NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2181691386|ref|WP_235378356|]
View 

nuclease-related domain-containing protein [Pseudoalteromonas sp. Cn5-37]

Protein Classification

nuclease-related domain-containing protein( domain architecture ID 10551559)

nuclease-related domain (NERD)-containing protein has distant similarity to endonucleases and DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

CATH:  3.40.960.10
Gene Ontology:  GO:0003677|GO:0004519
PubMed:  15055202|16011798|15972856
SCOP:  3000104

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 7-65 2.19e-05

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: 42.82  E-value: 2.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2181691386   7 YGFILIESKSITGEVAINGHQEWsrsYRGKWQGMPSPIKQVELQQALLKSLVTSNAEQL 65
Cdd:pfam08378  44 NGIFVIEVKNYSGWIFGDENGQW---TQKIGNGFPNPLEQNRRHAKALKKLLKAGGPRV 99
YrdD super family cl33943
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 154-261 6.24e-03

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: 37.92  E-value: 6.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181691386 154 LLAQNIKSTEQPVNDESPVTLNEPESIYKSEVKEEVLLSTEEPNVIHLKCKNCsnEHTLEARSGRYGYYVNCSN---CNT 230
Cdd:COG0551   540 ALLDKEEGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGEKCPKC--GKPLVIKKGRYGKFLGCSNypeCKY 617

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2181691386 231 NTPMK------APCIKCNDQNTKVSKRKDTYSLICDG 261
Cdd:COG0551   618 TKPLPkpevtgVKCPKCGKKLVLRKSKKGKVFYGCSN 654
 
Name Accession Description Interval E-value
NERD pfam08378
Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial ...
 7-65 2.19e-05

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: 42.82  E-value: 2.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2181691386   7 YGFILIESKSITGEVAINGHQEWsrsYRGKWQGMPSPIKQVELQQALLKSLVTSNAEQL 65
Cdd:pfam08378  44 NGIFVIEVKNYSGWIFGDENGQW---TQKIGNGFPNPLEQNRRHAKALKKLLKAGGPRV 99
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 154-261 6.24e-03

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: 37.92  E-value: 6.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181691386 154 LLAQNIKSTEQPVNDESPVTLNEPESIYKSEVKEEVLLSTEEPNVIHLKCKNCsnEHTLEARSGRYGYYVNCSN---CNT 230
Cdd:COG0551   540 ALLDKEEGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGEKCPKC--GKPLVIKKGRYGKFLGCSNypeCKY 617

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2181691386 231 NTPMK------APCIKCNDQNTKVSKRKDTYSLICDG 261
Cdd:COG0551   618 TKPLPkpevtgVKCPKCGKKLVLRKSKKGKVFYGCSN 654
PRK06599 PRK06599
DNA topoisomerase I; Validated
 183-269 6.33e-03

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 37.92  E-value: 6.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181691386 183 SEVKEEVLLSTEEPNVIHLKCKNCsNEHTLEARSGRYGYYVNCSN---CNTNTPMKAPcikcNDQNTKVSKRKDTysLIC 259
Cdd:PRK06599  568 EKVEEDVRTEKVTQEETDETCPKC-GGGPLVLKLGKNGKFLGCSGypeCKYTKNITRD----EDEPIEEEEIVEE--EKC 640

                          90
                  ....*....|
gi 2181691386 260 DGCGNKALIK 269
Cdd:PRK06599  641 PKCGGPLVLK 650
 
Name Accession Description Interval E-value
NERD pfam08378
Nuclease-related domain; The nuclease-related domain (NERD) is found in a range of bacterial ...
 7-65 2.19e-05

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: 42.82  E-value: 2.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2181691386   7 YGFILIESKSITGEVAINGHQEWsrsYRGKWQGMPSPIKQVELQQALLKSLVTSNAEQL 65
Cdd:pfam08378  44 NGIFVIEVKNYSGWIFGDENGQW---TQKIGNGFPNPLEQNRRHAKALKKLLKAGGPRV 99
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 154-261 6.24e-03

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: 37.92  E-value: 6.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181691386 154 LLAQNIKSTEQPVNDESPVTLNEPESIYKSEVKEEVLLSTEEPNVIHLKCKNCsnEHTLEARSGRYGYYVNCSN---CNT 230
Cdd:COG0551   540 ALLDKEEGKEDKVVEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGEKCPKC--GKPLVIKKGRYGKFLGCSNypeCKY 617

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2181691386 231 NTPMK------APCIKCNDQNTKVSKRKDTYSLICDG 261
Cdd:COG0551   618 TKPLPkpevtgVKCPKCGKKLVLRKSKKGKVFYGCSN 654
PRK06599 PRK06599
DNA topoisomerase I; Validated
 183-269 6.33e-03

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 37.92  E-value: 6.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181691386 183 SEVKEEVLLSTEEPNVIHLKCKNCsNEHTLEARSGRYGYYVNCSN---CNTNTPMKAPcikcNDQNTKVSKRKDTysLIC 259
Cdd:PRK06599  568 EKVEEDVRTEKVTQEETDETCPKC-GGGPLVLKLGKNGKFLGCSGypeCKYTKNITRD----EDEPIEEEEIVEE--EKC 640

                          90
                  ....*....|
gi 2181691386 260 DGCGNKALIK 269
Cdd:PRK06599  641 PKCGGPLVLK 650
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH