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Conserved domains on  [gi|488746061|ref|WP_002669390|]
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MULTISPECIES: HU family DNA-binding protein [Treponema]

Protein Classification

HU family DNA-binding protein( domain architecture ID 10194979)

HU family DNA-binding protein is a conserved nucleoid-associated protein, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein

Gene Ontology:  GO:0003677|GO:0030261
PubMed:  20484776|17097674|15102446
SCOP:  3000426

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 7-94 3.43e-28

Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


:

Pssm-ID: 259858  Cd Length: 89  Bit Score: 97.91  E-value: 3.43e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFK 86
Cdd:cd13836    3 KSELIKRIAEKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARI-GRNPKTGEKVVVPAKYVPHFK 81


                 ....*...
gi 488746061  87 PGKELKEA 94
Cdd:cd13836   82 PGKELKER 89
 
Name Accession Description Interval E-value
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 7-94 3.43e-28

Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259858  Cd Length: 89  Bit Score: 97.91  E-value: 3.43e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFK 86
Cdd:cd13836    3 KSELIKRIAEKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARI-GRNPKTGEKVVVPAKYVPHFK 81


                 ....*...
gi 488746061  87 PGKELKEA 94
Cdd:cd13836   82 PGKELKER 89
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
6-95 7.76e-23

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 84.10  E-value: 7.76e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061    6 SKIDIIDSVYRNNPqYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRF 85
Cdd:pfam00216   1 TKKELIKAIAEKTG-LSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAART-GRNPKTGETITIPAKKVVKF 78

                          90
                  ....*....|
gi 488746061   86 KPGKELKEAL 95
Cdd:pfam00216  79 KPGKALKEAV 88
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
7-97 5.26e-20

Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];


Pssm-ID: 440539  Cd Length: 92  Bit Score: 77.10  E-value: 5.26e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNnPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFdfaVLHGRK--NARNPKTGEAVLTADRCKVR 84
Cdd:COG0776    3 KSELIEAIAEK-TGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTF---SVRKRAarTGRNPKTGEEIKIPAKKVVK 78

                         90
                 ....*....|...
gi 488746061  85 FKPGKELKEALHK 97
Cdd:COG0776   79 FKPGKELKDAVNG 91
ihfB PRK00199
integration host factor subunit beta; Reviewed
 7-93 1.66e-16

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 68.36  E-value: 1.66e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGR--KNARNPKTGEAVLTADRCKVR 84
Cdd:PRK00199   3 KSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFS---LHYRppRVGRNPKTGEKVELEEKYVPH 79


                 ....*....
gi 488746061  85 FKPGKELKE 93
Cdd:PRK00199  80 FKPGKELRE 88
BHL smart00411
bacterial (prokaryotic) histone like domain;
6-95 1.21e-15

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 66.05  E-value: 1.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061     6 SKIDIIDSVYRNNPqYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGRK--NARNPKTGEAVLTADRCKV 83
Cdd:smart00411   2 TKSELIDAIAEKTG-LSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFE---VRERKarEGRNPKTGEEIEIPAKKVP 77

                           90
                   ....*....|..
gi 488746061    84 RFKPGKELKEAL 95
Cdd:smart00411  78 KFKPGKALKDAV 89
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 6-96 2.20e-13

integration host factor, beta subunit; This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130061  Cd Length: 94  Bit Score: 60.31  E-value: 2.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061    6 SKIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGR--KNARNPKTGEAVLTADRCKV 83
Cdd:TIGR00988   2 TKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFS---LHYRapRTGRNPKTGDSVELDGKYVP 78

                          90
                  ....*....|...
gi 488746061   84 RFKPGKELKEALH 96
Cdd:TIGR00988  79 HFKPGKELRDRAN 91
 
Name Accession Description Interval E-value
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 7-94 3.43e-28

Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259858  Cd Length: 89  Bit Score: 97.91  E-value: 3.43e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFK 86
Cdd:cd13836    3 KSELIKRIAEKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARI-GRNPKTGEKVVVPAKYVPHFK 81


                 ....*...
gi 488746061  87 PGKELKEA 94
Cdd:cd13836   82 PGKELKER 89
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
6-95 7.76e-23

