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Conserved domains on  [gi|2303863718|ref|WP_260397887|]
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MULTISPECIES: HU family DNA-binding protein [Dysgonomonas]

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 ...
 12-96 3.84e-32

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: 107.54  E-value: 3.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNT-GIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:cd13836     1 MTKSELIKRIAEKTpGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                  ....*.
gi 2303863718  91 KPAKTF 96
Cdd:cd13836    81 KPGKEL 86
 
Name Accession Description Interval E-value
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 12-96 3.84e-32

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: 107.54  E-value: 3.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNT-GIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:cd13836     1 MTKSELIKRIAEKTpGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                  ....*.
gi 2303863718  91 KPAKTF 96
Cdd:cd13836    81 KPGKEL 86
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
12-96 1.96e-29

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 100.98  E-value: 1.96e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:COG0776     1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80


                  ....*
gi 2303863718  92 PAKTF 96
Cdd:COG0776    81 PGKEL 85
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
13-96 5.09e-26

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 92.19  E-value: 5.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  13 TKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKP 92
Cdd:pfam00216   1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                  ....
gi 2303863718  93 AKTF 96
Cdd:pfam00216  81 GKAL 84
BHL smart00411
bacterial (prokaryotic) histone like domain;
12-96 1.41e-19

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 75.68  E-value: 1.41e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718   12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:smart00411   1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80


                   ....*
gi 2303863718   92 PAKTF 96
Cdd:smart00411  81 PGKAL 85
PRK10664 PRK10664
DNA-binding protein HU-beta;
12-96 1.29e-14

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 63.15  E-value: 1.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:PRK10664    1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80


                  ....*
gi 2303863718  92 PAKTF 96
Cdd:PRK10664   81 AGKAL 85
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 12-94 3.29e-12

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: 57.23  E-value: 3.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTG-IDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:TIGR00988   1 MTKSELIERIATQQShLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80


                  ....
gi 2303863718  91 KPAK 94
Cdd:TIGR00988  81 KPGK 84
 
Name Accession Description Interval E-value
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 12-96 3.84e-32

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: 107.54  E-value: 3.84e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNT-GIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:cd13836     1 MTKSELIKRIAEKTpGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                  ....*.
gi 2303863718  91 KPAKTF 96
Cdd:cd13836    81 KPGKEL 86
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 14-96 4.20e-31

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: 104.88  E-value: 4.20e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  14 KADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKPA 93
Cdd:cd13832     1 KADLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARIGRNPKTGEKIVIPARKVVKFKPS 80


                  ...
gi 2303863718  94 KTF 96
Cdd:cd13832    81 KEL 83
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
12-96 1.96e-29

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 100.98  E-value: 1.96e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:COG0776     1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80


                  ....*
gi 2303863718  92 PAKTF 96
Cdd:COG0776    81 PGKEL 85
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
13-96 5.09e-26

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 92.19  E-value: 5.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  13 TKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKP 92
Cdd:pfam00216   1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                  ....
gi 2303863718  93 AKTF 96
Cdd:pfam00216  81 GKAL 84
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 13-96 3.63e-23

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: 84.75  E-value: 3.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  13 TKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKP 92
Cdd:cd13831     1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                  ....
gi 2303863718  93 AKTF 96
Cdd:cd13831    81 GKAL 84
BHL smart00411
bacterial (prokaryotic) histone like domain;
12-96 1.41e-19

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 75.68  E-value: 1.41e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718   12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:smart00411   1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80


                   ....*
gi 2303863718   92 PAKTF 96
Cdd:smart00411  81 PGKAL 85
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 14-96 1.11e-17

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: 70.68  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  14 KADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKPA 93
Cdd:cd00591     1 KKELIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTGRNPATGETIEIPAKKVVKFTPS 80


                  ...
gi 2303863718  94 KTF 96
Cdd:cd00591    81 KAL 83
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 13-96 7.83e-17

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: 68.63  E-value: 7.83e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  13 TKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKP 92
Cdd:cd13835     1 TKADLAEAIYEKLGLSRKEAAELVESVFEEIKEALERGEDVKISGFGTFEVRDKKARPGRNPKTGEEVTISARRVVTFKP 80


                  ....
gi 2303863718  93 AKTF 96
Cdd:cd13835    81 SPKL 84
PRK10664 PRK10664
DNA-binding protein HU-beta;
12-96 1.29e-14

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 63.15  E-value: 1.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:PRK10664    1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80


                  ....*
gi 2303863718  92 PAKTF 96
Cdd:PRK10664   81 AGKAL 85
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 13-95 6.53e-13

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: 58.85  E-value: 6.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  13 TKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFKP 92
Cdd:cd14435     1 NKTELVAAIAQKAGLTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFERVERAARTGRNPQTGEAIQIPAGYGVKFSA 80


                  ...
gi 2303863718  93 AKT 95
Cdd:cd14435    81 GSK 83
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 12-94 3.29e-12

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: 57.23  E-value: 3.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTG-IDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:TIGR00988   1 MTKSELIERIATQQShLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80


                  ....
gi 2303863718  91 KPAK 94
Cdd:TIGR00988  81 KPGK 84
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 10-92 1.34e-10

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 53.30  E-value: 1.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  10 KKMTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPA 89
Cdd:PRK00285    1 MTLTKADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVT 80


                  ...
gi 2303863718  90 FKP 92
Cdd:PRK00285   81 FRP 83
ihfB PRK00199
integration host factor subunit beta; Reviewed
 12-94 2.65e-10

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 52.18  E-value: 2.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIA-KNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAF 90
Cdd:PRK00199    1 MTKSELIERLAaRNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80


                  ....
gi 2303863718  91 KPAK 94
Cdd:PRK00199   81 KPGK 84
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 12-94 8.79e-10

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: 51.05  E-value: 8.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:TIGR00987   2 LTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTFR 81


                  ...
gi 2303863718  92 PAK 94
Cdd:TIGR00987  82 PGQ 84
PRK10753 PRK10753
DNA-binding protein HU-alpha;
12-96 1.33e-08

DNA-binding protein HU-alpha;


Pssm-ID: 138142  Cd Length: 90  Bit Score: 47.85  E-value: 1.33e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQKTARNISKNTTIIIPAHSIPAFK 91
Cdd:PRK10753    1 MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80


                  ....*
gi 2303863718  92 PAKTF 96
Cdd:PRK10753   81 SGKAL 85
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 12-83 1.00e-04

HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains predominantly observed in the bacteroidetes lineage with a predicted role in recognition and possible interception of the DNA of parasitic elements, a counter-conflict strategy preventing incorporation of these elements into the host genome.


Pssm-ID: 436389  Cd Length: 125  Bit Score: 38.33  E-value: 1.00e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2303863718  12 MTKADIVNEIAKNTGIDKATVLKTVESFMDVVKDSLSKNENVYLRGFGSFIVKTRAQK-------TARNISKNTTIIIP 83
Cdd:pfam18291  32 VTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELGYFSLSLSSKGvddkkevRANSIKFRNINFRP 110
 
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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