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Conserved domains on  [gi|2278705417|ref|WP_255593097|]
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MULTISPECIES: RodZ domain-containing protein [unclassified Acidovorax]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12807598)

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; also contains a DUF4115 domain; similar to cytoskeleton protein RodZ, an inner membrane protein which functions in cell-shape control through regulation of the length of the long axis

CATH:  1.10.260.40
Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-68 2.27e-19

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: 80.23  E-value: 2.27e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2278705417   1 MTAGGLLREARQASGMHIAALAVALKVPVSKLEALEADNYEALPDTVFVRALASSICRTLKLDPAPVL 68
Cdd:COG1426     4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 221-287 2.34e-16

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: 71.83  E-value: 2.34e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2278705417 221 VLRARSESWVQVRDSAGAVALQRNLVAGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN 287
Cdd:pfam13464   1 VLTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
PRK10856 super family cl35960
cytoskeleton protein RodZ;
136-293 7.16e-08

cytoskeleton protein RodZ;


The actual alignment was detected with superfamily member PRK10856:

Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 52.72  E-value: 7.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 136 ATSTTGTAQAPAPVTAAPSVIAEPQASPAPTEVSSAPTgVAERKPESPAPVAAGRPDAAAPAAANGVASAPVAAASAAAP 215
Cdd:PRK10856  171 DPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNA-VVAPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 216 PAGALVLRARSESWVQVRDSAGAV---ALQRNlvaGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN-VARF 291
Cdd:PRK10856  250 DPNALVMNFTADCWLEVTDATGKKlfsGMQRK---GGNLNLTGQAPYKLKIGAPAAVQIQYQGKPVDLSRFIRTNqVARL 326


                  ..
gi 2278705417 292 EV 293
Cdd:PRK10856  327 TL 328
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-68 2.27e-19

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: 80.23  E-value: 2.27e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2278705417   1 MTAGGLLREARQASGMHIAALAVALKVPVSKLEALEADNYEALPDTVFVRALASSICRTLKLDPAPVL 68
Cdd:COG1426     4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-67 3.35e-18

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: 76.76  E-value: 3.35e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2278705417   6 LLREARQASGMHIAALAVALKVPVSKLEALEADNYEALPDTVFVRALASSICRTLKLDPAPV 67
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 221-287 2.34e-16

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: 71.83  E-value: 2.34e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2278705417 221 VLRARSESWVQVRDSAGAVALQRNLVAGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN 287
Cdd:pfam13464   1 VLTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
PRK10856 PRK10856
cytoskeleton protein RodZ;
136-293 7.16e-08

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 52.72  E-value: 7.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 136 ATSTTGTAQAPAPVTAAPSVIAEPQASPAPTEVSSAPTgVAERKPESPAPVAAGRPDAAAPAAANGVASAPVAAASAAAP 215
Cdd:PRK10856  171 DPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNA-VVAPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 216 PAGALVLRARSESWVQVRDSAGAV---ALQRNlvaGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN-VARF 291
Cdd:PRK10856  250 DPNALVMNFTADCWLEVTDATGKKlfsGMQRK---GGNLNLTGQAPYKLKIGAPAAVQIQYQGKPVDLSRFIRTNqVARL 326


                  ..
gi 2278705417 292 EV 293
Cdd:PRK10856  327 TL 328
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-68 2.27e-19

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: 80.23  E-value: 2.27e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2278705417   1 MTAGGLLREARQASGMHIAALAVALKVPVSKLEALEADNYEALPDTVFVRALASSICRTLKLDPAPVL 68
Cdd:COG1426     4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-67 3.35e-18

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: 76.76  E-value: 3.35e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2278705417   6 LLREARQASGMHIAALAVALKVPVSKLEALEADNYEALPDTVFVRALASSICRTLKLDPAPV 67
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 221-287 2.34e-16

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: 71.83  E-value: 2.34e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2278705417 221 VLRARSESWVQVRDSAGAVALQRNLVAGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN 287
Cdd:pfam13464   1 VLTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
PRK10856 PRK10856
cytoskeleton protein RodZ;
136-293 7.16e-08

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 52.72  E-value: 7.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 136 ATSTTGTAQAPAPVTAAPSVIAEPQASPAPTEVSSAPTgVAERKPESPAPVAAGRPDAAAPAAANGVASAPVAAASAAAP 215
Cdd:PRK10856  171 DPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNA-VVAPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2278705417 216 PAGALVLRARSESWVQVRDSAGAV---ALQRNlvaGESVSVAGSMPLAVVIGRADVTEVFVRGKPFDLTTVSREN-VARF 291
Cdd:PRK10856  250 DPNALVMNFTADCWLEVTDATGKKlfsGMQRK---GGNLNLTGQAPYKLKIGAPAAVQIQYQGKPVDLSRFIRTNqVARL 326


                  ..
gi 2278705417 292 EV 293
Cdd:PRK10856  327 TL 328
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-53 8.29e-04

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: 37.22  E-value: 8.29e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2278705417   4 GGLLREARQASGMHIAALAVALKVPVSKLEALEADnyEALPDTVFVRALA 53
Cdd:COG1813    14 GERIREAREARGLSQEELAEKLGVSESTIRRIERG--EATPSLDTLRKLE 61
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-70 7.61e-03

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: 34.43  E-value: 7.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2278705417   4 GGLLREARQASGMHIAALAVALKVPVSKLEALEADNYeALPDTVFVRALassiCRTLKLDPAPVLSL 70
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRR-GRPSPAVVERL----ARALGVDGAERAEL 64
 
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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