynthesis


Pssm-ID: 440277 [Multi-domain]  Cd Length: 136  Bit Score: 37.95  E-value: 5.65e-03
                        10        20
                ....*....|....*....|....*....
gi 67188550  84 RSERAGVVRELCAQPGQVVAPGAVLVRLE 112
Cdd:COG0511 108 EAPVSGTVVEILVENGQPVEYGQPLFVIE 136
RTT107_BRCT_5 pfam16770
Regulator of Ty1 transposition protein 107 BRCT domain; This is the fifth BRCT domain of ...
 630-728 8.31e-03

Regulator of Ty1 transposition protein 107 BRCT domain; This is the fifth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A.


Pssm-ID: 465266  Cd Length: 91  Bit Score: 36.34  E-value: 8.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67188550   630 KSKVLADVAIIFSGLHP----TNFPIEKTREhyhataLGAKILtrlvlspDAPDRATHLIAAR-AGTEKVLQAQECGHlH 704
Cdd:pfam16770   2 KSLPPYDIRAVLTGCERwidkEDLDKKKLRL------LGIKIV-------QDPSKCNHLIAPKiLRTEKFLCALAFAP-Y 67

                          90       100
                  ....*....|....*....|....
gi 67188550   705 VVNPDWLWSCLERWDKVEEQLFPL 728
Cdd:pfam16770  68 ILSPDFITDCLKEGKLPDEEDYLL 91
 
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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