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Conserved domains on  [gi|1541475614|gb|RTM20989|]
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DNA-binding protein HU-beta [Enterobacter bugandensis]

Protein Classification

HU family DNA-binding protein( domain architecture ID 10793437)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-90 8.04e-46

DNA-binding protein HU-beta;


:

Pssm-ID: 170612  Cd Length: 90  Bit Score: 141.73  E-value: 8.04e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:PRK10664   1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80

                         90
                 ....*....|
gi 1541475614 81 AGKALKDAVN 90
Cdd:PRK10664  81 AGKALKDAVN 90
 
Name Accession Description Interval E-value
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-90 8.04e-46

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 141.73  E-value: 8.04e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:PRK10664   1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80

                         90
                 ....*....|
gi 1541475614 81 AGKALKDAVN 90
Cdd:PRK10664  81 AGKALKDAVN 90
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 2-87 6.48e-43

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: 134.06  E-value: 6.48e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:cd13831    1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                 ....*.
gi 1541475614 82 GKALKD 87
Cdd:cd13831   81 GKALKD 86
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-90 7.06e-43

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 134.49  E-value: 7.06e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:COG0776    1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80

                         90
                 ....*....|
gi 1541475614 81 AGKALKDAVN 90
Cdd:COG0776   81 PGKELKDAVN 90
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-90 1.82e-37

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 120.75  E-value: 1.82e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614   1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:smart00411  1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80

                          90
                  ....*....|
gi 1541475614  81 AGKALKDAVN 90
Cdd:smart00411 81 PGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-89 4.88e-36

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 116.85  E-value: 4.88e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 1541475614 82 GKALKDAV 89
Cdd:pfam00216 81 GKALKEAV 88
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 1-90 1.12e-20

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: 78.41  E-value: 1.12e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAA-GADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGF 79
Cdd:TIGR00988  1 MTKSELIERIATqQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80

                         90
                 ....*....|.
gi 1541475614 80 RAGKALKDAVN 90
Cdd:TIGR00988 81 KPGKELRDRAN 91
 
Name Accession Description Interval E-value
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-90 8.04e-46

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 141.73  E-value: 8.04e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:PRK10664   1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80

                         90
                 ....*....|
gi 1541475614 81 AGKALKDAVN 90
Cdd:PRK10664  81 AGKALKDAVN 90
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 2-87 6.48e-43

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: 134.06  E-value: 6.48e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:cd13831    1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                 ....*.
gi 1541475614 82 GKALKD 87
Cdd:cd13831   81 GKALKD 86
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-90 7.06e-43

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 134.49  E-value: 7.06e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:COG0776    1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80

                         90
                 ....*....|
gi 1541475614 81 AGKALKDAVN 90
Cdd:COG0776   81 PGKELKDAVN 90
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-90 1.82e-37

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 120.75  E-value: 1.82e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614   1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:smart00411  1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80

                          90
                  ....*....|
gi 1541475614  81 AGKALKDAVN 90
Cdd:smart00411 81 PGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-89 4.88e-36

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 116.85  E-value: 4.88e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 1541475614 82 GKALKDAV 89
Cdd:pfam00216 81 GKALKEAV 88
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 3-87 6.68e-31

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: 103.80  E-value: 6.68e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  3 KSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRAG 82
Cdd:cd00591    1 KKELIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTGRNPATGETIEIPAKKVVKFTPS 80


                 ....*
gi 1541475614 83 KALKD 87
Cdd:cd00591   81 KALKD 85
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 1-88 5.32e-29

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: 99.07  E-value: 5.32e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAA-GADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGF 79
Cdd:cd13836    1 MTKSELIKRIAEkTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                 ....*....
gi 1541475614 80 RAGKALKDA 88
Cdd:cd13836   81 KPGKELKER 89
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 3-87 4.84e-28

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: 96.79  E-value: 4.84e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  3 KSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRAG 82
Cdd:cd13832    1 KADLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARIGRNPKTGEKIVIPARKVVKFKPS 80


                 ....*
gi 1541475614 83 KALKD 87
Cdd:cd13832   81 KELKE 85
PRK10753 PRK10753
DNA-binding protein HU-alpha;
1-89 5.92e-28

DNA-binding protein HU-alpha;


Pssm-ID: 138142  Cd Length: 90  Bit Score: 96.77  E-value: 5.92e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:PRK10753   1 MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80


                 ....*....
gi 1541475614 81 AGKALKDAV 89
Cdd:PRK10753  81 SGKALKDAV 89
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 2-88 2.00e-27

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: 95.06  E-value: 2.00e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:cd14435    1 NKTELVAAIAQKAGLTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFERVERAARTGRNPQTGEAIQIPAGYGVKFSA 80


                 ....*..
gi 1541475614 82 GKALKDA 88
Cdd:cd14435   81 GSKLKKA 87
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 2-89 6.75e-27

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: 93.66  E-value: 6.75e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRA 81
Cdd:cd13835    1 TKADLAEAIYEKLGLSRKEAAELVESVFEEIKEALERGEDVKISGFGTFEVRDKKARPGRNPKTGEEVTISARRVVTFKP 80


                 ....*...
gi 1541475614 82 GKALKDAV 89
Cdd:cd13835   81 SPKLKKRI 88
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-90 1.81e-23

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 85.31  E-value: 1.81e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAA-GADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGF 79
Cdd:PRK00199   1 MTKSELIERLAArNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80

                         90
                 ....*....|.
gi 1541475614 80 RAGKALKDAVN 90
Cdd:PRK00199  81 KPGKELRERVN 91
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 1-90 1.12e-20

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: 78.41  E-value: 1.12e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAA-GADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGF 79
Cdd:TIGR00988  1 MTKSELIERIATqQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80

                         90
                 ....*....|.
gi 1541475614 80 RAGKALKDAVN 90
Cdd:TIGR00988 81 KPGKELRDRAN 91
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 32-90 1.41e-17

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 70.64  E-value: 1.41e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1541475614 32 VTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFRAGKALKDAVN 90
Cdd:PRK00285  34 IRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVTFRPSQKLKSRVE 92
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 1-89 7.25e-15

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: 63.76  E-value: 7.25e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPGFR 80
Cdd:TIGR00987  2 LTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTFR 81


                 ....*....
gi 1541475614 81 AGKALKDAV 89
Cdd:TIGR00987 82 PGQKLKSRV 90
HU_like cd13834
DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins ...
 2-87 1.15e-08

DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins similar to HU 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).


Pssm-ID: 259856  Cd Length: 94  Bit Score: 47.60  E-value: 1.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614  2 NKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVA-----LVGFGTFAVKERAARTGRNPQTGKEITIA---A 73
Cdd:cd13834    1 TKSQLINALAEATGLSKKDVKAVLDSLEELITKELKKKGPGEftlpgLLKIKVVKKPATKARKGRNPFTGEEMTFKakpA 80

                         90
                 ....*....|....
gi 1541475614 74 AKVPGFRAGKALKD 87
Cdd:cd13834   81 SKVVKVRPLKKLKD 94
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-90 7.19e-06

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: 41.03  E-value: 7.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1541475614   1 MNKSQLIDKIAAGADISKAAAGRALDALIASVTESLQAGDDVALVGFGTFavkeRAARTGRNPQTGKEITIAAAKVPG-- 78
Cdd:pfam18291  32 VTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELGYF----SLSLSSKGVDDKKEVRANSIKFRNin 107

                          90
                  ....*....|..
gi 1541475614  79 FRAGKALKDAVN 90
Cdd:pfam18291 108 FRPGKKLKRELK 119
 
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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