RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C [Candidatus Liberibacter asiaticus str. psy62] (202 letters) >3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca} Length = 213 Score = 145 bits (367), Expect = 6e-36 Identities = 42/130 (32%), Positives = 65/130 (50%), Gaps = 2/130 (1%) Query: 5 IEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVD 64 +E I + ++ V GE++ V L+ + + LRDDP F + + GV Sbjct: 84 LERSLKEIGTPYDTAISRVVVDRGEITFHVQREHLLDVATRLRDDPALRFELCLGVTGVH 143 Query: 65 FLSR-SNRFDVVYHFLSPKYNRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDMYGI 122 + N VY S +N +R++++ + +PSIV +YP DW ERE WD +GI Sbjct: 144 YPEDEGNELHAVYALRSITHNYEIRLEVSCPDSDPHIPSIVSVYPTNDWHEREAWDFFGI 203 Query: 123 FFEGHPDLRR 132 F+GHP L R Sbjct: 204 IFDGHPALTR 213 >3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5* Length = 207 Score = 134 bits (337), Expect = 2e-32 Identities = 56/188 (29%), Positives = 87/188 (46%), Gaps = 32/188 (17%) Query: 25 NSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLS 80 N +G L + + + + F + D+ G+D+L+ R RF VVY +S Sbjct: 20 NGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVS 76 Query: 81 PKY-----NRRLRVKIAV-AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRIL 134 R V++ V E +P++ ++ A++ EREV+D++GI FEGHPDLR+IL Sbjct: 77 LPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKIL 136 Query: 135 TDYGFEGHPLRKDFPV----TGFVELHY----------DDKVKKVVYRPVELMQEHRDYD 180 T EGHPLRKD+P+ T F E Y K + + + +R Sbjct: 137 TPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPGLTFYKGGSRKGYR--- 193 Query: 181 FLSPWEGV 188 S W + Sbjct: 194 --SLWADL 199 >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 = 38.4 bits (89), Expect = 0.001 Identities = 26/165 (15%), Positives = 52/165 (31%), Gaps = 57/165 (34%) Query: 43 CSFLR-DDPHCCFVNIIDLCGVDFLSRSNRFDVV------YHFLSPKYNRR-----LRVK 90 +L +D H L + + +++ ++++ R Sbjct: 93 NCYLEGNDIHAL---AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR-- 147 Query: 91 IAVAEGKSVPSIVGIYPGA----DWFE--REVWDMYGIFFE-----GHPDLRRILTD--- 136 AV EG + +V I+ G D+FE R+++ Y + L ++ Sbjct: 148 -AVGEGNA--QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLD 204 Query: 137 ----Y--GFE-----GHP-LRKD----------FPVTGFVEL-HY 158 + G +P D P+ G ++L HY Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY 249 Score = 25.7 bits (56), Expect = 7.0 Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 38/99 (38%) Query: 22 FAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSP 81 FA +S+GE + D++S+ S + +VV++ Sbjct: 1759 FAGHSLGEYAALASLADVMSIESLV--------------------------EVVFY---- 1788 Query: 82 KYNRRLRVKIAVAE---GKSVPSIVGIYPG--ADWFERE 115 R + +++AV G+S ++ I PG A F +E Sbjct: 1789 ---RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824 Score = 25.7 bits (56), Expect = 8.2 Identities = 23/106 (21%), Positives = 27/106 (25%), Gaps = 52/106 (49%) Query: 39 LVSLCSFLRD---DPHCCFVNIIDLCGVD-----FLSR----SNRFDVV---YH--FLSP 81 L L LR G+D F R SNRF V +H L P Sbjct: 386 LYGLNLTLRKAKAPS-----------GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVP 434 Query: 82 ----------KYNRRLR---VKIAV-----------AEGKSVPSIV 103 K N ++I V G IV Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIV 480 >2b3w_A Hypothetical protein YBIA; structure, NESG, structural genomics, COG 3236, PSI, protein structure initiative; NMR {Escherichia coli} SCOP: d.336.1.1 Length = 168 Score = 32.2 bits (73), Expect = 0.090 Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 8/98 (8%) Query: 48 DDPHCCFVNI----IDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIV 103 D + F N I + G + + + F FL KY +R + + Sbjct: 23 SDDYGDFSNFAAWPIKVDGKTWPTSEHYF-QAQKFLDEKYREEIRRVSSPMVAARMGRDR 81 Query: 104 GIYPGADWFEREVWDMYGIF---FEGHPDLRRILTDYG 138 +W + M FE H +LR +L Sbjct: 82 SKPLRKNWESVKEQVMRKALRAKFEQHAELRALLLATA 119 >3gr7_A NADPH dehydrogenase; flavin, FMN, beta-alpha-barrel, oxidoreductase, flavoprotein; HET: FMN; 2.30A {Geobacillus kaustophilus} PDB: 3gr8_A* Length = 340 Score = 30.7 bits (69), Expect = 0.25 Identities = 15/109 (13%), Positives = 33/109 (30%), Gaps = 16/109 (14%) Query: 77 HFLSPKYNRRL---------RVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGH 127 FLSP NRR R + +V + P + G+ + + Sbjct: 173 EFLSPLSNRRQDEYGGSPENRYRFLGEVIDAVREVWD-GPLFVRISASDYHPDGLTAKDY 231 Query: 128 PDLRRILTDYGF------EGHPLRKDFPVTGFVELHYDDKVKKVVYRPV 170 + + + G G + V ++ + + +++ P Sbjct: 232 VPYAKRMKEQGVDLVDVSSGAIVPARMNVYPGYQVPFAELIRREADIPT 280 >3hgj_A Chromate reductase; TIM barrel, oxidoreductase; HET: FMN; 2.00A {Thermus scotoductus} PDB: 3hf3_A* Length = 349 Score = 29.7 bits (66), Expect = 0.43 Identities = 25/113 (22%), Positives = 38/113 (33%), Gaps = 17/113 (15%) Query: 75 VYHFLSPKYNRR---------------LRVKIAVAEGKSVPSIVGIYPGADWFEREVWDM 119 + FLSP N+R L+V AV E + + A + W + Sbjct: 179 LSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSL 238 Query: 120 --YGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPV 170 F +L L D G LR P+ ++ + D V+K V Sbjct: 239 EDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRT 291 >3khs_A Purine nucleoside phosphorylase; alpha-beta structure, mixed beta-barrel, hydrolase; 2.38A {Grouper iridovirus} Length = 285 Score = 28.3 bits (63), Expect = 1.2 Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 14/99 (14%) Query: 22 FAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSN--RFDVVYHFL 79 N+ G L+ GD + + D +N+ L G + L+ N + + Sbjct: 109 VLTNAAGGLNPSYRPGDFM-----VVRD----HINLPGLAGANPLTGPNDDTEGERFPSM 159 Query: 80 SPKYNRRLR---VKIAVAEGKSVPSIVGIYPGADWFERE 115 + Y++ LR + A G S + G+Y + E Sbjct: 160 TSVYDKTLRKYAISAARELGMSYATHEGVYCCVNGPSFE 198 >2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105 Score = 27.3 bits (60), Expect = 2.5 Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 9/84 (10%) Query: 27 VGELSLDVDCGDLVSLCSFLRDDPHCCFV--NIIDLCGVDFLSRSNRFDVVY-------H 77 VG L+ D++ L C + G F+ S+ + Sbjct: 20 VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79 Query: 78 FLSPKYNRRLRVKIAVAEGKSVPS 101 P + L VK A + +S PS Sbjct: 80 QTMPGASSSLVVKFADTDKESGPS 103 >2nl9_A Fusion protein consisting of induced myeloid leukemia cell differentiation protein...; apoptosis, MCL-1, BIM; HET: MSE; 1.55A {Rattus norvegicus} PDB: 2nla_A 3d7v_A 3io9_A 2pqk_A 1wsx_A 2jm6_B 2roc_A 2rod_A Length = 157 Score = 26.8 bits (59), Expect = 3.0 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 18/85 (21%) Query: 119 MYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRD 178 M +F +G + RI+T F + ++ + ++ + +++ Sbjct: 80 MIHVFSDGVTNWGRIVTLISFGAFVAKH------LKTINQESCIEPLAESITDVLVRT-- 131 Query: 179 YDFLSP-------WEGVNSLFAKED 196 W+G F ED Sbjct: 132 ---KRDWLVKQRGWDGFVEFFHVED 153 >2e7h_A Ephrin type-B receptor 4; FN3 domain, tyrosine- protein kinase receptor HTK, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 109 Score = 26.9 bits (58), Expect = 3.4 Identities = 7/78 (8%), Positives = 18/78 (23%) Query: 24 VNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKY 83 V SL + + + D + +++ L Sbjct: 16 VTRSSPSSLSLAWAVPRAPSGAVLDYEVKYHEKGAEGPSSVRFLKTSENRAELRGLKRGA 75 Query: 84 NRRLRVKIAVAEGKSVPS 101 + ++V+ G Sbjct: 76 SYLVQVRARSEAGYGPFG 93 >1u09_A Polyprotein; protein-DNA complex, RNA-dependent RNA polymerase, transferase; 1.91A {Foot-and-mouth disease virus c-s8c1} SCOP: e.8.1.4 PDB: 1wne_A 2e9r_X* 2e9t_A* 2e9z_A* 2ec0_A 2f8e_X* 2d7s_A* Length = 476 Score = 25.7 bits (56), Expect = 7.4 Identities = 10/38 (26%), Positives = 11/38 (28%) Query: 48 DDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNR 85 D FV + V FL R D F P Sbjct: 368 DKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMAS 405 >2nvv_A Acetyl-COA hydrolase/transferase family protein; alpha beta protein, structural genomics, PSI-2, protein structure initiative; 2.70A {Porphyromonas gingivalis W83} Length = 506 Score = 25.8 bits (56), Expect = 7.5 Identities = 9/29 (31%), Positives = 10/29 (34%), Gaps = 6/29 (20%) Query: 127 HPDLRRILTDY------GFEGHPLRKDFP 149 HPD R +L Y G L F Sbjct: 449 HPDYRPLLRQYLELGVKGQTPQNLDCCFA 477 >3nzo_A UDP-N-acetylglucosamine 4,6-dehydratase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, NAD; HET: MSE NAD; 2.10A {Vibrio fischeri} Length = 399 Score = 25.2 bits (54), Expect = 9.6 Identities = 10/78 (12%), Positives = 27/78 (34%), Gaps = 9/78 (11%) Query: 1 MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDL 60 + ++I ++ S E ++ D+ S ++ D ++I + Sbjct: 51 VTKEIFKRNPQKLHVVDIS---------ENNMVELVRDIRSSFGYINGDFQTFALDIGSI 101 Query: 61 CGVDFLSRSNRFDVVYHF 78 F+ ++D V + Sbjct: 102 EYDAFIKADGQYDYVLNL 119 >1fp2_A Isoflavone O-methytransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A* Length = 352 Score = 25.1 bits (54), Expect = 9.6 Identities = 20/158 (12%), Positives = 38/158 (24%), Gaps = 36/158 (22%) Query: 32 LDVDCGDLVSLCSFLRDDPHCCFVNI--------------IDLCGVDFLSRSNRFDVVYH 77 +DV G + P + + G D + D V Sbjct: 193 VDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLL 252 Query: 78 FLSPKYNRRLRVKIAVAE--------GKSVPSIVGIYPGADWFEREVW-------DMYGI 122 + + GK + + D+ Sbjct: 253 KYILHNWTDKDCLRILKKCKEAVTNDGKRGKVTIIDMVIDKKKDENQVTQIKLLMDVNMA 312 Query: 123 FFEGHP----DLRRILTDYGFEGHPLRKDFPVTGFVEL 156 G + +++ + GF+ K P+TGF+ L Sbjct: 313 CLNGKERNEEEWKKLFIEAGFQ---HYKISPLTGFLSL 347 >2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116 Score = 25.1 bits (54), Expect = 9.9 Identities = 13/88 (14%), Positives = 17/88 (19%), Gaps = 6/88 (6%) Query: 27 VGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCG------VDFLSRSNRFDVVYHFLS 80 VG L L D + V R+ Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP 81 Query: 81 PKYNRRLRVKIAVAEGKSVPSIVGIYPG 108 R+ V +A K G G Sbjct: 82 IIDGRKANVNLAYLGAKPRSLQTGFAIG 109 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 0.325 0.144 0.457 Gapped Lambda K H 0.267 0.0469 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,997,460 Number of extensions: 98307 Number of successful extensions: 391 Number of sequences better than 10.0: 1 Number of HSP's gapped: 384 Number of HSP's successfully gapped: 30 Length of query: 202 Length of database: 5,693,230 Length adjustment: 88 Effective length of query: 114 Effective length of database: 3,559,758 Effective search space: 405812412 Effective search space used: 405812412 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 54 (25.2 bits)