NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|490481162|ref|WP_004351484|]
View 

MULTISPECIES: RodZ family helix-turn-helix domain-containing protein [Pseudomonas]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11444431)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK10856 super family cl35960
cytoskeleton protein RodZ;
18-346 6.37e-41

cytoskeleton protein RodZ;


The actual alignment was detected with superfamily member PRK10856:

Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 145.94  E-value: 6.37e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  18 PGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENgafDKLPGH---TFSRGYIRAYAKLMGLDQAELVNSFD-HFTGTN 93
Cdd:PRK10856  15 TGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEE---DKAPADlasTFLRGYIRSYARLVHIPEEELLPGLEkQAPLRA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  94 ASGSTVQ--SLGRVaepvRLSRN---------VLRIVsllllallIGF-GYFWWQEHSARTPETAGLSLEHVEVESADGT 161
Cdd:PRK10856  92 AKVAPMQsfSLGKR----RKKRDgwlmtftwlVLFVV--------IGLtGAWWWQNHKAQQEEITTMADQSSAELSQNSG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 162 TEIH-TLDEPEDQAVIEAQKEGEQAPAEVSPEVAAQAEGAPPVASEGAQV-PAAPAQGTPAAPQQPVTAAPAGTAPAPGT 239
Cdd:PRK10856 160 QSVPlDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVvAPSQANVDTAATPAPAAPATPDGAAPLPT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 240 APAVPATaspaappapseptaapVVAGEGQGVVkvQFVADCWTQVTDANGKVLVSALKRKGDSLELAGKAPLELRLGFAR 319
Cdd:PRK10856 240 DQAGVST----------------PAADPNALVM--NFTADCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPA 301

                        330       340
                 ....*....|....*....|....*...
gi 490481162 320 GAQVSYNGQPVDVTPFVR-GETARLKVG 346
Cdd:PRK10856 302 AVQIQYQGKPVDLSRFIRtNQVARLTLN 329
 
Name Accession Description Interval E-value
PRK10856 PRK10856
cytoskeleton protein RodZ;
18-346 6.37e-41

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 145.94  E-value: 6.37e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  18 PGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENgafDKLPGH---TFSRGYIRAYAKLMGLDQAELVNSFD-HFTGTN 93
Cdd:PRK10856  15 TGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEE---DKAPADlasTFLRGYIRSYARLVHIPEEELLPGLEkQAPLRA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  94 ASGSTVQ--SLGRVaepvRLSRN---------VLRIVsllllallIGF-GYFWWQEHSARTPETAGLSLEHVEVESADGT 161
Cdd:PRK10856  92 AKVAPMQsfSLGKR----RKKRDgwlmtftwlVLFVV--------IGLtGAWWWQNHKAQQEEITTMADQSSAELSQNSG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 162 TEIH-TLDEPEDQAVIEAQKEGEQAPAEVSPEVAAQAEGAPPVASEGAQV-PAAPAQGTPAAPQQPVTAAPAGTAPAPGT 239
Cdd:PRK10856 160 QSVPlDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVvAPSQANVDTAATPAPAAPATPDGAAPLPT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 240 APAVPATaspaappapseptaapVVAGEGQGVVkvQFVADCWTQVTDANGKVLVSALKRKGDSLELAGKAPLELRLGFAR 319
Cdd:PRK10856 240 DQAGVST----------------PAADPNALVM--NFTADCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPA 301

                        330       340
                 ....*....|....*....|....*...
gi 490481162 320 GAQVSYNGQPVDVTPFVR-GETARLKVG 346
Cdd:PRK10856 302 AVQIQYQGKPVDLSRFIRtNQVARLTLN 329
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 13-83 7.48e-25

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 95.64  E-value: 7.48e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490481162  13 ASRQNPGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAFDKLPGHTFSRGYIRAYAKLMGLDQAELV 83
Cdd:COG1426    1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 273-339 2.05e-22

Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.


