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Conserved domains on  [gi|1635547078|gb|TKS65261|]
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ATP-dependent DNA helicase PIF1 [Collichthys lucidus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 977-1102 1.39e-57

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


:

Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 195.94  E-value: 1.39e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  977 CLSDTIVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQYSSVDQYLDASRMRYVGSWATEMEIQA 1056
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1057 TADFLGVNVYTYYND--RWLVYSCQNN----AISRQGIYLQHVNGCHYEVVV 1102
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKlgkrNGSREAIYLKNTNGNHFEPVV 132
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 1218-1343 2.57e-47

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


:

Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 166.67  E-value: 2.57e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1218 CKMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKAYNTVAEYIEDVKMKYVGTCISKVEIQA 1297
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1298 TANALGVDIFIFSAG--KWMGYFPKTKKQ----TGEAIYLSKCAENHFEAVI 1343
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKLGkrngSREAIYLKNTNGNHFEPVV 132
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 2720-3139 2.34e-43

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


:

Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 167.85  E-value: 2.34e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2720 HIFVTGGAGTGKSHLIKAIQYEATRILAPvchqpddicVLLTAPTGIAAYSLN------ATTIHSTFsiGKDVRLPYTPL 2793
Cdd:COG0507    142 VSVLTGGAGTGKTTTLRALLAALEALGLR---------VALAAPTGKAAKRLSestgieARTIHRLL--GLRPDSGRFRH 210

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2794 GEEKLnslrakYSSLQLLIIDEISMVDHNVLAYIhgrLRQIKQRGdsslfgnVAIIAVGDFFQLPPV-RGKPLYvqnvgi 2872
Cdd:COG0507    211 NRDNP------LTPADLLVVDEASMVDTRLMAAL---LEALPRAG-------ARLILVGDPDQLPSVgAGAVLR------ 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2873 DLW-SGVFNIAVLNTIVRQKDE-QFAKLLNRVRT------------------HSKGTAMLGCDVRLLKSRETGEESSALh 2932
Cdd:COG0507    269 DLIeSGTVPVVELTEVYRQADDsRIIELAHAIREgdapealnaryadvvfveAEDAEEAAEAIVELYADRPAGGEDIQV- 347

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2933 IFPTNRQVSAHNLEhirktcpdyvcigAQDYINSSKTGKLVLLKGhhsnarntcleEDLLLGKGARVMLCKNvDVADGLV 3012
Cdd:COG0507    348 LAPTNAGVDALNQA-------------IREALNPAGELERELAED-----------GELELYVGDRVMFTRN-DYDLGVF 402

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3013 NGVCGLVSEIvyadneNKFPRKVYVKFDhadvgklwrkrcahppgvdpasvgidaEEERVTDKGGMRRQfpLKLAWACTV 3092
Cdd:COG0507    403 NGDIGTVLSI------DEDEGRLTVRFD---------------------------GREIVTYDPSELDQ--LELAYAITV 447

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 3093 HKVQGLTVDEAVVSLDK----VFQPGQAYVALSRVRSLSGLIL-KDFKEKAI 3139
Cdd:COG0507    448 HKSQGSTFDRVILVLPSehspLLSRELLYTALTRARELLTLVGdRDALARAV 499
Helitron_like_N super family cl16715
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 1979-2173 9.87e-34

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


The actual alignment was detected with superfamily member pfam14214:

Pssm-ID: 464105  Cd Length: 199  Bit Score: 130.48  E-value: 9.87e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1979 RILHADGRFAQNVEYIFFAQYMSELEQVVSNVSIALRKGKGKGRNHKVscetfnTEESLRELLQ--FDDG---------Y 2047
Cdd:pfam14214    4 RLQHHDGRFARHPRFLFVAFNLFQQARAESRRLSFIRVNQKELRAESY------TGERLRDALEeeTDDPevlallgsiV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2048 RFLKPIRGTPAFWQGAQRDLLACVRQLGIPTWFCSFSAADMrWKNLLSSILKQAGRTDTVEQLEWadrCELLRRNPVTAA 2127
Cdd:pfam14214   78 ILPSSVPGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDL-WPEIKRELARYREWKLPGAQTRL---RRLASDRPDIVA 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1635547078 2128 RMFDFRWHCFLREVLMSPANPIGKIKDYFYRLEFQQRGSPHVHCLF 2173
Cdd:pfam14214  154 RVFHRKLELFLKDLLRFKEGVFGNVSAYVYTVEFQKRGLPHAHGLL 199
DUF6570 pfam20209
Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown ...
 1735-1864 3.40e-23

Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown function that is found in a wide range of proteins that includes eukaryotic transposon protein.


:

Pssm-ID: 466360  Cd Length: 134  Bit Score: 97.79  E-value: 3.40e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1735 KGEVPAESSKNNLTLGPIPSELACLNKLEQHLIALHIPFMKMLAL--PKGGQNGVHGPVTCVPANiVQTTNLLPRTSMD- 1811
Cdd:pfam20209    1 RGKLPKFSLANGLWIGEVPEELQDLTFVEELLIARVRPRVYVVKLrpKSGGQRGLRGNVIAFPQD-VGKLSVLPRPPEDl 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1635547078 1812 GSLLPIKLKR-KLTYKGHYEYEY-VDTTHIKQALQYLKDNNIYYKDVHFNTEWLN 1864
Cdd:pfam20209   80 DDVIAVLFIGpKKPTKEWLKKPFrVRRAKVRAALRWLKANNPLYRDIEIDEENLA 134
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 355-576 9.04e-06

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.86  E-value: 9.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  355 AEPEAEPPATPVPSSPYRPRFATQvvvvgEERQPRPEANPDGWltivkgQKVELKECFIPLTpvrfspsilALVEKTSPS 434
Cdd:PHA03247  2646 VPPPERPRDDPAPGRVSRPRRARR-----LGRAAQASSPPQRP------RRRAARPTVGSLT---------SLADPPPPP 2705

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  435 VLPSPEETTSAPvqvecvdvevcfvATPTSAVPTTAMDQDEATqcvvdlTLEPGPRSVVVTTRV-GDEPPPGLPQLSPTP 513
Cdd:PHA03247  2706 PTPEPAPHALVS-------------ATPLPPGPAAARQASPAL------PAAPAPPAVPAGPATpGGPARPARPPTTAGP 2766

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1635547078  514 GVNAAADGPGF---PQLSPTPGVNAAADGPGFPQPSPTPGVDAVVDGPGqrtdSAIKYVGSPRSLV 576
Cdd:PHA03247  2767 PAPAPPAAPAAgppRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA----AALPPAASPAGPL 2828
Borrelia_orfA super family cl20231
Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats ...
 1383-1600 2.45e-05

Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown.


The actual alignment was detected with superfamily member pfam02414:

Pssm-ID: 396813  Cd Length: 285  Bit Score: 48.95  E-value: 2.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1383 SNVNYCFSKYLKTKKHAQHRIKYQSNVLLREKKKYLLKRLYHQNMMFNEKkreiSLIRYrknqdiiknrlKLKYHEDDLY 1462
Cdd:pfam02414   23 SDILYYFNSNLKKNGQKEVKIRTLQNYLYKLEKEIKVTKNYYKHLGKNMG----TEIYY-----------KLNYPKKECY 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1463 RlkmKINKN----KKYREDNLYRTKLKDTCKQKYNVDDLH--REKIKQLSKTKYKVDDVHREKIKQLSKTKYKDDMYREK 1536
Cdd:pfam02414   88 K---KINKYfkekKEDRFQNRVNNYFKKNYNKNNSVKKWEciNNIYNNKENEEEKKKSIEKEQLKKYIKKCNFKSKESLS 164

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1635547078 1537 MINQ----------YKRKYKQDYLYRERVKNISK-----QKYENHLFREKaKIIYKQKYHKDLLYQNKAKERSQSKYRV 1600
Cdd:pfam02414  165 ILNLnikkdikiklIKIIKKEENLIKKNNNKIKKlknkqKTLKNILRNLK-KALEKEGYDEKQLEIEIQKIYEKYKNKP 242
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3277-3378 2.24e-04

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member pfam14529:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 118  Bit Score: 43.51  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3277 MLVAVVYRPPSYPMSLFRKNLGKLLDyvEPLSDSVTVMGDFN----------EDLVASKSICNFMTQRG--YVQHVSEAT 3344
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILR--SLDRPPIIIGGDFNahhplwgsnsTDVSRGEELIEFLNEHGlnLLNLPKSGP 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1635547078 3345 TAK----GTLIDHVYVNTTHFDVSCVVLQT-YFSDHDAI 3378
Cdd:pfam14529   79 TFIssngDSTIDLTLTSDPLAVRVLSDLGPdSGSDHRPI 117
Lipase_GDSL_2 pfam13472
GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are ...
 246-312 1.81e-03

GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are similar to pfam00657.


:

Pssm-ID: 463889  Cd Length: 176  Bit Score: 42.15  E-value: 1.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1635547078  246 PGATAAQLRTELVAAVLPRDPDAVVLLAPSNNLTACQGLEDSAADFASLLRCARSRWGNVAVLDFPP 312
Cdd:pfam13472   42 SGATTRLDLLERLDDVLRLKPDLVVILLGTNDLGRGVSAARAAANLEALIDALRAAGPDARVLLIGP 108
 
Name Accession Description Interval E-value
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 977-1102 1.39e-57

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 195.94  E-value: 1.39e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  977 CLSDTIVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQYSSVDQYLDASRMRYVGSWATEMEIQA 1056
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1057 TADFLGVNVYTYYND--RWLVYSCQNN----AISRQGIYLQHVNGCHYEVVV 1102
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKlgkrNGSREAIYLKNTNGNHFEPVV 132
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 1218-1343 2.57e-47

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 166.67  E-value: 2.57e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1218 CKMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKAYNTVAEYIEDVKMKYVGTCISKVEIQA 1297
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1298 TANALGVDIFIFSAG--KWMGYFPKTKKQ----TGEAIYLSKCAENHFEAVI 1343
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKLGkrngSREAIYLKNTNGNHFEPVV 132
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 2720-3139 2.34e-43

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 167.85  E-value: 2.34e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2720 HIFVTGGAGTGKSHLIKAIQYEATRILAPvchqpddicVLLTAPTGIAAYSLN------ATTIHSTFsiGKDVRLPYTPL 2793
Cdd:COG0507    142 VSVLTGGAGTGKTTTLRALLAALEALGLR---------VALAAPTGKAAKRLSestgieARTIHRLL--GLRPDSGRFRH 210

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2794 GEEKLnslrakYSSLQLLIIDEISMVDHNVLAYIhgrLRQIKQRGdsslfgnVAIIAVGDFFQLPPV-RGKPLYvqnvgi 2872
Cdd:COG0507    211 NRDNP------LTPADLLVVDEASMVDTRLMAAL---LEALPRAG-------ARLILVGDPDQLPSVgAGAVLR------ 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2873 DLW-SGVFNIAVLNTIVRQKDE-QFAKLLNRVRT------------------HSKGTAMLGCDVRLLKSRETGEESSALh 2932
Cdd:COG0507    269 DLIeSGTVPVVELTEVYRQADDsRIIELAHAIREgdapealnaryadvvfveAEDAEEAAEAIVELYADRPAGGEDIQV- 347

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2933 IFPTNRQVSAHNLEhirktcpdyvcigAQDYINSSKTGKLVLLKGhhsnarntcleEDLLLGKGARVMLCKNvDVADGLV 3012
Cdd:COG0507    348 LAPTNAGVDALNQA-------------IREALNPAGELERELAED-----------GELELYVGDRVMFTRN-DYDLGVF 402

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3013 NGVCGLVSEIvyadneNKFPRKVYVKFDhadvgklwrkrcahppgvdpasvgidaEEERVTDKGGMRRQfpLKLAWACTV 3092
Cdd:COG0507    403 NGDIGTVLSI------DEDEGRLTVRFD---------------------------GREIVTYDPSELDQ--LELAYAITV 447

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 3093 HKVQGLTVDEAVVSLDK----VFQPGQAYVALSRVRSLSGLIL-KDFKEKAI 3139
Cdd:COG0507    448 HKSQGSTFDRVILVLPSehspLLSRELLYTALTRARELLTLVGdRDALARAV 499
Helitron_like_N pfam14214
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 1979-2173 9.87e-34

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


Pssm-ID: 464105  Cd Length: 199  Bit Score: 130.48  E-value: 9.87e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1979 RILHADGRFAQNVEYIFFAQYMSELEQVVSNVSIALRKGKGKGRNHKVscetfnTEESLRELLQ--FDDG---------Y 2047
Cdd:pfam14214    4 RLQHHDGRFARHPRFLFVAFNLFQQARAESRRLSFIRVNQKELRAESY------TGERLRDALEeeTDDPevlallgsiV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2048 RFLKPIRGTPAFWQGAQRDLLACVRQLGIPTWFCSFSAADMrWKNLLSSILKQAGRTDTVEQLEWadrCELLRRNPVTAA 2127
Cdd:pfam14214   78 ILPSSVPGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDL-WPEIKRELARYREWKLPGAQTRL---RRLASDRPDIVA 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1635547078 2128 RMFDFRWHCFLREVLMSPANPIGKIKDYFYRLEFQQRGSPHVHCLF 2173
Cdd:pfam14214  154 RVFHRKLELFLKDLLRFKEGVFGNVSAYVYTVEFQKRGLPHAHGLL 199
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 2721-2860 3.12e-33

DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350795 [Multi-domain]  Cd Length: 183  Bit Score: 128.14  E-value: 3.12e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2721 IFVTGGAGTGKSHLIKAIQYEAtrilapvchQPDDICVLLTAPTGIAAYSLNATTIHSTFSIG-KDVRLPYTPLGEEKLN 2799
Cdd:cd18037     15 VFFTGSAGTGKSYLLRRIIRAL---------PSRPKRVAVTASTGIAACNIGGTTLHSFAGIGlGSEPAEDLLERVKRSP 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1635547078 2800 SLRAKYSSLQLLIIDEISMVDHNVLAYIHGRLRQIkqRGDSSLFGNVAIIAVGDFFQLPPV 2860
Cdd:cd18037     86 YLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREV--RGSDKPFGGIQLILCGDFLQLPPV 144
DUF6570 pfam20209
Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown ...
 1735-1864 3.40e-23

Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown function that is found in a wide range of proteins that includes eukaryotic transposon protein.


