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Conserved domains on  [gi|446909336|ref|WP_000986592|]
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helix-turn-helix domain-containing protein [Escherichia coli]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11514194)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator, which controls the expression of genes involved in stress response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-66 1.02e-12

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: 58.72  E-value: 1.02e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
PRK09706 super family cl27794
transcriptional repressor DicA; Reviewed
 11-129 4.43e-11

transcriptional repressor DicA; Reviewed


The actual alignment was detected with superfamily member PRK09706:

Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 56.40  E-value: 4.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLL--------PPEECEQiftpdTM 82
Cdd:PRK09706   9 RIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFgdedkqptPPVPLNQ-----PV 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446909336  83 KIGPRQRELLQAFSAFPEEDQEKMLQEIKDKKKSMEETIARWLAAQK 129
Cdd:PRK09706  84 ELSEDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARK 130
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-66 1.02e-12

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: 58.72  E-value: 1.02e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-72 8.46e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 8.46e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446909336   2 MSALEVSMY-RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLLPPEE 72
Cdd:COG1396    1 MSTLKKALGeRLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-66 2.97e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 54.83  E-value: 2.97e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336    11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 11-129 4.43e-11

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 56.40  E-value: 4.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLL--------PPEECEQiftpdTM 82
Cdd:PRK09706   9 RIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFgdedkqptPPVPLNQ-----PV 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446909336  83 KIGPRQRELLQAFSAFPEEDQEKMLQEIKDKKKSMEETIARWLAAQK 129
Cdd:PRK09706  84 ELSEDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARK 130
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-66 2.17e-09

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: 49.85  E-value: 2.17e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446909336   12 ISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-93 7.55e-08

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 48.64  E-value: 7.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446909336   2 MSALEVSM-YRISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLLPPEEceqiftPD 80
Cdd:PRK09943   1 MSDEGLAPgKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK------PD 74

                         90
                 ....*....|...
gi 446909336  81 TMKIGPRQRELLQ 93
Cdd:PRK09943  75 EPQVVINQDDLIE 87
transpos_IS481 NF033577
IS481 family transposase; null
 10-41 4.93e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 38.34  E-value: 4.93e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 446909336  10 YRISKLLQETGWSQAELARRIGVTQQTVQQWV 41
Cdd:NF033577   3 LELVRLVLEDGWSVREAARRFGISRKTVYKWL 34
PBP2_BCP_2 cd13643
Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline ...
 79-131 1.22e-03

Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold; This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270361 [Multi-domain]  Cd Length: 283  Bit Score: 37.27  E-value: 1.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446909336  79 PDTMKIGPRQRELLQAFSaFPEEDQEKMLQEIKDKKKSMEETIARWLAAQKSR 131
Cdd:cd13643  228 AGFADKWPAAYELLKNFT-LTNEDQAAMAALIDVDGMSVEDAAKKWLAANEAT 279
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 9-56 2.08e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 35.68  E-value: 2.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446909336    9 MYRISKLLqetGWSQAELARRIGVTQQTVQQWVSGKATPkASSLDKLV 56
Cdd:TIGR03830  70 IRRIRKKL---GLSQREAAELLGGGVNAFSRYERGEVRP-SKALDKLL 113
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-66 1.02e-12

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: 58.72  E-value: 1.02e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-72 8.46e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 8.46e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446909336   2 MSALEVSMY-RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLLPPEE 72
Cdd:COG1396    1 MSTLKKALGeRLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-66 2.97e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 54.83  E-value: 2.97e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336    11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 11-129 4.43e-11

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 56.40  E-value: 4.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLL--------PPEECEQiftpdTM 82
Cdd:PRK09706   9 RIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFgdedkqptPPVPLNQ-----PV 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446909336  83 KIGPRQRELLQAFSAFPEEDQEKMLQEIKDKKKSMEETIARWLAAQK 129
Cdd:PRK09706  84 ELSEDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARK 130
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
2-62 3.39e-10

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 52.24  E-value: 3.39e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446909336   2 MSALEVSMYRISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHP 62
Cdd:COG2944    1 MTKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHP 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 12-68 4.50e-10

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: 52.71  E-value: 4.50e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446909336  12 ISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLL 68
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
11-71 4.80e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 51.77  E-value: 4.80e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLLPPE 71
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-66 2.17e-09

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: 49.85  E-value: 2.17e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446909336   12 ISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
2-93 7.55e-08

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 48.64  E-value: 7.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446909336   2 MSALEVSM-YRISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFLLPPEEceqiftPD 80
Cdd:PRK09943   1 MSDEGLAPgKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK------PD 74

                         90
                 ....*....|...
gi 446909336  81 TMKIGPRQRELLQ 93
Cdd:PRK09943  75 EPQVVINQDDLIE 87
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 11-55 1.42e-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: 45.70  E-value: 1.42e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKL 55
Cdd:COG1813   16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKL 60
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
22-44 1.21e-06

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 42.98  E-value: 1.21e-06
                         10        20
                 ....*....|....*....|...
gi 446909336  22 SQAELARRIGVTQQTVQQWVSGK 44
Cdd:COG4197   10 SQSALARALGVSQQAVSQWLNGK 32
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
11-55 2.56e-06

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 42.05  E-value: 2.56e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKAT-PKASSLDKL 55
Cdd:COG3655    5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKI 50
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 15-45 2.98e-06

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.49  E-value: 2.98e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 446909336  15 LLQETGWSQAELARRIGVTQQTVQQWVSGKA 45
Cdd:COG3093   17 FLEPLGLSQTELAKALGVSRQRISEILNGKR 47
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
9-57 1.06e-05

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 41.41  E-value: 1.06e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446909336   9 MYRISKLLQETGWSQAELARRIGVTQQTVQQWVSGKatPKASSLDKLVE 57
Cdd:COG5606   34 MAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGK--ISKFSLDKLVN 80
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 10-67 1.73e-05

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: 39.96  E-value: 1.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 446909336   10 YRISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWFL 67
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 11-55 2.05e-05

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 39.83  E-value: 2.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 446909336   11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKA-TPKASSLDKL 55
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKI 46
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 12-44 1.21e-04

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 37.71  E-value: 1.21e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446909336   12 ISKLLQETGwSQAELARRIGVTQQTVQQWVSGK 44
Cdd:pfam15943   1 IKKAIEIVG-GQKALAEALGVTQQAVSQWLHGK 32
PHA01976 PHA01976
helix-turn-helix protein
 11-66 3.19e-04

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 36.86  E-value: 3.19e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446909336  11 RISKLLQETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSGHPLHWF 66
Cdd:PHA01976   6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWL 61
transpos_IS481 NF033577
IS481 family transposase; null
 10-41 4.93e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 38.34  E-value: 4.93e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 446909336  10 YRISKLLQETGWSQAELARRIGVTQQTVQQWV 41
Cdd:NF033577   3 LELVRLVLEDGWSVREAARRFGISRKTVYKWL 34
PBP2_BCP_2 cd13643
Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline ...
 79-131 1.22e-03

Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold; This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270361 [Multi-domain]  Cd Length: 283  Bit Score: 37.27  E-value: 1.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446909336  79 PDTMKIGPRQRELLQAFSaFPEEDQEKMLQEIKDKKKSMEETIARWLAAQKSR 131
Cdd:cd13643  228 AGFADKWPAAYELLKNFT-LTNEDQAAMAALIDVDGMSVEDAAKKWLAANEAT 279
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 17-60 1.85e-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: 1.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446909336   17 QETGWSQAELARRIGVTQQTVQQWVSGKAT-PKASSLDKLVEVSG 60
Cdd:pfam13560  11 ERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALG 55
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 9-56 2.08e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 35.68  E-value: 2.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446909336    9 MYRISKLLqetGWSQAELARRIGVTQQTVQQWVSGKATPkASSLDKLV 56
Cdd:TIGR03830  70 IRRIRKKL---GLSQREAAELLGGGVNAFSRYERGEVRP-SKALDKLL 113
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 15-41 6.23e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 35.21  E-value: 6.23e-03
                         10        20
                 ....*....|....*....|....*..
gi 446909336  15 LLQETGWSQAELARRIGVTQQTVQQWV 41
Cdd:COG3415   33 LLLAEGLSVREIAERLGVSRSTVYRWL 59
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 11-42 6.35e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 32.95  E-value: 6.35e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 446909336   11 RISKLLQEtGWSQAELARRIGVTQQTVQQWVS 42
Cdd:pfam13518   4 KIVLLALE-GESIKEAARLFGISRSTVYRWIR 34
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 18-60 8.53e-03

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 32.63  E-value: 8.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 446909336   18 ETGWSQAELARRIGVTQQTVQQWVSGKATPKASSLDKLVEVSG 60
Cdd:TIGR03070  13 ALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
HTH_23 pfam13384
Homeodomain-like domain;
10-42 9.03e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 32.63  E-value: 9.03e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446909336   10 YRISKLLQEtGWSQAELARRIGVTQQTVQQWVS 42
Cdd:pfam13384   8 ARALLLLAE-GLSVKEIAELLGVSRRTVYRWLK 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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