Replicase family; This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2070188773  28 LRIADVARALGARYIQPNGPTHRHWIVFDVDHAAATLSWDDVGAPAPNITVTNKANGHAHLIYGLDTPIRTAPDGNAAPL 107
Cdd:pfam03090   1 LKVRPREDALQYPYVQLNPPQLASWLVFDLDHPDAGLRWEDAGLPPPNLIVINPVNGHCHLLYGLKDPVYTTENARSKPL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2070188773 108 RYAAAIEAALREKLGADMGYSGLICKNPLHEHWLVQVWEPRLYDLAWL 155
Cdd:pfam03090  81 RYMKAVTEALRARLDADPAYSGLISKNPFHTAWRTHEQHPRVYDLGDL 128

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2070188773 176 GRNCTLFEKTRLWAYKAIRQgwpdypewlAACVDRASGYNAQFEQPLPANEVRHTAKSIAKWT 238
Cdd:pfam08708   9 GRNNALFRLAGALARRGIDR---------ESVLALLHALNSNLEPPLDESEVEKTVKSVYRYV 62

Replicase family; This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2070188773  28 LRIADVARALGARYIQPNGPTHRHWIVFDVDHAAATLSWDDVGAPAPNITVTNKANGHAHLIYGLDTPIRTAPDGNAAPL 107
Cdd:pfam03090   1 LKVRPREDALQYPYVQLNPPQLASWLVFDLDHPDAGLRWEDAGLPPPNLIVINPVNGHCHLLYGLKDPVYTTENARSKPL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2070188773 108 RYAAAIEAALREKLGADMGYSGLICKNPLHEHWLVQVWEPRLYDLAWL 155
Cdd:pfam03090  81 RYMKAVTEALRARLDADPAYSGLISKNPFHTAWRTHEQHPRVYDLGDL 128

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:COG2197    76 EVLRLLAEGLSNKEIAERLGISERTVKTHVSN 107

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:cd06170     7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRN 38

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2070188773  176 GRNCTLFEKTRlwayKAIRQGWPDyPEWLAACVDRASGYNAQfeQPLPANEVRHTAKSIAKWTH 239
Cdd:smart00942   9 NRNNTLFRLAG----RLLRRGYVD-EEEAYALLLAANSANCN--PPLPERELEKTAESAYRRES 65

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2070188773 281 EVLRLKA-QGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:TIGR02937 117 EVLVLRYlEGLSYKEIAEILGISVGTVKRRLKR 149

Replicase family; This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2070188773  28 LRIADVARALGARYIQPNGPTHRHWIVFDVDHAAATLSWDDVGAPAPNITVTNKANGHAHLIYGLDTPIRTAPDGNAAPL 107
Cdd:pfam03090   1 LKVRPREDALQYPYVQLNPPQLASWLVFDLDHPDAGLRWEDAGLPPPNLIVINPVNGHCHLLYGLKDPVYTTENARSKPL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2070188773 108 RYAAAIEAALREKLGADMGYSGLICKNPLHEHWLVQVWEPRLYDLAWL 155
Cdd:pfam03090  81 RYMKAVTEALRARLDADPAYSGLISKNPFHTAWRTHEQHPRVYDLGDL 128

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:COG2197    76 EVLRLLAEGLSNKEIAERLGISERTVKTHVSN 107

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:cd06170     7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRN 38

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:COG5905    19 EVLELLAEGLTNKEIARQLFISEKTVKNHVSN 50

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2070188773  176 GRNCTLFEKTRlwayKAIRQGWPDyPEWLAACVDRASGYNAQfeQPLPANEVRHTAKSIAKWTH 239
Cdd:smart00942   9 NRNNTLFRLAG----RLLRRGYVD-EEEAYALLLAANSANCN--PPLPERELEKTAESAYRRES 65

Homeodomain-like domain;

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:pfam13384   9 RALLLLAEGLSVKEIAELLGVSRRTVYRWLKR 40

transcriptional regulator NarL; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2070188773 268 PSNSGKDKSDLLP---EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:PRK10651  146 RATTERDVNQLTPrerDILKLIAQGLPNKMIARRLDITESTVKVHVKH 193

Transcriptional regulator [Transcription];

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKRDR 314
Cdd:COG1356    15 EVLALRERGLTQQEIADILGTSRANVSSIEKSAR 48

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2070188773 281 EVLRLKA-QGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:TIGR02937 117 EVLVLRYlEGLSYKEIAEILGISVGTVKRRLKR 149

IS630 family transposase;

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2070188773 282 VLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:NF033545    5 ILLLAAEGLSITEIAERLGVSRSTVYRWLKR 35

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2070188773 281 EVLRLKAQGYTNRDIADDLQISPSTVSVYLKR 312
Cdd:pfam13936  12 EIARLLAEGLSLREIARRLGRSPSTISRELRR 43