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Conserved domains on  [gi|1859666733|ref|YP_009854911|]
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major capsid protein [Flavobacterium phage vB_FspS_lillamy9-1]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Phage_capsid super family cl46099
Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.
1-363 4.40e-13

Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.


The actual alignment was detected with superfamily member TIGR01554:

Pssm-ID: 480439 [Multi-domain]  Cd Length: 386  Bit Score: 70.07  E-value: 4.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733   1 MEEIIKELGTKIDAMKNES------VSKTELDALKEELKAIEKmattdQVETLKGNLDELAEKLVEMQKGEKVEKTLLDE 74
Cdd:TIGR01554   4 LREALAELAKELRKLTEDEklaeaeEKKEEFDALKAEIDKLEA-----EIDRLEAALDELAAKAAAPGLGGGGEEEGREA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733  75 VIENKEKI--NALAKGDKKVEVELKALSNrASIANNTEAVRLSGIGQLGVKLRALYDFFPKVQVGN-GNHNGTIAYidwd 151
Cdd:TIGR01554  79 DEEKAAFRfrNYLRGGDAAGAEERKALST-GTDSDGGYLVPEEFSTEIIELLKEYSPLRQLATVIPvSSGSITIPV---- 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 152 eDTTVRAAAIVAEGATFPESTAKFAEYTKKLQKIGDTLPVTEEFMED-EVLASSELSKFININVNTVIDTKIAVGAgGAS 230
Cdd:TIGR01554 154 -DAGTPEAGWVGEGAARPESDPTFGQVELPVKKLAAIIPISNELLDDsAVDLEAYLADELAEAFARAENAAILNGD-GTG 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 231 DIEGLYTASPAYTPVASG----ITDANIKDLVRKMRTAivktrgskYAPNFV-AANSETIDRYFLKKDGENNYMF----- 300
Cdd:TIGR01554 232 KPKGILTYAAVGKVVTTGaagtITADDLIDLIYSLDPA--------YRANAVwVMNRSTLAALRKLKDGNGRYLWqpglt 303
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1859666733 301 DSETGTIAGLTIVEDNNLAD-----NTLVVGDSRYG-TIYEKGGVVLsEGFGDGQFVADMKTIKARVRM 363
Cdd:TIGR01554 304 AGQPATLLGRPVVETEDMPDvaagaKPILFGDFSRGyLIVDRKGMTI-RVLRDPYTEKDQVGFRATKRV 371
 
Name Accession Description Interval E-value
major_cap_HK97 TIGR01554
phage major capsid protein, HK97 family; This model family represents the major capsid protein ...
1-363 4.40e-13

phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273690 [Multi-domain]  Cd Length: 386  Bit Score: 70.07  E-value: 4.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733   1 MEEIIKELGTKIDAMKNES------VSKTELDALKEELKAIEKmattdQVETLKGNLDELAEKLVEMQKGEKVEKTLLDE 74
Cdd:TIGR01554   4 LREALAELAKELRKLTEDEklaeaeEKKEEFDALKAEIDKLEA-----EIDRLEAALDELAAKAAAPGLGGGGEEEGREA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733  75 VIENKEKI--NALAKGDKKVEVELKALSNrASIANNTEAVRLSGIGQLGVKLRALYDFFPKVQVGN-GNHNGTIAYidwd 151
Cdd:TIGR01554  79 DEEKAAFRfrNYLRGGDAAGAEERKALST-GTDSDGGYLVPEEFSTEIIELLKEYSPLRQLATVIPvSSGSITIPV---- 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 152 eDTTVRAAAIVAEGATFPESTAKFAEYTKKLQKIGDTLPVTEEFMED-EVLASSELSKFININVNTVIDTKIAVGAgGAS 230
Cdd:TIGR01554 154 -DAGTPEAGWVGEGAARPESDPTFGQVELPVKKLAAIIPISNELLDDsAVDLEAYLADELAEAFARAENAAILNGD-GTG 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 231 DIEGLYTASPAYTPVASG----ITDANIKDLVRKMRTAivktrgskYAPNFV-AANSETIDRYFLKKDGENNYMF----- 300
Cdd:TIGR01554 232 KPKGILTYAAVGKVVTTGaagtITADDLIDLIYSLDPA--------YRANAVwVMNRSTLAALRKLKDGNGRYLWqpglt 303
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1859666733 301 DSETGTIAGLTIVEDNNLAD-----NTLVVGDSRYG-TIYEKGGVVLsEGFGDGQFVADMKTIKARVRM 363
Cdd:TIGR01554 304 AGQPATLLGRPVVETEDMPDvaagaKPILFGDFSRGyLIVDRKGMTI-RVLRDPYTEKDQVGFRATKRV 371
Phage_capsid pfam05065
Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.
134-362 4.98e-08

Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.


Pssm-ID: 428287  Cd Length: 272  Bit Score: 53.54  E-value: 4.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 134 VQVGNGNHNGTIAYIDWDEDTTvraAAIVAEGATFPES-TAKFAEYTKKLQKIGDTLPVTEEFMEDevlASSELSKFINI 212
Cdd:pfam05065  21 ATVIRTSTSGTVRIPVDTGTAE---AGWVGETGAIPETdSPTFGQITLPVHKLAAWVPVSRELLDD---SAIDLEAYLAG 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 213 NVNTVIDTK----IAVGAGGASDIEGLYTASPAYTPVASGITDANIKDLVRKMRTAIVktrgSKYAPNFV-AANSETIDR 287
Cdd:pfam05065  95 RLAEAFARKedeaFLNGDGDGNQPKGILAASTGAVATGKAAAVTGTADNLIDLIYSLP----AAYRANASfVMNRSTLAA 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 288 YFLKKDGENNYMFD-----SETGTIAGLTIVEDN------NLADNTLVVGDSRYGTIYEKGGV---VLSEGFgdGQFVAD 353
Cdd:pfam05065 171 LRKLKDADGNYLWQpglaaGQPATLLGRPVVESEdmvaagAKPTGDILFGDFSAYIIVDRGGLeikRLRDPY--SFFEKD 248

                  ....*....
gi 1859666733 354 MKTIKARVR 362
Cdd:pfam05065 249 QVGFRATKR 257
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
14-104 7.47e-04

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 41.61  E-value: 7.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733  14 AMKNESVSkTELDALKEELKAIEK----------MATTDQVETLKGNLDELAEKLVEMQKGEKVEKTLLDEVIENKEKIN 83
Cdd:COG0542   403 RMEIDSKP-EELDELERRLEQLEIekealkkeqdEASFERLAELRDELAELEEELEALKARWEAEKELIEEIQELKEELE 481
                          90       100
                  ....*....|....*....|.
gi 1859666733  84 ALAKGDKKVEVELKALSNRAS 104
Cdd:COG0542   482 QRYGKIPELEKELAELEEELA 502
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
3-102 5.15e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 5.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733   3 EIIKELGTKIDAMKNESVSKTELDALKEELKAiEKMATTDQVETLKGNLDELAEKLvemqkgEKVEKtLLDEVIENKEKI 82
Cdd:PRK03918  169 EVIKEIKRRIERLEKFIKRTENIEELIKEKEK-ELEEVLREINEISSELPELREEL------EKLEK-EVKELEELKEEI 240
                          90       100
                  ....*....|....*....|
gi 1859666733  83 NALAKGDKKVEVELKALSNR 102
Cdd:PRK03918  241 EELEKELESLEGSKRKLEEK 260
 
Name Accession Description Interval E-value
major_cap_HK97 TIGR01554
phage major capsid protein, HK97 family; This model family represents the major capsid protein ...
1-363 4.40e-13

phage major capsid protein, HK97 family; This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273690 [Multi-domain]  Cd Length: 386  Bit Score: 70.07  E-value: 4.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733   1 MEEIIKELGTKIDAMKNES------VSKTELDALKEELKAIEKmattdQVETLKGNLDELAEKLVEMQKGEKVEKTLLDE 74
Cdd:TIGR01554   4 LREALAELAKELRKLTEDEklaeaeEKKEEFDALKAEIDKLEA-----EIDRLEAALDELAAKAAAPGLGGGGEEEGREA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733  75 VIENKEKI--NALAKGDKKVEVELKALSNrASIANNTEAVRLSGIGQLGVKLRALYDFFPKVQVGN-GNHNGTIAYidwd 151
Cdd:TIGR01554  79 DEEKAAFRfrNYLRGGDAAGAEERKALST-GTDSDGGYLVPEEFSTEIIELLKEYSPLRQLATVIPvSSGSITIPV---- 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 152 eDTTVRAAAIVAEGATFPESTAKFAEYTKKLQKIGDTLPVTEEFMED-EVLASSELSKFININVNTVIDTKIAVGAgGAS 230
Cdd:TIGR01554 154 -DAGTPEAGWVGEGAARPESDPTFGQVELPVKKLAAIIPISNELLDDsAVDLEAYLADELAEAFARAENAAILNGD-GTG 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 231 DIEGLYTASPAYTPVASG----ITDANIKDLVRKMRTAivktrgskYAPNFV-AANSETIDRYFLKKDGENNYMF----- 300
Cdd:TIGR01554 232 KPKGILTYAAVGKVVTTGaagtITADDLIDLIYSLDPA--------YRANAVwVMNRSTLAALRKLKDGNGRYLWqpglt 303
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1859666733 301 DSETGTIAGLTIVEDNNLAD-----NTLVVGDSRYG-TIYEKGGVVLsEGFGDGQFVADMKTIKARVRM 363
Cdd:TIGR01554 304 AGQPATLLGRPVVETEDMPDvaagaKPILFGDFSRGyLIVDRKGMTI-RVLRDPYTEKDQVGFRATKRV 371
Phage_capsid pfam05065
Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.
134-362 4.98e-08

