NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|339834436|gb|EGQ62201|]
View 

DNA-binding protein HU family protein [Acidithiobacillus sp. GGI-221]

Protein Classification

HU family DNA-binding protein( domain architecture ID 10194961)

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 4-89 1.25e-27

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: 95.54  E-value: 1.25e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  4 KKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKV 83
Cdd:cd13831   1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                ....*.
gi 339834436 84 AKSLQD 89
Cdd:cd13831  81 GKALKD 86
 
Name Accession Description Interval E-value
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 4-89 1.25e-27

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: 95.54  E-value: 1.25e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  4 KKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKV 83
Cdd:cd13831   1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                ....*.
gi 339834436 84 AKSLQD 89
Cdd:cd13831  81 GKALKD 86
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-93 4.14e-26

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 92.12  E-value: 4.14e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTlkKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVT 80
Cdd:COG0776   1 MT--KSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVK 78

                        90
                ....*....|...
gi 339834436 81 FKVAKSLQDKVNP 93
Cdd:COG0776  79 FKPGKELKDAVNG 91
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
4-91 1.54e-22

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 82.95  E-value: 1.54e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436   4 KKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKV 83
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 339834436  84 AKSLQDKV 91
Cdd:pfam00216 81 GKALKEAV 88
BHL smart00411
bacterial (prokaryotic) histone like domain;
5-92 3.15e-20

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 77.22  E-value: 3.15e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436    5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKVA 84
Cdd:smart00411  3 KSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFKPG 82


                  ....*...
gi 339834436   85 KSLQDKVN 92
Cdd:smart00411 83 KALKDAVN 90
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 1-92 2.37e-14

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 62.55  E-value: 2.37e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTLKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVT 80
Cdd:PRK00285  1 MTLTKADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVT 80

                        90
                ....*....|..
gi 339834436 81 FKVAKSLQDKVN 92
Cdd:PRK00285 81 FRPSQKLKSRVE 92
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 2-91 1.68e-11

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: 55.28  E-value: 1.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436   2 TLKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTF 81
Cdd:TIGR00987  1 ALTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTF 80

                         90
                 ....*....|
gi 339834436  82 KVAKSLQDKV 91
Cdd:TIGR00987 81 RPGQKLKSRV 90
 
Name Accession Description Interval E-value
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 4-89 1.25e-27

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: 95.54  E-value: 1.25e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  4 KKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKV 83
Cdd:cd13831   1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


                ....*.
gi 339834436 84 AKSLQD 89
Cdd:cd13831  81 GKALKD 86
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-93 4.14e-26

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 92.12  E-value: 4.14e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTlkKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVT 80
Cdd:COG0776   1 MT--KSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVK 78

                        90
                ....*....|...
gi 339834436 81 FKVAKSLQDKVNP 93
Cdd:COG0776  79 FKPGKELKDAVNG 91
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
4-91 1.54e-22

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 82.95  E-value: 1.54e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436   4 KKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKV 83
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 339834436  84 AKSLQDKV 91
Cdd:pfam00216 81 GKALKEAV 88
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 5-89 3.16e-21

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: 79.54  E-value: 3.16e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKVA 84
Cdd:cd00591   1 KKELIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTGRNPATGETIEIPAKKVVKFTPS 80


                ....*
gi 339834436 85 KSLQD 89
Cdd:cd00591  81 KALKD 85
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 5-87 6.12e-21

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: 78.88  E-value: 6.12e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKVA 84
Cdd:cd14435   2 KTELVAAIAQKAGLTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFERVERAARTGRNPQTGEAIQIPAGYGVKFSAG 81


                ...
gi 339834436 85 KSL 87
Cdd:cd14435  82 SKL 84
BHL smart00411
bacterial (prokaryotic) histone like domain;
5-92 3.15e-20

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 77.22  E-value: 3.15e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436    5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKVA 84
Cdd:smart00411  3 KSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFKPG 82


                  ....*...
gi 339834436   85 KSLQDKVN 92
Cdd:smart00411 83 KALKDAVN 90
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 5-91 3.15e-16

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: 66.70  E-value: 3.15e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  5 KSELVAALAYHAESSKAEAERFLEAFGKTI--HAEITKVVKIVvpEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFK 82
Cdd:cd13835   2 KADLAEAIYEKLGLSRKEAAELVESVFEEIkeALERGEDVKIS--GFGTFEVRDKKARPGRNPKTGEEVTISARRVVTFK 79


                ....*....
gi 339834436 83 VAKSLQDKV 91
Cdd:cd13835  80 PSPKLKKRI 88
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 5-87 1.68e-14

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: 62.51  E-value: 1.68e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFKVA 84
Cdd:cd13832   1 KADLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARIGRNPKTGEKIVIPARKVVKFKPS 80


                ...
gi 339834436 85 KSL 87
Cdd:cd13832  81 KEL 83
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 1-92 2.37e-14

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 62.55  E-value: 2.37e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTLKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVT 80
Cdd:PRK00285  1 MTLTKADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVT 80

                        90
                ....*....|..
gi 339834436 81 FKVAKSLQDKVN 92
Cdd:PRK00285 81 FRPSQKLKSRVE 92
PRK10664 PRK10664
DNA-binding protein HU-beta;
3-92 3.80e-14

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 61.60  E-value: 3.80e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  3 LKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFK 82
Cdd:PRK10664  1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80

                        90
                ....*....|
gi 339834436 83 VAKSLQDKVN 92
Cdd:PRK10664 81 AGKALKDAVN 90
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 1-90 3.92e-12

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: 56.31  E-value: 3.92e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTlkKSELVAALA-YHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGV 79
Cdd:cd13836   1 MT--KSELIKRIAeKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVP 78

                        90
                ....*....|.
gi 339834436 80 TFKVAKSLQDK 90
Cdd:cd13836  79 HFKPGKELKER 89
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 2-91 1.68e-11

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: 55.28  E-value: 1.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436   2 TLKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTF 81
Cdd:TIGR00987  1 ALTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTF 80

                         90
                 ....*....|
gi 339834436  82 KVAKSLQDKV 91
Cdd:TIGR00987 81 RPGQKLKSRV 90
PRK10753 PRK10753
DNA-binding protein HU-alpha;
3-91 1.01e-09

DNA-binding protein HU-alpha;


Pssm-ID: 138142  Cd Length: 90  Bit Score: 50.55  E-value: 1.01e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  3 LKKSELVAALAYHAESSKAEAERFLEAFGKTIHAEITKVVKIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAARNGVTFK 82
Cdd:PRK10753  1 MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80


                ....*....
gi 339834436 83 VAKSLQDKV 91
Cdd:PRK10753 81 SGKALKDAV 89
HU_like cd13834
DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins ...
 5-89 1.07e-07

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: 45.29  E-value: 1.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  5 KSELVAALAYHAESSKAEAERFLEAFGKTIHAEITK--VVKIVVPEVGTFQLSRK---EARKGRNPQTGEEIQIA---AR 76
Cdd:cd13834   2 KSQLINALAEATGLSKKDVKAVLDSLEELITKELKKkgPGEFTLPGLLKIKVVKKpatKARKGRNPFTGEEMTFKakpAS 81

                        90
                ....*....|...
gi 339834436 77 NGVTFKVAKSLQD 89
Cdd:cd13834  82 KVVKVRPLKKLKD 94
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-92 7.44e-06

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 40.63  E-value: 7.44e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 339834436  1 MTlkKSELVAALAYHAESSKAeaeRFLEAFGKTIHAEITKVV----KIVVPEVGTFQLSRKEARKGRNPQTGEEIQIAAR 76
Cdd:PRK00199  1 MT--KSELIERLAARNPHLSA---KDVENAVKEILEEMSDALargdRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEK 75

                        90
                ....*....|....*.
gi 339834436 77 NGVTFKVAKSLQDKVN 92
Cdd:PRK00199 76 YVPHFKPGKELRERVN 91
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH