Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460  96 IPKVRLKLQAGVMGVVTEPLPEEsgkttilraWVDKRGFQPEKLVAIEVKGESMEPTLYAGDTVFINLADTQPAENGVFA 175
Cdd:COG2932     1 VPLYDGEASAGGGAFNEVEEPVD---------KLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1585091460 176 VNYEGEAVVKRL-SRDAGDWWLTSDNSDQRKYHRKVCRGVDCLIVGRVV 223
Cdd:COG2932    72 VRTDGELLVKRLqRRPDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460  96 IPKVRLKLQAGVMGVVTEPLPEEsgkttilraWVDKRGFQPEKLVAIEVKGESMEPTLYAGDTVFINLADTQPAENGVFA 175
Cdd:COG2932     1 VPLYDGEASAGGGAFNEVEEPVD---------KLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1585091460 176 VNYEGEAVVKRL-SRDAGDWWLTSDNSDQRKYHRKVCRGVDCLIVGRVV 223
Cdd:COG2932    72 VRTDGELLVKRLqRRPDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460 140 VAIEVKGESMEPTLYAGDTVFINLADTqPAENGVFAVNYEGEAVVKRLSRD-AGDWWLTSDNSDqrkYHRKVCRGVDCLI 218
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRgGGRLRLISDNPA---YPPIEIDEEELEI 76

                  ....*
gi 1585091460 219 VGRVV 223
Cdd:cd06529    77 VGVVG 81

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1585091460   5 QRLTQARVEKNLSKSELARAINVSPATITQWESGTTKeLKGENLTAVCSVLGLAAEWL 62
Cdd:cd00093     2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDEL 58

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1585091460   9 QARVEKNLSKSELARAINVSPATITQWESGTTkELKGENLTAVCSVLGLAAEWL 62
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55

nickel-type superoxide dismutase maturation protease; Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad. [Cellular processes, Detoxification, Protein fate, Protein modification and repair]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460 143 EVKGESMEPTLYAGDTVFINLADTQP--AENGVFAV----NYEGEAVVKRLS-RDAGDWWLTSDNSDQRKYHRK---VCR 212
Cdd:TIGR02754   2 KVTGVSMSPTLPPGDRIIVVPWLKIFrvPPIGNVVVvrhpLQPYGLIIKRLAaVDDNGLFLLGDNPKASTDSRQlgpVPR 81

                          90
                  ....*....|.
gi 1585091460 213 GvdcLIVGRVV 223
Cdd:TIGR02754  82 S---LLLGKVL 89

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460  96 IPKVRLKLQAGVMGVVTEPLPEEsgkttilraWVDKRGFQPEKLVAIEVKGESMEPTLYAGDTVFINLADTQPAENGVFA 175
Cdd:COG2932     1 VPLYDGEASAGGGAFNEVEEPVD---------KLEFPGLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIYV 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1585091460 176 VNYEGEAVVKRL-SRDAGDWWLTSDNSDQRKYHRKVCRGVDCLIVGRVV 223
Cdd:COG2932    72 VRTDGELLVKRLqRRPDGKLRLISDNPAYPPIEIPPEDADEIEIIGRVV 120

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460 140 VAIEVKGESMEPTLYAGDTVFINLADTqPAENGVFAVNYEGEAVVKRLSRD-AGDWWLTSDNSDqrkYHRKVCRGVDCLI 218
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDT-PRDGDIVVARLDGELTVKRLQRRgGGRLRLISDNPA---YPPIEIDEEELEI 76

                  ....*
gi 1585091460 219 VGRVV 223
Cdd:cd06529    77 VGVVG 81

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460 136 PEKLVAIEVKGESM-EPTLYAGDTVFINLADTqpAENG-VFAVNYEGEAVVKRLSRDAGDWWLTSDNSDqrkYHRKVCRG 213
Cdd:COG1974   109 PGATFALRVKGDSMiDAGILDGDLVIVDRQLE--AENGdIVVALIDGEATVKRLYKEGGRVRLQPENPA---YPPIIIEG 183

                          90
                  ....*....|
gi 1585091460 214 VDCLIVGRVV 223
Cdd:COG1974   184 DDVEILGVVV 193

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1585091460   5 QRLTQARVEKNLSKSELARAINVSPATITQWESGTTKeLKGENLTAVCSVLGLAAEWL 62
Cdd:cd00093     2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDEL 58

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1585091460   9 QARVEKNLSKSELARAINVSPATITQWESGTTkELKGENLTAVCSVLGLAAEWL 62
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585091460   1 MNWNQRLTQARVEKNLSKSELARAINVSPATITQWESGTTKeLKGENLTAVCSVLGLAAEWLL 63
Cdd:COG1476     3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYN-PSLELALKIARALGVSLEELF 64

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1585091460   6 RLTQARVEKNLSKSELARAINVSPATITQWESGTTKELKGENLTAVCSVLG 56
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALG 51

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1585091460   2 NWNQRLTQARVEKNLSKSELARAINVSPATITQWESGTTKeLKGENLTAVCSVLGLAAEW 61
Cdd:COG1813    12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEAT-PSLDTLRKLEKALGISLAE 70

bifunctional HTH-domain containing protein/aminotransferase; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1585091460   6 RLTQARVEKNLSKSELARA-----INVSPATITQWESGTTkELKGENLTAVCSVLGLAAEWLLHGRGPKALDPTAL 76
Cdd:PRK13355    7 RLKQAMKARGLKQEDLVHAaeargVKLGKSHISQYVSGKT-GPRRDVLPFLAAILGVSEDWLLGGESPADQESDAS 81

The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa) belong to this family and they process many proteins that enter the ER for retention or for export to the Golgi apparatus, secretory vesicles, plasma membranes or vacuole. An atypical member of the S26 SPase type I family is the TraF peptidase which has the remarkable activity of producing a cyclic protein of the Pseudomonas pilin system. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism.

                          10
                  ....*....|....*....
gi 1585091460 144 VKGESMEPTLYAGDTVFIN 162
Cdd:cd06530     5 VPGGSMEPTLQPGDLVLVN 23

Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1585091460 123 TILRAWVdkrgFQPeklvaIEVKGESMEPTLYAGDTVFIN 162
Cdd:COG0681    26 LLIRTFV----FEP-----FVIPSGSMEPTLLVGDRLLVN 56