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Conserved domains on  [gi|1763716485|gb|KAB5024088|]
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topoisomerase I [Bacteroides thetaiotaomicron]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NERD pfam08378
Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial ...
 24-134 6.73e-28

Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.


:

Pssm-ID: 462454  Cd Length: 108  Bit Score: 102.53  E-value: 6.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1763716485  24 KGKYSEKLVNNKIqELPEEYVIFNDLLFESNGYSTQIDHIVVSPYGVFVIETKGYKGWILGGENsEYWTQTIyksKHQFY 103
Cdd:pfam08378   1 KGAKGERRVAEYL-KLPGGYIVLHNLRLPPGTGTAEIDHLVISPNGIFVIEVKNYSGWIFGDEN-GQWTQKI---GNGFP 75

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1763716485 104 NPIKQNAGHVRFLRHLLRCSV-DIPFIPIVVF 134
Cdd:pfam08378  76 NPLEQNRRHAKALKKLLKAGGpRVPVESVVVF 107
zf-C4_Topoisom pfam01396
Topoisomerase DNA binding C4 zinc finger;
211-245 5.29e-16

Topoisomerase DNA binding C4 zinc finger;


:

Pssm-ID: 307520 [Multi-domain]  Cd Length: 39  Bit Score: 69.59  E-value: 5.29e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1763716485 211 QGICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:pfam01396   1 GGKCPKCGGDLVLKRGRFGKFVGCSNYPECRFTRP 35
YrdD super family cl33943
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 170-245 8.82e-14

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0551:

Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 70.28  E-value: 8.82e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1763716485 170 ETTDWIVRTINQNRIIADKEKLKQHKHNAKARQYRSSDLINQgICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:COG0551   546 EGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGE-KCPKCGKPLVIKKGRYGKFLGCSNYPECKYTKP 620
 
Name Accession Description Interval E-value
NERD pfam08378
Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial ...
 24-134 6.73e-28

Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.


Pssm-ID: 462454  Cd Length: 108  Bit Score: 102.53  E-value: 6.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1763716485  24 KGKYSEKLVNNKIqELPEEYVIFNDLLFESNGYSTQIDHIVVSPYGVFVIETKGYKGWILGGENsEYWTQTIyksKHQFY 103
Cdd:pfam08378   1 KGAKGERRVAEYL-KLPGGYIVLHNLRLPPGTGTAEIDHLVISPNGIFVIEVKNYSGWIFGDEN-GQWTQKI---GNGFP 75

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1763716485 104 NPIKQNAGHVRFLRHLLRCSV-DIPFIPIVVF 134
Cdd:pfam08378  76 NPLEQNRRHAKALKKLLKAGGpRVPVESVVVF 107
zf-C4_Topoisom pfam01396
Topoisomerase DNA binding C4 zinc finger;
211-245 5.29e-16

Topoisomerase DNA binding C4 zinc finger;


Pssm-ID: 307520 [Multi-domain]  Cd Length: 39  Bit Score: 69.59  E-value: 5.29e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1763716485 211 QGICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:pfam01396   1 GGKCPKCGGDLVLKRGRFGKFVGCSNYPECRFTRP 35
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 170-245 8.82e-14

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 70.28  E-value: 8.82e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1763716485 170 ETTDWIVRTINQNRIIADKEKLKQHKHNAKARQYRSSDLINQgICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:COG0551   546 EGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGE-KCPKCGKPLVIKKGRYGKFLGCSNYPECKYTKP 620
PRK07219 PRK07219
DNA topoisomerase I; Validated
 212-244 1.27e-13

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 70.03  E-value: 1.27e-13
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1763716485 212 GICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTL 244
Cdd:PRK07219  689 GPCPKCGGELAIKQLKYGSFLGCTNYPKCKYTL 721
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 214-245 6.05e-12

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 64.89  E-value: 6.05e-12
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1763716485 214 CPQCGGQLLLRHGKYG-TFYGCSNYPKCKFTLN 245
Cdd:COG0551   631 CPKCGKKLVLRKSKKGkVFYGCSNYPKCKFTEW 663
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
 200-240 6.43e-07

DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273420 [Multi-domain]  Cd Length: 618  Bit Score: 49.83  E-value: 6.43e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1763716485 200 ARQYRSSDLInqGICPQCGGQLLLRHGKYGTFYGCSNYPKC 240
Cdd:TIGR01057 580 GKSLGSVEVV--GKCPKCGGKLVSKYAKKGRFVGCSNYPEC 618
 
Name Accession Description Interval E-value
NERD pfam08378
Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial ...
 24-134 6.73e-28

Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.


Pssm-ID: 462454  Cd Length: 108  Bit Score: 102.53  E-value: 6.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1763716485  24 KGKYSEKLVNNKIqELPEEYVIFNDLLFESNGYSTQIDHIVVSPYGVFVIETKGYKGWILGGENsEYWTQTIyksKHQFY 103
Cdd:pfam08378   1 KGAKGERRVAEYL-KLPGGYIVLHNLRLPPGTGTAEIDHLVISPNGIFVIEVKNYSGWIFGDEN-GQWTQKI---GNGFP 75

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1763716485 104 NPIKQNAGHVRFLRHLLRCSV-DIPFIPIVVF 134
Cdd:pfam08378  76 NPLEQNRRHAKALKKLLKAGGpRVPVESVVVF 107
zf-C4_Topoisom pfam01396
Topoisomerase DNA binding C4 zinc finger;
211-245 5.29e-16

Topoisomerase DNA binding C4 zinc finger;


Pssm-ID: 307520 [Multi-domain]  Cd Length: 39  Bit Score: 69.59  E-value: 5.29e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1763716485 211 QGICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:pfam01396   1 GGKCPKCGGDLVLKRGRFGKFVGCSNYPECRFTRP 35
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 170-245 8.82e-14

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 70.28  E-value: 8.82e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1763716485 170 ETTDWIVRTINQNRIIADKEKLKQHKHNAKARQYRSSDLINQgICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:COG0551   546 EGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGE-KCPKCGKPLVIKKGRYGKFLGCSNYPECKYTKP 620
PRK07219 PRK07219
DNA topoisomerase I; Validated
 212-244 1.27e-13

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 70.03  E-value: 1.27e-13
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1763716485 212 GICPQCGGQLLLRHGKYGTFYGCSNYPKCKFTL 244
Cdd:PRK07219  689 GPCPKCGGELAIKQLKYGSFLGCTNYPKCKYTL 721
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 214-245 6.05e-12

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 64.89  E-value: 6.05e-12
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1763716485 214 CPQCGGQLLLRHGKYG-TFYGCSNYPKCKFTLN 245
Cdd:COG0551   631 CPKCGKKLVLRKSKKGkVFYGCSNYPKCKFTEW 663
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 214-245 4.33e-11

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 62.53  E-value: 4.33e-11
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1763716485 214 CPQCGGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:PRK06319  648 CPLCGGEMKVRHGRFGTFLGCENYPECRGIIN 679
PRK06599 PRK06599
DNA topoisomerase I; Validated
 189-245 8.03e-10

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 58.33  E-value: 8.03e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1763716485 189 EKLKQHKHNAKARQYRSSDlinqgICPQC-GGQLLLRHGKYGTFYGCSNYPKCKFTLN 245
Cdd:PRK06599  568 EKVEEDVRTEKVTQEETDE-----TCPKCgGGPLVLKLGKNGKFLGCSGYPECKYTKN 620
PRK06599 PRK06599
DNA topoisomerase I; Validated
 214-241 1.41e-09

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 57.56  E-value: 1.41e-09
                          10        20
                  ....*....|....*....|....*...
gi 1763716485 214 CPQCGGQLLLRHGKYGTFYGCSNYPKCK 241
Cdd:PRK06599  640 CPKCGGPLVLKKGRYGKFLACSGYPECK 667
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 213-245 9.16e-08

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 52.49  E-value: 9.16e-08
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1763716485 213 ICPQCGGQLLLRHGKYGTFYGCSNY---PKCKFTLN 245
Cdd:PRK07561  589 DCPTCGRGMGIRTGKTGVFLGCSGYalkERCKTTRN 624
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
 200-240 6.43e-07

DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273420 [Multi-domain]  Cd Length: 618  Bit Score: 49.83  E-value: 6.43e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1763716485 200 ARQYRSSDLInqGICPQCGGQLLLRHGKYGTFYGCSNYPKC 240
Cdd:TIGR01057 580 GKSLGSVEVV--GKCPKCGGKLVSKYAKKGRFVGCSNYPEC 618
PRK07219 PRK07219
DNA topoisomerase I; Validated
 204-245 9.07e-07

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 49.23  E-value: 9.07e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1763716485 204 RSSDLInqGICPQCGGQLLLRHGKYGT-FYGCSNYPKCKFTLN 245
Cdd:PRK07219  597 RSLKTI--GKCPECGGDLIIIRTDKGSrFVGCSGYPDCRNTFP 637
PRK07220 PRK07220
DNA topoisomerase I; Validated
 212-244 1.08e-06

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 48.99  E-value: 1.08e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1763716485 212 GICPQCGGQLLLRHGKYGT-FYGCSNYPKCKFTL 244
Cdd:PRK07220  590 GKCPLCGSDLMVRRSKRGSrFIGCEGYPECTFSL 623
PRK07219 PRK07219
DNA topoisomerase I; Validated
 212-243 2.20e-06

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 48.07  E-value: 2.20e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1763716485 212 GICPQCGGQLLLRHGKYGTFYGCSNYPKCKFT 243
Cdd:PRK07219  734 EKCPECGLPLLRVKGGFGDELGCCNNPKCNYT 765
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 204-242 5.41e-05

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 44.07  E-value: 5.41e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1763716485 204 RSSDLINQGICPQCGGQLLLRHGKYGTFYGCSNYPKCKF 242
Cdd:PRK14973  581 RTAEELTIGPCPVCGKDLRIKHIGSSQFIGCSGYPDCTF 619
PRK07726 PRK07726
DNA topoisomerase 3;
214-241 2.16e-03

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 38.99  E-value: 2.16e-03
                          10        20
                  ....*....|....*....|....*...
gi 1763716485 214 CPQCGGQLLLRHGKYGTFYGCSNYPKCK 241
Cdd:PRK07726  613 CPDCGKPMLKVKGKNGKMLVCQDRECGK 640
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 214-245 4.32e-03

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 38.26  E-value: 4.32e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1763716485 214 CP--QCGGQLLLRHGKYG-TFYGCSNYPKCKFTLN 245
Cdd:PRK06319  696 CPaiGCTGHIVKRRSRFNkMFYSCSEYPACSVIGN 730
COG1754 COG1754
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
214-243 7.39e-03

Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];


Pssm-ID: 441360 [Multi-domain]  Cd Length: 892  Bit Score: 37.49  E-value: 7.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1763716485 214 CPQCGGQLLLRHGKYGTFYGCSNY-------PKCKFT 243
Cdd:COG1754   605 CPLGTGGLSLRVGRYGPFIECSNYeprrasiPECLAP 641
 
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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