Pssm-ID: 433229 [Multi-domain]  Cd Length: 67  Bit Score: 89.17  E-value: 2.05e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490481162  273 KVQFVADCWTQVTDANGKVLVSALKRKGDSLELAGKAPLELRLGFARGAQVSYNGQPVDVTPFVRGE 339
Cdd:pfam13464   1 VLTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-82 8.29e-09

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 51.01  E-value: 8.29e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490481162  19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGafdklpGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENG------KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
22-82 8.74e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.59  E-value: 8.74e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490481162    22 LRQAREQKGLSLSQVAGQLNLTENSLRQLENGafdklpGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENG------KRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
PRK10856 PRK10856
cytoskeleton protein RodZ;
18-346 6.37e-41

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 145.94  E-value: 6.37e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  18 PGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENgafDKLPGH---TFSRGYIRAYAKLMGLDQAELVNSFD-HFTGTN 93
Cdd:PRK10856  15 TGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEE---DKAPADlasTFLRGYIRSYARLVHIPEEELLPGLEkQAPLRA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  94 ASGSTVQ--SLGRVaepvRLSRN---------VLRIVsllllallIGF-GYFWWQEHSARTPETAGLSLEHVEVESADGT 161
Cdd:PRK10856  92 AKVAPMQsfSLGKR----RKKRDgwlmtftwlVLFVV--------IGLtGAWWWQNHKAQQEEITTMADQSSAELSQNSG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 162 TEIH-TLDEPEDQAVIEAQKEGEQAPAEVSPEVAAQAEGAPPVASEGAQV-PAAPAQGTPAAPQQPVTAAPAGTAPAPGT 239
Cdd:PRK10856 160 QSVPlDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVvAPSQANVDTAATPAPAAPATPDGAAPLPT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162 240 APAVPATaspaappapseptaapVVAGEGQGVVkvQFVADCWTQVTDANGKVLVSALKRKGDSLELAGKAPLELRLGFAR 319
Cdd:PRK10856 240 DQAGVST----------------PAADPNALVM--NFTADCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPA 301

                        330       340
                 ....*....|....*....|....*...
gi 490481162 320 GAQVSYNGQPVDVTPFVR-GETARLKVG 346
Cdd:PRK10856 302 AVQIQYQGKPVDLSRFIRtNQVARLTLN 329
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 13-83 7.48e-25

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 95.64  E-value: 7.48e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490481162  13 ASRQNPGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAFDKLPGHTFSRGYIRAYAKLMGLDQAELV 83
Cdd:COG1426    1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 273-339 2.05e-22

Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.


Pssm-ID: 433229 [Multi-domain]  Cd Length: 67  Bit Score: 89.17  E-value: 2.05e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490481162  273 KVQFVADCWTQVTDANGKVLVSALKRKGDSLELAGKAPLELRLGFARGAQVSYNGQPVDVTPFVRGE 339
Cdd:pfam13464   1 VLTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 21-82 1.72e-20

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 83.70  E-value: 1.72e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490481162   21 TLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAFDKLPGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-82 8.29e-09

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 51.01  E-value: 8.29e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490481162  19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGafdklpGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENG------KRNPSLETLEKLAKALGVSLDEL 58
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 19-82 5.39e-08

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 49.06  E-value: 5.39e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490481162   19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAfdklpGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGR-----RGRPSPAVVERLARALGVDGAER 61
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 19-78 3.08e-07

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 47.24  E-value: 3.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGafDKLPghtfSRGYIRAYAKLMGLD 78
Cdd:COG1813   14 GERIREAREARGLSQEELAEKLGVSESTIRRIERG--EATP----SLDTLRKLEKALGIS 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
19-87 3.15e-07

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 47.68  E-value: 3.15e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490481162  19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAfdklpgHTFSRGYIRAYAKLMGLDQAELVNSFD 87
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGR------RNPSLETLLKLAKALGVSLDELLGGAD 71
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 19-84 5.18e-07

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 46.13  E-value: 5.18e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490481162   19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAFDklpghtFSRGYIRAYAKLMGLDQAELVN 84
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSV------PPAETLYKIAELLGVPANWLLQ 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
22-82 8.74e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.59  E-value: 8.74e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490481162    22 LRQAREQKGLSLSQVAGQLNLTENSLRQLENGafdklpGHTFSRGYIRAYAKLMGLDQAEL 82
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENG------KRKPSLETLKKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
19-78 7.10e-05

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 40.22  E-value: 7.10e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490481162  19 GETLRQAREQKGLSLSQVAGQLNLTENSLRQLENGAfdklpgHTFSRGYIRAYAKLMGLD 78
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGK------YNPSLELALKIARALGVS 59
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 22-53 2.39e-04

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 38.68  E-value: 2.39e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 490481162   22 LRQAREQKGLSLSQVAGQLNLTENSLRQLENG 53
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENG 32
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-53 3.82e-03

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 36.15  E-value: 3.82e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 490481162   7 PEVVATASRQNPGETLRQAREQKGLSLSQVAGQLNLTENSLRQLENG 53
Cdd:COG3620    7 RDVVTVSPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESG 53
 
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