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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  177 LHRNRKLVLMVDLDQTLIHTTEQHCPQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435 611 DIRKIVPELKSKVLADVAVIFSGLHPTNFPVEKTREHYHATALGAKVLTQLVlspdapDRATHLIAARAGTEKVRQAQEC 690
Cdd:cd17729    1 DVKDILPELRSKVLKGCVIVFSGVIPTGIDPERSRLWKLAESLGAKVVTDLS------PRTTHLVAAKLGTEKVKQALKM 74

                         90       100
                 ....*....|....*....|...
gi 569005435 691 KHLHVVSPDWLWSCLERWDKVEE 713
Cdd:cd17729   75 PGIHVVHPDWLWACAERWERVDE 97

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  177 LHRNRKLVLMVDLDQTLIHTTEQHCPQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  706 ERWDKVEEQLFPLIDDDTRTHRDNSPAVFPDRHSVLPTALFHPTPIHSKAHPGPEVRIYDSNTGKLIRMGPQGSAPAPSS 785
Cdd:pfam09309   1 ERWDRVEEQLFPLKDDYTKTQRENSPAAFPDRQGALPTALFHPTPIHPKAQPGPEVRIYDPNTGKLIRKGPQGSSPGPPG 80

                          90
                  ....*....|....
gi 569005435  786 APLNHGEPSSFRST 799
Cdd:pfam09309  81 SLPVHGEHSSFRAV 94

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435 182 KLVLMVDLDQTLIHTTEQHCPQMSNKgiFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:cd07521    1 KLTLVLDLDETLVHSTWKPVLSEDFK--IPVLPDGREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 569005435 262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLFPCgDSMVCIIDD-REDVWKFAPNLITV 317
Cdd:cd07521   79 PNGLFIDRR-LFRDSCVYVDGNyVKDLSKLFRD-LSKVVIIDDsPGSYWLQPENAIPI 134

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  27 PTPLRLLEWKVAAGATVRIGSVLAVCEtaasaqpagpaparaasggcvrAARTERRLRSERAGVVRELCAQPGQVVAPGA 106
Cdd:cd06850    5 PMPGTVVKVLVKEGDKVEAGQPLAVLE----------------------AMKMENEVTAPVAGVVKEILVKEGDQVEAGQ 62

                 ....*
gi 569005435 107 LLVRL 111
Cdd:cd06850   63 LLVVI 67

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  620 KSKVLADVAVIFSGLhptnfpVEKTREHYH--ATALGAKVltqlvlSPDAPDRATHLIAArAGTEKVRQAQECKhLHVVS 697
Cdd:pfam00533   2 KEKLFSGKTFVITGL------DGLERDELKelIEKLGGKV------TDSLSKKTTHVIVE-ARTKKYLKAKELG-IPIVT 67

                  ....*...
gi 569005435  698 PDWLWSCL 705
Cdd:pfam00533  68 EEWLLDCI 75

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  177 LHRNRKLVLMVDLDQTLIHTTEQHCPQMSNK------------GIFHFQLGRgePMLHTRLRPHCKDFLEKIAKLYELHV 244
Cdd:TIGR02250   1 LLREKKLHLVLDLDQTLIHTTKDPTLSEWEKydieepnsetrrDLRKFNLGT--MWYLTKLRPFLHEFLKEASKLYEMHV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  245 FTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTgnLRNLFPCGDSMVCIIDDREDVWKFAP-NLITVKKYVYF 323
Cdd:TIGR02250  79 YTMGTRAYAQAIAKLIDPDGKYFGDRIISRDESGSPHTKS--LLRLFPADESMVVIIDDREDVWPWHKrNLIQIEPYNYF 156

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  706 ERWDKVEEQLFPLIDDDTRTHRDNSPAVFPDRHSVLPTALFHPTPIHSKAHPGPEVRIYDSNTGKLIRMGPQGSAPAPSS 785
Cdd:pfam09309   1 ERWDRVEEQLFPLKDDYTKTQRENSPAAFPDRQGALPTALFHPTPIHPKAQPGPEVRIYDPNTGKLIRKGPQGSSPGPPG 80

                          90
                  ....*....|....
gi 569005435  786 APLNHGEPSSFRST 799
Cdd:pfam09309  81 SLPVHGEHSSFRAV 94

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435 182 KLVLMVDLDQTLIHTTEQHCPQMSNKgiFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:cd07521    1 KLTLVLDLDETLVHSTWKPVLSEDFK--IPVLPDGREHGYYVKKRPGVDEFLERLSKLYEIVIFTAGTRAYADPVADKLD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 569005435 262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLFPCgDSMVCIIDD-REDVWKFAPNLITV 317
Cdd:cd07521   79 PNGLFIDRR-LFRDSCVYVDGNyVKDLSKLFRD-LSKVVIIDDsPGSYWLQPENAIPI 134

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435  182 KLVLMVDLDQTLIHTTeQHCPQMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLYELHVFTFGSRLYAHTIAGFLD 261
Cdd:TIGR02251   1 KKTLVLDLDETLVHST-FKMPKVDADFKVPVLIDGKIIQVYVFKRPHVDEFLERVSKWYELVIFTASLEEYADPVLDILD 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 569005435  262 PEKKLFSHRiLSRDECIDPFSK-TGNLRNLfpCGD-SMVCIIDDREDVWKFAP-NLITVKKYVYFP 324
Cdd:TIGR02251  80 RGGKVISRR-LYRESCVFTNGKyVKDLSLV--GKDlSKVIIIDNSPYSYSLQPdNAIPIKSWFSDP 142

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 569005435 629 VIFSGLHPTnfpvEKTREHYHATALGAKVltqlvlSPDAPDRATHLIAARAGTEKVRQAQECKHLHVVSPDWLWSC 704
Cdd:cd00027    3 ICFSGLDDE----EREELKKLIEALGGKV------SESLSSKVTHLIAKSPSGEKYYLAALAWGIPIVSPEWLLDC 68

breast cancer carboxy-terminal domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435   621 SKVLADVAVIFSGlhptNFPVEKTREHYH-ATALGAKVLTQLVlspdaPDRATHLIAARAGTEKVRQAQECKH-LHVVSP 698
Cdd:smart00292   1 PKLFKGKTFYITG----SFDKEERDELKElIEALGGKVTSSLS-----SKTTTHVIVGSPEGGKLELLKAIALgIPIVKE 71

                   ....*..
gi 569005435   699 DWLWSCL 705
Cdd:smart00292  72 EWLLDCL 78

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 569005435 650 ATALGAKvltqlvLSPDAPDRATHLIAARAGTEKVRQAQECKHLhVVSPDWLWSC 704
Cdd:cd17725   21 ALEMGAK------YRPDWTADCTHLICAFANTPKYKQVKGAGGI-IVSKEWILDC 68

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569005435   3 APPAAGVPTECTPAVAGAEVRCPGPTPLR-----------LLEWK--VAAGATVRIGSVLAVcetaasaqpagpaparaa 69
Cdd:COG0511   36 AAPAAAAPAAAAPAAAAAAAAASGGGAVKspmvgtfyrapSPGAKpfVKVGDKVKAGDTLCI------------------ 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 569005435  70 sggcVRAARTERRLRSERAGVVRELCAQPGQVVAPGALLVRLE 112
Cdd:COG0511   98 ----IEAMKMMNEIEAPVSGTVVEILVENGQPVEYGQPLFVIE 136

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 569005435  651 TALGAKVLTQLVLSpdapdrATHLIAARAGTEKVRQAQECKhLHVVSPDW 700
Cdd:pfam12738  21 EAMGAEYTKDLTKS------VTHLICKSGEGEKYEKAKEWG-IPVVSPLW 63