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Conserved domains on  [gi|1158912424|ref|XP_020361191|]
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CCR4-NOT transcription complex subunit 3 isoform X4 [Oncorhynchus kisutch]

Protein Classification

CCR4-NOT transcription complex subunit 3( domain architecture ID 13694822)

CCR4-NOT transcription complex subunit 3 is a component of one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Not3 pfam04065
Not1 N-terminal domain, CCR4-Not complex component;
3-229 5.06e-140

Not1 N-terminal domain, CCR4-Not complex component;


:

Pssm-ID: 461155 [Multi-domain]  Cd Length: 228  Bit Score: 416.18  E-value: 5.06e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRDQIKTWVASNEIKDKRQLVENRK 82
Cdd:pfam04065   1 AARKLQQEIDRTLKKVAEGLEEFDDIYEKLESATNSSQKEKLEADLKKEIKKLQRLRDQIKTWLSSNDIKDKKKLLENRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  83 LIETQMERFKIVERETKTKAYSKEGLGLAQ--KVDPAQREKEEVGNWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDK 160
Cdd:pfam04065  81 LIEEAMERFKAVEKESKTKAFSKEGLSLAAasKLDPKEKEKAEARDWLSDSIDELNRQIEALEAEIESLQAQKKKKKKDS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1158912424 161 EKQdRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKDDVEYYMDSSQDPDFEENEFLYDDL 229
Cdd:pfam04065 161 EKA-RLEELEKLIERHKFHIEKLELILRLLENGELDPEQVDDIKEDIEYYVESNQDPDFVEDEDIYDDL 228
NOT2_3_5 pfam04153
NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that ...
 801-926 9.28e-58

NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5.


:

Pssm-ID: 461199  Cd Length: 121  Bit Score: 193.58  E-value: 9.28e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 801 SAWTHMPHPSDSERIRQYLMRNPCPtlpfHHQVPPPHSDSVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFH 880
Cdd:pfam04153   1 YSTFNSPWPLDAERPYEPDFRNPAC----YPQEPLPRLESPEKFSKFDDETLFYIFYSMPGDYAQYLAAKELKKRSWRYH 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1158912424 881 TKYMMWFQRHEEPKTITDEFEQGTYIYFDYeKWGQRKKEGFTFEYR 926
Cdd:pfam04153  77 KKLRTWFTRDEEPKVITNEYERGTYIYFDY-TWEQRRKKDFTLDYE 121
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 623-836 1.18e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 52.46  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 623 PPSGQKQNGSTSYS-AVVADSTPDSALNIANQLQSSQPSSLISTTNQLKDSGPSLLGSMTLPTSTPSPSYIESKPSGSSM 701
Cdd:pfam03154 134 PKDIDQDNRSTSPSiPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPA 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 702 LN----------GPLSYTQASESMKPQE---PLSTVKSMAE---------QAALGSAMEGELPPLHLTTDIFPSTTAPPG 759
Cdd:pfam03154 214 TSqppnqtqstaAPHTLIQQTPTLHPQRlpsPHPPLQPMTQppppsqvspQPLPQPSLHGQMPPMPHSLQTGPSHMQHPV 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 760 PPSA-PQQPSLSEVSIPPslgvcplGPVPlskdqlyQQAMQESAWTHMPHPSDSERIRQYLMRNPCP--TLPFHHQVPPP 836
Cdd:pfam03154 294 PPQPfPLTPQSSQSQVPP-------GPSP-------AAPGQSQQRIHTPPSQSQLQSQQPPREQPLPpaPLSMPHIKPPP 359
 
Name Accession Description Interval E-value
Not3 pfam04065
Not1 N-terminal domain, CCR4-Not complex component;
3-229 5.06e-140

Not1 N-terminal domain, CCR4-Not complex component;


Pssm-ID: 461155 [Multi-domain]  Cd Length: 228  Bit Score: 416.18  E-value: 5.06e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRDQIKTWVASNEIKDKRQLVENRK 82
Cdd:pfam04065   1 AARKLQQEIDRTLKKVAEGLEEFDDIYEKLESATNSSQKEKLEADLKKEIKKLQRLRDQIKTWLSSNDIKDKKKLLENRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  83 LIETQMERFKIVERETKTKAYSKEGLGLAQ--KVDPAQREKEEVGNWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDK 160
Cdd:pfam04065  81 LIEEAMERFKAVEKESKTKAFSKEGLSLAAasKLDPKEKEKAEARDWLSDSIDELNRQIEALEAEIESLQAQKKKKKKDS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1158912424 161 EKQdRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKDDVEYYMDSSQDPDFEENEFLYDDL 229
Cdd:pfam04065 161 EKA-RLEELEKLIERHKFHIEKLELILRLLENGELDPEQVDDIKEDIEYYVESNQDPDFVEDEDIYDDL 228
NOT2_3_5 pfam04153
NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that ...
 801-926 9.28e-58

NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5.


