Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as UBXN3A) and similar proteins; UBX domain-containing protein 3A (UBXN3A),also termed UBX domain-containing protein 12 (UBXD12), or FAF1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem ubiquitin-like (Ubl) domains, which shows high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to UBX domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370451704 563 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAK 641
Cdd:cd01771     2 EPISKLRFRLPGGEFLTRRFLASEPLQVLLNFVASKGYPPDEYKLLTTFPRRDLTQLDPSKTLEELKLFPQETLFLEER 80

ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin (Ub) regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the first Ubl domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370451704  92 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTP 164
Cdd:cd17129     1 MLTFNVEYRDRTIDVVLPDTETVGDIKQILENELGIPPCKQILKGWKARTVSDSTVLRSLHLPKENSLYLLTP 73

Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 482 QQQEDIKDEDEREARENVKrEQDEAYRlslEADRAKREAHEREMAEQfrLEQIRKEQEEEREAIRLSLEQALPPEPKEEN 561
Cdd:pfam09731 301 KKLAELKKREEKHIERALE-KQKEELD---KLAEELSARLEEVRAAD--EAQLRLEFEREREEIRESYEEKLRTELERQA 374

                          90       100
                  ....*....|....*....|....*...
gi 1370451704 562 AEPVSKLR--IRTPSGEfLERRFLASNK 587
Cdd:pfam09731 375 EAHEEHLKdvLVEQEIE-LQREFLQDIK 401

Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as UBXN3A) and similar proteins; UBX domain-containing protein 3A (UBXN3A),also termed UBX domain-containing protein 12 (UBXD12), or FAF1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem ubiquitin-like (Ubl) domains, which shows high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to UBX domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370451704 563 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAK 641
Cdd:cd01771     2 EPISKLRFRLPGGEFLTRRFLASEPLQVLLNFVASKGYPPDEYKLLTTFPRRDLTQLDPSKTLEELKLFPQETLFLEER 80

ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin (Ub) regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the first Ubl domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1370451704  92 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTP 164
Cdd:cd17129     1 MLTFNVEYRDRTIDVVLPDTETVGDIKQILENELGIPPCKQILKGWKARTVSDSTVLRSLHLPKENSLYLLTP 73

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370451704 562 AEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDE-YKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE 639
Cdd:pfam00789   1 AEDVTRLQIRLPDGSRLVRRFNSSDKLQTVYDFVDSNRYDDLEpFSLNTPFPRRPLTDLDYSKTLKEAGLLPNSTLVLE 79

UBA-like domain found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is a multi-functional Fas associating protein that contains an N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains, p150 subunit of a chromatin assembly factor like domain (CAF) and a novel nuclear localization signal (NLS). FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP) which is involved in the ubiquitin-proteosome pathway.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1370451704   6 FSACTGIENIDEAITLLEQNNWDLVAAINGVIP 38
Cdd:cd14413     1 FQACTGIEDIDECIMLLEQNNWNLVAAVNAVIP 33

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704  475 AMEIFTAQQQEDIKDEDEREARENVKREQDEAyRLSLEADRAKREAHEREMAEQFRLEQIRK-EQEEEREAIRLSLEQal 553
Cdd:PTZ00121  1649 AEELKKAEEENKIKAAEEAKKAEEDKKKAEEA-KKAEEDEKKAAEALKKEAEEAKKAEELKKkEAEEKKKAEELKKAE-- 1725

                           90
                   ....*....|....*.
gi 1370451704  554 ppepkEENAEPVSKLR 569
Cdd:PTZ00121  1726 -----EENKIKAEEAK 1736

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 477 EIFTAQQQEDI------KDEDEREARENVKREQDEAYRLSLEADRAKREAHEREMAEQFRLEQIR--KEQEEERE-AIRL 547
Cdd:COG2268   202 RIAEAEAERETeiaiaqANREAEEAELEQEREIETARIAEAEAELAKKKAEERREAETARAEAEAayEIAEANAErEVQR 281

                  ....*
gi 1370451704 548 SLEQA 552
Cdd:COG2268   282 QLEIA 286

Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as UBXN3A) and similar proteins; UBX domain-containing protein 3A (UBXN3A),also termed UBX domain-containing protein 12 (UBXD12), or FAF1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem ubiquitin-like (Ubl) domains, which shows high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to UBX domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370451704 563 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAK 641
Cdd:cd01771     2 EPISKLRFRLPGGEFLTRRFLASEPLQVLLNFVASKGYPPDEYKLLTTFPRRDLTQLDPSKTLEELKLFPQETLFLEER 80

ubiquitin-like (Ubl) domain 2 found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the second Ubl domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1370451704 185 NFMLIITHREVQREYNLNFSGSSTIQEVKRNVYDLTSIPVRHQLWEGWPTSATDDSMcLAESGLSYPCHRLTVGRR 260
Cdd:cd17130     1 NYTLNITDTTSQREYNLNFPGSKTIQEVKQDVSDLTSIPVRHQRWTGWPSGASDDTM-LLALGLDFPCHRLTVSRR 75

UAS family; UAS is a domain of unknown function. Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. ETEA is the protein product of a highly expressed gene in T-cells and eosinophils of atopic dermatitis patients. The presence of the ubiquitin-associated UBX domain in the proteins of this family suggests the possibility of their involvement in ubiquitination. Recently, FAF1 has been shown to interact with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. Some members of this family are uncharacterized proteins containing only a UAS domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 344 FFIGSLEAAFQEAFyvkaRDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLTKdSNRARFLTMCnrh 423
Cdd:cd02958     1 FFQGSFEDAKQEAK----SEKKWLLVYLQSEDEFDSQVLNRDLWSNESVKEFIRENFIFWQCDIDS-SEGQRFLQSY--- 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1370451704 424 fgsvvaqtirtqKTDQFPLFLIIMGKrsSNEVLNVIQGNTTVDELMMRLMAAMEIF 479
Cdd:cd02958    73 ------------KVDKYPHIAIIDPR--TGEVLKVWSGNITPEDLLSQLIEFLEEF 114

UBX domain; This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370451704 562 AEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDE-YKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE 639
Cdd:pfam00789   1 AEDVTRLQIRLPDGSRLVRRFNSSDKLQTVYDFVDSNRYDDLEpFSLNTPFPRRPLTDLDYSKTLKEAGLLPNSTLVLE 79

Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold; The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370451704 567 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE 639
Cdd:cd01767     1 RIQIRLPDGSRIQRRFSKSDTLQDLYDFVESNlGDSPSSFSLVTSFPRRVLTDEDSDKTLEELGLTPNAVLFVE 74

UBA-like domain found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is a multi-functional Fas associating protein that contains an N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains, p150 subunit of a chromatin assembly factor like domain (CAF) and a novel nuclear localization signal (NLS). FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP) which is involved in the ubiquitin-proteosome pathway.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1370451704   6 FSACTGIENIDEAITLLEQNNWDLVAAINGVIP 38
Cdd:cd14413     1 FQACTGIEDIDECIMLLEQNNWNLVAAVNAVIP 33

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 8 (UBXN8) and similar proteins; UBXN8, also termed reproduction 8 protein (Rep8), or UBX domain-containing protein 6 (UBXD6), or D8S2298E, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN8 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN8 is a transmembrane protein that localizes to the endoplasmic reticulum (ER) membrane with its UBX domain facing the cytoplasm. It facilitates efficient ER-associated degradation (ERAD) by tethering p97 to the ER membrane.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370451704 565 VSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQlDPNKSLLEVKLFPQETLFLE 639
Cdd:cd01774     2 AVTIALRFPGGRVHRRRFLTTENIQVLLDWMTKLGYHQTLYTLSTTYPRTILSD-DADKTLEDLGITKDVALNVE 75

UAS family, ETEA subfamily; composed of proteins similar to human ETEA protein, the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. ETEA shows homology to Fas-associated factor 1 (FAF1); both containing UAS and UBX (ubiquitin-associated) domains. Compared to FAF1, however, ETEA lacks the ubiquitin-associated UBA domain and a nuclear targeting domain. The function of ETEA is still unknown. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that ETEA could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 344 FFIGSLEAAFQEAfyvkARDRKLLAIYLHHDESVLTNVFCSQMLCAESIVSYLSQNFITWAWDLtkdsnrarfltmcNRH 423
Cdd:cd02991     1 FYQGTYSQALNDA----KQELRFLLVYLHGDDHQDTDEFCRNTLCAPEVIEYINTRMLFWACSV-------------AKP 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1370451704 424 FGSVVAQTIRTQktdQFPLFLIIMGKRSSNEVLNVIQGNTTVDELMMRLMAAME 477
Cdd:cd02991    64 EGYRVSQALRER---TYPFLAMIMLKDNRMTIVGRLEGLIQPEDLINRLTFIMD 114

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 4 (UBXN4) and similar proteins; UBXN4, also termed ERAD (endoplasmic-reticulum-associated protein degradation) substrate erasing protein (erasin), or UBX domain-containing protein 2 (UBXD2), or UBXDC1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN4 is an endoplasmic reticulum (ER) localized protein that interacts with p97 (also known as VCP or Cdc48) via its UBX domain. Erasin exists in a complex with other p97/VCP-associated factors involved in endoplasmic-reticulum-associated protein degradation (ERAD). p97 is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The overexpression of UBXN4 increases degradation of a classical ERAD substrate and UBXN4 levels are increased in ER stressed cells. Anti-UBXN4 staining is increased in neuropathological lesions in brains of patients with Alzheimer's disease.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1370451704 565 VSKLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFL 638
Cdd:cd16117     1 TARIQFRLPDGSSFTNQFPSDAPLEEARQFVAQTvGPAYGPFSLATTFPRREFTDDDYQKTLLELELAPSAALVV 75

Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 482 QQQEDIKDEDEREARENVKrEQDEAYRlslEADRAKREAHEREMAEQfrLEQIRKEQEEEREAIRLSLEQALPPEPKEEN 561
Cdd:pfam09731 301 KKLAELKKREEKHIERALE-KQKEELD---KLAEELSARLEEVRAAD--EAQLRLEFEREREEIRESYEEKLRTELERQA 374

                          90       100
                  ....*....|....*....|....*...
gi 1370451704 562 AEPVSKLR--IRTPSGEfLERRFLASNK 587
Cdd:pfam09731 375 EAHEEHLKdvLVEQEIE-LQREFLQDIK 401

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins; UBXN6, also termed UBX domain-containing protein 1 (UBXD1), and UBXDC2, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN6 acts as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Unlike other p97 cofactors that binds the N-domain of p97 through their UBX domain, UBXN6 binds p97 in two regions, at the p97 C terminus via a PUB domain and at the p97 N-domain with a short linear interaction motif termed VIM. Its UBX domain is not functional for the binding of p97. The UBXN6-p97 complex regulates the endolysosomal sorting of ubiquitylated plasma membrane protein caveolin-1 (CAV1), as well as the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53. In addition, UBXN6 is a regulatory component of endoplasmic reticulum-associated degradation (ERAD) that may modulate the adaptor binding to p97.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 568 LRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLlsTFPRRDVTQLDpNKSLLEVKLFPQETL 636
Cdd:cd16119     4 IRVRFPDGVILQGTFYAREKLSAVREFVREAlANDWLPFEL--VTPGGQKLTDE-DATLAELGLVPAALL 70

Chromatin assembly factor 1 complex p150 subunit, N-terminal; CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 484 QEDIKDEDEReARENVKREQDEAYRLSLEADRAKREAHEREMAEQFRL-EQIRKEQEEEREAirlSLEQALPPEpkEENA 562
Cdd:pfam11600  42 KEEAKAEKER-AKEEARRKKEEEKELKEKERREKKEKDEKEKAEKLRLkEEKRKEKQEALEA---KLEEKRKKE--EEKR 115

                          90       100
                  ....*....|....*....|....*....
gi 1370451704 563 EPVSKLRIRTPSGEFleRRFLASNKLQIV 591
Cdd:pfam11600 116 LKEEEKRIKAEKAEI--TRFLQKPKTQQA 142

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 470 MRLMAAMEIFTAQQQEDIKDEDEREArenvKREQDEAYRLSLEADRAKR------EAHER--EMAEQFRLEQIRKEQEEE 541
Cdd:pfam15709 412 LQLQAAQERARQQQEEFRRKLQELQR----KKQQEEAERAEAEKQRQKElemqlaEEQKRlmEMAEEERLEYQRQKQEAE 487

                          90       100
                  ....*....|....*....|....*
gi 1370451704 542 --------------REAIRLSLEQA 552
Cdd:pfam15709 488 ekarleaeerrqkeEEAARLALEEA 512

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1370451704  96 RVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLK 135
Cdd:cd17055     4 RVRSRDGTERVEVPDDATVGDLKEKIAEQLSVPVSDQTLS 43

UBA-like domain;

                          10        20
                  ....*....|....*....|....*....
gi 1370451704   6 FSACTGIENiDEAITLLEQNNWDLVAAIN 34
Cdd:pfam14555   7 FQAITGADE-EVARQYLEAHNWDLEAAVN 34

UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity.

                          10        20
                  ....*....|....*....|....*....
gi 1370451704   6 FSACTGIeNIDEAITLLEQNNWDLVAAIN 34
Cdd:cd14273     1 FMEITGA-DPETARQYLESNNWDLEAAIN 28

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704  481 AQQQEDIKDEDEREAR--ENVKREQDEAyrlSLEADRAKREAHEremaEQFRLEQIRKEQEEEREAIRLSLEQALPPEPK 558
Cdd:PTZ00121  1701 AKKAEELKKKEAEEKKkaEELKKAEEEN---KIKAEEAKKEAEE----DKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEI 1773

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1370451704  559 EENAEPVSKLRIRTpsgEFLERRFLASNKLQIVFD 593
Cdd:PTZ00121  1774 RKEKEAVIEEELDE---EDEKRRMEVDKKIKDIFD 1805

recombination and DNA strand exchange inhibitor protein; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 482 QQQEDIKDEDEREA------RENVKREQDEAYRLSLEAdrAKREAHE-----REMAEQFRLEQIRKEQEEEREAIRLSLE 550
Cdd:PRK00409  544 KEAEKLKEELEEKKeklqeeEDKLLEEAEKEAQQAIKE--AKKEADEiikelRQLQKGGYASVKAHELIEARKRLNKANE 621

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1370451704 551 --QALPPEPKEENAEPVSKLRIRTPS----GEFLE 579
Cdd:PRK00409  622 kkEKKKKKQKEKQEELKVGDEVKYLSlgqkGEVLS 656

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370451704 467 ELMMRLMAAMEIFTAQQQEDIKDEDEREARENVK-----REQDEAYRLSLEADRAKREAHEREMAEQFRLEQIRKEQEEE 541
Cdd:pfam13868 123 EKQRQLREEIDEFNEEQAEWKELEKEEEREEDERileylKEKAEREEEREAEREEIEEEKEREIARLRAQQEKAQDEKAE 202

                          90
                  ....*....|.
gi 1370451704 542 REAIRLSLEQA 552
Cdd:pfam13868 203 RDELRAKLYQE 213

F0F1 ATP synthase subunit B;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1370451704 496 RENVKREQDEAYRLSLEADRAKrEAHEREMAE---------QFRLEQIRKEQEEEREAIRLSLEQAL 553
Cdd:PRK09174   86 RDRIAQDLDQAARLKQEADAAV-AAYEQELAQarakahsiaQAAREAAKAKAEAERAAIEASLEKKL 151