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 84.10  E-value: 7.76e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061    6 SKIDIIDSVYRNNPqYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRF 85
Cdd:pfam00216   1 TKKELIKAIAEKTG-LSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAART-GRNPKTGETITIPAKKVVKF 78

                          90
                  ....*....|
gi 488746061   86 KPGKELKEAL 95
Cdd:pfam00216  79 KPGKALKEAV 88
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 7-93 3.62e-22

Integration host factor (IHF) and similar proteins; This subfamily includes integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. This subfamily also includes the protein Hbb from tick-borne spirochete Borrelia burgdorferi, responsible for causing Lyme disease in humans. Hbb, a homodimer, shows DNA sequence preferences that are related, yet distinct from those of IHF.


Pssm-ID: 259854  Cd Length: 85  Bit Score: 82.54  E-value: 3.62e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNpQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFK 86
Cdd:cd13832    1 KADLIEEIAEKT-GLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARI-GRNPKTGEKIVIPARKVVKFK 78


                 ....*..
gi 488746061  87 PGKELKE 93
Cdd:cd13832   79 PSKELKE 85
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
7-97 5.26e-20

Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];


Pssm-ID: 440539  Cd Length: 92  Bit Score: 77.10  E-value: 5.26e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNnPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFdfaVLHGRK--NARNPKTGEAVLTADRCKVR 84
Cdd:COG0776    3 KSELIEAIAEK-TGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTF---SVRKRAarTGRNPKTGEEIKIPAKKVVK 78

                         90
                 ....*....|...
gi 488746061  85 FKPGKELKEALHK 97
Cdd:COG0776   79 FKPGKELKDAVNG 91
ihfB PRK00199
integration host factor subunit beta; Reviewed
 7-93 1.66e-16

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 68.36  E-value: 1.66e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGR--KNARNPKTGEAVLTADRCKVR 84
Cdd:PRK00199   3 KSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFS---LHYRppRVGRNPKTGEKVELEEKYVPH 79


                 ....*....
gi 488746061  85 FKPGKELKE 93
Cdd:PRK00199  80 FKPGKELRE 88
BHL smart00411
bacterial (prokaryotic) histone like domain;
6-95 1.21e-15

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 66.05  E-value: 1.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061     6 SKIDIIDSVYRNNPqYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGRK--NARNPKTGEAVLTADRCKV 83
Cdd:smart00411   2 TKSELIDAIAEKTG-LSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFE---VRERKarEGRNPKTGEEIEIPAKKVP 77

                           90
                   ....*....|..
gi 488746061    84 RFKPGKELKEAL 95
Cdd:smart00411  78 KFKPGKALKDAV 89
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 6-96 2.20e-13

integration host factor, beta subunit; This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130061  Cd Length: 94  Bit Score: 60.31  E-value: 2.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061    6 SKIDIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfavLHGR--KNARNPKTGEAVLTADRCKV 83
Cdd:TIGR00988   2 TKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFS---LHYRapRTGRNPKTGDSVELDGKYVP 78

                          90
                  ....*....|...
gi 488746061   84 RFKPGKELKEALH 96
Cdd:TIGR00988  79 HFKPGKELRDRAN 91
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 24-93 7.89e-11

histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). In E. coli, HU binds uniformly to the chromosome, with a preference for damaged or distorted DNA structures and can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Anabaena HU (AHU) shows preference for A/T-rich region in the center of its DNA binding site.


Pssm-ID: 259853  Cd Length: 86  Bit Score: 53.55  E-value: 7.89e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061  24 KQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFKPGKELKE 93
Cdd:cd13831   18 KDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAART-GRNPQTGEKIKIPASKVPKFKPGKALKD 86
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 7-95 2.88e-10

Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259857  Cd Length: 88  Bit Score: 52.06  E-value: 2.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   7 KIDIIDSVYrNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfaVLhgRKNAR---NPKTGEAVLTADRCKV 83
Cdd:cd13835    2 KADLAEAIY-EKLGLSRKEAAELVESVFEEIKEALERGEDVKISGFGTFE--VR--DKKARpgrNPKTGEEVTISARRVV 76

                         90
                 ....*....|..
gi 488746061  84 RFKPGKELKEAL 95
Cdd:cd13835   77 TFKPSPKLKKRI 88
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 24-94 2.08e-09

Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to bacillus phage SPO1-encoded transcription factor 1 (TF1), a type II DNA-binding protein related to the DNA sequence specific (IHF) and non-specific (HU) domains. Type II DNA-binding proteins bind and bend DNA as dimers. Like IHF, TF1 binds DNA specifically and bends DNA sharply. Bacteriophage SPO1-encoded TF1 recognizes SPO1 phage DNA containing 5-(hydroxymethyl)-2'-deoxyuridine as opposed to thymine, Related family members includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups).


Pssm-ID: 259859  Cd Length: 87  Bit Score: 49.99  E-value: 2.08e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488746061  24 KQINAIANLFLDELSVLLQQGIPVEIRGLGSFDfAVLHGRKNARNPKTGEAVLTADRCKVRFKPGKELKEA 94
Cdd:cd14435   18 AQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFE-RVERAARTGRNPQTGEAIQIPAGYGVKFSAGSKLKKA 87
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 24-93 2.16e-09

DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). Bacillus phage SPO1-encoded transcription factor 1 (TF1) is another related type II DNA-binding protein. Like IHF, TF1 binds DNA specifically and bends DNA sharply.


Pssm-ID: 259852  Cd Length: 85  Bit Score: 49.88  E-value: 2.16e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061  24 KQINAIANLFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKNaRNPKTGEAVLTADRCKVRFKPGKELKE 93
Cdd:cd00591   17 KQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTG-RNPATGETIEIPAKKVVKFTPSKALKD 85
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 6-97 2.39e-09

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 50.22  E-value: 2.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   6 SKIDIIDSVYRnnpQYQL-KQINA-IANLFLDELSVLLQQGIPVEIRGLGSFDFAvlhgRKNAR---NPKTGEAVLTADR 80
Cdd:PRK00285   4 TKADLAEALFE---KVGLsKREAKeLVELFFEEIRDALENGEQVKLSGFGNFQLR----DKNQRpgrNPKTGEEIPISAR 76

                         90
                 ....*....|....*..
gi 488746061  81 CKVRFKPGKELKEALHK 97
Cdd:PRK00285  77 RVVTFRPSQKLKSRVEN 93
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 32-93 2.38e-07

integration host factor, alpha subunit; This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130060  Cd Length: 96  Bit Score: 44.88  E-value: 2.38e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488746061   32 LFLDELSVLLQQGIPVEIRGLGSFDFAVLHGRKnARNPKTGEAVLTADRCKVRFKPGKELKE 93
Cdd:TIGR00987  28 LFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP-GRNPKTGEEIPITARRVVTFRPGQKLKS 88
HU_IHF_like cd13833
Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; ...
 9-95 2.80e-06

Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; This subfamily consists of uncharacterized proteins similar to integration host factor (IHF) and HU domains, including hypothetical protein Bvu_2165 from Bacteroides vulgatus. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259855  Cd Length: 97  Bit Score: 42.28  E-value: 2.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061   9 DIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPVEIrGLGSFDFAVlHGRKNARNPKTGEAVltaDRCKVRFKPG 88
Cdd:cd13833   16 DIIDRIVAKGSTLRAETIEHILELFDKVVSEALQEGYSVNT-GLGYLYIAI-SGVFEGETDSFDPAK---HSITVSFTPG 90


                 ....*..
gi 488746061  89 KELKEAL 95
Cdd:cd13833   91 KLLREAL 97
HU-DNA_bdg pfam14848
DNA-binding domain;
9-98 9.26e-06

DNA-binding domain;


Pssm-ID: 434264  Cd Length: 123  Bit Score: 41.17  E-value: 9.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488746061    9 DIIDSVYRNNPQYQLKQINAIANLFLDELSVLLQQGIPV-------EIRGLGSFDfavlhGRKNARNPKTgeavltaDRC 81
Cdd:pfam14848  33 DIIDEMVKKGTEVRKETILHILNLFNREVSEAVLNGYSVntglgrtSPTIKGVFD-----GKTSAFDPNR-------HSI 100

                          90
                  ....*....|....*..
gi 488746061   82 KVRFKPGKELKEALHKI 98
Cdd:pfam14848 101 YVNLTQGAALREALANT 117
 
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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