Pssm-ID: 461199  Cd Length: 121  Bit Score: 193.58  E-value: 9.28e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 801 SAWTHMPHPSDSERIRQYLMRNPCPtlpfHHQVPPPHSDSVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFH 880
Cdd:pfam04153   1 YSTFNSPWPLDAERPYEPDFRNPAC----YPQEPLPRLESPEKFSKFDDETLFYIFYSMPGDYAQYLAAKELKKRSWRYH 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1158912424 881 TKYMMWFQRHEEPKTITDEFEQGTYIYFDYeKWGQRKKEGFTFEYR 926
Cdd:pfam04153  77 KKLRTWFTRDEEPKVITNEYERGTYIYFDY-TWEQRRKKDFTLDYE 121
CDC36 COG5601
General negative regulator of transcription subunit [Transcription];
833-929 1.52e-14

General negative regulator of transcription subunit [Transcription];


Pssm-ID: 227888  Cd Length: 172  Bit Score: 72.32  E-value: 1.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 833 VPPPHSDSVEFYQR----LSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMW--FQRHEEPKTITDEFEQGTYI 906
Cdd:COG5601    71 APNPPIFKVNIEDMkmdnFHDETLFYIFYSFPNDVLQEKAYDELLKRNWRFHKMLKCWltFNPGMSPATADHVKERGSYV 150

                          90       100
                  ....*....|....*....|...
gi 1158912424 907 YFDYEKWGQRKKEgFTFEYRYLE 929
Cdd:COG5601   151 FFDPFSWSKVSLD-FLLDYKAVR 172
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 623-836 1.18e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 52.46  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 623 PPSGQKQNGSTSYS-AVVADSTPDSALNIANQLQSSQPSSLISTTNQLKDSGPSLLGSMTLPTSTPSPSYIESKPSGSSM 701
Cdd:pfam03154 134 PKDIDQDNRSTSPSiPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPA 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 702 LN----------GPLSYTQASESMKPQE---PLSTVKSMAE---------QAALGSAMEGELPPLHLTTDIFPSTTAPPG 759
Cdd:pfam03154 214 TSqppnqtqstaAPHTLIQQTPTLHPQRlpsPHPPLQPMTQppppsqvspQPLPQPSLHGQMPPMPHSLQTGPSHMQHPV 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 760 PPSA-PQQPSLSEVSIPPslgvcplGPVPlskdqlyQQAMQESAWTHMPHPSDSERIRQYLMRNPCP--TLPFHHQVPPP 836
Cdd:pfam03154 294 PPQPfPLTPQSSQSQVPP-------GPSP-------AAPGQSQQRIHTPPSQSQLQSQQPPREQPLPpaPLSMPHIKPPP 359
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 16-205 3.24e-06

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: 51.17  E-value: 3.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  16 KKVTEGVEQFEDIWQKLHNAANANQKEKyeADLKKEIKKLQrlrDQIKTWVASNEiKDKRQLVENRKLIETQMErfKIVE 95
Cdd:TIGR04523 214 KSLESQISELKKQNNQLKDNIEKKQQEI--NEKTTEISNTQ---TQLNQLKDEQN-KIKKQLSEKQKELEQNNK--KIKE 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  96 RETKTKAYSKEGLGLAQK------------VDPAQREKEEVGNWLTNT---IDTLNMQVDQFESEVESL-SVQTRKKKGD 159
Cdd:TIGR04523 286 LEKQLNQLKSEISDLNNQkeqdwnkelkseLKNQEKKLEEIQNQISQNnkiISQLNEQISQLKKELTNSeSENSEKQREL 365

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1158912424 160 KEKQDRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKD 205
Cdd:TIGR04523 366 EEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKD 411
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
8-205 9.69e-06