Pssm-ID: 466360  Cd Length: 134  Bit Score: 97.79  E-value: 3.40e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1735 KGEVPAESSKNNLTLGPIPSELACLNKLEQHLIALHIPFMKMLAL--PKGGQNGVHGPVTCVPANiVQTTNLLPRTSMD- 1811
Cdd:pfam20209    1 RGKLPKFSLANGLWIGEVPEELQDLTFVEELLIARVRPRVYVVKLrpKSGGQRGLRGNVIAFPQD-VGKLSVLPRPPEDl 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1635547078 1812 GSLLPIKLKR-KLTYKGHYEYEY-VDTTHIKQALQYLKDNNIYYKDVHFNTEWLN 1864
Cdd:pfam20209   80 DDVIAVLFIGpKKPTKEWLKKPFrVRRAKVRAALRWLKANNPLYRDIEIDEENLA 134
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 2692-3021 3.09e-21

PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.


Pssm-ID: 428699 [Multi-domain]  Cd Length: 361  Bit Score: 98.61  E-value: 3.09e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2692 LNETQMGIFYQVRQwCVQQAQGQkpdpfHIFVTGGAGTGKSHLIKAIqyeATRIlapvchQPDDICVLLTAPTGIAAYSL 2771
Cdd:pfam05970    1 LNDEQKKVFDAIIE-SVINNKGG-----VFFVYGYGGTGKTFLWKAI---ITSL------RSEGKIVLAVASSGVAALLL 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2772 -NATTIHSTFSIGKDVrlpytplGEEKLNSLR--AKYSSL----QLLIIDEISMVDHNVLAYIHGRLRQIKQRGDSSLFG 2844
Cdd:pfam05970   66 pGGRTAHSRFGIPLDI-------DELSTCKIKrgSKLAELlektSLIVWDEAPMTHRHCFEALDRTLRDILSETDDKPFG 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2845 NVAIIAVGDFFQLPPVRGKPLYVQNVGID-----LWSGVFNI----------AVLNTIVRQKDEQFAKLLNRVR------ 2903
Cdd:pfam05970  139 GKTVVLGGDFRQILPVIPKGSRPEIVNASitnsyLWKHVKVLeltknmrllaDSLDQTEAKELQDFSDWLLAIGdgkind 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2904 THSKGTAMLGCDVRLLKSRETGEESSALHIFPTNRQVSahnlehirkTCPDYVCIGAQ--------DYINSSKTGKL--- 2972
Cdd:pfam05970  219 ENEREQLIDIPIDILLNTGGDPIEAIVSEVYPDILQNS---------TDPNYLEERAIlcptnedvDEINNYRLSQLpge 289

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1635547078 2973 --------VLLKGHHSNARNTCLEEDLL--------------LGKGARVMLCKNVDVADGLVNGVCGLVSE 3021
Cdd:pfam05970  290 ekeylssdSISKSDNDSEIDALYPTEFLnslnanglpnhvlkLKVGAPVMLLRNLDQSRGLCNGTRLIVTQ 360
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 2708-3151 3.11e-14

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 79.44  E-value: 3.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2708 VQQAQGQKpdpFHIfVTGGAGTGKSHLIKAIQYEATRILAPvchQPddicVLLTAPTGIAAYSLN------ATTIHSTfs 2781
Cdd:TIGR01448  332 LDTAIQHK---VVI-LTGGPGTGKTTITRAIIELAEELGGL---LP----VGLAAPTGRAAKRLGevtgltASTIHRL-- 398

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2782 IGKDvrlpytplGEEKLNSLRAKYSSLQLLIIDEISMVDhNVLAyihgrlrqikqrgdSSLFGNVA----IIAVGDFFQL 2857
Cdd:TIGR01448  399 LGYG--------PDTFRHNHLEDPIDCDLLIVDESSMMD-TWLA--------------LSLLAALPdharLLLVGDTDQL 455

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2858 PPVR-GKPLyvqnvgIDL-WSGVFNIAVLNTIVRQKDEQ-FAKLLNRVRthsKGTAMLGCDVRLLKSRETGEESSALHI- 2933
Cdd:TIGR01448  456 PSVGpGQVL------KDLiLSQAIPVTRLTKVYRQAAGSpIITLAHGIL---HGEAPAWGDFKFLNLTRSEPEGAARHIp 526

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2934 -----FPTNRQVSAHNLEHIRKTCPDY---VCIGA-----QDYINSSKTGKLVL-LKGHHsnARntcleedlllgKGARV 2999
Cdd:TIGR01448  527 lmvekIVGMARVGGIPGADIQVLAPMYkgpLGIDAlnqhlQALLNPYQKGQGGIeIAEGE--YR-----------KGDRV 593

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3000 MLCKNvDVADGLVNGVCGLVSEIVYADNENKfpRKVYVKFDhadvgklwrkrcahppgvdpasvgidaEEERVTDKGGMr 3079
Cdd:TIGR01448  594 MQTKN-DYNNEIFNGDLGMIVKIEGAKQGKK--DQVVVDFD---------------------------GNEVELTRAEL- 642

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1635547078 3080 rqFPLKLAWACTVHKVQG----LTVDEAVVSLDKVFQPGQAYVALSRVRslSGLILKDFKEKAIYCKDSIKEALNS 3151
Cdd:TIGR01448  643 --FNLTLAYATSIHKSQGsefpTVILPIHTAHMRMLYRNLLYTALTRAK--KRVILVGSAEAFDIAAARQGQARNT 714
OTU pfam02338
OTU-like cysteine protease; This family is comprised of a group of predicted cysteine ...
 984-1072 1.66e-08

OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.


Pssm-ID: 426728 [Multi-domain]  Cd Length: 127  Bit Score: 55.53  E-value: 1.66e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  984 ADGNCFFRAVAQAV-----SGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSqyssvDQYLDASRMRYVGSWATEMEIQATA 1058
Cdd:pfam02338    2 GDGNCLYRSISHQLwgvhdVLRKMLVQELRETLAEYMREHKEEFEPFLED-----DETGDIIEIEQTGAWGGEIEIFALA 76

                           90
                   ....*....|....
gi 1635547078 1059 DFLGVNVYTYYNDR 1072
Cdd:pfam02338   77 HILRRPIIVYKSEG 90
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 2720-2851 7.75e-06

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 48.52  E-value: 7.75e-06
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  2720 HIFVTGGAGTGKSHLIKAIQYEAtrilapvchQPDDICVLLTAPTGIAAYSLNATTIHSTFSIGKDVRlpytplGEEKLN 2799
Cdd:smart00382    4 VILIVGPPGSGKTTLARALAREL---------GPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS------GELRLR 68

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1635547078  2800 SL--RAKYSSLQLLIIDEISMVDHNVLAYIHGRLRQIKQRGDSSLFGNVAIIAV 2851
Cdd:smart00382   69 LAlaLARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
PHA03247 PHA03247
large tegument protein UL36; Provisional
 355-576 9.04e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.86  E-value: 9.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  355 AEPEAEPPATPVPSSPYRPRFATQvvvvgEERQPRPEANPDGWltivkgQKVELKECFIPLTpvrfspsilALVEKTSPS 434
Cdd:PHA03247  2646 VPPPERPRDDPAPGRVSRPRRARR-----LGRAAQASSPPQRP------RRRAARPTVGSLT---------SLADPPPPP 2705

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  435 VLPSPEETTSAPvqvecvdvevcfvATPTSAVPTTAMDQDEATqcvvdlTLEPGPRSVVVTTRV-GDEPPPGLPQLSPTP 513
Cdd:PHA03247  2706 PTPEPAPHALVS-------------ATPLPPGPAAARQASPAL------PAAPAPPAVPAGPATpGGPARPARPPTTAGP 2766

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1635547078  514 GVNAAADGPGF---PQLSPTPGVNAAADGPGFPQPSPTPGVDAVVDGPGqrtdSAIKYVGSPRSLV 576
Cdd:PHA03247  2767 PAPAPPAAPAAgppRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA----AALPPAASPAGPL 2828
Borrelia_orfA pfam02414
Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats ...
 1383-1600 2.45e-05

Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown.


Pssm-ID: 396813  Cd Length: 285  Bit Score: 48.95  E-value: 2.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1383 SNVNYCFSKYLKTKKHAQHRIKYQSNVLLREKKKYLLKRLYHQNMMFNEKkreiSLIRYrknqdiiknrlKLKYHEDDLY 1462
Cdd:pfam02414   23 SDILYYFNSNLKKNGQKEVKIRTLQNYLYKLEKEIKVTKNYYKHLGKNMG----TEIYY-----------KLNYPKKECY 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1463 RlkmKINKN----KKYREDNLYRTKLKDTCKQKYNVDDLH--REKIKQLSKTKYKVDDVHREKIKQLSKTKYKDDMYREK 1536
Cdd:pfam02414   88 K---KINKYfkekKEDRFQNRVNNYFKKNYNKNNSVKKWEciNNIYNNKENEEEKKKSIEKEQLKKYIKKCNFKSKESLS 164

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1635547078 1537 MINQ----------YKRKYKQDYLYRERVKNISK-----QKYENHLFREKaKIIYKQKYHKDLLYQNKAKERSQSKYRV 1600
Cdd:pfam02414  165 ILNLnikkdikiklIKIIKKEENLIKKNNNKIKKlknkqKTLKNILRNLK-KALEKEGYDEKQLEIEIQKIYEKYKNKP 242
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1393-1617 2.89e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 50.02  E-value: 2.89e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1393 LKTKKHAQHRIKYQsnvlLREKKKYL------LKRLYHQnmmFNEKKREISLIRYRKNQDIIKNrLK--LKYHEDDLYRL 1464
Cdd:TIGR04523  255 LNQLKDEQNKIKKQ----LSEKQKELeqnnkkIKELEKQ---LNQLKSEISDLNNQKEQDWNKE-LKseLKNQEKKLEEI 326

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1465 KMKINKN-KKYREDNLYRTKLKdtcKQKYNVDDLHREKIKQLSKTKYKVDDVHREkikqlsKTKYKDDMYR-EKMINQYK 1542
Cdd:TIGR04523  327 QNQISQNnKIISQLNEQISQLK---KELTNSESENSEKQRELEEKQNEIEKLKKE------NQSYKQEIKNlESQINDLE 397

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1635547078 1543 RKykqdylyrervknISKQKYENHLFREKAKIIYKQKYHKDLLYQNKAKERSQSKYRV-NLTHKH---NIKVRSAKTYR 1617
Cdd:TIGR04523  398 SK-------------IQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSEIkDLTNQDsvkELIIKNLDNTR 463
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 3277-3378 2.24e-04

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 43.51  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3277 MLVAVVYRPPSYPMSLFRKNLGKLLDyvEPLSDSVTVMGDFN----------EDLVASKSICNFMTQRG--YVQHVSEAT 3344
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILR--SLDRPPIIIGGDFNahhplwgsnsTDVSRGEELIEFLNEHGlnLLNLPKSGP 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1635547078 3345 TAK----GTLIDHVYVNTTHFDVSCVVLQT-YFSDHDAI 3378
Cdd:pfam14529   79 TFIssngDSTIDLTLTSDPLAVRVLSDLGPdSGSDHRPI 117
Lipase_GDSL_2 pfam13472
GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are ...
 246-312 1.81e-03

GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are similar to pfam00657.


