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Conserved domains on  [gi|56405014|sp|P68574|]
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RecName: Full=DNA-binding protein HU 2

Protein Classification

HU family DNA-binding protein( domain architecture ID 10002493)

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:0030527|GO:0030261
PubMed:  4038648

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-92 7.83e-42

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


:

Pssm-ID: 440539  Cd Length: 92  Bit Score: 131.80  E-value: 7.83e-42
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:COG0776  1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80

                       90
               ....*....|..
gi 56405014 81 PAKALKDAVKAK 92
Cdd:COG0776 81 PGKELKDAVNGS 92
 
Name Accession Description Interval E-value
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-92 7.83e-42

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 131.80  E-value: 7.83e-42
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:COG0776  1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80

                       90
               ....*....|..
gi 56405014 81 PAKALKDAVKAK 92
Cdd:COG0776 81 PGKELKDAVNGS 92
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 2-87 4.03e-41

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: 129.82  E-value: 4.03e-41
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:cd13831  1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


               ....*.
gi 56405014 82 AKALKD 87
Cdd:cd13831 81 GKALKD 86
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-90 3.38e-36

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 117.67  E-value: 3.38e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014     1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:smart00411  1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80

                          90
                  ....*....|
gi 56405014    81 PAKALKDAVK 90
Cdd:smart00411 81 PGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-89 4.53e-34

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 112.22  E-value: 4.53e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014    2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 56405014   82 AKALKDAV 89
Cdd:pfam00216 81 GKALKEAV 88
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-89 1.10e-26

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 93.58  E-value: 1.10e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014   1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:PRK10664  1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80


                ....*....
gi 56405014  81 PAKALKDAV 89
Cdd:PRK10664 81 AGKALKDAV 89
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 1-92 1.03e-21

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: 81.09  E-value: 1.03e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014    1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:TIGR00987  2 LTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTFR 81

                         90
                 ....*....|..
gi 56405014   81 PAKALKDAVKAK 92
Cdd:TIGR00987 82 PGQKLKSRVENA 93
 
Name Accession Description Interval E-value
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-92 7.83e-42

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 131.80  E-value: 7.83e-42
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:COG0776  1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKFK 80

                       90
               ....*....|..
gi 56405014 81 PAKALKDAVKAK 92
Cdd:COG0776 81 PGKELKDAVNGS 92
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 2-87 4.03e-41

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: 129.82  E-value: 4.03e-41
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:cd13831  1 NKAELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFKP 80


               ....*.
gi 56405014 82 AKALKD 87
Cdd:cd13831 81 GKALKD 86
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-90 3.38e-36

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 117.67  E-value: 3.38e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014     1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:smart00411  1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKFK 80

                          90
                  ....*....|
gi 56405014    81 PAKALKDAVK 90
Cdd:smart00411 81 PGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-89 4.53e-34

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 112.22  E-value: 4.53e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014    2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:pfam00216  1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFKP 80


                 ....*...
gi 56405014   82 AKALKDAV 89
Cdd:pfam00216 81 GKALKEAV 88
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 1-88 4.11e-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: 107.16  E-value: 4.11e-32
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  1 MNKTELIAKVAEK-QGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAF 79
Cdd:cd13836  1 MTKSELIKRIAEKtPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


               ....*....
gi 56405014 80 KPAKALKDA 88
Cdd:cd13836 81 KPGKELKER 89
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 2-88 1.35e-31

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: 105.85  E-value: 1.35e-31
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:cd14435  1 NKTELVAAIAQKAGLTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFERVERAARTGRNPQTGEAIQIPAGYGVKFSA 80


               ....*..
gi 56405014 82 AKALKDA 88
Cdd:cd14435 81 GSKLKKA 87
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 3-87 4.22e-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: 104.50  E-value: 4.22e-31
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  3 KTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKPA 82
Cdd:cd13832  1 KADLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARIGRNPKTGEKIVIPARKVVKFKPS 80


               ....*
gi 56405014 83 KALKD 87
Cdd:cd13832 81 KELKE 85
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 3-87 4.51e-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: 104.57  E-value: 4.51e-31
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  3 KTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKPA 82
Cdd:cd00591  1 KKELIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTGRNPATGETIEIPAKKVVKFTPS 80


               ....*
gi 56405014 83 KALKD 87
Cdd:cd00591 81 KALKD 85
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 2-89 1.48e-30

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: 103.29  E-value: 1.48e-30
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKP 81
Cdd:cd13835  1 TKADLAEAIYEKLGLSRKEAAELVESVFEEIKEALERGEDVKISGFGTFEVRDKKARPGRNPKTGEEVTISARRVVTFKP 80


               ....*...
gi 56405014 82 AKALKDAV 89
Cdd:cd13835 81 SPKLKKRI 88
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-89 1.10e-26

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 93.58  E-value: 1.10e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014   1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:PRK10664  1 MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFR 80


                ....*....
gi 56405014  81 PAKALKDAV 89
Cdd:PRK10664 81 AGKALKDAV 89
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 3-89 3.03e-25

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 89.90  E-value: 3.03e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014   3 KTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFKPA 82
Cdd:PRK00285  5 KADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVTFRPS 84


                ....*..
gi 56405014  83 KALKDAV 89
Cdd:PRK00285 85 QKLKSRV 91
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-89 6.52e-25

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 89.16  E-value: 6.52e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014   1 MNKTELIAKVAEKQG-VSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAF 79
Cdd:PRK00199  1 MTKSELIERLAARNPhLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80

                        90
                ....*....|
gi 56405014  80 KPAKALKDAV 89
Cdd:PRK00199 81 KPGKELRERV 90
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 1-92 1.03e-21

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: 81.09  E-value: 1.03e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014    1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:TIGR00987  2 LTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTFR 81

                         90
                 ....*....|..
gi 56405014   81 PAKALKDAVKAK 92
Cdd:TIGR00987 82 PGQKLKSRVENA 93
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 1-89 2.13e-21

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: 80.34  E-value: 2.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014    1 MNKTELIAKVAEKQG-VSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAF 79
Cdd:TIGR00988  1 MTKSELIERIATQQShLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80

                         90
                 ....*....|
gi 56405014   80 KPAKALKDAV 89
Cdd:TIGR00988 81 KPGKELRDRA 90
PRK10753 PRK10753
DNA-binding protein HU-alpha;
1-90 2.57e-21

DNA-binding protein HU-alpha;


Pssm-ID: 138142  Cd Length: 90  Bit Score: 79.82  E-value: 2.57e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014   1 MNKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGEKVSIPGFGTFEVRERAARKGRNPQTGEEIDIPATKAPAFK 80
Cdd:PRK10753  1 MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFV 80

                        90
                ....*....|
gi 56405014  81 PAKALKDAVK 90
Cdd:PRK10753 81 SGKALKDAVK 90
HU_like cd13834
DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins ...
 2-87 1.25e-10

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: 52.61  E-value: 1.25e-10
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56405014  2 NKTELIAKVAEKQGVSKKEGAPSVEKVFDTISEALKSGE--KVSIPGFGTFEVRE---RAARKGRNPQTGEEIDI---PA 73
Cdd:cd13834  1 TKSQLINALAEATGLSKKDVKAVLDSLEELITKELKKKGpgEFTLPGLLKIKVVKkpaTKARKGRNPFTGEEMTFkakPA 80

                       90
               ....*....|....
gi 56405014 74 TKAPAFKPAKALKD 87
Cdd:cd13834 81 SKVVKVRPLKKLKD 94
 
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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