RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780444|ref|YP_003064857.1| bacteriophage repressor protein C1 [Candidatus Liberibacter asiaticus str. psy62] (223 letters) >gnl|CDD|32756 COG2932, COG2932, Predicted transcriptional regulator [Transcription]. Length = 214 Score = 127 bits (319), Expect = 3e-30 Identities = 78/221 (35%), Positives = 108/221 (48%), Gaps = 14/221 (6%) Query: 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64 SH AID +AER + SGLARK GLDPTSFN SKR + RW ST S K+L A Sbjct: 3 SHDSGGRAIDALAERGKASSSGLARKEGLDPTSFNLSKRASADVSARWLSTGSGEKVLEA 62 Query: 65 TNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIR 124 DL D IP+ +G+ GFFD FP G W+ + P Sbjct: 63 AGAPT----DLTAGDASENPVV-PLIPVSGAAGAGADGFFDENGFPVGFGWDEIERPPGI 117 Query: 125 SPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKV 184 P +G++A++ SM P Y GD L+++ + GDR+ ++ G++ K Sbjct: 118 DPDSGVFALR-------VTGDSMEPTYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKK 170 Query: 185 LISRRGRSIDLMSLNCCYPVDTV--EMSDIEWIARILWASQ 223 L G + L+SLN Y D + E D+E I R++W S+ Sbjct: 171 LQREPGGLLRLVSLNPDYYPDEIFSEDDDVEIIGRVVWVSR 211 >gnl|CDD|119397 cd06529, S24_LexA-like, 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.. Length = 81 Score = 49.1 bits (118), Expect = 8e-07 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 1/76 (1%) Query: 143 QDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCY 202 + SM P GD+++++ + GD ++ + G++ K L R G + L+S N Y Sbjct: 6 KGDSMEPTIPDGDLVLVDPSDTPRDGDIVVAR-LDGELTVKRLQRRGGGRLRLISDNPAY 64 Query: 203 PVDTVEMSDIEWIARI 218 P ++ ++E + + Sbjct: 65 PPIEIDEEELEIVGVV 80 >gnl|CDD|119396 cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: 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 S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique 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.. Length = 84 Score = 36.5 bits (85), Expect = 0.006 Identities = 18/81 (22%), Positives = 29/81 (35%), Gaps = 20/81 (24%) Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVA----------KVLISRRGR-SID 194 SM P GD++++ D+ +P+ GDIV K +I G Sbjct: 9 SMEPTIPDGDLVLV---------DKSSYEPKRGDIVVFRLPGGELTVKRVIGLPGEGHYF 59 Query: 195 LMSLNCCYPVDTVEMSDIEWI 215 L+ N P ++ I Sbjct: 60 LLGDNPNSPDSRIDGPPELDI 80 >gnl|CDD|144350 pfam00717, Peptidase_S24, Peptidase S24-like. Length = 67 Score = 34.5 bits (80), Expect = 0.021 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%) Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYP 203 SM P GD+L+++ + GD ++ + + K LI G I L+ N YP Sbjct: 6 SMEPTIPDGDLLLVDKTSEPKRGDIVVARLPGEEAYVKRLIGLPGDII-LLPSNPEYP 62 >gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.. Length = 58 Score = 31.3 bits (71), Expect = 0.21 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%) Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 E + + + LT LA K G+ ++ ++ IE R PS E++ K+ A ++ Sbjct: 2 ERLKELRKEKGLTQEELAEKLGVSRSTISR-----IENGKRNPSLETLEKLAKALGVSL 55 >gnl|CDD|29994 cd01128, rho_factor, Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.. Length = 249 Score = 31.4 bits (71), Expect = 0.23 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%) Query: 11 EAIDRMAERHNLT--PSGLARKAGLDPTSFNKSKRFGIEGRN 50 ++I R+A +N PSG G+D + +K KRF RN Sbjct: 110 DSITRLARAYNTVVPPSGKILSGGVDANALHKPKRFFGAARN 151 >gnl|CDD|31352 COG1158, Rho, Transcription termination factor [Transcription]. Length = 422 Score = 31.0 bits (70), Expect = 0.26 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%) Query: 11 EAIDRMAERHNLT--PSGLARKAGLDPTSFNKSKRFGIEGRN 50 ++I R+A +N SG G+D + ++ KRF RN Sbjct: 267 DSITRLARAYNTVVPSSGKVLSGGVDANALHRPKRFFGAARN 308 >gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators [Transcription]. Length = 120 Score = 29.6 bits (64), Expect = 0.69 Identities = 15/80 (18%), Positives = 38/80 (47%), Gaps = 4/80 (5%) Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 