Pssm-ID: 463889  Cd Length: 176  Bit Score: 42.15  E-value: 1.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1635547078  246 PGATAAQLRTELVAAVLPRDPDAVVLLAPSNNLTACQGLEDSAADFASLLRCARSRWGNVAVLDFPP 312
Cdd:pfam13472   42 SGATTRLDLLERLDDVLRLKPDLVVILLGTNDLGRGVSAARAAANLEALIDALRAAGPDARVLLIGP 108
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
1430-1578 3.67e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 42.21  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1430 NEKKREISLIRYR---------KNQDIIK--NRLKLKYHEddlyrLKMKINKNKKYREDnlyRTKLKDTCKQkynVDDLH 1498
Cdd:COG1340    112 DKLRKEIERLEWRqqtevlspeEEKELVEkiKELEKELEK-----AKKALEKNEKLKEL---RAELKELRKE---AEEIH 180

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1499 ------REKI----KQLSKTKYKVDDVhREKIKQLSKT--KYKD--DMYREKMINQYK--RKY-KQDYLYRERVKNISKQ 1561
Cdd:COG1340    181 kkikelAEEAqelhEEMIELYKEADEL-RKEADELHKEivEAQEkaDELHEEIIELQKelRELrKELKKLRKKQRALKRE 259

                          170
                   ....*....|....*..
gi 1635547078 1562 KYENHLfREKAKIIYKQ 1578
Cdd:COG1340    260 KEKEEL-EEKAEEIFEK 275
TesA COG2755
Lysophospholipase L1 or related esterase. Includes spore coat protein LipC/YcsK [Cell cycle ...
 246-349 5.20e-03

Lysophospholipase L1 or related esterase. Includes spore coat protein LipC/YcsK [Cell cycle control, cell division, chromosome partitioning, Lipid transport and metabolism];


Pssm-ID: 442045 [Multi-domain]  Cd Length: 191  Bit Score: 40.78  E-value: 5.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  246 PGATAAQLRTELVAAVLPRDPDAVVLLAPSNNLTACQG--LEDSAADFASLLRCARSRWG-------------------- 303
Cdd:COG2755     51 SGATTADLLARLDRDLLALKPDLVVIELGTNDLLRGLGvsPEEFRANLEALIDRLRAAGPgarvvlvtppprlrpnylne 130

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1635547078  304 ----------------NVAVLDFPPRLSVEQRSQELlrMAYNSTHLSDnAGMPILAYLLWQA 349
Cdd:COG2755    131 rieaynaairelaaeyGVPLVDLYAALRDAGDLPDL--LTADGLHPNA-AGYRLIAEAVLPA 189
uS4m cd23691
Tetrahymena thermophila ribosomal protein uS4m, and similar proteins; Ribosomal protein uS4m, ...
 1414-1601 5.43e-03

Tetrahymena thermophila ribosomal protein uS4m, and similar proteins; Ribosomal protein uS4m, also called Ymf76, is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosome (mitoribosome), which reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit; its large subunit (LSU) lacks 5S rRNA.


Pssm-ID: 467905  Cd Length: 398  Bit Score: 42.09  E-value: 5.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1414 KKKYLLKRLYhQNMMFNEKKREISLIrYRKNQDIIKNRLKLKYheddlyrlkMKINKNKKYRedNLyrtkLKDTCKQKYN 1493
Cdd:cd23691      6 KLKKKLKKFY-KKYNYNSNKLNNFYL-KKPNILNLYNKINNFF---------LKIFKYIKYL--NL----IKKIISKKKL 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1494 VDDLHREKIKQLSKTKYKVDDVHREKIKQL--SKTKYKDDMYREKMINQY-KRKYKQDYLYRERV---------KNISKQ 1561
Cdd:cd23691     69 FKFLNNPKIRNKKKFKYKYSDKFKFILNILksKKTKINNLLYFLKYFSVFrKRQSRIFNLSKVKSrlskrkffkKKFKKK 148

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1635547078 1562 KYENHLFREKAKIIYKQKYHKDLLYQNKAKERSQSKYRVN 1601
Cdd:cd23691    149 KIAKYFFKMFKKLKFKRKKHINLINLDLYFIRNKRFFRLH 188
 
Name Accession Description Interval E-value
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 977-1102 1.39e-57

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 195.94  E-value: 1.39e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  977 CLSDTIVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQYSSVDQYLDASRMRYVGSWATEMEIQA 1056
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1057 TADFLGVNVYTYYND--RWLVYSCQNN----AISRQGIYLQHVNGCHYEVVV 1102
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKlgkrNGSREAIYLKNTNGNHFEPVV 132
OTU_CeDUB-like cd22755
OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and ...
 1218-1343 2.57e-47

OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins; This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438592 [Multi-domain]  Cd Length: 132  Bit Score: 166.67  E-value: 2.57e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1218 CKMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKAYNTVAEYIEDVKMKYVGTCISKVEIQA 1297
Cdd:cd22755      1 CKTIKIVGDGNCFFRALSYAITGSEKYHRKIRKAIVDFLEKNPDEFRNLLRSDYESVEEYLEKSRMRYDGTWATDVEIFA 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1298 TANALGVDIFIFSAG--KWMGYFPKTKKQ----TGEAIYLSKCAENHFEAVI 1343
Cdd:cd22755     81 AATLLGVDIYVYSKGgyKWLLYSPRFKLGkrngSREAIYLKNTNGNHFEPVV 132
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 2720-3139 2.34e-43

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 167.85  E-value: 2.34e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2720 HIFVTGGAGTGKSHLIKAIQYEATRILAPvchqpddicVLLTAPTGIAAYSLN------ATTIHSTFsiGKDVRLPYTPL 2793
Cdd:COG0507    142 VSVLTGGAGTGKTTTLRALLAALEALGLR---------VALAAPTGKAAKRLSestgieARTIHRLL--GLRPDSGRFRH 210

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2794 GEEKLnslrakYSSLQLLIIDEISMVDHNVLAYIhgrLRQIKQRGdsslfgnVAIIAVGDFFQLPPV-RGKPLYvqnvgi 2872
Cdd:COG0507    211 NRDNP------LTPADLLVVDEASMVDTRLMAAL---LEALPRAG-------ARLILVGDPDQLPSVgAGAVLR------ 268

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2873 DLW-SGVFNIAVLNTIVRQKDE-QFAKLLNRVRT------------------HSKGTAMLGCDVRLLKSRETGEESSALh 2932
Cdd:COG0507    269 DLIeSGTVPVVELTEVYRQADDsRIIELAHAIREgdapealnaryadvvfveAEDAEEAAEAIVELYADRPAGGEDIQV- 347

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2933 IFPTNRQVSAHNLEhirktcpdyvcigAQDYINSSKTGKLVLLKGhhsnarntcleEDLLLGKGARVMLCKNvDVADGLV 3012
Cdd:COG0507    348 LAPTNAGVDALNQA-------------IREALNPAGELERELAED-----------GELELYVGDRVMFTRN-DYDLGVF 402

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3013 NGVCGLVSEIvyadneNKFPRKVYVKFDhadvgklwrkrcahppgvdpasvgidaEEERVTDKGGMRRQfpLKLAWACTV 3092
Cdd:COG0507    403 NGDIGTVLSI------DEDEGRLTVRFD---------------------------GREIVTYDPSELDQ--LELAYAITV 447

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 3093 HKVQGLTVDEAVVSLDK----VFQPGQAYVALSRVRSLSGLIL-KDFKEKAI 3139
Cdd:COG0507    448 HKSQGSTFDRVILVLPSehspLLSRELLYTALTRARELLTLVGdRDALARAV 499
Helitron_like_N pfam14214
Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently ...
 1979-2173 9.87e-34

Helitron helicase-like domain at N-terminus; This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.


Pssm-ID: 464105  Cd Length: 199  Bit Score: 130.48  E-value: 9.87e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1979 RILHADGRFAQNVEYIFFAQYMSELEQVVSNVSIALRKGKGKGRNHKVscetfnTEESLRELLQ--FDDG---------Y 2047
Cdd:pfam14214    4 RLQHHDGRFARHPRFLFVAFNLFQQARAESRRLSFIRVNQKELRAESY------TGERLRDALEeeTDDPevlallgsiV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2048 RFLKPIRGTPAFWQGAQRDLLACVRQLGIPTWFCSFSAADMrWKNLLSSILKQAGRTDTVEQLEWadrCELLRRNPVTAA 2127
Cdd:pfam14214   78 ILPSSVPGSPRYMLQLRQDAMAIVRRLGKPDLFITFTPNDL-WPEIKRELARYREWKLPGAQTRL---RRLASDRPDIVA 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1635547078 2128 RMFDFRWHCFLREVLMSPANPIGKIKDYFYRLEFQQRGSPHVHCLF 2173
Cdd:pfam14214  154 RVFHRKLELFLKDLLRFKEGVFGNVSAYVYTVEFQKRGLPHAHGLL 199
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 2721-2860 3.12e-33

DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350795 [Multi-domain]  Cd Length: 183  Bit Score: 128.14  E-value: 3.12e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2721 IFVTGGAGTGKSHLIKAIQYEAtrilapvchQPDDICVLLTAPTGIAAYSLNATTIHSTFSIG-KDVRLPYTPLGEEKLN 2799
Cdd:cd18037     15 VFFTGSAGTGKSYLLRRIIRAL---------PSRPKRVAVTASTGIAACNIGGTTLHSFAGIGlGSEPAEDLLERVKRSP 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1635547078 2800 SLRAKYSSLQLLIIDEISMVDHNVLAYIHGRLRQIkqRGDSSLFGNVAIIAVGDFFQLPPV 2860
Cdd:cd18037     86 YLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREV--RGSDKPFGGIQLILCGDFLQLPPV 144
OTU cd22744
OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved ...
 982-1101 4.96e-27

OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation.


Pssm-ID: 438581 [Multi-domain]  Cd Length: 128  Bit Score: 108.29  E-value: 4.96e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQY---RSFLRSQYSSVDQYLDasRMRYVGSWATEMEIQATA 1058
Cdd:cd22744      5 VPGDGNCLFRALAHALYGDQESHRELRQEVVDYLRENPDLYepaELADEDDGEDFDEYLQ--RMRKPGTWGGELELQALA 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1635547078 1059 DFLGVNVYTYYND----RWLVYSCQNNAISRQgIYLQHVNGCHYEVV 1101
Cdd:cd22744     83 NALNVPIVVYSEDggflPVSVFGPGPGPSGRP-IHLLYTGGNHYDAL 128
DUF6570 pfam20209
Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown ...
 1735-1864 3.40e-23

Domain of unknown function (DUF6570); This entry represents a presumed domain of unknown function that is found in a wide range of proteins that includes eukaryotic transposon protein.


Pssm-ID: 466360  Cd Length: 134  Bit Score: 97.79  E-value: 3.40e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1735 KGEVPAESSKNNLTLGPIPSELACLNKLEQHLIALHIPFMKMLAL--PKGGQNGVHGPVTCVPANiVQTTNLLPRTSMD- 1811
Cdd:pfam20209    1 RGKLPKFSLANGLWIGEVPEELQDLTFVEELLIARVRPRVYVVKLrpKSGGQRGLRGNVIAFPQD-VGKLSVLPRPPEDl 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1635547078 1812 GSLLPIKLKR-KLTYKGHYEYEY-VDTTHIKQALQYLKDNNIYYKDVHFNTEWLN 1864
Cdd:pfam20209   80 DDVIAVLFIGpKKPTKEWLKKPFrVRRAKVRAALRWLKANNPLYRDIEIDEENLA 134
OTU_plant_OTU7-like cd22771
OTU (ovarian tumor) domain of Arabidopsis thaliana deubiquitinating enzyme OTU7 and similar ...
 981-1098 5.20e-22

OTU (ovarian tumor) domain of Arabidopsis thaliana deubiquitinating enzyme OTU7 and similar proteins; Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. DUBs catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. OTU7 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438608 [Multi-domain]  Cd Length: 124  Bit Score: 93.77  E-value: 5.20e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  981 TIVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLrSQYSSVDQYLdaSRMRYVGSWATEMEIQATADF 1060
Cdd:cd22771      6 DVEGDGNCLFRALADQLYGDEERHAELRKKVVDYMEAHEEDFEPFF-EDDETFEDYV--SRMREDGTWGGNLELQAASLV 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1635547078 1061 LGVN--VYTYYNDRWLVySCQNNAISRQgIYLQHVNGCHY 1098
Cdd:cd22771     83 YRVNivVHQLGQPRWEI-ENFPDKGART-IHLSYHDGEHY 120
OTU_232R-like cd22758
OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase ...
 984-1098 1.87e-21

OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase 232R and similar proteins; This subfamily contains putative ubiquitin thioesterases 232R from Invertebrate iridescent virus and L96 from Tipula iridescent virus (TIV), Dictyostelium discoideum OTU domain-containing protein DDB_G0284757, and similar proteins. L96 may be involved in TIV genomic DNA packaging in a manner related to the Gag polyproteins of the mammalian viruses. Proteins in this subfamily contain an OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438595 [Multi-domain]  Cd Length: 135  Bit Score: 92.72  E-value: 1.87e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  984 ADGNCFFRAVAQAVSGTQ--KSHVKLRRAVVRHIEKNAVQYRSFLRSQ---YSSVDQYLDasRMRYVGSWATEMEIQATA 1058
Cdd:cd22758     13 GDGNCFFHAVSDQLYGNGieHSHKELRQQAVNYLRENPELYDGFFLSEfdeEESWEEYLN--RMSKDGTWGDHIILQAAA 90

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1635547078 1059 DFLGVNVY---TYYNDRWLVYSCQNNAISRQgIYLQHVNGCHY 1098
Cdd:cd22758     91 NLFNVRIViisSDGSDETTIIEPGNSKNGRT-IYLGHIGENHY 132
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 2692-3021 3.09e-21

PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.


