RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781147|ref|YP_003065560.1| transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62] (83 letters) >3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, structural genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141 Score = 50.3 bits (120), Expect = 9e-08 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 6/85 (7%) Query: 2 PRRK----RDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 PRRK R ++D I + F ++R + TQ E+ G Q ++S +E Sbjct: 47 PRRKAAMDRAAARIADKIALKA--GGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENS 104 Query: 58 KSTINIDNMIILAHTLDTPLWKLLK 82 K ++ + LA+ L ++ Sbjct: 105 KQSLQDKTVQKLANALGVSPLEVRA 129 >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 = 50.2 bits (120), Expect = 1e-07 Identities = 15/59 (25%), Positives = 31/59 (52%) Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 F R +R L+Q+ + +G +S++ +E G+ +++ N++ LA LD +L Sbjct: 14 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPREL 72 >3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomics; 1.80A {Silicibacter pomeroyi} Length = 86 Score = 50.2 bits (120), Expect = 1e-07 Identities = 12/57 (21%), Positives = 26/57 (45%) Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 E + R R +A LTQ ++ R QS+++++ET + +++ + Sbjct: 11 EHVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE 67 >2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 Length = 77 Score = 49.8 bits (119), Expect = 1e-07 Identities = 16/65 (24%), Positives = 33/65 (50%) Query: 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 + F + IR + ++Q+E+ + G +++ISE+E G I++ N+ + LD P Sbjct: 8 KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAS 67 Query: 79 KLLKP 83 + Sbjct: 68 TFFRK 72 >1adr_A P22 C2 repressor; transcription regulation; NMR {Bacteriophage P22} SCOP: a.35.1.2 Length = 76 Score = 47.5 bits (113), Expect = 7e-07 Identities = 16/63 (25%), Positives = 28/63 (44%) Query: 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWK 79 + R RK+ K+ Q + G + IS+ E ++ N +N++ L+ L Sbjct: 4 QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY 63 Query: 80 LLK 82 LLK Sbjct: 64 LLK 66 >2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 68 Score = 47.5 bits (113), Expect = 7e-07 Identities = 16/59 (27%), Positives = 27/59 (45%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 R RK+ K+ Q + G + IS+ E ++ N +N++ L+ L LLK Sbjct: 8 ERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLK 66 >2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, bacterial persistence, serine kinase, mercury derivative, SAD; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* Length = 88 Score = 46.5 bits (110), Expect = 1e-06 Identities = 11/60 (18%), Positives = 23/60 (38%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLKP 83 N + +R++ TQ E+ + G Q+ IS E + + +L+ + Sbjct: 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK 74 >3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp} Length = 111 Score = 46.4 bits (110), Expect = 1e-06 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 4/68 (5%) Query: 18 ERMIFVNNF----RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 E + F +N + +R + LTQKE+ + + I +E + I + Sbjct: 16 ENLYFQSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAF 75 Query: 74 DTPLWKLL 81 + + Sbjct: 76 NVKYDDIF 83 >2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A Length = 99 Score = 46.4 bits (110), Expect = 2e-06 Identities = 13/53 (24%), Positives = 25/53 (47%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 +RK L+++++ + TG +S E+G+ST D M+ + T Sbjct: 7 EKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFT 59 >2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, helix-turn-helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae TIGR4} Length = 158 Score = 46.3 bits (109), Expect = 2e-06 Identities = 13/61 (21%), Positives = 30/61 (49%) Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 + N +++RK LTQ E G +++ +S E G S+++ + + I+ + + Sbjct: 1 MIGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDI 60 Query: 81 L 81 + Sbjct: 61 V 61 >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 = 46.1 bits (109), Expect = 2e-06 Identities = 15/62 (24%), Positives = 35/62 (56%) Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 + +NN + IR++ K++Q E+ ++ I+ +E K ++ + +A+ L+TPL + Sbjct: 1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDI 60 Query: 81 LK 82 + Sbjct: 61 FQ 62 >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 = 44.9 bits (105), Expect = 5e-06 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 2/71 (2%) Query: 11 LSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILA 70 L+D + + + N +N+RK L+ TG +++ + ++E G+S+ I + +A Sbjct: 3 LTDVMFKSQ--IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIA 60 Query: 71 HTLDTPLWKLL 81 L+ Sbjct: 61 SGLEASFSAFF 71 >3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} Length = 80 Score = 43.0 bits (101), Expect = 2e-05 Identities = 12/56 (21%), Positives = 26/56 (46%) Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 + + E L+ + + ++ G QS ++ L G + +N N +LA L + + Sbjct: 17 WEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEFS 72 >3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73 Score = 42.9 bits (101), Expect = 2e-05 Identities = 8/62 (12%), Positives = 25/62 (40%) Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 N +++ E T + ++ +S+ T +++ + +A L+ + +L+ Sbjct: 9 IFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRELI 68 Query: 82 KP 83 Sbjct: 69 VS 70 >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 = 42.8 bits (101), Expect = 2e-05 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 + ++ R + L Q E+ + G Q I +LE GK T + LA L + LL Sbjct: 4 SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSVDWLL 60 >1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Length = 91 Score = 42.7 bits (100), Expect = 2e-05 Identities = 11/61 (18%), Positives = 25/61 (40%) Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 R + + R+ LTQK++ + I++ E+G++ N + + + Sbjct: 9 RVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLK 68 Query: 77 L 77 L Sbjct: 69 L 69 >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 = 42.5 bits (100), Expect = 3e-05 Identities = 12/63 (19%), Positives = 27/63 (42%) Query: 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 + F N ++KE L +I ++ +G++ +I+ +I LA + Sbjct: 7 QHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSID 66 Query: 79 KLL 81 +L+ Sbjct: 67 ELV 69 >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 = 42.3 bits (99), Expect = 3e-05 Identities = 15/71 (21%), Positives = 30/71 (42%) Query: 11 LSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILA 70 L+ L + + + E L+Q+ + ++ G QS + L G + +N N +LA Sbjct: 7 LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLA 66 Query: 71 HTLDTPLWKLL 81 L + + Sbjct: 67 KILKVSVEEFS 77 >2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A Length = 198 Score = 41.8 bits (97), Expect = 4e-05 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 1/67 (1%) Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTP 76 F ++ R++ K+ + + G ++ E G+ + + + +AH L T Sbjct: 7 ASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTS 66 Query: 77 LWKLLKP 83 + L P Sbjct: 67 IGALTPP 73 >3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response element family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} Length = 83 Score = 41.5 bits (97), Expect = 5e-05 Identities = 15/61 (24%), Positives = 29/61 (47%) Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 ++ R A +TQKE+ R G QS++S+ E + +++ + + T + LL Sbjct: 15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALL 74 Query: 82 K 82 Sbjct: 75 S 75 >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 = 40.7 bits (95), Expect = 9e-05 Identities = 16/61 (26%), Positives = 29/61 (47%) Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 