DNA-binding protein, histone-like, putative; This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547311085   11 RKYVNQEDSQVLYYVR-QKSGtvrVMDVNKLADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHITLS 89
Cdd:TIGR01201   9 RKAKIGKTGKTMWYPQtVKSG---VMDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTFRLSAT 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 547311085   90 SEGT--EKEKDCTVRSIRRVNVRFVADKALhlvntsHTATRSEN 131
Cdd:TIGR01201  86 AKGSgvEEAEEVSAEQVNKARVLFTPEKTL------KTATREIR 123

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 547311085  38 NK--LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHIT 87
Cdd:cd13831    1 NKaeLIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVR 52

integration host factor subunit alpha; Reviewed

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 547311085  40 LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHI 86
Cdd:PRK00285   8 LAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQL 54

DNA-binding protein, histone-like, putative; This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547311085   11 RKYVNQEDSQVLYYVR-QKSGtvrVMDVNKLADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHITLS 89
Cdd:TIGR01201   9 RKAKIGKTGKTMWYPQtVKSG---VMDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTFRLSAT 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 547311085   90 SEGT--EKEKDCTVRSIRRVNVRFVADKALhlvntsHTATRSEN 131
Cdd:TIGR01201  86 AKGSgvEEAEEVSAEQVNKARVLFTPEKTL------KTATREIR 123

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 547311085  38 NK--LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHIT 87
Cdd:cd13831    1 NKaeLIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVR 52

Bacterial DNA-binding protein;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547311085   40 LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHItlsSEGTEKekdcTVRSIR---------RVNVR 110
Cdd:pfam00216   5 LIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEV---RERAAR----TGRNPKtgetitipaKKVVK 77

                  ....*..
gi 547311085  111 FVADKAL 117
Cdd:pfam00216  78 FKPGKAL 84

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 547311085  40 LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTF 84
Cdd:cd00591    4 LIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKF 48

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).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 547311085  38 NK--LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTF 84
Cdd:cd14435    1 NKteLVAAIAQKAGLTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTF 49

integration host factor subunit alpha; Reviewed

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 547311085  40 LADAIEANSSLTAGDVKHAIEAFVEQLRLSLTQGDKVKIDGLGTFHI 86
Cdd:PRK00285   8 LAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQL 54

CCDC81-like prokaryotic HU domain 2; Second of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 547311085   57 HAIEAFVEQLRLSLTQGDKVKIDGLGTFhiTLSSEGT 93
Cdd:pfam18175  20 QRIEKEVEELKQELQEGGRVELPNIGTL--SLNEEGN 54