Pssm-ID: 428699 [Multi-domain]  Cd Length: 361  Bit Score: 98.61  E-value: 3.09e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2692 LNETQMGIFYQVRQwCVQQAQGQkpdpfHIFVTGGAGTGKSHLIKAIqyeATRIlapvchQPDDICVLLTAPTGIAAYSL 2771
Cdd:pfam05970    1 LNDEQKKVFDAIIE-SVINNKGG-----VFFVYGYGGTGKTFLWKAI---ITSL------RSEGKIVLAVASSGVAALLL 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2772 -NATTIHSTFSIGKDVrlpytplGEEKLNSLR--AKYSSL----QLLIIDEISMVDHNVLAYIHGRLRQIKQRGDSSLFG 2844
Cdd:pfam05970   66 pGGRTAHSRFGIPLDI-------DELSTCKIKrgSKLAELlektSLIVWDEAPMTHRHCFEALDRTLRDILSETDDKPFG 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2845 NVAIIAVGDFFQLPPVRGKPLYVQNVGID-----LWSGVFNI----------AVLNTIVRQKDEQFAKLLNRVR------ 2903
Cdd:pfam05970  139 GKTVVLGGDFRQILPVIPKGSRPEIVNASitnsyLWKHVKVLeltknmrllaDSLDQTEAKELQDFSDWLLAIGdgkind 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2904 THSKGTAMLGCDVRLLKSRETGEESSALHIFPTNRQVSahnlehirkTCPDYVCIGAQ--------DYINSSKTGKL--- 2972
Cdd:pfam05970  219 ENEREQLIDIPIDILLNTGGDPIEAIVSEVYPDILQNS---------TDPNYLEERAIlcptnedvDEINNYRLSQLpge 289

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1635547078 2973 --------VLLKGHHSNARNTCLEEDLL--------------LGKGARVMLCKNVDVADGLVNGVCGLVSE 3021
Cdd:pfam05970  290 ekeylssdSISKSDNDSEIDALYPTEFLnslnanglpnhvlkLKVGAPVMLLRNLDQSRGLCNGTRLIVTQ 360
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 2721-2888 6.98e-20

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 89.15  E-value: 6.98e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2721 IFVTGGAGTGKSHLIKAI--QYEATRilapvchqpddICVLLTAPTGIAAYSLN------ATTIHstfsigkdvRLPYTP 2792
Cdd:cd17933     15 SVLTGGAGTGKTTTLKALlaALEAEG-----------KRVVLAAPTGKAAKRLSestgieASTIH---------RLLGIN 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2793 LGEEKLNSLRAKYSSLQLLIIDEISMVD----HNVLAYIHGRLRqikqrgdsslfgnvaIIAVGDFFQLPPV-RGKPLyv 2867
Cdd:cd17933     75 PGGGGFYYNEENPLDADLLIVDEASMVDtrlmAALLSAIPAGAR---------------LILVGDPDQLPSVgAGNVL-- 137

                          170       180
                   ....*....|....*....|.
gi 1635547078 2868 qnvGIDLWSGVFNIAVLNTIV 2888
Cdd:cd17933    138 ---RDLIASKGVPTVELTEVF 155
OTU_OTUD3-like cd22756
OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This ...
 982-1101 9.47e-18

OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This subfamily includes bilaterial OTU domain-containing protein 3 (OTUD3), Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, and similar proteins. OTUD3 is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. OTU7 is a DUB that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438593 [Multi-domain]  Cd Length: 131  Bit Score: 81.84  E-value: 9.47e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQYS-----SVDQYLDasRMRYVGSWATEMEIQA 1056
Cdd:cd22756      5 ITGDGNCLFRALSDQLYGDPDRHLEIRAEVVEYMRANPDDFKPFSEAATFaeddeAFEDYLA--RMAKDGTYGDNLEIVA 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1635547078 1057 TADFLGVNVYTYYNDRWLVYSC---QNNAISRQGIYLQHVNGCHYEVV 1101
Cdd:cd22756     83 FARAYNVDVKVYQPDPVYVISApedGSPGPARRVLHIAYHNWEHYSSV 130
OTU cd22744
OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved ...
 1226-1342 6.56e-17

OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation.


Pssm-ID: 438581 [Multi-domain]  Cd Length: 128  Bit Score: 79.40  E-value: 6.56e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1226 DGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKA---YNTVAEYIEDvkMKYVGTCISKVEIQATANAL 1302
Cdd:cd22744      8 DGNCLFRALAHALYGDQESHRELRQEVVDYLRENPDLYEPAELADeddGEDFDEYLQR--MRKPGTWGGELELQALANAL 85

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1635547078 1303 GVDIFIFSAGKWMG---YFPKTKKQTGEAIYLSKCAENHFEAV 1342
Cdd:cd22744     86 NVPIVVYSEDGGFLpvsVFGPGPGPSGRPIHLLYTGGNHYDAL 128
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 2723-2904 1.05e-16

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 81.07  E-value: 1.05e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2723 VTGGAGTGKSHLIKAIQ--YEAtrilapvchqpDDICVLLTAPTGIAA------YSLNATTIHSTFSIGKDvrlpytplg 2794
Cdd:pfam13604   23 LVGPAGTGKTTALKALReaWEA-----------AGYRVIGLAPTGRAAkvlgeeLGIPADTIAKLLHRLGG--------- 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2795 eeklnslRAKYSSLQLLIIDEISMVDHNVLAYIhgrLRQIKQRGDSslfgnvaIIAVGDFFQLPPV-RGKPLYvqnvgiD 2873
Cdd:pfam13604   83 -------RAGLDPGTLLIVDEAGMVGTRQMARL---LKLAEDAGAR-------VILVGDPRQLPSVeAGGAFR------D 139

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1635547078 2874 LWSGVFNIAVLNTIVRQKDEQFAKLLNRVRT 2904
Cdd:pfam13604  140 LLAAGIGTAELTEIVRQRDPWQRAASLALRD 170
OTU_ALG13-like cd22753
OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and ...
 982-1102 7.10e-16

OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 and similar proteins; Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is alco called asparagine-linked glycosylation 13 homolog, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homolog. It displays both glycosyltransferase (EC 2.4.1.141) and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyzes the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum. ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures, neurodevelopmental impairment, and poor prognosis; given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). This subfamily also contains OTU domain-containing protein 4 (OTUD4), also called HIV-1-induced protein HIN-1, a DUB that specifically deubiquitinates 'Lys-63'-polyubiquitinated MYD88 adapter protein upon phosphorylation, triggering down-regulation of NF-kappa-B-dependent transcription of inflammatory mediators. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438590 [Multi-domain]  Cd Length: 130  Bit Score: 76.81  E-value: 7.10e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFlrSQYsSVDQYLDasRMRYVGSWATEMEIQATADFL 1061
Cdd:cd22753     15 IPRDGSCLFRAVSEQLFFTQSYHQQVRQACVEYLEKNREEFEKF--SEI-SFDDYLE--RLSDPKEWGGLLELEALSLLY 89

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1635547078 1062 GVNVYTYYNDRWLVYSCQNNAISRQgIYLQHVNGCHYEVVV 1102
Cdd:cd22753     90 KVDFIVYSIPDQPPSNITNNGYPKK-IMLCYSGGNHYDSVY 129
OTU_plant_OTU9-like cd22751
OTU (ovarian tumor) domain of plant deubiquitinating enzyme OTU9 and similar proteins; This ...
 982-1098 3.11e-15

OTU (ovarian tumor) domain of plant deubiquitinating enzyme OTU9 and similar proteins; This subfamily contains Arabidopsis thaliana deubiquitinating enzymes OTU8, OTU9, OTU10, OTU11, and OTU12, and similar proteins from plants and other eukaryotes. OTU8-OTU12 are deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438588 [Multi-domain]  Cd Length: 134  Bit Score: 74.89  E-value: 3.11e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNA-VQYRSFLRSQYssvDQYLDasRMRYVGSWATEMEIQATADF 1060
Cdd:cd22751     15 VEGDGNCQFRALSDQLFGTQDHHAEVRELVVKQLRAHPeLYYEFYVPEEY---DEYLK--KMSKDGEWGDELTLQAAADA 89

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1635547078 1061 LGVN--VYTYYNDRW-LVYSCQNNAISRQGIYLQHVNGCHY 1098
Cdd:cd22751     90 FGVKihVITSFEDNWfLEIEPRGLVRSKRVLFLSYWAEVHY 130
OTU_P87_VP80-like cd22757
OTU (ovarian tumor) domain of nucleopolyhedrovirus P87/VP80 protein and similar proteins; The ...
 982-1072 9.63e-15

OTU (ovarian tumor) domain of nucleopolyhedrovirus P87/VP80 protein and similar proteins; The VP80 protein is a capsid-associated structural protein that was first identified as P87 in Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV); its homologs are found only in NPV genomes. The Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) VP80 protein is essential for the formation of both budded virus (BV) and occlusion-derived virus (ODV). It has also been shown to interact with the virus-triggered, nuclear F-actin cytoskeleton. P87/VP80 contains an N-terminal OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438594 [Multi-domain]  Cd Length: 128  Bit Score: 73.39  E-value: 9.63e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQ----YSSVDQYldASRMRYVGSWATEMEIQAT 1057
Cdd:cd22757      6 IPGDGACLFRALSYLLYGTQSRHLEVRKEVVDYVVNNWDEFSIYTHDSegnnYKSAEEY--RADMSKPGTYGTLCELVAA 83

                           90
                   ....*....|....*
gi 1635547078 1058 ADFLGVNVYTYYNDR 1072
Cdd:cd22757     84 AELYPFHFEVYRNGK 98
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 2708-3151 3.11e-14

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 79.44  E-value: 3.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2708 VQQAQGQKpdpFHIfVTGGAGTGKSHLIKAIQYEATRILAPvchQPddicVLLTAPTGIAAYSLN------ATTIHSTfs 2781
Cdd:TIGR01448  332 LDTAIQHK---VVI-LTGGPGTGKTTITRAIIELAEELGGL---LP----VGLAAPTGRAAKRLGevtgltASTIHRL-- 398

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2782 IGKDvrlpytplGEEKLNSLRAKYSSLQLLIIDEISMVDhNVLAyihgrlrqikqrgdSSLFGNVA----IIAVGDFFQL 2857
Cdd:TIGR01448  399 LGYG--------PDTFRHNHLEDPIDCDLLIVDESSMMD-TWLA--------------LSLLAALPdharLLLVGDTDQL 455

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2858 PPVR-GKPLyvqnvgIDL-WSGVFNIAVLNTIVRQKDEQ-FAKLLNRVRthsKGTAMLGCDVRLLKSRETGEESSALHI- 2933
Cdd:TIGR01448  456 PSVGpGQVL------KDLiLSQAIPVTRLTKVYRQAAGSpIITLAHGIL---HGEAPAWGDFKFLNLTRSEPEGAARHIp 526

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2934 -----FPTNRQVSAHNLEHIRKTCPDY---VCIGA-----QDYINSSKTGKLVL-LKGHHsnARntcleedlllgKGARV 2999
Cdd:TIGR01448  527 lmvekIVGMARVGGIPGADIQVLAPMYkgpLGIDAlnqhlQALLNPYQKGQGGIeIAEGE--YR-----------KGDRV 593

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3000 MLCKNvDVADGLVNGVCGLVSEIVYADNENKfpRKVYVKFDhadvgklwrkrcahppgvdpasvgidaEEERVTDKGGMr 3079
Cdd:TIGR01448  594 MQTKN-DYNNEIFNGDLGMIVKIEGAKQGKK--DQVVVDFD---------------------------GNEVELTRAEL- 642

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1635547078 3080 rqFPLKLAWACTVHKVQG----LTVDEAVVSLDKVFQPGQAYVALSRVRslSGLILKDFKEKAIYCKDSIKEALNS 3151
Cdd:TIGR01448  643 --FNLTLAYATSIHKSQGsefpTVILPIHTAHMRMLYRNLLYTALTRAK--KRVILVGSAEAFDIAAARQGQARNT 714
AAA_19 pfam13245
AAA domain;
2720-2860 6.83e-14

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 71.10  E-value: 6.83e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2720 HIFVTGGAGTGKSHLIKAIQYEATRILapvchqPDDICVLLTAPTGIAAYSLN------ATTIHStfSIGKDVRLPYTPL 2793
Cdd:pfam13245   13 VVLLTGGPGTGKTTTIRHIVALLVALG------GVSFPILLAAPTGRAAKRLSertglpASTIHR--LLGFDDLEAGGFL 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1635547078 2794 GEEKlNSLRAkysslQLLIIDEISMVDhNVLAYihGRLRQIKQRgdsslfgnVAIIAVGDFFQLPPV 2860
Cdd:pfam13245   85 RDEE-EPLDG-----DLLIVDEFSMVD-LPLAY--RLLKALPDG--------AQLLLVGDPDQLPSV 134
OTU_plant_OTU7-like cd22771
OTU (ovarian tumor) domain of Arabidopsis thaliana deubiquitinating enzyme OTU7 and similar ...
 1218-1342 2.74e-13