V +RKEA L+Q E+ G +QS IS++E+ + ++ + L + + Sbjct: 6 HRYRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASR 65 Query: 77 L 77 L Sbjct: 66 L 66 >3gn5_A HTH-type transcriptional regulator MQSA (YGIT/B3021); Zn-binding protein, HTH-XRE DNA binding motif, DNA-binding, transcription regulation; HET: MEQ; 2.15A {Escherichia coli k-12} PDB: 3gn5_B* Length = 133 Score = 40.1 bits (93), Expect = 1e-04 Identities = 14/76 (18%), Positives = 24/76 (31%) Query: 3 RRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62 + A + + +RK+ LTQKE G + S E G + + Sbjct: 53 DAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPH 112 Query: 63 IDNMIILAHTLDTPLW 78 + +L P Sbjct: 113 PSTIKLLRVLDKHPEL 128 >2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovarisraelensis atcc 35646} Length = 293 Score = 40.2 bits (92), Expect = 1e-04 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 + + IR LTQK++ QS +S +E+G ++D + +A L P+ Sbjct: 8 SEIKKIRVLRGLTQKQLSEN-ICHQSEVSRIESGAVYPSMDILQGIAAKLQIPII 61 >2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1 Length = 170 Score = 39.9 bits (93), Expect = 1e-04 Identities = 10/59 (16%), Positives = 16/59 (27%), Gaps = 1/59 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINID-NMIILAHTLDTPLWKLL 81 F + L+ G ++ +S T I + L P K L Sbjct: 93 EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGWEATRPETKTL 151 >1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L* Length = 71 Score = 39.8 bits (93), Expect = 2e-04 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 1/58 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 + R K+TQ E+ + G Q I +E G T + +A L+ L Sbjct: 6 ERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGV-TKRPRFLFEIAMALNCDPVWLQ 62 >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 = 39.3 bits (91), Expect = 2e-04 Identities = 8/60 (13%), Positives = 24/60 (40%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLKP 83 + RK+ LT++++ +++ +E ++ + L L+ + + P Sbjct: 15 LAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFFLP 74 >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 = 39.2 bits (91), Expect = 2e-04 Identities = 10/59 (16%), Positives = 28/59 (47%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 + IR E +TQ+++ ++ +++IS +E + I ++ ++ L+ + Sbjct: 14 FVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFE 72 >3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A Length = 99 Score = 39.3 bits (91), Expect = 2e-04 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 7/82 (8%) Query: 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST 60 +PR E L + + IR E +TQ+++ ++ +++IS +E Sbjct: 15 VPRGSHMESFLLSKV-------SFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRN 67 Query: 61 INIDNMIILAHTLDTPLWKLLK 82 + I ++ ++ L+ + Sbjct: 68 LTIKSLELIMKGLEVSDVVFFE 89 >1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 Length = 111 Score = 39.3 bits (91), Expect = 2e-04 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 1/61 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG-KSTINIDNMIILAHTLDTPLWKLLK 82 + RKE + E+ + G A+S++S +E ++ +I + ++ LD + LL Sbjct: 4 QRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLD 63 Query: 83 P 83 Sbjct: 64 E 64 >2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3 Length = 99 Score = 39.2 bits (91), Expect = 2e-04 Identities = 13/59 (22%), Positives = 21/59 (35%) Query: 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 + + IR+ KLTQ+E R + + E G+S + L P Sbjct: 27 ASAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKIIAVDP 85 >2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain, transcription; 2.25A {Enterococcus faecalis} SCOP: a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A 2grl_A 2grm_A Length = 317 Score = 38.8 bits (90), Expect = 3e-04 Identities = 9/58 (15%), Positives = 27/58 (46%), Gaps = 1/58 (1%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 + + IR+E Q ++ + ++S ++E I+++ + + L +++L Sbjct: 6 