UAS domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931    173 RDYGSNNAFKidFVVEGFMDALQRSRSSFKLLFVYLHSPDHPDTPVFCGGTLCNEAVVAFVNENFVSWGGSIRSSEGFKM 252
Cdd:smart00594   1 KLFRPPYGPL--FYQGSLEAAKQEASRQRRLLWLYLHSQDSPDSQVFNRDVLCNEAVKSLIRENFIFWQVDVDTSEGQRV 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 15236931    253 SNSLKASRFPFCAVVMPAANQR-IALLQQVEGPKSPEEMLAILQ 295
Cdd:smart00594  79 SQFYKLDSFPYVAIVDPRTGQRvIEWVGVVEGEISPEELMTFLE 122

UBA-like domain found in FAS-associated factor FAF1, FAF2 and similar proteins; FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, 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. FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, 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. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 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
                ....*....|....*....|....*....|..
gi 15236931  11 FQAITGLEDADLCTEILQAHGWDLELAISSFT 42
Cdd:cd14353   1 FQSITGIEDSDQCRQILEAHNWDLEAAIQTAL 32

UAS domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931    173 RDYGSNNAFKidFVVEGFMDALQRSRSSFKLLFVYLHSPDHPDTPVFCGGTLCNEAVVAFVNENFVSWGGSIRSSEGFKM 252
Cdd:smart00594   1 KLFRPPYGPL--FYQGSLEAAKQEASRQRRLLWLYLHSQDSPDSQVFNRDVLCNEAVKSLIRENFIFWQVDVDTSEGQRV 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 15236931    253 SNSLKASRFPFCAVVMPAANQR-IALLQQVEGPKSPEEMLAILQ 295
Cdd:smart00594  79 SQFYKLDSFPYVAIVDPRTGQRvIEWVGVVEGEISPEELMTFLE 122

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 15236931   400 GPDVTQVLVRFPNGERKGRMFKSETKIQTLYDYVDSLGLLDTEEYSLITNFPRTVYGRDKESMSLKDAGLHPQASLFIE 478
Cdd:pfam00789   1 AEDVTRLQIRLPDGSRLVRRFNSSDKLQTVYDFVDSNRYDDLEPFSLNTPFPRRPLTDLDYSKTLKEAGLLPNSTLVLE 79

UBA-like domain found in FAS-associated factor FAF1, FAF2 and similar proteins; FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, 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. FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, 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. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 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
                ....*....|....*....|....*....|..
gi 15236931  11 FQAITGLEDADLCTEILQAHGWDLELAISSFT 42
Cdd:cd14353   1 FQSITGIEDSDQCRQILEAHNWDLEAAIQTAL 32

UBA-like domain;

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 15236931     6 DKLGYFQAITGLeDADLCTEILQAHGWDLELAISSF 41
Cdd:pfam14555   2 ELIAQFQAITGA-DEEVARQYLEAHNWDLEAAVNAF 36

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931   278 LQQVEGPKSPEEMLAilQRIVEDSSPTLVTARVEAEERRtnlrLREEQDAayRAALEADQAREQQRQEEKERLEREAAEA 357
Cdd:pfam05672  35 LEKEEEERLRKEELR--RRAEEERARREEEARRLEEERR----REEEERQ--RKAEEEAEEREQREQEEQERLQKQKEEA 106

                  ....*
gi 15236931   358 ERKLK 362
Cdd:pfam05672 107 EAKAR 111

Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model characterizes proteins similar to prohibitin (a lipid raft-associated integral membrane protein). Individual proteins of the SPFH (band 7) domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains, in addition to being stable scaffolds, may also be dynamic units with their own regulatory functions. Prohibitin is a mitochondrial inner-membrane protein which may act as a chaperone for the stabilization of mitochondrial proteins. Human prohibitin forms a hetero-oligomeric complex with Bap-37 (prohibitin 2, an SPFH domain carrying homolog). This complex may protect non-assembled membrane proteins against proteolysis by the m-AAA protease. Prohibitin and Bap-37 yeast homologs have been implicated in yeast longevity and in the maintenance of mitochondrial morphology.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15236931 317 TNLRLreeqDAAYRAALEADQAREQQRQEEKERLEREAAEAERK 360
Cdd:cd03401 145 TNIDF----PDEYEKAIEAKQVAEQEAERAKFELEKAEQEAERK 184

polarized growth protein Scy;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15236931   289 EMLAILQRIVEDSSPTLVTARVEAEERRtnlrlREEQDAAYRAALEADQAREQQRQEEKE-------RLEREAAEAER 359
Cdd:NF041483  685 EAAAAAERVGTEAAEALAAAQEEAARRR-----REAEETLGSARAEADQERERAREQSEEllasarkRVEEAQAEAQR 757

UAS domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931    173 RDYGSNNAFKidFVVEGFMDALQRSRSSFKLLFVYLHSPDHPDTPVFCGGTLCNEAVVAFVNENFVSWGGSIRSSEGFKM 252
Cdd:smart00594   1 KLFRPPYGPL--FYQGSLEAAKQEASRQRRLLWLYLHSQDSPDSQVFNRDVLCNEAVKSLIRENFIFWQVDVDTSEGQRV 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 15236931    253 SNSLKASRFPFCAVVMPAANQR-IALLQQVEGPKSPEEMLAILQ 295
Cdd:smart00594  79 SQFYKLDSFPYVAIVDPRTGQRvIEWVGVVEGEISPEELMTFLE 122

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 15236931   400 GPDVTQVLVRFPNGERKGRMFKSETKIQTLYDYVDSLGLLDTEEYSLITNFPRTVYGRDKESMSLKDAGLHPQASLFIE 478
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 15236931 406 VLVRFPNGERKGRMFKSETKIQTLYDYVDSLGLLDTEEYSLITNFPRTVYGRDKESMSLKDAGLHPQASLFIE 478
Cdd:cd01767   2 IQIRLPDGSRIQRRFSKSDTLQDLYDFVESNLGDSPSSFSLVTSFPRRVLTDEDSDKTLEELGLTPNAVLFVE 74

Ubiquitin regulatory domain X (UBX) found in UBX domain protein 7 (UBXN7) and similar proteins; UBXN7, also termed UBX domain-containing protein 7 (UBXD7), 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. UBXN7 functions as a ubiquitin-binding adaptor that mediates the interaction between the AAA+ ATPase p97 (also known as VCP or Cdc48) and the transcription factor HIF1-alpha. It binds only to the active, NEDD8- or Rub1-modified form of cullins. In addition to having a UBX domain, UBXD7 contains a ubiquitin-associated (UBA), ubiquitin-associating (UAS), and ubiquitin-interacting motif (UIM) domains. Either UBA or UIM could serve as a docking site for neddylated-cullins. UBA domain is required for binding ubiquitylated-protein substrates, while the UIM motif is responsible for the binding to cullin RING ligases (CRLs), and the UBX domain is essential for p97 binding.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236931 404 TQVLVRFPNGERKGRMFKSETKIQTLYDYVDSLGlLDTEEYSLITNFPRTVYGRDKESMSLKDAGLHPQASLFI 477
Cdd:cd01773   2 SKLMLRFPDGKREQLSLPASAKLKALVKYVSSKG-YPNERYELVTNFPRRKLSHLDYDITLKEAGLCPQETIFV 74

UBA-like domain found in FAS-associated factor FAF1, FAF2 and similar proteins; FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, 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. FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, 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. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 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
                ....*....|....*....|....*....|..
gi 15236931  11 FQAITGLEDADLCTEILQAHGWDLELAISSFT 42
Cdd:cd14353   1 FQSITGIEDSDQCRQILEAHNWDLEAAIQTAL 32

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 15236931 402 DVTQVLVRFPNGERKGRMFKSETKIQTLYDYVDSLGlLDTEEYSLITNFPRTVYgRDKESMSLKDAGLHPQASLFIE 478
Cdd:cd01774   1 GAVTIALRFPGGRVHRRRFLTTENIQVLLDWMTKLG-YHQTLYTLSTTYPRTIL-SDDADKTLEDLGITKDVALNVE 75

UBA-like TAP-C domain found in FAS-associated factor 2 (FAF2) and similar proteins; FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, 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. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 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
                ....*....|....*....|....*....|...
gi 15236931   6 DKLGYFQAITGLEDADLCTEILQAHGWDLELAI 38
Cdd:cd14414   1 EKLLQFQDLTGIEDMDQCREVLERHNWDIEAAV 33

UAS family, FAS-associated factor 1 (FAF1) subfamily; FAF1 contains a UAS domain of unknown function N-terminal to a ubiquitin-associated UBX domain. FAF1 also contains ubiquitin-associated UBA and nuclear targeting domains, N-terminal to the UAS 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. It 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-kB (NF-kB) by interfering with the nuclear translocation of the p65 subunit. FAF1 also interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931 185 FVVEGFMDALQ----RSRSSFKLLFVYLHSPDHPDTPVFCGGTLCNEAVVAFVNENFVSWGGSI-RSSEGFKMSNSLKAS 259
Cdd:cd02990   1 FFIGSLEAAFQeacyRKARDRKLLAIYLHHDESVLSNVFCSQLLCAESIVQYLSQNFITWGWDMtKESNKARFLSSCTRH 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 15236931 260 RFPFCAVVMPAAN-QRIALLQQVEGPKSPEEMLAILQ 295
Cdd:cd02990  81 FGSVAAQTIRNIKtDQLPAILIIMGKRSSNEVLNVIQ 117

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 15236931  11 FQAITGLEDADLCTEILQAHGWDLELAISS 40
Cdd:cd14413   1 FQACTGIEDIDECIMLLEQNNWNLVAAVNA 30

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        30
                ....*....|....*....|....*....|.
gi 15236931  11 FQAITGLeDADLCTEILQAHGWDLELAISSF 41
Cdd:cd14273   1 FMEITGA-DPETARQYLESNNWDLEAAINLY 30

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931   278 LQQVEGPKSPEEMLAilQRIVEDSSPTLVTARVEAEERRtnlrLREEQDAayRAALEADQAREQQRQEEKERLEREAAEA 357
Cdd:pfam05672  35 LEKEEEERLRKEELR--RRAEEERARREEEARRLEEERR----REEEERQ--RKAEEEAEEREQREQEEQERLQKQKEEA 106

                  ....*
gi 15236931   358 ERKLK 362
Cdd:pfam05672 107 EAKAR 111

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15236931 288 EEMLAILQRIVEDSSPTLVTARVEAEERRTNLRLREEQDAAYRAALEADQAREQQRQEEKERLEREAAEAERKLK 362
Cdd:COG1196 386 EELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEA 460

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
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15236931   308 ARVEAEERRTNLRLREEQDAAYRAALEAD--QAREQQRQEEKERLEREAAEAER 359
Cdd:pfam13868 208 AKLYQEEQERKERQKEREEAEKKARQRQElqQAREEQIELKERRLAEEAEREEE 261

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15236931   307 TARVEAEERRTNLRLREEQDAAYRAALEADQAREQQR---QEEKERLEREAAEAERKLK 362
Cdd:pfam20492  35 TAEELEEERRQAEEEAERLEQKRQEAEEEKERLEESAemeAEEKEQLEAELAEAQEEIA 93

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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 15236931   308 ARVEAEERRTNLRLREEQDAAYRAALEADQAREQQRQEEKERLER--EAAEAERKLK 362
Cdd:pfam13868 176 EEIEEEKEREIARLRAQQEKAQDEKAERDELRAKLYQEEQERKERqkEREEAEKKAR 232

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15236931 307 TARVEAEERRTNLRLREEQDAAYRAAlEADQAREQQRQEEKERLER--EAAEAERKLK 362
Cdd:COG2268 246 LAKKKAEERREAETARAEAEAAYEIA-EANAEREVQRQLEIAEREReiELQEKEAERE 302

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15236931   272 NQRIAllQQVEGPKSPEEMLAILQRIVEDSSPTLVTARVEAEE-RRTNLRLREEQDAAyraALEADQAREQQRQEEKERL 350
Cdd:pfam17380 391 NERVR--QELEAARKVKILEEERQRKIQQQKVEMEQIRAEQEEaRQREVRRLEEERAR---EMERVRLEEQERQQQVERL 465

                          90
                  ....*....|
gi 15236931   351 EREAAEAERK 360
Cdd:pfam17380 466 RQQEEERKRK 475

polarized growth protein Scy;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15236931   289 EMLAILQRIVEDSSPTLVTARVEAEERRtnlrlREEQDAAYRAALEADQAREQQRQEEKE-------RLEREAAEAER 359
Cdd:NF041483  685 EAAAAAERVGTEAAEALAAAQEEAARRR-----REAEETLGSARAEADQERERAREQSEEllasarkRVEEAQAEAQR 757

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15236931 288 EEMLAILQRIVEDSSpTLVTARVEAEERRTNLRLREEQDAAYRAALEADQAREQQRQEEKERLEREAAEAERKL 361
Cdd:COG1196 323 EELAELEEELEELEE-ELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAA 395

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                        10        20
                ....*....|....*....|....*....
gi 15236931  11 FQAITGlEDADLCTEILQAHGWDLELAIS 39
Cdd:cd00194   1 LVDITG-ASQEEAQQALEACGGNLNIAAN 28

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15236931 308 ARVEAEERRTNLRLREEQDAA-YRAALEADQAREQQRQEEKERLEREAAEAERKLK 362
Cdd:COG1196 376 EAEEELEELAEELLEALRAAAeLAAQLEELEEAEEALLERLERLEEELEELEEALA 431