Phage capsid family; Family of bacteriophage hypothetical proteins and capsid proteins.


Pssm-ID: 428287  Cd Length: 272  Bit Score: 53.54  E-value: 4.98e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 134 VQVGNGNHNGTIAYIDWDEDTTvraAAIVAEGATFPES-TAKFAEYTKKLQKIGDTLPVTEEFMEDevlASSELSKFINI 212
Cdd:pfam05065  21 ATVIRTSTSGTVRIPVDTGTAE---AGWVGETGAIPETdSPTFGQITLPVHKLAAWVPVSRELLDD---SAIDLEAYLAG 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 213 NVNTVIDTK----IAVGAGGASDIEGLYTASPAYTPVASGITDANIKDLVRKMRTAIVktrgSKYAPNFV-AANSETIDR 287
Cdd:pfam05065  95 RLAEAFARKedeaFLNGDGDGNQPKGILAASTGAVATGKAAAVTGTADNLIDLIYSLP----AAYRANASfVMNRSTLAA 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733 288 YFLKKDGENNYMFD-----SETGTIAGLTIVEDN------NLADNTLVVGDSRYGTIYEKGGV---VLSEGFgdGQFVAD 353
Cdd:pfam05065 171 LRKLKDADGNYLWQpglaaGQPATLLGRPVVESEdmvaagAKPTGDILFGDFSAYIIVDRGGLeikRLRDPY--SFFEKD 248

                  ....*....
gi 1859666733 354 MKTIKARVR 362
Cdd:pfam05065 249 QVGFRATKR 257
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
14-104 7.47e-04

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 41.61  E-value: 7.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733  14 AMKNESVSkTELDALKEELKAIEK----------MATTDQVETLKGNLDELAEKLVEMQKGEKVEKTLLDEVIENKEKIN 83
Cdd:COG0542   403 RMEIDSKP-EELDELERRLEQLEIekealkkeqdEASFERLAELRDELAELEEELEALKARWEAEKELIEEIQELKEELE 481
                          90       100
                  ....*....|....*....|.
gi 1859666733  84 ALAKGDKKVEVELKALSNRAS 104
Cdd:COG0542   482 QRYGKIPELEKELAELEEELA 502
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
3-102 5.15e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 5.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733   3 EIIKELGTKIDAMKNESVSKTELDALKEELKAiEKMATTDQVETLKGNLDELAEKLvemqkgEKVEKtLLDEVIENKEKI 82
Cdd:PRK03918  169 EVIKEIKRRIERLEKFIKRTENIEELIKEKEK-ELEEVLREINEISSELPELREEL------EKLEK-EVKELEELKEEI 240
                          90       100
                  ....*....|....*....|
gi 1859666733  83 NALAKGDKKVEVELKALSNR 102
Cdd:PRK03918  241 EELEKELESLEGSKRKLEEK 260
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
2-104 5.32e-03

chromosome segregation protein SMC, common bacterial 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. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 38.88  E-value: 5.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859666733    2 EEIIKELGTKIDAMKNESVSKTELDALKEELKAIEKMATTDQVETLKGNLDELAEKLVEMQKGEKVEKTLLDEVIENKEK 81
Cdd:TIGR02168  192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEE 271
                           90       100
                   ....*....|....*....|....*..
gi 1859666733   82 IN-ALAKGDKKVEV---ELKALSNRAS 104
Cdd:TIGR02168  272 LRlEVSELEEEIEElqkELYALANEIS 298
 
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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