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Conserved domains on  [gi|333804239|dbj|BAK25446|]
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60 kDa protein [Porphyromonas gingivalis TDC60]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OmpA super family cl34510
Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall ...
 204-290 5.03e-06

Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall/membrane/envelope biogenesis];


The actual alignment was detected with superfamily member COG2885:

Pssm-ID: 442131 [Multi-domain]  Cd Length: 294  Bit Score: 48.24  E-value: 5.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 204 YQVGKYVVLPQFDgnpAELARIDSKLKEIGNdsdiifEKLSMVGYASPEGGVEYNAKLSKDRAHSFASYLVNKyPILKSR 283
Cdd:COG2885  191 FDFDSAELTPEAK---AALDELAALLKENPD------LRIEIEGHTDSRGSDAYNLALSERRAEAVKDYLVSK-GIPASR 260


                 ....*..
gi 333804239 284 FEYDWKG 290
Cdd:COG2885  261 ITAVGYG 267
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 376-488 3.33e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 43.64  E-value: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 376 RLSLAEVYAVAQSYPEGsherYETWTIAEKTFPKAIEPTANAAIIDLRAGRYPQALARL----EARKSEPKLWMLLGLAY 451
Cdd:COG4783    7 LYALAQALLLAGDYDEA----EALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLhealELDPDEPEARLNLGLAL 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 333804239 452 AYSEKWAEAESYLTRAAQQ--GRPGAQHNLNELRRYMQD 488
Cdd:COG4783   83 LKAGDYDEALALLEKALKLdpEHPEAYLRLARAYRALGR 121
DUF3868 super family cl15216
Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides ...
 4-88 2.37e-04

Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture.


The actual alignment was detected with superfamily member pfam12984:

Pssm-ID: 432918  Cd Length: 109  Bit Score: 40.55  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239    4 SRYIILSFLFGMSTLAVTGQTHLGGIKVSEKHVVKKtGHTANVKMDLDLTAIpDMNSNLLMVVTPIIRSNTSNDQVALRP 83
Cdd:pfam12984   2 KKTFILLSLAICGLVAQAQNAYEGVISVKPHQLEVR-GDSVFVNMDIDLENV-KLKSKQMVILTPILRSQDGTELQQLPK 79


                  ....*
gi 333804239   84 FLLMG 88
Cdd:pfam12984  80 VVIKG 84
 
Name Accession Description Interval E-value
OmpA COG2885
Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall ...
 204-290 5.03e-06

Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442131 [Multi-domain]  Cd Length: 294  Bit Score: 48.24  E-value: 5.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 204 YQVGKYVVLPQFDgnpAELARIDSKLKEIGNdsdiifEKLSMVGYASPEGGVEYNAKLSKDRAHSFASYLVNKyPILKSR 283
Cdd:COG2885  191 FDFDSAELTPEAK---AALDELAALLKENPD------LRIEIEGHTDSRGSDAYNLALSERRAEAVKDYLVSK-GIPASR 260


                 ....*..
gi 333804239 284 FEYDWKG 290
Cdd:COG2885  261 ITAVGYG 267
OmpA_C-like cd07185
Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; ...
 207-292 1.21e-05

Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.


Pssm-ID: 143586 [Multi-domain]  Cd Length: 106  Bit Score: 44.08  E-value: 1.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 207 GKYVVLPQFDgnpAELARIDSKLKEIGNdsdiifEKLSMVGYASPEGGVEYNAKLSKDRAHSFASYLVNKYpILKSRFEY 286
Cdd:cd07185    9 GSAELTPEAK---PLLDKLAEVLKKNPD------AKIRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKG-VDASRITA 78


                 ....*.
gi 333804239 287 DWKGQD 292
Cdd:cd07185   79 VGYGES 84
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 376-488 3.33e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 43.64  E-value: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 376 RLSLAEVYAVAQSYPEGsherYETWTIAEKTFPKAIEPTANAAIIDLRAGRYPQALARL----EARKSEPKLWMLLGLAY 451
Cdd:COG4783    7 LYALAQALLLAGDYDEA----EALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLhealELDPDEPEARLNLGLAL 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 333804239 452 AYSEKWAEAESYLTRAAQQ--GRPGAQHNLNELRRYMQD 488
Cdd:COG4783   83 LKAGDYDEALALLEKALKLdpEHPEAYLRLARAYRALGR 121
DUF3868 pfam12984
Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides ...
 4-88 2.37e-04

Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture.


Pssm-ID: 432918  Cd Length: 109  Bit Score: 40.55  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239    4 SRYIILSFLFGMSTLAVTGQTHLGGIKVSEKHVVKKtGHTANVKMDLDLTAIpDMNSNLLMVVTPIIRSNTSNDQVALRP 83
Cdd:pfam12984   2 KKTFILLSLAICGLVAQAQNAYEGVISVKPHQLEVR-GDSVFVNMDIDLENV-KLKSKQMVILTPILRSQDGTELQQLPK 79


                  ....*
gi 333804239   84 FLLMG 88
Cdd:pfam12984  80 VVIKG 84
OmpA pfam00691
OmpA family; The Pfam entry also includes MotB and related proteins which are not included in ...
 220-276 1.03e-03

OmpA family; The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.


Pssm-ID: 425825 [Multi-domain]  Cd Length: 95  Bit Score: 38.50  E-value: 1.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 333804239  220 AELARIDSKLKEIGNDSDIIFEklsmvGYASPEGGVEYNAKLSKDRAHSFASYLVNK 276
Cdd:pfam00691  14 ATLDEIADLLKFPELKNTITIE-----GHTDTVGSAAYNWELSQRRAEAVRRYLVNF 65
 
Name Accession Description Interval E-value
OmpA COG2885
Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall ...
 204-290 5.03e-06

Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442131 [Multi-domain]  Cd Length: 294  Bit Score: 48.24  E-value: 5.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 204 YQVGKYVVLPQFDgnpAELARIDSKLKEIGNdsdiifEKLSMVGYASPEGGVEYNAKLSKDRAHSFASYLVNKyPILKSR 283
Cdd:COG2885  191 FDFDSAELTPEAK---AALDELAALLKENPD------LRIEIEGHTDSRGSDAYNLALSERRAEAVKDYLVSK-GIPASR 260


                 ....*..
gi 333804239 284 FEYDWKG 290
Cdd:COG2885  261 ITAVGYG 267
OmpA_C-like cd07185
Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; ...
 207-292 1.21e-05

Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.


Pssm-ID: 143586 [Multi-domain]  Cd Length: 106  Bit Score: 44.08  E-value: 1.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 207 GKYVVLPQFDgnpAELARIDSKLKEIGNdsdiifEKLSMVGYASPEGGVEYNAKLSKDRAHSFASYLVNKYpILKSRFEY 286
Cdd:cd07185    9 GSAELTPEAK---PLLDKLAEVLKKNPD------AKIRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKG-VDASRITA 78


                 ....*.
gi 333804239 287 DWKGQD 292
Cdd:cd07185   79 VGYGES 84
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 376-488 3.33e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 43.64  E-value: 3.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 376 RLSLAEVYAVAQSYPEGsherYETWTIAEKTFPKAIEPTANAAIIDLRAGRYPQALARL----EARKSEPKLWMLLGLAY 451
Cdd:COG4783    7 LYALAQALLLAGDYDEA----EALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLhealELDPDEPEARLNLGLAL 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 333804239 452 AYSEKWAEAESYLTRAAQQ--GRPGAQHNLNELRRYMQD 488
Cdd:COG4783   83 LKAGDYDEALALLEKALKLdpEHPEAYLRLARAYRALGR 121
DUF3868 pfam12984
Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides ...
 4-88 2.37e-04

Domain of unknown function, B. Theta Gene description (DUF3868); Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture.


Pssm-ID: 432918  Cd Length: 109  Bit Score: 40.55  E-value: 2.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239    4 SRYIILSFLFGMSTLAVTGQTHLGGIKVSEKHVVKKtGHTANVKMDLDLTAIpDMNSNLLMVVTPIIRSNTSNDQVALRP 83
Cdd:pfam12984   2 KKTFILLSLAICGLVAQAQNAYEGVISVKPHQLEVR-GDSVFVNMDIDLENV-KLKSKQMVILTPILRSQDGTELQQLPK 79


                  ....*
gi 333804239   84 FLLMG 88
Cdd:pfam12984  80 VVIKG 84
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 363-470 1.01e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 39.40  E-value: 1.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 363 LDKAREIIKTHPS----RLSLAEVYAVAQSYPEGShERYETwtiAEKTFPKAIEPTANAAIIDLRAGRYPQALA----RL 434
Cdd:COG4783   24 EALLEKALELDPDnpeaFALLGEILLQLGDLDEAI-VLLHE---ALELDPDEPEARLNLGLALLKAGDYDEALAllekAL 99

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 333804239 435 EARKSEPKLWMLLGLAYAYSEKWAEAESYLTRAAQQ 470
Cdd:COG4783  100 KLDPEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
OmpA pfam00691
OmpA family; The Pfam entry also includes MotB and related proteins which are not included in ...
 220-276 1.03e-03

OmpA family; The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.


Pssm-ID: 425825 [Multi-domain]  Cd Length: 95  Bit Score: 38.50  E-value: 1.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 333804239  220 AELARIDSKLKEIGNDSDIIFEklsmvGYASPEGGVEYNAKLSKDRAHSFASYLVNK 276
Cdd:pfam00691  14 ATLDEIADLLKFPELKNTITIE-----GHTDTVGSAAYNWELSQRRAEAVRRYLVNF 65
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 363-476 1.17e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.22  E-value: 1.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 363 LDKAREIIKTHP----SRLSLAEVYAVAQSYPEgSHERYETwtiAEKTFPKAIEPTANAAIIDLRAGRYPQALARLE-AR 437
Cdd:COG4235    3 IARLRQALAANPndaeGWLLLGRAYLRLGRYDE-ALAAYEK---ALRLDPDNADALLDLAEALLAAGDTEEAEELLErAL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 333804239 438 KSEP---KLWMLLGLAYAYSEKWAEAESYLTRAAQQGRPGAQ 476
Cdd:COG4235   79 ALDPdnpEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAP 120
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 361-488 2.10e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 38.79  E-value: 2.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 361 FELDKAREIIKTHPSRLSLAEVYAVAQSYPEGSHERYETWTIAEKTFPKAIEPTANAAIIDLRAGRYPQALAR----LEA 436
Cdd:COG5010    4 LEGFDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALleqaLQL 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 333804239 437 RKSEPKLWMLLGLAYAYSEKWAEAESYLTRAAQ--QGRPGAQHNLNELRRYMQD 488
Cdd:COG5010   84 DPNNPELYYNLALLYSRSGDKDEAKEYYEKALAlsPDNPNAYSNLAALLLSLGQ 137
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 417-476 3.16e-03

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 39.51  E-value: 3.16e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 333804239 417 AAIIDLRAGRYPQALARLEAR-KSEPK---LWMLLGLAYAYSEKWAEAESYLTRAAQQgRPGAQ 476
Cdd:COG3071  230 RLYGRLQGGDPAKQLKRAEKWlKKHPNdpdLLLALGRLCLRNQLWGKAREYLEAALAL-RPSAE 292
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 362-470 6.98e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 38.56  E-value: 6.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333804239 362 ELDKA----REIIKTHP----SRLSLAEVYAVAQSYPEGsherYETWTIAEKTFPKAIEPTANAAIIDLRAGRYPQALAR 433
Cdd:COG2956   91 LLDRAeellEKLLELDPddaeALRLLAEIYEQEGDWEKA----IEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEA 166

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 333804239 434 LE-ARKSEPKL---WMLLGLAYAYSEKWAEAESYLTRAAQQ 470
Cdd:COG2956  167 LEkALKLDPDCaraLLLLAELYLEQGDYEEAIAALERALEQ 207
 
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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