SVLKQIRQELNYHQIDLYSG-IMSKSVYIKVEADSRPISVEELSKFSERLGVNFFEIL 62 >2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94 Score = 39.0 bits (90), Expect = 3e-04 Identities = 12/66 (18%), Positives = 27/66 (40%) Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 +++ IF N + +++ TQ EI G + + G + + + LA + Sbjct: 5 KQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNIN 64 Query: 77 LWKLLK 82 L++ Sbjct: 65 KSDLIE 70 >3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* Length = 133 Score = 38.6 bits (89), Expect = 4e-04 Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 2/81 (2%) Query: 2 PRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-- 59 + A + + +RK+ LTQKE G + S E G + Sbjct: 52 SDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQP 111 Query: 60 TINIDNMIILAHTLDTPLWKL 80 + ++ + L ++ Sbjct: 112 HPSTIKLLRVLDKHPELLNEI 132 >3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236 Score = 36.9 bits (84), Expect = 0.001 Identities = 13/53 (24%), Positives = 25/53 (47%) Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 + + E L+Q+ + ++ G QS + L G + +N N +LA L + Sbjct: 22 YEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE 74 >3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A Length = 443 Score = 36.1 bits (83), Expect = 0.002 Identities = 7/64 (10%), Positives = 14/64 (21%), Gaps = 1/64 (1%) Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE-TGKSTINIDNMIILAHTLDTPLWK 79 + T+ G + + + S + + L L Sbjct: 230 SAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRV 289 Query: 80 LLKP 83 LL Sbjct: 290 LLPA 293 >2jvl_A TRMBF1; coactivator, helix-turn-helix, protein binding, transcription; NMR {Trichoderma reesei} Length = 107 Score = 35.7 bits (82), Expect = 0.003 Identities = 10/48 (20%), Positives = 22/48 (45%) Query: 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77 + E +TQ E+ G + ++ E G +T + + + + L+ L Sbjct: 45 KFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKL 92 >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 = 34.8 bits (80), Expect = 0.005 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 1/62 (1%) Query: 14 AILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 A + + +RK+ LTQKE G + S E G + + + I L L Sbjct: 4 ASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHP-STIKLLRVL 62 Query: 74 DT 75 D Sbjct: 63 DK 64 >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 = 34.6 bits (79), Expect = 0.005 Identities = 8/62 (12%), Positives = 18/62 (29%), Gaps = 1/62 (1%) Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET-GKSTINIDNMIILAHTLDTPLWK 79 + + + LT + G QS ++ + I + + TL + Sbjct: 7 FVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVHD 66 Query: 80 LL 81 Sbjct: 67 FF 68 >3cec_A Putative antidote protein of plasmid maintenance system; ZP_00107635.1, structural genomics, joint center for structural genomics; HET: MSE; 1.60A {Nostoc punctiforme pcc 73102} Length = 104 Score = 32.2 bits (73), Expect = 0.032 Identities = 11/55 (20%), Positives = 19/55 (34%) Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 +I + + G + I E+ G+ +I +D I L L L Sbjct: 24 ADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKALGNGPRLWL 78 >2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 1.63A {Escherichia coli CFT073} SCOP: a.35.1.3 PDB: 2icp_A Length = 94 Score = 31.9 bits (72), Expect = 0.040 Identities = 12/55 (21%), Positives = 22/55 (40%) Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 + E ++ +E A S S L TGK+ + + I L+ + + L Sbjct: 14 QESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWL 68 >2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli} Length = 113 Score = 30.3 bits (68), Expect = 0.11 Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 10/81 (12%) Query: 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST 60 M + R D +L E + + L E+ ++ +S L Sbjct: 1 MKQATRKPTTPGDILLYEYL----------EPLDLKINELAELLHVHRNSVSALINNNRK 50 Query: 61 INIDNMIILAHTLDTPLWKLL 81 + + LA DT + L Sbjct: 51 LTTEMAFRLAKVFDTTVDFWL 71 >3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp} Length = 130 Score = 29.7 bits (66), Expect = 0.16 Identities = 7/46 (15%), Positives = 16/46 (34%) Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAH 71 + R+ +T E+ RTG + + +E + + Sbjct: 8 LKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGF 53 >2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.83A {Rhodopseudomonas palustris CGA009} SCOP: a.35.1.13 Length = 120 Score = 28.9 bits (65), Expect = 0.26 Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 1/60 (1%) Query: 16 LRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK-STINIDNMIILAHTLD 74 + ++ + A+L+Q R G Q +S L K +++ ++ L + LD Sbjct: 35 RQTKLRLAYALNAVIDRARLSQXXXXXRLGINQPKVSALRNYKLEGFSVERLMTLLNALD 94 >2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima} Length = 112 Score = 28.5 bits (63), Expect = 0.43 Identities = 9/33 (27%), Positives = 15/33 (45%) Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 FR R+E ++T + T S + +E G Sbjct: 12 FRKKREERRITLLDASLFTNINPSKLKRIEEGD 44 >3bg1_B Nucleoporin NUP145; NPC, transport, WD repeat, autocatalytic cleavage, mRNA transport, nuclear pore complex, nucleus, phosphoprotein; 3.00A {Saccharomyces cerevisiae} PDB: 3bg0_B Length = 442 Score = 26.4 bits (58), Expect = 1.6 Identities = 12/46 (26%), Positives = 13/46 (28%), Gaps = 4/46 (8%) Query: 10 HLSDAILRERMI--FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 L+D E I V R I T I NR I Sbjct: 386 FLNDDKAAEDTIKRLVM--REITLLRASTNDHILNRLKIPSQLIFN 429 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 24.9 bits (54), Expect = 4.2 Identities = 5/27 (18%), Positives = 10/27 (37%), Gaps = 4/27 (14%) Query: 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQ 48 R + + L Q +R F++ Sbjct: 389 LNLTLRKAKAPSGLDQ----SRIPFSE 411 >1nm8_A Carnitine O-acetyltransferase; two equally sized domains, anti-parallel beta-strand; 1.60A {Homo sapiens} SCOP: c.43.1.3 c.43.1.3 PDB: 1s5o_A* 2h3u_A* 2h3p_A* 1t7q_A* 1t7n_A 1t7o_A* 1ndb_A 1ndf_A* 1ndi_A* 2h3w_A* Length = 616 Score = 24.6 bits (53), Expect = 6.0 Identities = 10/47 (21%), Positives = 20/47 (42%) Query: 8 EPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 +P +S+ V+ F+ + QK + R ++W+SE Sbjct: 34 QPIVSEEEWAHTKQLVDEFQASGGVGERLQKGLERRARKTENWLSEW 80 >1t1u_A Choline O-acetyltransferase; choline acetyltransferase; 1.55A {Rattus norvegicus} SCOP: c.43.1.3 c.43.1.3 PDB: 1q6x_A 2fy2_A 2fy3_A 2fy4_A* 2fy5_A* Length = 639 Score = 24.6 bits (53), Expect = 6.2 Identities = 8/46 (17%), Positives = 18/46 (39%) Query: 8 EPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 + + + R+ V F + Q+++ R +W+SE Sbjct: 42 QHLVPEEQFRKSQAIVKRFGAPGGLGETLQEKLLERQEKTANWVSE 87 >3e7m_A Nitric oxide synthase, inducible; NOS, heme, tetrahydrobiopterin, oxidoreductase calmodulin-binding, FAD, FMN, iron, metal- binding, NADP; HET: HEM H4B AT2; 2.00A {Mus musculus} SCOP: d.174.1.1 PDB: 1r35_A* 3e67_A* 3e68_A* 3e6l_A* 3e6n_A* 3e6o_A* 3e6t_A* 3e7i_A* 3e65_A* 3e7t_A* 3eai_A* 3ebd_A* 3ebf_A* 1m8d_A* 1m8e_A* 1m8h_A* 1m8i_A* 1m9t_A* 1qom_A* 1jwj_A* ... Length = 433 Score = 23.9 bits (52), Expect = 8.0 Identities = 12/41 (29%), Positives = 21/41 (51%) Query: 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIR 41 + R RD+P + +L + F+N + KEAK+ + R Sbjct: 54 LTRGPRDKPTPLEELLPHAIEFINQYYGSFKEAKIEEHLAR 94 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 0.321 0.135 0.398 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: 706,778 Number of extensions: 26867 Number of successful extensions: 148 Number of sequences better than 10.0: 1 Number of HSP's gapped: 146 Number of HSP's successfully gapped: 59 Length of query: 83 Length of database: 5,693,230 Length adjustment: 51 Effective length of query: 32 Effective length of database: 4,456,786 Effective search space: 142617152 Effective search space used: 142617152 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 (21.9 bits) S2: 50 (23.2 bits)