OTU (ovarian tumor) domain of Arabidopsis thaliana deubiquitinating enzyme OTU7 and similar proteins; Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. DUBs catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. OTU7 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438608 [Multi-domain]  Cd Length: 124  Bit Score: 69.12  E-value: 2.74e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1218 CKMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDiHMQLIGKAYNTVAEYIEDvkMKYVGTCISKVEIQA 1297
Cdd:cd22771      2 LRIRDVEGDGNCLFRALADQLYGDEERHAELRKKVVDYMEAHEE-DFEPFFEDDETFEDYVSR--MREDGTWGGNLELQA 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1635547078 1298 TANALGVDIFIFSAG--KW-MGYFPKTKKQTgeaIYLSKCAENHFEAV 1342
Cdd:cd22771     79 ASLVYRVNIVVHQLGqpRWeIENFPDKGART---IHLSYHDGEHYNSV 123
OTU_OTUD4 cd22794
OTU (ovarian tumor) domain of OTU domain-containing protein 4 and similar proteins; OTU ...
 981-1101 7.29e-13

OTU (ovarian tumor) domain of OTU domain-containing protein 4 and similar proteins; OTU domain-containing protein 4 (OTUD4), also called HIV-1-induced protein HIN-1, is a deubiquitinase that specifically deubiquitinates 'Lys-63'-polyubiquitinated MYD88 adapter protein upon phosphorylation, triggering down-regulation of NF-kappa-B-dependent transcription of inflammatory mediators. OTUD4 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438615 [Multi-domain]  Cd Length: 130  Bit Score: 68.17  E-value: 7.29e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  981 TIVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRsqySSVDQYLDasRMRYVGSWATEMEIQATADF 1060
Cdd:cd22794     14 QIAKDGSCLFRAVAEQVFHTQSRHLEVRKACVDYLRRNREKFEAFIE---GPFEQYLK--NLENPKEWAGQVEISALSLM 88

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1635547078 1061 lgvnvytyYNDRWLVY--------SCQNNAISRQgIYLQHVNGCHYEVV 1101
Cdd:cd22794     89 --------YKRDFIIYqepgkppsNVTENGFPDK-ILLCFSNGNHYDSV 128
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 3085-3130 6.26e-12

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 63.73  E-value: 6.26e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1635547078 3085 KLAWACTVHKVQGLTVDEAVVSLDKV---FQPGQAYVALSRVRSLSGLI 3130
Cdd:cd18809     31 LQAYAMTIHKSQGSEFDRVIVVLPTShpmLSRGLLYTALTRARKLLTLV 79
OTU_232R-like cd22758
OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase ...
 1222-1342 2.28e-11

OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase 232R and similar proteins; This subfamily contains putative ubiquitin thioesterases 232R from Invertebrate iridescent virus and L96 from Tipula iridescent virus (TIV), Dictyostelium discoideum OTU domain-containing protein DDB_G0284757, and similar proteins. L96 may be involved in TIV genomic DNA packaging in a manner related to the Gag polyproteins of the mammalian viruses. Proteins in this subfamily contain an OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438595 [Multi-domain]  Cd Length: 135  Bit Score: 63.83  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1222 KIVN---DGNSFFRAVCHVIS--GSQKNHRKLRLFVVKYMLNNS---DIHMQLIGKAYNTVAEYIEdvKMKYVGTCISKV 1293
Cdd:cd22758      7 EIRDvpgDGNCFFHAVSDQLYgnGIEHSHKELRQQAVNYLRENPelyDGFFLSEFDEEESWEEYLN--RMSKDGTWGDHI 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 1294 EIQATANALGVDIFIFSAGKWMGYF---PKTKKQTgEAIYLSKCAENHFEAV 1342
Cdd:cd22758     85 ILQAAANLFNVRIVIISSDGSDETTiiePGNSKNG-RTIYLGHIGENHYVSL 135
OTU_OTUD5-like cd22752
OTU (ovarian tumor) domain of OTU domain-containing protein 5 and similar proteins; OTU ...
 982-1102 3.68e-11

OTU (ovarian tumor) domain of OTU domain-containing protein 5 and similar proteins; OTU domain-containing protein 5 (OTUD5), also called deubiquitinating enzyme A (DUBA), is a phosphorylation-dependent deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that can hydrolyze 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, and may function as negative regulator of the innate immune system. It limits type I interferon production in macrophages and suppresses interleukin-17A production in T cells. OTUD5 also functions in an apoptotic signaling cascade by mediating the sequential activation of PDCD5 (programmed cell death 5) and p53 in response to genotoxic stress. In Drosophila, OTUD5/DUBA is essential for spermatogenesis. This subfamily also includes Arabidopsis thaliana OTU domain-containing protein 6, also called deubiquitinating enzyme OTU6 or otubain-like deubiquitinase 1 (OTLD1), which binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It also includes plant OTU6.


Pssm-ID: 438589 [Multi-domain]  Cd Length: 124  Bit Score: 62.95  E-value: 3.68e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLrsqYSSVDQYLdaSRMRYVGSWATEMEIQATADFL 1061
Cdd:cd22752      7 MEEDGNCLFRAVADQVYGDQEMHDVVRKHCMDYMEKNRDYFSQFV---TEDFEEYI--NRKRQDGVWGNHIEIQAMSELY 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1635547078 1062 G--VNVYTYYNDRWLVYSCQNNAISRQgIYLQHVNGCHYEVVV 1102
Cdd:cd22752     82 NrpIEVYAYSTEPINTFHEASSSDNEP-IRLSYHGNSHYNSIV 123
OTU_plant_OTU9-like cd22751
OTU (ovarian tumor) domain of plant deubiquitinating enzyme OTU9 and similar proteins; This ...
 1218-1342 1.05e-10

OTU (ovarian tumor) domain of plant deubiquitinating enzyme OTU9 and similar proteins; This subfamily contains Arabidopsis thaliana deubiquitinating enzymes OTU8, OTU9, OTU10, OTU11, and OTU12, and similar proteins from plants and other eukaryotes. OTU8-OTU12 are deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438588 [Multi-domain]  Cd Length: 134  Bit Score: 61.79  E-value: 1.05e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1218 CKMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKA-YNtvaEYIEdvKMKYVGTCISKVEIQ 1296
Cdd:cd22751     10 LVERKVEGDGNCQFRALSDQLFGTQDHHAEVRELVVKQLRAHPELYYEFYVPEeYD---EYLK--KMSKDGEWGDELTLQ 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1635547078 1297 ATANALGVDIFI---FSAGKWMGYFPKTKKQTGEAIYLSKCAENHFEAV 1342
Cdd:cd22751     85 AAADAFGVKIHVitsFEDNWFLEIEPRGLVRSKRVLFLSYWAEVHYNSI 133
OTU_OTUD1 cd22747
OTU (ovarian tumor) domain of OTU domain-containing protein 1 and similar proteins; OTU ...
 982-1101 5.18e-10

OTU (ovarian tumor) domain of OTU domain-containing protein 1 and similar proteins; OTU domain-containing protein 1 (OTUD1), also called DUBA-7 in humans, is a deubiquitinating enzyme/ubiquitinyl hydrolase (EC 3.4.19.12) that specifically hydrolyzes 'Lys-63'-linked polyubiquitin to monoubiquitin; this specificity is facilitated by the C-terminal Ub-interacting motif (UIM) of OTUD1. It interacts and promotes the deubiquitination of myeloid cell leukemia 1 (MCL1), a pro-survival Bcl-2 family protein that plays important roles in cell survival, proliferation, differentiation and tumorigenesis. OTUD1 also deubiquitinates IFN regulatory factor 3 (IRF3) and attenuates its function; IRF3 is critical for the transcription of type I IFNs in defensing virus and promoting inflammatory responses. Loss-of-function mutations of OTUD1 associated with multiple autoimmune diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), ulcerative colitis (UC) and Hashimoto's thyroiditis (HT). OTUD1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438584 [Multi-domain]  Cd Length: 149  Bit Score: 60.59  E-value: 5.18e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRsqySSVDQYLDASRMRyvGSWATEMEIQATADFL 1061
Cdd:cd22747     26 IIPDGNCLYRAVSKAVYGDQALHRELREQTVHYIADHLDEFNPIIE---GDVGEFLIKAAQD--GAWAGYPELLAMGQML 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1635547078 1062 GVNVYTYYNDRW-------LVYSCQNNAISRQGIYLQHVNGCHYEVV 1101
Cdd:cd22747    101 NVNIRLTTGGSLesptvstMVHYLGPEDSGKPSIWLSWLSNGHYDAV 147
OTU_P87_VP80-like cd22757
OTU (ovarian tumor) domain of nucleopolyhedrovirus P87/VP80 protein and similar proteins; The ...
 1222-1313 8.55e-10

OTU (ovarian tumor) domain of nucleopolyhedrovirus P87/VP80 protein and similar proteins; The VP80 protein is a capsid-associated structural protein that was first identified as P87 in Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV); its homologs are found only in NPV genomes. The Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) VP80 protein is essential for the formation of both budded virus (BV) and occlusion-derived virus (ODV). It has also been shown to interact with the virus-triggered, nuclear F-actin cytoskeleton. P87/VP80 contains an N-terminal OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438594 [Multi-domain]  Cd Length: 128  Bit Score: 59.14  E-value: 8.55e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1222 KIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNN----SDIHMQLIGKAYNTVAEYIEDvkMKYVGTCISKVEIQA 1297
Cdd:cd22757      5 PIPGDGACLFRALSYLLYGTQSRHLEVRKEVVDYVVNNwdefSIYTHDSEGNNYKSAEEYRAD--MSKPGTYGTLCELVA 82

                           90
                   ....*....|....*.
gi 1635547078 1298 TANALGVDIFIFSAGK 1313
Cdd:cd22757     83 AAELYPFHFEVYRNGK 98
OTU_OTUD3-like cd22756
OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This ...
 1222-1312 1.27e-09

OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This subfamily includes bilaterial OTU domain-containing protein 3 (OTUD3), Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, and similar proteins. OTUD3 is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. OTU7 is a DUB that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438593 [Multi-domain]  Cd Length: 131  Bit Score: 58.73  E-value: 1.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1222 KIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQL--------IGKAYNtvaEYIEdvKMKYVGTCISKV 1293
Cdd:cd22756      4 DITGDGNCLFRALSDQLYGDPDRHLEIRAEVVEYMRANPDDFKPFseaatfaeDDEAFE---DYLA--RMAKDGTYGDNL 78

                           90
                   ....*....|....*....
gi 1635547078 1294 EIQATANALGVDIFIFSAG 1312
Cdd:cd22756     79 EIVAFARAYNVDVKVYQPD 97
OTU_ALG13-like cd22753
OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and ...
 1223-1342 3.49e-09

OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 and similar proteins; Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is alco called asparagine-linked glycosylation 13 homolog, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homolog. It displays both glycosyltransferase (EC 2.4.1.141) and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyzes the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum. ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures, neurodevelopmental impairment, and poor prognosis; given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). This subfamily also contains OTU domain-containing protein 4 (OTUD4), also called HIV-1-induced protein HIN-1, a DUB that specifically deubiquitinates 'Lys-63'-polyubiquitinated MYD88 adapter protein upon phosphorylation, triggering down-regulation of NF-kappa-B-dependent transcription of inflammatory mediators. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438590 [Multi-domain]  Cd Length: 130  Bit Score: 57.55  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1223 IVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKAYNtvaEYIEDvkMKYVGTCISKVEIQATANAL 1302
Cdd:cd22753     15 IPRDGSCLFRAVSEQLFFTQSYHQQVRQACVEYLEKNREEFEKFSEISFD---DYLER--LSDPKEWGGLLELEALSLLY 89

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1635547078 1303 GVDIFIFSAgkwMGYFPK--TKKQTGEAIYLSKCAENHFEAV 1342
Cdd:cd22753     90 KVDFIVYSI---PDQPPSniTNNGYPKKIMLCYSGGNHYDSV 128
OTU_fungi_OTU2-like cd22762
OTU (ovarian tumor) domain of fungal OTU domain-containing protein 2 and similar proteins; ...
 982-1065 8.53e-09

OTU (ovarian tumor) domain of fungal OTU domain-containing protein 2 and similar proteins; This subfamily includes Schizosaccharomyces pombe and Saccharomyces cerevisiae OTU domain-containing protein 2 (OTU2) and similar proteins. S. pombe OTU2 is a ubiquitin thioesterase/hydrolase (EC 3.4.19.12) that can remove conjugated ubiquitin from protein substrates and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Fungal OTU2 bbelongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438599 [Multi-domain]  Cd Length: 142  Bit Score: 56.85  E-value: 8.53e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVA----QAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQY---SSVDQYLDasRMRYVGSWATEMEI 1054
Cdd:cd22762     12 IKPDGHCLFAAIAdqlqLRGSEINLDYKELRKLAAEYIRKHPDDFEPFLFEETdelEDIDEYCK--KIENTAEWGGELEL 89

                           90
                   ....*....|.
gi 1635547078 1055 QATADFLGVNV 1065
Cdd:cd22762     90 LALAKAFGVPI 100
OTU pfam02338
OTU-like cysteine protease; This family is comprised of a group of predicted cysteine ...
 984-1072 1.66e-08

OTU-like cysteine protease; This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.