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 49.68  E-value: 9.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   8 QGEID----------RCLKKVTeGVEQFEDIWQKLhnaananqkekyeADLKKEIK-KLQRLRDQIKtwvASNEIKDkrq 76
Cdd:PRK03918  134 QGEIDailesdesreKVVRQIL-GLDDYENAYKNL-------------GEVIKEIKrRIERLEKFIK---RTENIEE--- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  77 lvenrkLIETQMERFKIVERETKTKaySKEGLGLAQKVDPAQREKEEVGNwLTNTIDTLNMQVDQFESEVESLSVQTRK- 155
Cdd:PRK03918  194 ------LIKEKEKELEEVLREINEI--SSELPELREELEKLEKEVKELEE-LKEEIEELEKELESLEGSKRKLEEKIREl 264

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 156 KKGDKEKQDRIEELK--------------------RFIEKHRYHIRMLETILRMLDNDTLPVdsIRKIKD 205
Cdd:PRK03918  265 EERIEELKKEIEELEekvkelkelkekaeeyiklsEFYEEYLDELREIEKRLSRLEEEINGI--EERIKE 332
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
5-190 6.30e-05

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


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 46.06  E-value: 6.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   5 RKLQGEIDRCLKKVTEGVEQFEDIWQKLhnaANANQKEKYEADLKKEIkklQRLRDQIKTWVAS--------NEIKDKRQ 76
Cdd:COG1340    74 KELKEERDELNEKLNELREELDELRKEL---AELNKAGGSIDKLRKEI---ERLEWRQQTEVLSpeeekelvEKIKELEK 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  77 LVENRKLIETQMErfKIVERETKTKAYSKEGLGLAQKV----DPAQREKEEVGNwLTNTIDTLNMQVDQFESEVEslsvq 152
Cdd:COG1340   148 ELEKAKKALEKNE--KLKELRAELKELRKEAEEIHKKIkelaEEAQELHEEMIE-LYKEADELRKEADELHKEIV----- 219

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1158912424 153 trkkkgdkEKQDRIEELKRFIEKHRYHIRMLETILRML 190
Cdd:COG1340   220 --------EAQEKADELHEEIIELQKELRELRKELKKL 249
PHA03247 PHA03247
large tegument protein UL36; Provisional
 574-842 2.55e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.31  E-value: 2.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  574 PPLVSPSPIGggLAPGSSLGAIGSIGGNSGSGAPSNSLGIGGGNAAIARPPSGQKQNGSTSYSAVVAD---STPDSALNI 650
Cdd:PHA03247  2713 HALVSATPLP--PGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGpprRLTRPAVAS 2790

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  651 ANQLQSSQPSSLISTTNQLKDSGPSLLGSMTLPTSTPSPSYIESKPSGSSMLNGPL-SYTQASESMKPQEPLS---TVKS 726
Cdd:PHA03247  2791 LSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPpPSLPLGGSVAPGGDVRrrpPSRS 2870

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  727 MAEQAALGS---AMEGELPPLHLTTDIF---PSTTAPPGPPSAPQQPSLSEVSIPPSLGVCPLGPVPLSKDQLYQQAMQE 800
Cdd:PHA03247  2871 PAAKPAAPArppVRRLARPAVSRSTESFalpPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1158912424  801 SAwthmPHPSDSERIRQYLMRNPCPTLPFHHQVPPPhSDSVE 842
Cdd:PHA03247  2951 GA----GEPSGAVPQPWLGALVPGRVAVPRFRVPQP-APSRE 2987
 
Name Accession Description Interval E-value
Not3 pfam04065
Not1 N-terminal domain, CCR4-Not complex component;
3-229 5.06e-140

Not1 N-terminal domain, CCR4-Not complex component;


Pssm-ID: 461155 [Multi-domain]  Cd Length: 228  Bit Score: 416.18  E-value: 5.06e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRDQIKTWVASNEIKDKRQLVENRK 82
Cdd:pfam04065   1 AARKLQQEIDRTLKKVAEGLEEFDDIYEKLESATNSSQKEKLEADLKKEIKKLQRLRDQIKTWLSSNDIKDKKKLLENRK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  83 LIETQMERFKIVERETKTKAYSKEGLGLAQ--KVDPAQREKEEVGNWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDK 160
Cdd:pfam04065  81 LIEEAMERFKAVEKESKTKAFSKEGLSLAAasKLDPKEKEKAEARDWLSDSIDELNRQIEALEAEIESLQAQKKKKKKDS 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1158912424 161 EKQdRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKDDVEYYMDSSQDPDFEENEFLYDDL 229
Cdd:pfam04065 161 EKA-RLEELEKLIERHKFHIEKLELILRLLENGELDPEQVDDIKEDIEYYVESNQDPDFVEDEDIYDDL 228
NOT2_3_5 pfam04153
NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that ...
 801-926 9.28e-58

NOT2 / NOT3 / NOT5 family; NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5.


