RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780444|ref|YP_003064857.1| bacteriophage repressor protein C1 [Candidatus Liberibacter asiaticus str. psy62] (223 letters) >2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A Length = 189 Score = 45.1 bits (106), Expect = 1e-05 Identities = 25/213 (11%), Positives = 55/213 (25%), Gaps = 41/213 (19%) Query: 11 EAIDRMAERHNL-TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69 + +DR+ E + LA + +S + G + ET Sbjct: 9 DVLDRICEAYGFSQKIQLANHFDIASSSLSNRYTRGAISYD---------FAAHCALETG 59 Query: 70 CQLLDLPFSDGRTTEKKEKEIPLLYFP--PSGSGGFFDSGVFPTGNKWNTVGVPEIRSPH 127 L L +G + ++ T + Sbjct: 60 ANLQWLLTGEGEAFVNNRESSDAKRIEGFTLSEEILKSDKQLSVDAQFFTKPL------- 112 Query: 128 NGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLIS 187 T + + +G I ++ ++ G L+ I + L Sbjct: 113 -----------------TDGMAIRSEGKIYFVDKQASLSDGLWLVDIKGAISI--RELTK 153 Query: 188 RRGRSIDLMSLNCCYPVDTVEMSDIEWIARILW 220 GR + + + + DI+ + R++ Sbjct: 154 LPGRKLHVAGGKVPFE---CGIDDIKTLGRVVG 183 >3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236 Score = 38.9 bits (89), Expect = 8e-04 Identities = 22/224 (9%), Positives = 62/224 (27%), Gaps = 20/224 (8%) Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66 +++ ++ L+ +A K G+ + + + + + Sbjct: 16 RRLKAIYEKKKNELGLSQESVADKMGMGQSGVGA-----LFNGINALNAYNAALLAKILK 70 Query: 67 ETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSP 126 ++ + + E + + G + Sbjct: 71 VSVEE----FSPSIAREIYEMYEAVSMQPSLRSEYEYPVFSHVQAGMFSPELRTFTKGDA 126 Query: 127 HNGIYAIQTQDTRH---KTQDTSML------PLYRKGDILILNSAIQVNCGDRLLIKPRT 177 + + + + SM P + G +++++ V GD + + Sbjct: 127 ERWVSTTKKASDSAFWLEVEGNSMTAPTGSKPSFPDGMLILVDPEQAVEPGDFCIARLGG 186 Query: 178 GDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWA 221 + K LI R + L LN YP+ + +++ + Sbjct: 187 DEFTFKKLI-RGSGQVFLQPLNPQYPMIPCN-ESCSVVGKVIAS 228 >3ivp_A Putative transposon-related DNA-binding protein; APC62618, structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile 630} Length = 126 Score = 37.4 bits (86), Expect = 0.003 Identities = 15/95 (15%), Positives = 41/95 (43%), Gaps = 5/95 (5%) Query: 4 FSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILA 63 + + + AI ++ LT + +DP IE + + PS + ++ +++ Sbjct: 8 YDFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTN-----IENKGQHPSLQVLYDLVS 62 Query: 64 ATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPS 98 N ++ + S ++T++++ E + F + Sbjct: 63 LLNVSVDEFFLPASSQVKSTKRRQLENKIDNFTDA 97 >2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 Length = 77 Score = 35.1 bits (81), Expect = 0.012 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 5/69 (7%) Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 +K + ++ + ++ LA AGL T ++ +E +R S +I KI AA Sbjct: 8 KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISE-----VERGDRNISLINIHKICAAL 62 Query: 66 NETICQLLD 74 + Sbjct: 63 DIPASTFFR 71 >3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, structural genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141 Score = 34.5 bits (79), Expect = 0.020 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 5/67 (7%) Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66 K E + + T S LA AGL ++ IE + +++ K+ A Sbjct: 67 KAGGETFVSLRMKKGFTQSELATAAGLPQPYLSR-----IENSKQSLQDKTVQKLANALG 121 Query: 67 ETICQLL 73 + ++ Sbjct: 122 VSPLEVR 128 >3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Length = 114 Score = 33.3 bits (76), Expect = 0.045 Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 5/85 (5%) Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 + E + R+ + H L +A + + P E + ++ Sbjct: 7 QHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAY-----YMSGETKPDIEKLIRLATYF 61 Query: 66 NETICQLLDLPFSDGRTTEKKEKEI 90 + +I +L+ D + K+ Sbjct: 62 HLSIDELVGYVQEDKVWNDLSLKQW 86 >1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3 Length = 74 Score = 32.1 bits (73), Expect = 0.11 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 5/65 (7%) Query: 8 KIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNE 67 K + + + L+ LA +GLD + +E R S +I K+ A + Sbjct: 13 KFGQRLRELRTAKGLSQETLAFLSGLDRSYVGG-----VERGQRNVSLVNILKLATALDI 67 Query: 68 TICQL 72 +L Sbjct: 68 EPREL 72 >3clc_A Regulatory protein; protein-DNA complex, transcriptional regulator, helix-turn- helix, DNA-bending, plasmid, transcription regulator/DNA complex; 2.80A {Enterobacter SP} Length = 82 Score = 31.9 bits (72), Expect = 0.11 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 5/75 (6%) Query: 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFK 60 M SF K+ I ++ +T LA K+ LD T + IE +R + +S+ Sbjct: 4 MESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISG-----IERNSRNLTIKSLEL 58 Query: 61 ILAATNETICQLLDL 75 I+ + ++ Sbjct: 59 IMKGLEVSDVVFFEM 73 >2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, helix-turn-helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae TIGR4} Length = 158 Score = 31.6 bits (71), Expect = 0.16 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 5/63 (7%) Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 + I + + H+LT AR G+ S ++ E STE I I N + Sbjct: 4 KNIKSLRKTHDLTQLEFARIVGISRNSLSR-----YENGTSSVSTELIDIICQKFNVSYV 58 Query: 71 QLL 73 ++ Sbjct: 59 DIV 61 >1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A Length = 69 Score = 30.5 bits (69), Expect = 0.31 Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 6/64 (9%) Query: 11 EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETIC 70 + + L + LA+K G S + +E + + ++ +A ++ Sbjct: 4 SRVKSKRIQLGLNQAELAQKVGTTQQSIEQ-----LE-NGKTKRPRFLPELASALGVSVD 57 Query: 71 QLLD 74 LL+ Sbjct: 58 WLLN 61 >1y4w_A EXO-inulinase; glycoside hydrolase family 32, crystallographic structure, native structure; HET: NAG; 1.55A {Aspergillus awamori} SCOP: b.29.1.19 b.67.2.3 PDB: 1y9g_A* 1y9m_A* Length = 518 Score = 29.5 bits (65), Expect = 0.59 Identities = 9/47 (19%), Positives = 16/47 (34%) Query: 70 CQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWN 116 Q + DG T + P++ PPS + + P + Sbjct: 131 SQSIAYSLDDGLTWTTYDAANPVIPNPPSPYEAEYQNFRDPFVFWHD 177 >3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73 Score = 29.0 bits (65), Expect = 0.94 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 5/69 (7%) Query: 5 SHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64 + +KI+ + + T L + T+ +K + PS E++F I A Sbjct: 5 TERKIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSK-----WCTNDVQPSLETLFDIAEA 59 Query: 65 TNETICQLL 73 N + +L+ Sbjct: 60 LNVDVRELI 68 >3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1} Length = 78 Score = 28.8 bits (64), Expect = 1.1 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%) Query: 1 MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFK 60 M + + + E + + + NLT + +A AGL+ ++ N R++ P+ +I K Sbjct: 1 MKTDG-EFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEG----RSKRPTITTIRK 55 Query: 61 ILAATNETICQLLDLP 76 + ++ D P Sbjct: 56 VCGTLGISVHDFFDFP 71 >1utx_A CYLR2; DNA-binding protein, transcriptional repressor, regulation of cytolysin operon, helix-turn-helix; 1.90A {Enterococcus faecalis} SCOP: a.35.1.3 PDB: 2gzu_A Length = 66 Score = 28.4 bits (63), Expect = 1.3 Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 5/63 (7%) Query: 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72 + + E+ ++ S LA + + N IE PS + KI N + + Sbjct: 6 LKLIREKKKISQSELAALLEVSRQTING-----IEKNKYNPSLQLALKIAYYLNTPLEDI 60 Query: 73 LDL 75 Sbjct: 61 FQW 63 >1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A* Length = 92 Score = 28.4 bits (63), Expect = 1.4 Identities = 4/68 (5%), Positives = 20/68 (29%), Gaps = 5/68 (7%) Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66 +++ ++ L+ +A K G+ + + + + + Sbjct: 16 RRLKAIYEKKKNELGLSQESVADKMGMGQSGVGA-----LFNGINALNAYNAALLAKILK 70 Query: 67 ETICQLLD 74 ++ + Sbjct: 71 VSVEEFSP 78 >3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum} Length = 113 Score = 28.1 bits (63), Expect = 1.5 Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 2/38 (5%) Query: 5 SHKKIWEAIDRMAER--HNLTPSGLARKAGLDPTSFNK 40 S K+ EA+ M L+ +A G+ + Sbjct: 5 SQPKLTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLER 42 >2dig_A Lamin-B receptor; tudor domain, integral nuclear envelope inner membrane protein, nuclear protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.34.9.1 Length = 68 Score = 27.6 bits (61), Expect = 2.1 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 4/65 (6%) Query: 26 GLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEK 85 G + +G+ F G R RWP + +++ ++++ QL + + DG E Sbjct: 1 GSSGSSGMPSRKFAD----GEVVRGRWPGSSLYYEVEILSHDSTSQLYTVKYKDGTELEL 56 Query: 86 KEKEI 90 KE +I Sbjct: 57 KENDI 61 >3kwo_A Putative bacterioferritin; alpha-helix, bacterial ferritin fold, structural genomics, center for structural genomics of infectious diseases; 1.99A {Campylobacter jejuni} Length = 152 Score = 27.2 bits (60), Expect = 3.1 Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 5/65 (7%) Query: 9 IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNET 68 + E D AER L KA ++ + ++ + E I +++ E Sbjct: 50 MAELFDSCAERVL----QLGEKAITCQKVLMENAKSPKVAKDCFTPLEVI-ELIKQDYEY 104 Query: 69 ICQLL 73 + Sbjct: 105 LLAEF 109 >1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15 Length = 192 Score = 27.2 bits (59), Expect = 3.3 Identities = 9/68 (13%), Positives = 23/68 (33%), Gaps = 5/68 (7%) Query: 7 KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATN 66 +I + + + L+ A+ G+ + IE P+ +++KI + Sbjct: 10 SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQ-----IERGESSPTIATLWKIASGLE 64 Query: 67 ETICQLLD 74 + Sbjct: 65 ASFSAFFA 72 >3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12} Length = 73 Score = 26.8 bits (59), Expect = 3.8 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 7/76 (9%) Query: 1 MTSFSHKKIW-EAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIF 59 M S + + + E I ++ ++ +LT + G +F++ E N P S Sbjct: 3 MASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSR-----YEKGNAXPH-PSTI 56 Query: 60 KILAATNETICQLLDL 75 K+L ++ L ++ Sbjct: 57 KLLRVLDKHPELLNEI 72 >1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 1jhc_A 1jhe_A 1lea_A 1leb_A Length = 202 Score = 26.6 bits (58), Expect = 4.2 Identities = 25/210 (11%), Positives = 67/210 (31%), Gaps = 36/210 (17%) Query: 7 KKIWEAIDRMAERHNLTPS--GLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAA 64 +++++ I + + P+ +A++ G S + + L A Sbjct: 9 QEVFDLIRDHISQTGMPPTRAEIAQRLGFR-------------------SPNAAEEHLKA 49 Query: 65 TNETICQLLDLPFSDGRT-TEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEI 123 + S G +++E+ +PL+ + + V Sbjct: 50 LARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAADEPLLAQQ------HIEGHYQVDPS 103 Query: 124 RSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAK 183 N + ++ + GD+L ++ V G ++ + ++ K Sbjct: 104 LFKPNADFLLRVSG------MSMKDIGIMDGDLLAVHKTQDVRNGQVVVAR-IDDEVTVK 156 Query: 184 VLISRRGRSIDLMSLNCCYPVDTVEMSDIE 213 L ++G ++L+ N + V++ Sbjct: 157 RLK-KQGNKVELLPENSEFKPIVVDLRQQS 185 >3kdp_B Sodium/potassium-transporting ATPase subunit beta-1; alpha helical, heterotrimeric membrane protein complex, ATP- binding, hydrolase, ION transport; HET: CLR; 3.50A {Sus scrofa} Length = 286 Score = 26.5 bits (58), Expect = 5.0 Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 1/41 (2%) Query: 79 DGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVG 119 G+ E KEK + YF G G F +P K Sbjct: 197 TGKRDEDKEKVGTMEYFGLGGYPG-FPLQYYPYYGKLLQPK 236 >2iny_A Hexon protein, late protein 2; avian adenovirus, CELO, major coat protein, crystal packing, nanotechnology, viral jelly roll, viral protein; 3.90A {Fowl adenovirus 1} Length = 942 Score = 26.2 bits (58), Expect = 6.2 Identities = 11/33 (33%), Positives = 15/33 (45%) Query: 87 EKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVG 119 E+ +P F P G G D+G + K T G Sbjct: 371 EEGVPTYAFLPDGHGAGEDNGPDLSNVKIYTNG 403 >2obe_A Hexon, PII; trimer, double-barrel subunit, viral jellyroll, base, hypervariable tower, viral protein; 2.10A {Simian adenovirus 25} PDB: 1p2z_A* 1p30_A 2bvi_F Length = 932 Score = 25.8 bits (57), Expect = 7.3 Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 1/32 (3%) Query: 87 EKEIPLLYFPPSGSG-GFFDSGVFPTGNKWNT 117 E E+P FP G G+ G T Sbjct: 388 EDELPNYCFPLDAVGRTDTYQGIKANGTDQTT 419 >2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2} Length = 84 Score = 25.7 bits (56), Expect = 8.5 Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 5/74 (6%) Query: 6 HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65 ++ + + + ++ + +L+ S LA GL + +K IE R +F++L Sbjct: 8 YRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISK-----IESFERRLDALELFELLEVV 62 Query: 66 NETICQLLDLPFSD 79 + +D+ D Sbjct: 63 ASRLGLPMDILLKD 76 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.319 0.136 0.418 Gapped Lambda K H 0.267 0.0632 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,002,709 Number of extensions: 88717 Number of successful extensions: 300 Number of sequences better than 10.0: 1 Number of HSP's gapped: 297 Number of HSP's successfully gapped: 28 Length of query: 223 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 134 Effective length of database: 3,535,514 Effective search space: 473758876 Effective search space used: 473758876 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)