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Conserved domains on  [gi|489182353|ref|WP_003091802|]
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MULTISPECIES: transcriptional regulator AmrZ [Pseudomonas]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arc super family cl46767
Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor ...
 13-62 4.04e-18

Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove.


The actual alignment was detected with superfamily member pfam03869:

Pssm-ID: 481107  Cd Length: 50  Bit Score: 71.48  E-value: 4.04e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489182353   13 SRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALQD 62
Cdd:pfam03869   1 SRTAPKFVVRLPEEVREQIAEVAESNGRS*NSEIIQRVEQSLLKEGALQD 50
 
Name Accession Description Interval E-value
Arc pfam03869
Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor ...
 13-62 4.04e-18

Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove.


Pssm-ID: 397789  Cd Length: 50  Bit Score: 71.48  E-value: 4.04e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489182353   13 SRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALQD 62
Cdd:pfam03869   1 SRTAPKFVVRLPEEVREQIAEVAESNGRS*NSEIIQRVEQSLLKEGALQD 50
HicB COG4226
Predicted nuclease of the RNAse H fold, HicB family [General function prediction only];
18-54 5.00e-03

Predicted nuclease of the RNAse H fold, HicB family [General function prediction only];


Pssm-ID: 443370 [Multi-domain]  Cd Length: 110  Bit Score: 33.62  E-value: 5.00e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 489182353  18 KFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSL 54
Cdd:COG4226   71 KFNVRIPPELHRALAIAAAEEGVSLNQWVVEALSEAL 107
mnt PHA01513
Mnt
 14-83 5.03e-03

Mnt


Pssm-ID: 164855 [Multi-domain]  Cd Length: 82  Bit Score: 33.42  E-value: 5.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182353  14 RTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALqdnLGVRLDSPELSLHERELLQR 83
Cdd:PHA01513   3 RDDPQFNLRLPYELKEKLKQRAKANGRSLNAELVQIVQDALSKPSPV---TGYRDDAERLADEQSELVKK 69
 
Name Accession Description Interval E-value
Arc pfam03869
Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor ...
 13-62 4.04e-18

Arc-like DNA binding domain; Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove.


Pssm-ID: 397789  Cd Length: 50  Bit Score: 71.48  E-value: 4.04e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489182353   13 SRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALQD 62
Cdd:pfam03869   1 SRTAPKFVVRLPEEVREQIAEVAESNGRS*NSEIIQRVEQSLLKEGALQD 50
HicB COG4226
Predicted nuclease of the RNAse H fold, HicB family [General function prediction only];
18-54 5.00e-03

Predicted nuclease of the RNAse H fold, HicB family [General function prediction only];


Pssm-ID: 443370 [Multi-domain]  Cd Length: 110  Bit Score: 33.62  E-value: 5.00e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 489182353  18 KFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSL 54
Cdd:COG4226   71 KFNVRIPPELHRALAIAAAEEGVSLNQWVVEALSEAL 107
mnt PHA01513
Mnt
 14-83 5.03e-03

Mnt


Pssm-ID: 164855 [Multi-domain]  Cd Length: 82  Bit Score: 33.42  E-value: 5.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182353  14 RTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGALqdnLGVRLDSPELSLHERELLQR 83
Cdd:PHA01513   3 RDDPQFNLRLPYELKEKLKQRAKANGRSLNAELVQIVQDALSKPSPV---TGYRDDAERLADEQSELVKK 69
 
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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