Pssm-ID: 461199  Cd Length: 121  Bit Score: 193.58  E-value: 9.28e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 801 SAWTHMPHPSDSERIRQYLMRNPCPtlpfHHQVPPPHSDSVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFH 880
Cdd:pfam04153   1 YSTFNSPWPLDAERPYEPDFRNPAC----YPQEPLPRLESPEKFSKFDDETLFYIFYSMPGDYAQYLAAKELKKRSWRYH 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1158912424 881 TKYMMWFQRHEEPKTITDEFEQGTYIYFDYeKWGQRKKEGFTFEYR 926
Cdd:pfam04153  77 KKLRTWFTRDEEPKVITNEYERGTYIYFDY-TWEQRRKKDFTLDYE 121
CDC36 COG5601
General negative regulator of transcription subunit [Transcription];
833-929 1.52e-14

General negative regulator of transcription subunit [Transcription];


Pssm-ID: 227888  Cd Length: 172  Bit Score: 72.32  E-value: 1.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 833 VPPPHSDSVEFYQR----LSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMW--FQRHEEPKTITDEFEQGTYI 906
Cdd:COG5601    71 APNPPIFKVNIEDMkmdnFHDETLFYIFYSFPNDVLQEKAYDELLKRNWRFHKMLKCWltFNPGMSPATADHVKERGSYV 150

                          90       100
                  ....*....|....*....|...
gi 1158912424 907 YFDYEKWGQRKKEgFTFEYRYLE 929
Cdd:COG5601   151 FFDPFSWSKVSLD-FLLDYKAVR 172
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 623-836 1.18e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 52.46  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 623 PPSGQKQNGSTSYS-AVVADSTPDSALNIANQLQSSQPSSLISTTNQLKDSGPSLLGSMTLPTSTPSPSYIESKPSGSSM 701
Cdd:pfam03154 134 PKDIDQDNRSTSPSiPSPQDNESDSDSSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPA 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 702 LN----------GPLSYTQASESMKPQE---PLSTVKSMAE---------QAALGSAMEGELPPLHLTTDIFPSTTAPPG 759
Cdd:pfam03154 214 TSqppnqtqstaAPHTLIQQTPTLHPQRlpsPHPPLQPMTQppppsqvspQPLPQPSLHGQMPPMPHSLQTGPSHMQHPV 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 760 PPSA-PQQPSLSEVSIPPslgvcplGPVPlskdqlyQQAMQESAWTHMPHPSDSERIRQYLMRNPCP--TLPFHHQVPPP 836
Cdd:pfam03154 294 PPQPfPLTPQSSQSQVPP-------GPSP-------AAPGQSQQRIHTPPSQSQLQSQQPPREQPLPpaPLSMPHIKPPP 359
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 16-205 3.24e-06

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: 51.17  E-value: 3.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  16 KKVTEGVEQFEDIWQKLHNAANANQKEKyeADLKKEIKKLQrlrDQIKTWVASNEiKDKRQLVENRKLIETQMErfKIVE 95
Cdd:TIGR04523 214 KSLESQISELKKQNNQLKDNIEKKQQEI--NEKTTEISNTQ---TQLNQLKDEQN-KIKKQLSEKQKELEQNNK--KIKE 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  96 RETKTKAYSKEGLGLAQK------------VDPAQREKEEVGNWLTNT---IDTLNMQVDQFESEVESL-SVQTRKKKGD 159
Cdd:TIGR04523 286 LEKQLNQLKSEISDLNNQkeqdwnkelkseLKNQEKKLEEIQNQISQNnkiISQLNEQISQLKKELTNSeSENSEKQREL 365

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1158912424 160 KEKQDRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKD 205
Cdd:TIGR04523 366 EEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKD 411
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 3-170 3.26e-06

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: 51.17  E-value: 3.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIwqklhnaananqkEKYEADLKKEIKKLQRLRDQIKTWVA--SNEIKDkrqlvEN 80
Cdd:TIGR04523 420 EKELLEKEIERLKETIIKNNSEIKDL-------------TNQDSVKELIIKNLDNTRESLETQLKvlSRSINK-----IK 481

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  81 RKLIETQMErfkIVERETKTKAYSKEGLGLAQKVDPAQREKEEvgnwLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDK 160
Cdd:TIGR04523 482 QNLEQKQKE---LKSKEKELKKLNEEKKELEEKVKDLTKKISS----LKEKIEKLESEKKEKESKISDLEDELNKDDFEL 554

                         170       180
                  ....*....|....*....|
gi 1158912424 161 ----------EKQDRIEELK 170
Cdd:TIGR04523 555 kkenlekeidEKNKEIEELK 574
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
8-205 9.69e-06

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 49.68  E-value: 9.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   8 QGEID----------RCLKKVTeGVEQFEDIWQKLhnaananqkekyeADLKKEIK-KLQRLRDQIKtwvASNEIKDkrq 76
Cdd:PRK03918  134 QGEIDailesdesreKVVRQIL-GLDDYENAYKNL-------------GEVIKEIKrRIERLEKFIK---RTENIEE--- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  77 lvenrkLIETQMERFKIVERETKTKaySKEGLGLAQKVDPAQREKEEVGNwLTNTIDTLNMQVDQFESEVESLSVQTRK- 155
Cdd:PRK03918  194 ------LIKEKEKELEEVLREINEI--SSELPELREELEKLEKEVKELEE-LKEEIEELEKELESLEGSKRKLEEKIREl 264

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 156 KKGDKEKQDRIEELK--------------------RFIEKHRYHIRMLETILRMLDNDTLPVdsIRKIKD 205
Cdd:PRK03918  265 EERIEELKKEIEELEekvkelkelkekaeeyiklsEFYEEYLDELREIEKRLSRLEEEINGI--EERIKE 332
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
5-190 6.30e-05

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


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 46.06  E-value: 6.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   5 RKLQGEIDRCLKKVTEGVEQFEDIWQKLhnaANANQKEKYEADLKKEIkklQRLRDQIKTWVAS--------NEIKDKRQ 76
Cdd:COG1340    74 KELKEERDELNEKLNELREELDELRKEL---AELNKAGGSIDKLRKEI---ERLEWRQQTEVLSpeeekelvEKIKELEK 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  77 LVENRKLIETQMErfKIVERETKTKAYSKEGLGLAQKV----DPAQREKEEVGNwLTNTIDTLNMQVDQFESEVEslsvq 152
Cdd:COG1340   148 ELEKAKKALEKNE--KLKELRAELKELRKEAEEIHKKIkelaEEAQELHEEMIE-LYKEADELRKEADELHKEIV----- 219

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1158912424 153 trkkkgdkEKQDRIEELKRFIEKHRYHIRMLETILRML 190
Cdd:COG1340   220 --------EAQEKADELHEEIIELQKELRELRKELKKL 249
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 3-208 9.71e-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: 46.17  E-value: 9.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHNAANANQKEKYEADLKK-EIKKLQRLRDQIKTWVAS--NEIKDKRQLVE 79
Cdd:TIGR04523 322 KLEEIQNQISQNNKIISQLNEQISQLKKELTNSESENSEKQRELEEKQnEIEKLKKENQSYKQEIKNleSQINDLESKIQ 401

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  80 NRKLIETQME-RFKIVERETKTKaySKEglglaQKVDPAQREKEEvgnwltNTIDTLNMQVDQFESEVESLsvqtrKKKG 158
Cdd:TIGR04523 402 NQEKLNQQKDeQIKKLQQEKELL--EKE-----IERLKETIIKNN------SEIKDLTNQDSVKELIIKNL-----DNTR 463

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1158912424 159 DKEKQdRIEELKRFIEKHRyhiRMLETILRMLDNDTLPVDSIRKIKDDVE 208
Cdd:TIGR04523 464 ESLET-QLKVLSRSINKIK---QNLEQKQKELKSKEKELKKLNEEKKELE 509
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 2-191 1.32e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 45.83  E-value: 1.32e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424    2 ADKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHnaananQKEKYEADLKKEIKKLQRLRD-QIKTWVASNEIkDKRQLVEN 80
Cdd:TIGR02169  237 RQKEAIERQLASLEEELEKLTEEISELEKRLE------EIEQLLEELNKKIKDLGEEEQlRVKEKIGELEA-EIASLERS 309

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   81 RKLIETQMERF-----KIVERETKTKAyskEGLGLAQKVDPAQREKEEVGNWLTNTIDTLNMQVDQFEsEVESLSVQTRK 155
Cdd:TIGR02169  310 IAEKERELEDAeerlaKLEAEIDKLLA---EIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELE-EVDKEFAETRD 385

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1158912424  156 KKgdKEKQDRIEELKRFIEKHRYHIRMLETILRMLD 191
Cdd:TIGR02169  386 EL--KDYREKLEKLKREINELKRELDRLQEELQRLS 419
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
3-234 1.63e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.44  E-value: 1.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   3 DKRKLQGEIDRCLKKVTEGVEQFEDIWQKLHNaananQKEKYEADLKKE--IKKLQRLRDQIKTWVASNEIKDKRQLVEN 80
Cdd:PRK03918  449 HRKELLEEYTAELKRIEKELKEIEEKERKLRK-----ELRELEKVLKKEseLIKLKELAEQLKELEEKLKKYNLEELEKK 523

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  81 RKLIETQMERF-------KIVERE-TKTKAYSKEGLGLAQKVDPAQREKEEvgnwLTNTIDTLNMQ-VDQFESEVESLSV 151
Cdd:PRK03918  524 AEEYEKLKEKLiklkgeiKSLKKElEKLEELKKKLAELEKKLDELEEELAE----LLKELEELGFEsVEELEERLKELEP 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 152 QTRK-------KKGDKEKQDRIEELKRFIEKHRYHIRMLETILRMLDNDtlpVDSIRKIKDDVEY------YMDSSQ--- 215
Cdd:PRK03918  600 FYNEylelkdaEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKE---LEELEKKYSEEEYeelreeYLELSRela 676

                         250       260
                  ....*....|....*....|...
gi 1158912424 216 --DPDFEENEFLYDDL--DLEEL 234
Cdd:PRK03918  677 glRAELEELEKRREEIkkTLEKL 699
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
5-202 2.25e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 2.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   5 RKLQGEIDRCLKKVTEGVEQFEDIWQKLHNA----ANANQKEKYEADLKKEIKKLQRLRDQIKTWVasneikdkrQLVEN 80
Cdd:PRK03918  296 IKLSEFYEEYLDELREIEKRLSRLEEEINGIeeriKELEEKEERLEELKKKLKELEKRLEELEERH---------ELYEE 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  81 RKLIETQMERFKivereTKTKAYSKEglGLAQKVDPAQREKEEVgnwlTNTIDTLNMQVDQFESEVESLS---VQTRKKK 157
Cdd:PRK03918  367 AKAKKEELERLK-----KRLTGLTPE--KLEKELEELEKAKEEI----EEEISKITARIGELKKEIKELKkaiEELKKAK 435

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1158912424 158 G----------DKEKQDRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRK 202
Cdd:PRK03918  436 GkcpvcgreltEEHRKELLEEYTAELKRIEKELKEIEEKERKLRKELRELEKVLK 490
PHA03247 PHA03247
large tegument protein UL36; Provisional
 574-842 2.55e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.31  E-value: 2.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  574 PPLVSPSPIGggLAPGSSLGAIGSIGGNSGSGAPSNSLGIGGGNAAIARPPSGQKQNGSTSYSAVVAD---STPDSALNI 650
Cdd:PHA03247  2713 HALVSATPLP--PGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGpprRLTRPAVAS 2790

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  651 ANQLQSSQPSSLISTTNQLKDSGPSLLGSMTLPTSTPSPSYIESKPSGSSMLNGPL-SYTQASESMKPQEPLS---TVKS 726
Cdd:PHA03247  2791 LSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPpPSLPLGGSVAPGGDVRrrpPSRS 2870

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  727 MAEQAALGS---AMEGELPPLHLTTDIF---PSTTAPPGPPSAPQQPSLSEVSIPPSLGVCPLGPVPLSKDQLYQQAMQE 800
Cdd:PHA03247  2871 PAAKPAAPArppVRRLARPAVSRSTESFalpPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPA 2950

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1158912424  801 SAwthmPHPSDSERIRQYLMRNPCPTLPFHHQVPPPhSDSVE 842
Cdd:PHA03247  2951 GA----GEPSGAVPQPWLGALVPGRVAVPRFRVPQP-APSRE 2987
COG4487 COG4487
Uncharacterized conserved protein, contains DUF2130 domain [Function unknown];
36-175 3.58e-04

Uncharacterized conserved protein, contains DUF2130 domain [Function unknown];


Pssm-ID: 443580 [Multi-domain]  Cd Length: 425  Bit Score: 44.17  E-value: 3.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  36 ANANQKEKYEADLKKEIKKLQRLRDQIKtwvasNEIKDKRQLVENRKLIETQMERFKIVERETK---TKAYSKEGLGLAQ 112
Cdd:COG4487    52 AEAKAKAQLQEQVAEKDAEIAELRARLE-----AEERKKALAVAEEKEKELAALQEALAEKDAKlaeLQAKELELLKKER 126

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1158912424 113 KVDPAQREKE-EVGNWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDKE---KQDRIEELKRFIEK 175
Cdd:COG4487   127 ELEDAKREAElTVEKERDEELDELKEKLKKEEEEKQLAEKSLKVAEYEKQlkdMQEQIEELKRKKEQ 193
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 7-204 4.74e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 44.19  E-value: 4.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424    7 LQGEIDRCLKKVTEGVEQFEDIwqklhnAANANQKEKYEADLKKEIKKLQRLRDQIktWVASNEIKDKRQLVENRK-LIE 85
Cdd:pfam02463  140 QGGKIEIIAMMKPERRLEIEEE------AAGSRLKRKKKEALKKLIEETENLAELI--IDLEELKLQELKLKEQAKkALE 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   86 TQMERFKIVERETKTKAYSKEGLglaqkvdpaqrekeeVGNWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDKEKQDR 165
Cdd:pfam02463  212 YYQLKEKLELEEEYLLYLDYLKL---------------NEERIDLLQELLRDEQEEIESSKQEIEKEEEKLAQVLKENKE 276

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1158912424  166 IEELKRFIEKHRYHIRMLETILR--MLDNDTLPVDSIRKIK 204
Cdd:pfam02463  277 EEKEKKLQEEELKLLAKEEEELKseLLKLERRKVDDEEKLK 317
fliJ PRK07720
flagellar biosynthesis chaperone FliJ;
10-101 2.32e-03

flagellar biosynthesis chaperone FliJ;


Pssm-ID: 181091 [Multi-domain]  Cd Length: 146  Bit Score: 39.28  E-value: 2.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  10 EIDRCLKKVTEGVEQFEDIWQKLHNaaNANQKEKYEADLKKEIKK----------------LQRLRD--QIKTWVASNEI 71
Cdd:PRK07720   17 EKEKALGEYEEAVSRFEQVAEKLYE--LLKQKEDLEQAKEEKLQSglsiqeirhyqqfvtnLERTIDhyQLLVMQAREQM 94

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1158912424  72 KDK-RQLVEN-------RKLIETQMERFKIVERETKTK 101
Cdd:PRK07720   95 NRKqQDLTEKnievkkyEKMKEKKQEMFALEEKAAEMK 132
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
41-175 3.37e-03

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


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 40.66  E-value: 3.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  41 KEKYEaDLKKEIKKLQRLRD----QIKTWVAS--NEIKDKRQLVE-NRKLIEtqmERFKIVE--RETKTK--AYSKEGLG 109
Cdd:COG1340    14 EEKIE-ELREEIEELKEKRDelneELKELAEKrdELNAQVKELREeAQELRE---KRDELNEkvKELKEErdELNEKLNE 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 110 LAQKVDPAQREKEEvgnwltntIDTLNMQVDQFESEVESL--SVQTRKKKGDKEKQ--DRIEELKRFIEK 175
Cdd:COG1340    90 LREELDELRKELAE--------LNKAGGSIDKLRKEIERLewRQQTEVLSPEEEKElvEKIKELEKELEK 151
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 37-208 4.42e-03

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: 40.77  E-value: 4.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  37 NANQKEKYEADLKKEIKKLQRLRDQIKtwvasNEIKDKRQLVE-----NRKLIEtqmerfKIVERETKTKAYSKEGLGLA 111
Cdd:TIGR04523 118 QKNKLEVELNKLEKQKKENKKNIDKFL-----TEIKKKEKELEklnnkYNDLKK------QKEELENELNLLEKEKLNIQ 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 112 QKVDPAqREKEEVGNWLTNTIDTLNMQVDQFESEVESLSVQTRK-KKGDKEKQDRIEELKRFIEKHRYHIRML----ETI 186
Cdd:TIGR04523 187 KNIDKI-KNKLLKLELLLSNLKKKIQKNKSLESQISELKKQNNQlKDNIEKKQQEINEKTTEISNTQTQLNQLkdeqNKI 265

                         170       180
                  ....*....|....*....|..
gi 1158912424 187 LRMLDNDTLPVDSIRKIKDDVE 208
Cdd:TIGR04523 266 KKQLSEKQKELEQNNKKIKELE 287
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
5-204 4.57e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.82  E-value: 4.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   5 RKLQGEidrcLKKVTEGVEQFEDIWQKLHNAANanQKEKYEADLKKEIKKLQRLRDQIKtwvasnEIKDK-RQLVENRKL 83
Cdd:PRK03918  217 PELREE----LEKLEKEVKELEELKEEIEELEK--ELESLEGSKRKLEEKIRELEERIE------ELKKEiEELEEKVKE 284

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  84 IEtqmerfkivERETKTKAYSKEGLGLAQKVDPAQREKEEVGNWltntidtlnmqvdqfESEVESlsVQTRKKKGDkEKQ 163
Cdd:PRK03918  285 LK---------ELKEKAEEYIKLSEFYEEYLDELREIEKRLSRL---------------EEEING--IEERIKELE-EKE 337

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1158912424 164 DRIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIK 204
Cdd:PRK03918  338 ERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLK 378
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
16-233 5.27e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 40.27  E-value: 5.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  16 KKVTEGVEQFEDIWQKLHNAAN-----ANQKEKYEADLKKEIKKLQRLRDQIKTW------------VASNEIKDKRQLV 78
Cdd:COG4372    31 EQLRKALFELDKLQEELEQLREeleqaREELEQLEEELEQARSELEQLEEELEELneqlqaaqaelaQAQEELESLQEEA 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  79 EN--RKLIETQMERFKIVERETKTKAYSKEglgLAQKVDPAQREKEEvgnwLTNTIDTLNMQVDQFESEVESLSVQTRKK 156
Cdd:COG4372   111 EElqEELEELQKERQDLEQQRKQLEAQIAE---LQSEIAEREEELKE----LEEQLESLQEELAALEQELQALSEAEAEQ 183

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1158912424 157 KGDKEKQD--RIEELKRFIEKHRYHIRMLETILRMLDNDTLPVDSIRKIKDDVEYYMDSSQDPDFEENEFLYDDLDLEE 233
Cdd:COG4372   184 ALDELLKEanRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEE 262
mukB PRK04863
chromosome partition protein MukB;
42-193 5.86e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 40.71  E-value: 5.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424   42 EKYeADLKKEIKKLQRLRDQIKTWVASN-----------EIKDKRQlveNRKLIETQMERFKIVERETKTKA-YSKEGLG 109
Cdd:PRK04863   800 ERY-ATLSFDVQKLQRLHQAFSRFIGSHlavafeadpeaELRQLNR---RRVELERALADHESQEQQQRSQLeQAKEGLS 875

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424  110 LAQKVDPaqrekeevgnwLTNTIDtlnmqVDQFESEVESLsvqtrkkkgdKEKQDRIEELKRFIEKHRYHIRMLETILRM 189
Cdd:PRK04863   876 ALNRLLP-----------RLNLLA-----DETLADRVEEI----------REQLDEAEEAKRFVQQHGNALAQLEPIVSV 929


                   ....
gi 1158912424  190 LDND 193
Cdd:PRK04863   930 LQSD 933
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 620-838 8.79e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 40.14  E-value: 8.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 620 IARPPSGQKQNGSTSYSAVVADSTpdsalnianqlqSSQPSSlISTTNqlKDSGPSLlgsmtlptstPSPSYIESKPSGS 699
Cdd:pfam03154 107 ISRPNSPSEGEGESSDGRSVNDEG------------SSDPKD-IDQDN--RSTSPSI----------PSPQDNESDSDSS 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1158912424 700 smlngplsytqASESMKPQEPLstvksmAEQAALGSAMEGELPPLHLTTdiFPSTTAPPGPPSAPQQPSlSEVSIPPSLG 779
Cdd:pfam03154 162 -----------AQQQILQTQPP------VLQAQSGAASPPSPPPPGTTQ--AATAGPTPSAPSVPPQGS-PATSQPPNQT 221

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1158912424 780 VCPLGPVPL--SKDQLYQQAM--QESAWTHMPHPSDSERIRQylmrNPCPTLPFHHQVPP-PHS 838
Cdd:pfam03154 222 QSTAAPHTLiqQTPTLHPQRLpsPHPPLQPMTQPPPPSQVSP----QPLPQPSLHGQMPPmPHS 281
 
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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