Pssm-ID: 426728 [Multi-domain]  Cd Length: 127  Bit Score: 55.53  E-value: 1.66e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  984 ADGNCFFRAVAQAV-----SGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSqyssvDQYLDASRMRYVGSWATEMEIQATA 1058
Cdd:pfam02338    2 GDGNCLYRSISHQLwgvhdVLRKMLVQELRETLAEYMREHKEEFEPFLED-----DETGDIIEIEQTGAWGGEIEIFALA 76

                           90
                   ....*....|....
gi 1635547078 1059 DFLGVNVYTYYNDR 1072
Cdd:pfam02338   77 HILRRPIIVYKSEG 90
OTU_OTUD6-like cd22748
OTU (ovarian tumor) domain of OTU domain-containing proteins 6A, 6B, and similar proteins; ...
 982-1068 1.89e-08

OTU (ovarian tumor) domain of OTU domain-containing proteins 6A, 6B, and similar proteins; This subfamily is composed of mammalian OTU domain-containing protein 6A (OTUD6A, also called DUBA-2, vertebrate OTU domain-containing protein 6B (OTUD6B, also called DUBA-5), fungal OTU domain-containing protein 2 (OTU2), and similar proteins. OTUD6A, OTUD6B, and Schizosaccharomyces pombe OTU2 are deubiquitinating enzymes/ubiquitinyl hydrolases (EC 3.4.19.12). OTUD6A hydrolyzes 'Lys-27'-, 'Lys-29'-, and 'Lys-33'-linked polyubiquitin chains, and may also be able to hydrolyze 'Lys-11'-linked ubiquitin chains. It deubiquitylates and stabilizes dynamin-related protein 1 (Drp1), a cytosolic protein responsible for mitochondrial fission and is essential in the initiation and development of several human diseases including cancer, thereby facilitating tumorigenesis. OTUD6B is a functional deubiquitinase in in vitro enzyme assays. It may play a role in the ubiquitin-dependent regulation of protein synthesis downstream of mTORC1, and may modify the ubiquitination of the protein synthesis initiation complex to repress translation. Biallelic variants in OTUD6B cause an intellectual disability syndrome that is associated with seizures and dysmorphic features. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438585 [Multi-domain]  Cd Length: 144  Bit Score: 55.65  E-value: 1.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVA-----QAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQ---YSSVDQYLD-ASRMRYVGSWATEM 1052
Cdd:cd22748     11 IPPDGHCLYRAIAdqlklRGGSEEPYSYKELRKLAADYMRAHRDDFLPFLTNDdgdLMTEEEFEEyCDKIENTAEWGGQL 90

                           90
                   ....*....|....*.
gi 1635547078 1053 EIQATADFLGVNVYTY 1068
Cdd:cd22748     91 ELRALSKALKRPIHVY 106
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3065-3124 5.69e-08

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 52.82  E-value: 5.69e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1635547078 3065 IDAEEERVTDKGGMRRQFPLKLAWACTVHKVQGLTVDEAVVSLD--KVFQPGQAYVALSRVR 3124
Cdd:cd18786     21 RDRAYLNQYLQGLSLDEFDLQLVGAITIDSSQGLTFDVVTLYLPtaNSLTPRRLYVALTRAR 82
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 2722-2860 2.57e-07

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 56.69  E-value: 2.57e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2722 FVTGGAGTGKSHLIkaiqyeaTRILAPVCHQ---PDDICVLLTAPTGIAAYSLN-----------------------ATT 2775
Cdd:TIGR01447  163 LITGGPGTGKTTTV-------ARLLLALVKQspkQGKLRIALAAPTGKAAARLAeslrkavknlaaaealiaalpseAVT 235

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2776 IHSTFSIGKDvrlpytplgEEKLNSLRAKYSSLQLLIIDEISMVDHNVLAyihgRLRQikqrgdsSLFGNVAIIAVGDFF 2855
Cdd:TIGR01447  236 IHRLLGIKPD---------TKRFRHHERNPLPLDVLVVDEASMVDLPLMA----KLLK-------ALPPNTKLILLGDKN 295


                   ....*
gi 1635547078 2856 QLPPV 2860
Cdd:TIGR01447  296 QLPSV 300
OTU_plant_OTU6-like cd22796
OTU (ovarian tumor) domain of deubiquitinating enzyme OTU6 from plants and similar proteins; ...
 983-1071 2.70e-07

OTU (ovarian tumor) domain of deubiquitinating enzyme OTU6 from plants and similar proteins; Deubiquitinating enzyme OTU6, also called OTU domain-containing protein 6 or otubain-like deubiquitinase 1 (OTLD1), is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU6 binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. OTU6 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438617 [Multi-domain]  Cd Length: 128  Bit Score: 52.04  E-value: 2.70e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  983 VADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQYssvDQYLdaSRMRYVGSWATEMEIQATADFLG 1062
Cdd:cd22796     11 DGDGNCLFRAVADQVYGDQEMHDEVREMCMDYMEKERDHFSQFVTEDF---TQYV--KRKRRDRVFGNNLEIQAMSEIYN 85

                           90
                   ....*....|.
gi 1635547078 1063 --VNVYTYYND 1071
Cdd:cd22796     86 rpIEVYSYSNG 96
OTU_VRTN cd22791
OTU (ovarian tumor) domain of vertnin and similar proteins; Vertnin (VRTN) is an OTU ...
 982-1069 6.82e-07

OTU (ovarian tumor) domain of vertnin and similar proteins; Vertnin (VRTN) is an OTU domain-containing protein that is required for the development of thoracic vertebrae in mammals. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. Vertnin and some subfamily members do not possess the conserved catalytic residues and may not have DUB activity. VRTN gene is associated with variations in vertebral number.


Pssm-ID: 438612  Cd Length: 137  Bit Score: 51.07  E-value: 6.82e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRsflrsqySSVDQYLDASRMRyvGSWATEMEIQATADFL 1061
Cdd:cd22791      6 VTGDGNCLFRAASLLLFGDESLHLELRLRTVLELVLNSEFYE-------AIYEAEIKATCKP--GSYSGIWHIYALSSVL 76


                   ....*...
gi 1635547078 1062 GVNVYTYY 1069
Cdd:cd22791     77 QRPIFSVY 84
OTU_OTUD5-like cd22752
OTU (ovarian tumor) domain of OTU domain-containing protein 5 and similar proteins; OTU ...
 1222-1343 1.20e-06

OTU (ovarian tumor) domain of OTU domain-containing protein 5 and similar proteins; OTU domain-containing protein 5 (OTUD5), also called deubiquitinating enzyme A (DUBA), is a phosphorylation-dependent deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that can hydrolyze 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, and may function as negative regulator of the innate immune system. It limits type I interferon production in macrophages and suppresses interleukin-17A production in T cells. OTUD5 also functions in an apoptotic signaling cascade by mediating the sequential activation of PDCD5 (programmed cell death 5) and p53 in response to genotoxic stress. In Drosophila, OTUD5/DUBA is essential for spermatogenesis. This subfamily also includes Arabidopsis thaliana OTU domain-containing protein 6, also called deubiquitinating enzyme OTU6 or otubain-like deubiquitinase 1 (OTLD1), which binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It also includes plant OTU6.


Pssm-ID: 438589 [Multi-domain]  Cd Length: 124  Bit Score: 49.85  E-value: 1.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1222 KIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIgkaYNTVAEYIEdvKMKYVGTCISKVEIQATANA 1301
Cdd:cd22752      6 EMEEDGNCLFRAVADQVYGDQEMHDVVRKHCMDYMEKNRDYFSQFV---TEDFEEYIN--RKRQDGVWGNHIEIQAMSEL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1635547078 1302 LGVDIFIFSA-GKWMGYFPKTKKQTGEAIYLSKCAENHFEAVI 1343
Cdd:cd22752     81 YNRPIEVYAYsTEPINTFHEASSSDNEPIRLSYHGNSHYNSIV 123
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 2720-2851 7.75e-06

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 48.52  E-value: 7.75e-06
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  2720 HIFVTGGAGTGKSHLIKAIQYEAtrilapvchQPDDICVLLTAPTGIAAYSLNATTIHSTFSIGKDVRlpytplGEEKLN 2799
Cdd:smart00382    4 VILIVGPPGSGKTTLARALAREL---------GPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS------GELRLR 68

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1635547078  2800 SL--RAKYSSLQLLIIDEISMVDHNVLAYIHGRLRQIKQRGDSSLFGNVAIIAV 2851
Cdd:smart00382   69 LAlaLARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
PHA03247 PHA03247
large tegument protein UL36; Provisional
 355-576 9.04e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.86  E-value: 9.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  355 AEPEAEPPATPVPSSPYRPRFATQvvvvgEERQPRPEANPDGWltivkgQKVELKECFIPLTpvrfspsilALVEKTSPS 434
Cdd:PHA03247  2646 VPPPERPRDDPAPGRVSRPRRARR-----LGRAAQASSPPQRP------RRRAARPTVGSLT---------SLADPPPPP 2705

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  435 VLPSPEETTSAPvqvecvdvevcfvATPTSAVPTTAMDQDEATqcvvdlTLEPGPRSVVVTTRV-GDEPPPGLPQLSPTP 513
Cdd:PHA03247  2706 PTPEPAPHALVS-------------ATPLPPGPAAARQASPAL------PAAPAPPAVPAGPATpGGPARPARPPTTAGP 2766

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1635547078  514 GVNAAADGPGF---PQLSPTPGVNAAADGPGFPQPSPTPGVDAVVDGPGqrtdSAIKYVGSPRSLV 576
Cdd:PHA03247  2767 PAPAPPAAPAAgppRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPA----AALPPAASPAGPL 2828
OTU_OTUD1 cd22747
OTU (ovarian tumor) domain of OTU domain-containing protein 1 and similar proteins; OTU ...
 1223-1342 1.25e-05

OTU (ovarian tumor) domain of OTU domain-containing protein 1 and similar proteins; OTU domain-containing protein 1 (OTUD1), also called DUBA-7 in humans, is a deubiquitinating enzyme/ubiquitinyl hydrolase (EC 3.4.19.12) that specifically hydrolyzes 'Lys-63'-linked polyubiquitin to monoubiquitin; this specificity is facilitated by the C-terminal Ub-interacting motif (UIM) of OTUD1. It interacts and promotes the deubiquitination of myeloid cell leukemia 1 (MCL1), a pro-survival Bcl-2 family protein that plays important roles in cell survival, proliferation, differentiation and tumorigenesis. OTUD1 also deubiquitinates IFN regulatory factor 3 (IRF3) and attenuates its function; IRF3 is critical for the transcription of type I IFNs in defensing virus and promoting inflammatory responses. Loss-of-function mutations of OTUD1 associated with multiple autoimmune diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), ulcerative colitis (UC) and Hashimoto's thyroiditis (HT). OTUD1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438584 [Multi-domain]  Cd Length: 149  Bit Score: 47.88  E-value: 1.25e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1223 IVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGkayNTVAEYIedVKMKYVGTCISKVEIQATANAL 1302
Cdd:cd22747     26 IIPDGNCLYRAVSKAVYGDQALHRELREQTVHYIADHLDEFNPIIE---GDVGEFL--IKAAQDGAWAGYPELLAMGQML 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1635547078 1303 GVDIFIFSAGKW-------MGYFPKTKKQTGEAIYLSKCAENHFEAV 1342
Cdd:cd22747    101 NVNIRLTTGGSLesptvstMVHYLGPEDSGKPSIWLSWLSNGHYDAV 147
Borrelia_orfA pfam02414
Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats ...
 1383-1600 2.45e-05

Borrelia ORF-A; This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown.


Pssm-ID: 396813  Cd Length: 285  Bit Score: 48.95  E-value: 2.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1383 SNVNYCFSKYLKTKKHAQHRIKYQSNVLLREKKKYLLKRLYHQNMMFNEKkreiSLIRYrknqdiiknrlKLKYHEDDLY 1462
Cdd:pfam02414   23 SDILYYFNSNLKKNGQKEVKIRTLQNYLYKLEKEIKVTKNYYKHLGKNMG----TEIYY-----------KLNYPKKECY 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1463 RlkmKINKN----KKYREDNLYRTKLKDTCKQKYNVDDLH--REKIKQLSKTKYKVDDVHREKIKQLSKTKYKDDMYREK 1536
Cdd:pfam02414   88 K---KINKYfkekKEDRFQNRVNNYFKKNYNKNNSVKKWEciNNIYNNKENEEEKKKSIEKEQLKKYIKKCNFKSKESLS 164

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1635547078 1537 MINQ----------YKRKYKQDYLYRERVKNISK-----QKYENHLFREKaKIIYKQKYHKDLLYQNKAKERSQSKYRV 1600
Cdd:pfam02414  165 ILNLnikkdikiklIKIIKKEENLIKKNNNKIKKlknkqKTLKNILRNLK-KALEKEGYDEKQLEIEIQKIYEKYKNKP 242
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1393-1617 2.89e-05

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 50.02  E-value: 2.89e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1393 LKTKKHAQHRIKYQsnvlLREKKKYL------LKRLYHQnmmFNEKKREISLIRYRKNQDIIKNrLK--LKYHEDDLYRL 1464
Cdd:TIGR04523  255 LNQLKDEQNKIKKQ----LSEKQKELeqnnkkIKELEKQ---LNQLKSEISDLNNQKEQDWNKE-LKseLKNQEKKLEEI 326

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1465 KMKINKN-KKYREDNLYRTKLKdtcKQKYNVDDLHREKIKQLSKTKYKVDDVHREkikqlsKTKYKDDMYR-EKMINQYK 1542
Cdd:TIGR04523  327 QNQISQNnKIISQLNEQISQLK---KELTNSESENSEKQRELEEKQNEIEKLKKE------NQSYKQEIKNlESQINDLE 397

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1635547078 1543 RKykqdylyrervknISKQKYENHLFREKAKIIYKQKYHKDLLYQNKAKERSQSKYRV-NLTHKH---NIKVRSAKTYR 1617
Cdd:TIGR04523  398 SK-------------IQNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSEIkDLTNQDsvkELIIKNLDNTR 463
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 2714-2816 5.96e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 45.99  E-value: 5.96e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2714 QKPDPFHIFVTGGAGTGKSHLIKAIQYEATRILAPVChqpddicvlltaptgiaaySLNATTIHSTFSIGKDVRLPytpl 2793
Cdd:cd00009     15 ELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFL-------------------YLNASDLLEGLVVAELFGHF---- 71

                           90       100
                   ....*....|....*....|...
gi 1635547078 2794 gEEKLNSLRAKYSSLQLLIIDEI 2816
Cdd:cd00009     72 -LVRLLFELAEKAKPGVLFIDEI 93
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 360-549 6.21e-05

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 48.77  E-value: 6.21e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  360 EPPATPVPSSPY-RPRFATQV--VVVGEERQPRPEANPDGWLTIVKGQKVELKECFiPLTP-VRFSPsilaLVEKTSPSv 435
Cdd:PLN03209   381 KPPTSPIPTPPSsSPASSKSVdaVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTR-PLSPyARYED----LKPPTSPS- 454

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  436 lPSPEETTSAPVQVECVDVEVCFVATPTSAVPTTAMDqdeatqcvvdltlEPGPRSVVVTTRVGDEPPPGLPQLSPTPGV 515
Cdd:PLN03209   455 -PTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAPP-------------PANMRPLSPYAVYDDLKPPTSPSPAAPVGK 520

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1635547078  516 NAAADGPGFPQLSPTPGVNAAADGPGFPQPSPTP 549
Cdd:PLN03209   521 VAPSSTNEVVKVGNSAPPTALADEQHHAQPKPRP 554
OTU_OTUD6-like cd22748
OTU (ovarian tumor) domain of OTU domain-containing proteins 6A, 6B, and similar proteins; ...
 1219-1312 1.35e-04

OTU (ovarian tumor) domain of OTU domain-containing proteins 6A, 6B, and similar proteins; This subfamily is composed of mammalian OTU domain-containing protein 6A (OTUD6A, also called DUBA-2, vertebrate OTU domain-containing protein 6B (OTUD6B, also called DUBA-5), fungal OTU domain-containing protein 2 (OTU2), and similar proteins. OTUD6A, OTUD6B, and Schizosaccharomyces pombe OTU2 are deubiquitinating enzymes/ubiquitinyl hydrolases (EC 3.4.19.12). OTUD6A hydrolyzes 'Lys-27'-, 'Lys-29'-, and 'Lys-33'-linked polyubiquitin chains, and may also be able to hydrolyze 'Lys-11'-linked ubiquitin chains. It deubiquitylates and stabilizes dynamin-related protein 1 (Drp1), a cytosolic protein responsible for mitochondrial fission and is essential in the initiation and development of several human diseases including cancer, thereby facilitating tumorigenesis. OTUD6B is a functional deubiquitinase in in vitro enzyme assays. It may play a role in the ubiquitin-dependent regulation of protein synthesis downstream of mTORC1, and may modify the ubiquitination of the protein synthesis initiation complex to repress translation. Biallelic variants in OTUD6B cause an intellectual disability syndrome that is associated with seizures and dysmorphic features. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438585 [Multi-domain]  Cd Length: 144  Bit Score: 44.48  E-value: 1.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1219 KMEKIVNDGNSFFRAVCHVI-----SGSQKNHRKLRLFVVKYMLNNSD--IHMQLIGKAY----NTVAEYIEDVK--MKY 1285
Cdd:cd22748      7 RIKEIPPDGHCLYRAIADQLklrggSEEPYSYKELRKLAADYMRAHRDdfLPFLTNDDGDlmteEEFEEYCDKIEntAEW 86

                           90       100
                   ....*....|....*....|....*..
gi 1635547078 1286 VGtcisKVEIQATANALGVDIFIFSAG 1312
Cdd:cd22748     87 GG----QLELRALSKALKRPIHVYQAG 109
OTU_plant_OTU3_4-like cd22746
OTU (ovarian tumor) domain of deubiquitinating enzymes OTU3 and OTU4 from plants, and similar ...
 979-1102 2.03e-04

OTU (ovarian tumor) domain of deubiquitinating enzymes OTU3 and OTU4 from plants, and similar proteins; Deubiquitinating enzyme OTU3 (also called OTU domain-containing protein 3) and deubiquitinating enzyme OTU4 (also called OTU domain-containing protein 4) are deubiquitinases (DUBs) or ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU3 and OTU4 may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438583 [Multi-domain]  Cd Length: 141  Bit Score: 44.18  E-value: 2.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  979 SDTIVADGNCFFRAVAQAVS----GTQKSHV-------KLRRAVVRHIEKNavQYRSFLRSQY--SSVDQYLDasRMRYV 1045
Cdd:cd22746      4 VVPVKGDGRCLFRAVARGLAlatgGRPLSERreradadALRKAVVEEIRKR--RDELFEGSLVieGDFDAYCQ--RMSHP 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1046 GSWATEMEIQATADFLGVNVytyyndrwLVYSCQNNA-----ISRQG--------IYLQHVNGCHYEVVV 1102
Cdd:cd22746     80 DTWGGEPELLMLADVLQRPI--------AVYLPTPGKgglrkIQEYGeeylggepIRLLYNGGNHYDLLL 141
OTU_OTUD3 cd22770
OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; OTU ...
 982-1101 2.15e-04

OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; OTU domain-containing protein 3 (OTUD3) is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438607 [Multi-domain]  Cd Length: 145  Bit Score: 44.20  E-value: 2.15e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRSQySSVDQYLdaSRMRYVGSWATEMEIQATADFL 1061
Cdd:cd22770     19 IPGDGNCLFRALGDQLEGHSRNHLKHRQETVQYMIEHREDFEPFVEDD-VPFDKHV--ANLSKPGTYAGNDAIVAFARLH 95

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1635547078 1062 GVNVYTYYND--RWLVYSCqNNAISRQgIYLQHVNGCHYEVV 1101
Cdd:cd22770     96 QVNVVIHQLNapLWQIRGT-EKSSSRE-LHISYHNGDHYSSV 135
OTU_plant_OTU6-like cd22796
OTU (ovarian tumor) domain of deubiquitinating enzyme OTU6 from plants and similar proteins; ...
 1219-1343 2.17e-04

OTU (ovarian tumor) domain of deubiquitinating enzyme OTU6 from plants and similar proteins; Deubiquitinating enzyme OTU6, also called OTU domain-containing protein 6 or otubain-like deubiquitinase 1 (OTLD1), is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU6 binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. OTU6 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438617 [Multi-domain]  Cd Length: 128  Bit Score: 43.57  E-value: 2.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1219 KMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDIHMQLIGKAYntvAEYIEDVKMKYV-GtciSKVEIQA 1297
Cdd:cd22796      6 EIRRMDGDGNCLFRAVADQVYGDQEMHDEVREMCMDYMEKERDHFSQFVTEDF---TQYVKRKRRDRVfG---NNLEIQA 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1635547078 1298 TANALG--VDIFIFSAGKWMGYFPKTKKQTGEAIYLSKCAENHFEAVI 1343
Cdd:cd22796     80 MSEIYNrpIEVYSYSNGEPINIFHGSYEGDDPPIRLSYHDGNHYNSII 127
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 3277-3378 2.24e-04

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 43.51  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 3277 MLVAVVYRPPSYPMSLFRKNLGKLLDyvEPLSDSVTVMGDFN----------EDLVASKSICNFMTQRG--YVQHVSEAT 3344
Cdd:pfam14529    1 ILIISVYCPPSDQLRNLLDTLEDILR--SLDRPPIIIGGDFNahhplwgsnsTDVSRGEELIEFLNEHGlnLLNLPKSGP 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1635547078 3345 TAK----GTLIDHVYVNTTHFDVSCVVLQT-YFSDHDAI 3378
Cdd:pfam14529   79 TFIssngDSTIDLTLTSDPLAVRVLSDLGPdSGSDHRPI 117
OTU_VRTN cd22791
OTU (ovarian tumor) domain of vertnin and similar proteins; Vertnin (VRTN) is an OTU ...
 1226-1307 3.46e-04

OTU (ovarian tumor) domain of vertnin and similar proteins; Vertnin (VRTN) is an OTU domain-containing protein that is required for the development of thoracic vertebrae in mammals. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. Vertnin and some subfamily members do not possess the conserved catalytic residues and may not have DUB activity. VRTN gene is associated with variations in vertebral number.


Pssm-ID: 438612  Cd Length: 137  Bit Score: 43.36  E-value: 3.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1226 DGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSDihmqligkayntvaEYIEDVKMKYVGTCISKV-----EIQATAN 1300
Cdd:cd22791      9 DGNCLFRAASLLLFGDESLHLELRLRTVLELVLNSE--------------FYEAIYEAEIKATCKPGSysgiwHIYALSS 74


                   ....*..
gi 1635547078 1301 ALGVDIF 1307
Cdd:cd22791     75 VLQRPIF 81
OTU_RNAP_L_virus cd21880
OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase ...
 983-1099 3.73e-04

OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438580  Cd Length: 148  Bit Score: 43.36  E-value: 3.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  983 VADGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKN------AVQYrsflrsqYSSVDQYL-DASRMRYVGSwATEMEIQ 1055
Cdd:cd21880     28 PGDGNCFFRSIAELLFDTEDEWRLVKNTIESYARANwdecpeARLY-------YLSLEEYLrDAMKDGYWGG-SLEAEIL 99

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1635547078 1056 ATAdfLGVNVYTYY--NDRWLVYSCQ--NNAISRQgIYLQHVNGcHYE 1099
Cdd:cd21880    100 SKA--LGITIIIWVvdDSDWVTAAVRfgDGDVSTS-LNLLHSGG-HFD 143
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 1412-1644 4.13e-04

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.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 45.68  E-value: 4.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1412 REKKKYLLKRLYHQN----MMFNEKKREISLIRYRKNQDIIKNRLKlKYHEDDLYRLKMKINKNKKYRED----NLYRTK 1483
Cdd:pfam13868   63 KEEERKEERKRYRQEleeqIEEREQKRQEEYEEKLQEREQMDEIVE-RIQEEDQAEAEEKLEKQRQLREEidefNEEQAE 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1484 LKDTCKQKYNVDDL-----HREKIKQLSKTKYKVDDVHREK-------IKQLSKTK-YKDDM-------YREKMINQYKR 1543
Cdd:pfam13868  142 WKELEKEEEREEDErileyLKEKAEREEEREAEREEIEEEKereiarlRAQQEKAQdEKAERdelraklYQEEQERKERQ 221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1544 KYKQDYLYRERVKNISKQKYENHL-FREKAKIIYKQkyhKDLLYQNKAKERSQSKYRVNlthkhniKVRSAKTYRGNVEF 1622
Cdd:pfam13868  222 KEREEAEKKARQRQELQQAREEQIeLKERRLAEEAE---REEEEFERMLRKQAEDEEIE-------QEEAEKRRMKRLEH 291

                          250       260
                   ....*....|....*....|..
gi 1635547078 1623 RKRVSAGVRNKRQQIKAQAQDF 1644
Cdd:pfam13868  292 RRELEKQIEEREEQRAAEREEE 313
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1389-1593 4.65e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 46.17  E-value: 4.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1389 FSKYLKTKKHAQHRIKYQSNVLLREKKKylLKRlyHQNMMFNEKKREISLIRY--RKNQDIIKNRLKLKYHEDDLYRLKM 1466
Cdd:TIGR04523  108 INSEIKNDKEQKNKLEVELNKLEKQKKE--NKK--NIDKFLTEIKKKEKELEKlnNKYNDLKKQKEELENELNLLEKEKL 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1467 KINKN-----KKYREDNLYRTKLKdTCKQKYN-----VDDLhREKIKQLSKTKYKVDDVHREKIKQLSKTK-----YKDD 1531
Cdd:TIGR04523  184 NIQKNidkikNKLLKLELLLSNLK-KKIQKNKslesqISEL-KKQNNQLKDNIEKKQQEINEKTTEISNTQtqlnqLKDE 261

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1635547078 1532 myREKMINQYKRKYKQdylyRERVKNISKQKyENHLFREKAKI--IYKQK---YHKDLLYQNKAKER 1593
Cdd:TIGR04523  262 --QNKIKKQLSEKQKE----LEQNNKKIKEL-EKQLNQLKSEIsdLNNQKeqdWNKELKSELKNQEK 321
OTU_plant_OTU5-like cd22797
OTU (ovarian tumor) domain of deubiquitinating enzyme OTU5 from plants and similar proteins; ...
 982-1066 7.72e-04

OTU (ovarian tumor) domain of deubiquitinating enzyme OTU5 from plants and similar proteins; Deubiquitinating enzyme OTU5, also called OTU domain-containing protein 6, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU5 is an inactive cysteine protease. It regulates gene expression by contributing to chromatin organization and DNA methylation patterns (e.g. H3K4me3 and H3K27me3). It is required for phosphate (Pi) homeostasis. OTU5 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438618 [Multi-domain]  Cd Length: 149  Bit Score: 42.72  E-value: 7.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVA---QAVSGT--QKSHVKLRRAVVRHIEKNAVQYRSFLRSQYSSVD------QYLDAsrMRYVGSWAT 1050
Cdd:cd22797     15 IKADGHCLYRAVEdqlQLRGGGapAPDYQQLRELAADYMRAHPDDFLPFLEDEDEGGDgdeafeAYCRE--VESTAAWGG 92

                           90
                   ....*....|....*...
gi 1635547078 1051 EMEIQATADFLG--VNVY 1066
Cdd:cd22797     93 QLELGALAHALRrhIKVY 110
OTU_ALG13 cd22795
OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and ...
 985-1101 8.22e-04

OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13; Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is also called asparagine-linked glycosylation 13 homolog, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homolog. It displays both glycosyltransferase (EC 2.4.1.141) and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyzes the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum. ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures, neurodevelopmental impairment, and poor prognosis; given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). ALG13 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438616 [Multi-domain]  Cd Length: 130  Bit Score: 42.11  E-value: 8.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  985 DGNCFFRAVAQAVSGTQKSHVKLRRAVVRHIEKNAVQYRSFLRsqySSVDQYLDasRMRYVGSWATEMEIQATADFLGVN 1064
Cdd:cd22795     18 DASCLFRAVSEQLFLCQIHHLEIRKACVSYMRANQCNFESYVE---GSFEKYLE--RLEDPKESAGQLEISALSLIYNRD 92

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1635547078 1065 VYTY-YNDRWLVYSCQNNAISRqgIYLQHVNGCHYEVV 1101
Cdd:cd22795     93 FILYrYPGKPPTYATDNGFEDK--ILLCCSSNGHYDSV 128
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1380-1594 8.62e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 45.01  E-value: 8.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1380 SVKSNVNYCFSKYLKTKKHAQHRIKyqsnVLLREKkkyllkrlyhqnmmfNEKKREISLIRyrknQDIIKNRLKLKYHED 1459
Cdd:TIGR04523  391 SQINDLESKIQNQEKLNQQKDEQIK----KLQQEK---------------ELLEKEIERLK----ETIIKNNSEIKDLTN 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1460 DLYRLKMKINKNKKYREDnlYRTKLKDTCKQ----KYNVDDLHRE---KIKQLSKTKY-------KVDDVHR------EK 1519
Cdd:TIGR04523  448 QDSVKELIIKNLDNTRES--LETQLKVLSRSinkiKQNLEQKQKElksKEKELKKLNEekkeleeKVKDLTKkisslkEK 525

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1520 IKQLSKTKYKddmyREKMINQYKRKYKQD-----YLYRERVKNiSKQKYENHLFREKAKIIYKQKyHKDLLYQNKAKERS 1594
Cdd:TIGR04523  526 IEKLESEKKE----KESKISDLEDELNKDdfelkKENLEKEID-EKNKEIEELKQTQKSLKKKQE-EKQELIDQKEKEKK 599
Lipase_GDSL_2 pfam13472
GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are ...
 246-312 1.81e-03

GDSL-like Lipase/Acylhydrolase family; This family of presumed lipases and related enzymes are similar to pfam00657.


Pssm-ID: 463889  Cd Length: 176  Bit Score: 42.15  E-value: 1.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1635547078  246 PGATAAQLRTELVAAVLPRDPDAVVLLAPSNNLTACQGLEDSAADFASLLRCARSRWGNVAVLDFPP 312
Cdd:pfam13472   42 SGATTRLDLLERLDDVLRLKPDLVVILLGTNDLGRGVSAARAAANLEALIDALRAAGPDARVLLIGP 108
OTU_OTUD6 cd22761
OTU (ovarian tumor) domain of OTU domain-containing proteins 6A and 6B and similar proteins; ...
 982-1061 1.84e-03

OTU (ovarian tumor) domain of OTU domain-containing proteins 6A and 6B and similar proteins; This subfamily is composed of mammalian OTU domain-containing protein 6A (OTUD6A, also called DUBA-2) and vertebrate OTU domain-containing protein 6B (OTUD6B, also called DUBA-5), which are deubiquitinating enzymes/ubiquitinyl hydrolases (EC 3.4.19.12). OTUD6A hydrolyzes 'Lys-27'-, 'Lys-29'-, and 'Lys-33'-linked polyubiquitin chains, and may also be able to hydrolyze 'Lys-11'-linked ubiquitin chains. It deubiquitylates and stabilizes dynamin-related protein 1 (Drp1), a cytosolic protein responsible for mitochondrial fission and is essential in the initiation and development of several human diseases including cancer, thereby facilitating tumorigenesis. OTUD6B is a functional deubiquitinase in in vitro enzyme assays. It may play a role in the ubiquitin-dependent regulation of protein synthesis downstream of mTORC1, and may modify the ubiquitination of the protein synthesis initiation complex to repress translation. Biallelic variants in OTUD6B cause an intellectual disability syndrome that is associated with seizures and dysmorphic features. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438598 [Multi-domain]  Cd Length: 146  Bit Score: 41.33  E-value: 1.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  982 IVADGNCFFRAVAQAVS--GTQKSHVKLRRAVVRHIEKNAVQYRSFL----------RSQYssvDQYLDasRMRYVGSWA 1049
Cdd:cd22761     15 IPSDGDCLYNAIAHQLSlrGIETSVEELRKQTADYMRENKDDFLPFLtnpdtgdpltEEEF---EKYCD--DVENTGAWG 89

                           90
                   ....*....|..
gi 1635547078 1050 TEMEIQATADFL 1061
Cdd:cd22761     90 GQLELRALSHVL 101
OTU_OTUD3 cd22770
OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; OTU ...
 1219-1261 3.47e-03

OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; OTU domain-containing protein 3 (OTUD3) is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438607 [Multi-domain]  Cd Length: 145  Bit Score: 40.73  E-value: 3.47e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1635547078 1219 KMEKIVNDGNSFFRAVCHVISGSQKNHRKLRLFVVKYMLNNSD 1261
Cdd:cd22770     15 KLRDIPGDGNCLFRALGDQLEGHSRNHLKHRQETVQYMIEHRE 57
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
1430-1578 3.67e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 42.21  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1430 NEKKREISLIRYR---------KNQDIIK--NRLKLKYHEddlyrLKMKINKNKKYREDnlyRTKLKDTCKQkynVDDLH 1498
Cdd:COG1340    112 DKLRKEIERLEWRqqtevlspeEEKELVEkiKELEKELEK-----AKKALEKNEKLKEL---RAELKELRKE---AEEIH 180

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1499 ------REKI----KQLSKTKYKVDDVhREKIKQLSKT--KYKD--DMYREKMINQYK--RKY-KQDYLYRERVKNISKQ 1561
Cdd:COG1340    181 kkikelAEEAqelhEEMIELYKEADEL-RKEADELHKEivEAQEkaDELHEEIIELQKelRELrKELKKLRKKQRALKRE 259

                          170
                   ....*....|....*..
gi 1635547078 1562 KYENHLfREKAKIIYKQ 1578
Cdd:COG1340    260 KEKEEL-EEKAEEIFEK 275
AAA_22 pfam13401
AAA domain;
2720-2828 4.44e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.02  E-value: 4.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 2720 HIFVTGGAGTGKSHLIKAIQYEATRilapvcHQPDDICVLLTAPTGIAAYslnATTIHSTFSIGKDVRLPYTPLGEEKLN 2799
Cdd:pfam13401    7 ILVLTGESGTGKTTLLRRLLEQLPE------VRDSVVFVDLPSGTSPKDL---LRALLRALGLPLSGRLSKEELLAALQQ 77

                           90       100
                   ....*....|....*....|....*....
gi 1635547078 2800 SLRAkYSSLQLLIIDEISMVDHNVLAYIH 2828
Cdd:pfam13401   78 LLLA-LAVAVVLIIDEAQHLSLEALEELR 105
TesA COG2755
Lysophospholipase L1 or related esterase. Includes spore coat protein LipC/YcsK [Cell cycle ...
 246-349 5.20e-03

Lysophospholipase L1 or related esterase. Includes spore coat protein LipC/YcsK [Cell cycle control, cell division, chromosome partitioning, Lipid transport and metabolism];


Pssm-ID: 442045 [Multi-domain]  Cd Length: 191  Bit Score: 40.78  E-value: 5.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  246 PGATAAQLRTELVAAVLPRDPDAVVLLAPSNNLTACQG--LEDSAADFASLLRCARSRWG-------------------- 303
Cdd:COG2755     51 SGATTADLLARLDRDLLALKPDLVVIELGTNDLLRGLGvsPEEFRANLEALIDRLRAAGPgarvvlvtppprlrpnylne 130

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1635547078  304 ----------------NVAVLDFPPRLSVEQRSQELlrMAYNSTHLSDnAGMPILAYLLWQA 349
Cdd:COG2755    131 rieaynaairelaaeyGVPLVDLYAALRDAGDLPDL--LTADGLHPNA-AGYRLIAEAVLPA 189
uS4m cd23691
Tetrahymena thermophila ribosomal protein uS4m, and similar proteins; Ribosomal protein uS4m, ...
 1414-1601 5.43e-03

Tetrahymena thermophila ribosomal protein uS4m, and similar proteins; Ribosomal protein uS4m, also called Ymf76, is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosome (mitoribosome), which reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit; its large subunit (LSU) lacks 5S rRNA.


Pssm-ID: 467905  Cd Length: 398  Bit Score: 42.09  E-value: 5.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1414 KKKYLLKRLYhQNMMFNEKKREISLIrYRKNQDIIKNRLKLKYheddlyrlkMKINKNKKYRedNLyrtkLKDTCKQKYN 1493
Cdd:cd23691      6 KLKKKLKKFY-KKYNYNSNKLNNFYL-KKPNILNLYNKINNFF---------LKIFKYIKYL--NL----IKKIISKKKL 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078 1494 VDDLHREKIKQLSKTKYKVDDVHREKIKQL--SKTKYKDDMYREKMINQY-KRKYKQDYLYRERV---------KNISKQ 1561
Cdd:cd23691     69 FKFLNNPKIRNKKKFKYKYSDKFKFILNILksKKTKINNLLYFLKYFSVFrKRQSRIFNLSKVKSrlskrkffkKKFKKK 148

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1635547078 1562 KYENHLFREKAKIIYKQKYHKDLLYQNKAKERSQSKYRVN 1601
Cdd:cd23691    149 KIAKYFFKMFKKLKFKRKKHINLINLDLYFIRNKRFFRLH 188
OTU_OTU1 cd22745
OTU (ovarian tumor) domain of ubiquitin thioesterase OTU1 and similar proteins; Ubiquitin ...
 984-1102 9.95e-03

OTU (ovarian tumor) domain of ubiquitin thioesterase OTU1 and similar proteins; Ubiquitin thioesterase (EC 3.4.19.12) OTU1 is also called OTU domain-containing protein 1 in yeast, while human OTU1 is also called HIV-1-induced protease 7 (HIN7), DUBA-8, or OTU domain-containing protein 2 (OTUD2). OTU1 is a deubiquitinase (DUB) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU1 has been implicated in the ER-associated degradation (ERAD) pathway. In yeast, it counteracts the activity of Ufd2 by deubiquitinating Ufd2 substrates; Ufd2 is a E4 ubiquitin ligase that interacts with Cdc48, an AAA ATPase that plays a central role in the ERAD pathway by chaperoning proteins to the proteasome for destruction. OTU1 also functions as a substrate-processing factor of valosin-containing protein (VCP, the mammalian counterpart of yeast Cdc48) that is required for the retrotranslocation of the ERAD pathway. OTU1 has been shown to preferentially hydrolyze polyubiquitin chains with Lys48 linkages. It contains ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a C2H2-type zinc finger, and an OTU (ovarian tumor) domain. This model represents the OTU domain that interacts with ubiquitin and possesses catalytic activity. OTU1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. This family also contains plant OTU1 and OTU2.


Pssm-ID: 438582  Cd Length: 161  Bit Score: 39.39  E-value: 9.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1635547078  984 ADGNCFFRAVAQAVSGTQKSHV-KLRRAVVRHIEKNAVQYRS-FL-RsqysSVDQYldASRMRYVGSWATEMEIQATADF 1060
Cdd:cd22745     10 DDNSCLFTSISYLLEGGLLDSApELREIVADAILSDPDTYNEaILgK----PPDEY--CAWILKPDSWGGAIELSILSKH 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1635547078 1061 LGVNVYT---------------YYNDR-WLVYScqnnaisrqGIylqhvngcHYEVVV 1102
Cdd:cd22745     84 FGVEICVvdvqtgrvdrfgedkGYSKRiFLLYS---------GI--------HYDALA 124
 
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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