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Conserved domains on  [gi|1789128599|ref|WP_158213256|]
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RodZ domain-containing protein [Pigmentiphaga sp. NML080357]

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 ...
 28-93 4.49e-20

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: 82.16  E-value: 4.49e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALENENWAELPQGMPLRGFVRNYARLLEIDPAPML 93
Cdd:COG1426     6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 228-294 4.55e-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: 71.06  E-value: 4.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789128599 228 LTLKQASWVEIRRADGTVAVSRIIPANEPYALDPsGAPYRVVIGNVNGVDLSWRGAPVDLAPYRRDN 294
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTG-KPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
PRK10856 super family cl35960
cytoskeleton protein RodZ;
34-300 4.35e-06

cytoskeleton protein RodZ;


The actual alignment was detected with superfamily member PRK10856:

Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 47.33  E-value: 4.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599  34 RLREAR---GWSQEYVSDRLKFAVRQIRALENENwaeLPQGMP---LRGFVRNYARLLEIDPAPMLQALSPQLQV-ADPV 106
Cdd:PRK10856   18 RLRQAReqlGLTQQAVAERLCLKVSTVRDIEEDK---APADLAstfLRGYIRSYARLVHIPEEELLPGLEKQAPLrAAKV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 107 SLEQASSLssplaqssgrawpaagGRKR--------LAPWLVggVMAVLALVLLGYALN---QQGKL------SFGQQSA 169
Cdd:PRK10856   95 APMQSFSL----------------GKRRkkrdgwlmTFTWLV--LFVVIGLTGAWWWQNhkaQQEEIttmadqSSAELSQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 170 ------------STDLDVAGSKTAIQVETPLAPATTAETPAAPPATPAPA----------LEPVAPPEPAPAPAPEPGLA 227
Cdd:PRK10856  157 nsgqsvpldtstTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQnavvapsqanVDTAATPAPAAPATPDGAAP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 228 LTLKQAS-------------------WVEIRRADGTVAVSRIIPANEpyALDPSG-APYRVVIGNVNGVDLSWRGAPVDL 287
Cdd:PRK10856  237 LPTDQAGvstpaadpnalvmnftadcWLEVTDATGKKLFSGMQRKGG--NLNLTGqAPYKLKIGAPAAVQIQYQGKPVDL 314

                         330
                  ....*....|....
gi 1789128599 288 APYRRDN-VARLTL 300
Cdd:PRK10856  315 SRFIRTNqVARLTL 328
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 28-93 4.49e-20

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: 82.16  E-value: 4.49e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALENENWAELPQGMPLRGFVRNYARLLEIDPAPML 93
Cdd:COG1426     6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 32-92 1.01e-17

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: 75.61  E-value: 1.01e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1789128599  32 LARLREARGWSQEYVSDRLKFAVRQIRALENENWAELPQGMPLRGFVRNYARLLEIDPAPM 92
Cdd:pfam13413   2 LRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 228-294 4.55e-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: 71.06  E-value: 4.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789128599 228 LTLKQASWVEIRRADGTVAVSRIIPANEPYALDPsGAPYRVVIGNVNGVDLSWRGAPVDLAPYRRDN 294
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTG-KPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
PRK10856 PRK10856
cytoskeleton protein RodZ;
34-300 4.35e-06

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 47.33  E-value: 4.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599  34 RLREAR---GWSQEYVSDRLKFAVRQIRALENENwaeLPQGMP---LRGFVRNYARLLEIDPAPMLQALSPQLQV-ADPV 106
Cdd:PRK10856   18 RLRQAReqlGLTQQAVAERLCLKVSTVRDIEEDK---APADLAstfLRGYIRSYARLVHIPEEELLPGLEKQAPLrAAKV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 107 SLEQASSLssplaqssgrawpaagGRKR--------LAPWLVggVMAVLALVLLGYALN---QQGKL------SFGQQSA 169
Cdd:PRK10856   95 APMQSFSL----------------GKRRkkrdgwlmTFTWLV--LFVVIGLTGAWWWQNhkaQQEEIttmadqSSAELSQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 170 ------------STDLDVAGSKTAIQVETPLAPATTAETPAAPPATPAPA----------LEPVAPPEPAPAPAPEPGLA 227
Cdd:PRK10856  157 nsgqsvpldtstTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQnavvapsqanVDTAATPAPAAPATPDGAAP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 228 LTLKQAS-------------------WVEIRRADGTVAVSRIIPANEpyALDPSG-APYRVVIGNVNGVDLSWRGAPVDL 287
Cdd:PRK10856  237 LPTDQAGvstpaadpnalvmnftadcWLEVTDATGKKLFSGMQRKGG--NLNLTGqAPYKLKIGAPAAVQIQYQGKPVDL 314

                         330
                  ....*....|....
gi 1789128599 288 APYRRDN-VARLTL 300
Cdd:PRK10856  315 SRFIRTNqVARLTL 328
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 29-90 2.88e-04

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: 38.30  E-value: 2.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789128599  29 GRELARLREARGWSQEYVSDRLKFAVRQIRALENENwaelpqGMPLRGFVRNYARLLEIDPA 90
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGK------RNPSLETLEKLAKALGVSLD 56
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
31-90 1.30e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 1.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599   31 ELARLREARGWSQEYVSDRLKFAVRQIRALENENWaelpqgMPLRGFVRNYARLLEIDPA 90
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR------KPSLETLKKLAKALGVSLD 54
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 28-93 4.49e-20

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: 82.16  E-value: 4.49e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALENENWAELPQGMPLRGFVRNYARLLEIDPAPML 93
Cdd:COG1426     6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 32-92 1.01e-17

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: 75.61  E-value: 1.01e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1789128599  32 LARLREARGWSQEYVSDRLKFAVRQIRALENENWAELPQGMPLRGFVRNYARLLEIDPAPM 92
Cdd:pfam13413   2 LRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 228-294 4.55e-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: 71.06  E-value: 4.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789128599 228 LTLKQASWVEIRRADGTVAVSRIIPANEPYALDPsGAPYRVVIGNVNGVDLSWRGAPVDLAPYRRDN 294
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTG-KPPLTLVLGNAGAVEVSVNGKPVDLLGYARGN 67
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 29-89 3.88e-06

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: 43.82  E-value: 3.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1789128599  29 GRELARLREARGWSQEYVSDRLKFAVRQIRALENENWaelpqgMPLRGFVRNYARLLEIDP 89
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKS------VPPAETLYKIAELLGVPA 55
PRK10856 PRK10856
cytoskeleton protein RodZ;
34-300 4.35e-06

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 47.33  E-value: 4.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599  34 RLREAR---GWSQEYVSDRLKFAVRQIRALENENwaeLPQGMP---LRGFVRNYARLLEIDPAPMLQALSPQLQV-ADPV 106
Cdd:PRK10856   18 RLRQAReqlGLTQQAVAERLCLKVSTVRDIEEDK---APADLAstfLRGYIRSYARLVHIPEEELLPGLEKQAPLrAAKV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 107 SLEQASSLssplaqssgrawpaagGRKR--------LAPWLVggVMAVLALVLLGYALN---QQGKL------SFGQQSA 169
Cdd:PRK10856   95 APMQSFSL----------------GKRRkkrdgwlmTFTWLV--LFVVIGLTGAWWWQNhkaQQEEIttmadqSSAELSQ 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 170 ------------STDLDVAGSKTAIQVETPLAPATTAETPAAPPATPAPA----------LEPVAPPEPAPAPAPEPGLA 227
Cdd:PRK10856  157 nsgqsvpldtstTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQnavvapsqanVDTAATPAPAAPATPDGAAP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599 228 LTLKQAS-------------------WVEIRRADGTVAVSRIIPANEpyALDPSG-APYRVVIGNVNGVDLSWRGAPVDL 287
Cdd:PRK10856  237 LPTDQAGvstpaadpnalvmnftadcWLEVTDATGKKLFSGMQRKGG--NLNLTGqAPYKLKIGAPAAVQIQYQGKPVDL 314

                         330
                  ....*....|....
gi 1789128599 288 APYRRDN-VARLTL 300
Cdd:PRK10856  315 SRFIRTNqVARLTL 328
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 28-88 2.47e-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: 38.77  E-value: 2.47e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALENEnwaelpQGMPLRGFVRNYARLLEID 88
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERG------EATPSLDTLRKLEKALGIS 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 29-90 2.88e-04

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: 38.30  E-value: 2.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789128599  29 GRELARLREARGWSQEYVSDRLKFAVRQIRALENENwaelpqGMPLRGFVRNYARLLEIDPA 90
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGK------RNPSLETLEKLAKALGVSLD 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
28-90 1.18e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 37.28  E-value: 1.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALENEnwaelpQGMPLRGFVRNYARLLEIDPA 90
Cdd:COG1396     8 LGERLRELRKARGLTQEELAERLGVSRSTISRIERG------RRNPSLETLLKLAKALGVSLD 64
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 29-90 1.26e-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: 36.74  E-value: 1.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789128599  29 GRELARLREARGWSQEYVSDRLKFAVRQIRALENEnwaelPQGMPLRGFVRNYARLLEIDPA 90
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETG-----RRGRPSPAVVERLARALGVDGA 59
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
31-90 1.30e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 1.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789128599   31 ELARLREARGWSQEYVSDRLKFAVRQIRALENENWaelpqgMPLRGFVRNYARLLEIDPA 90
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR------KPSLETLKKLAKALGVSLD 54
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
28-62 2.71e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 35.59  E-value: 2.71e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1789128599  28 VGRELARLREARGWSQEYVSDRLKFAVRQIRALEN 62
Cdd:COG1476     5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIEN 39
 
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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