E + + ++ L+ LA + G+ ++ ++ +R GR+ PS E + ++ AA ++ Sbjct: 4 ERLKELRKKKGLSQEELAERLGVSRSTISRIER----GRSESPSLELLARLAAALGVSLD 59 Query: 71 QLLDLPFSDGRTTEKKEKEI 90 +LL+ + ++ Sbjct: 60 ELLEEEEELEIEELNELAKL 79 >gnl|CDD|145926 pfam03036, Perilipin, Perilipin family. The perilipin family includes lipid droplet-associated protein (perilipin) and adipose differentiation-related protein (adipophilin). Length = 390 Score = 28.2 bits (63), Expect = 1.9 Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 10/36 (27%) Query: 62 LAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPP 97 +AA NE C+ LD K E+++P+L PP Sbjct: 78 IAAANELACKGLD----------KLEEKLPILQQPP 103 >gnl|CDD|30773 COG0424, Maf, Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]. Length = 193 Score = 28.2 bits (63), Expect = 2.0 Identities = 12/59 (20%), Positives = 25/59 (42%) Query: 155 DILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIE 213 D L++ + V R+L KP+ + ++L GR+ + + S++E Sbjct: 64 DALVIGADTVVVLDGRILGKPKDEEEAREMLRKLSGRTHQVYTGVALIDPGKRVQSEVE 122 >gnl|CDD|119398 cd06530, S26_SPase_I, 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.. Length = 85 Score = 27.5 bits (62), Expect = 2.7 Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 6/36 (16%) Query: 146 SMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIV 181 SM P + GD++++N +P+ GD+V Sbjct: 9 SMEPTLQPGDLVLVNKL------SYGFREPKRGDVV 38 >gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Length = 55 Score = 27.5 bits (62), Expect = 2.8 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 5/55 (9%) Query: 18 ERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 E L+ LA K G+ ++ +K IE R PS E++ K+ A ++ +L Sbjct: 6 EELGLSQEELAEKLGVSRSTISK-----IENGKREPSLETLKKLAEALGVSLDEL 55 >gnl|CDD|31036 COG0692, Ung, Uracil DNA glycosylase [DNA replication, recombination, and repair]. Length = 223 Score = 26.7 bits (59), Expect = 5.2 Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 14/70 (20%) Query: 55 TESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYF---------PPSGSGGFFD 105 T+++ K L E + +L G +KK+K I P S GFF Sbjct: 145 TDAVIKALNERREPVVFVLW-----GSHAQKKKKLIDNKKHLILEAPHPSPLSAHRGFFG 199 Query: 106 SGVFPTGNKW 115 F N+W Sbjct: 200 CKHFSKANEW 209 >gnl|CDD|33190 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]. Length = 978 Score = 26.5 bits (58), Expect = 6.2 Identities = 6/22 (27%), Positives = 12/22 (54%) Query: 168 GDRLLIKPRTGDIVAKVLISRR 189 GD + + G+I + L++ R Sbjct: 872 GDLVRLTSEFGEIKLRALVTDR 893 >gnl|CDD|146768 pfam04303, PrpF, PrpF protein. PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerize trans-aconitate to cis-aconitate. Length = 371 Score = 26.3 bits (58), Expect = 6.5 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 15/69 (21%) Query: 63 AATNETICQLLDLPFSDGRTTEKKE----------KEIPLLYFPPSGSGGFFDSGVFPTG 112 T +TI +P +G+ + I L + +G G +FPTG Sbjct: 124 VNTGKTI--EAHVPTPNGQVQYDGDFEIDGVPGPGAPIALTFLDAAGDGT---GALFPTG 178 Query: 113 NKWNTVGVP 121 N +T+ VP Sbjct: 179 NLIDTLDVP 187 >gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]. Length = 604 Score = 26.0 bits (57), Expect = 8.6 Identities = 9/25 (36%), Positives = 13/25 (52%) Query: 154 GDILILNSAIQVNCGDRLLIKPRTG 178 G L+ +V G+RLLI +G Sbjct: 405 GQTLLSELNFEVRPGERLLITGESG 429 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.136 0.418 Gapped Lambda K H 0.267 0.0616 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,815,335 Number of extensions: 141586 Number of successful extensions: 312 Number of sequences better than 10.0: 1 Number of HSP's gapped: 307 Number of HSP's successfully gapped: 24 Length of query: 223 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 133 Effective length of database: 4,318,927 Effective search space: 574417291 Effective search space used: 574417291 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.2 bits)