RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus Liberibacter asiaticus str. psy62] (160 letters) >2kgw_A Outer membrane protein A; OMPA- like, cell membrane, transmembrane; NMR {Mycobacterium tuberculosis} Length = 129 Score = 105 bits (263), Expect = 5e-24 Identities = 33/110 (30%), Positives = 50/110 (45%), Gaps = 1/110 (0%) Query: 40 LQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSS 98 LQ ++ G + F S+ PAD ++L+ + L+ D I G+ D GS + Sbjct: 14 LQSAINAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGIN 73 Query: 99 IALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148 I L +RA V +Y VARG++ + G P + AKNRR Sbjct: 74 IPLSAQRAKIVADYLVARGVAGDHIATVGLGSVNPIASNATPEGRAKNRR 123 >2zf8_A MOTY, component of sodium-driven polar flagellar motor; beta barrel, 2-layer sandwich, flagellum, structural protein; 2.85A {Vibrio alginolyticus} Length = 278 Score = 96.9 bits (241), Expect = 2e-21 Identities = 26/116 (22%), Positives = 51/116 (43%), Gaps = 2/116 (1%) Query: 40 LQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHD--CDFLIEGHADELGSRNS 97 L+ F + ++ + A + LS + ++ + L+ + D +++ Sbjct: 152 LKYSFEDIAFTILHYERQGDQLTKASKKRLSQIADYIRHNQDIDLVLVATYTDSTDGKSA 211 Query: 98 SIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153 S +L RRA ++ +YF + G+ R++V YGK P KNRR ++ L Sbjct: 212 SQSLSERRAESLRDYFQSLGLPEDRIQVQGYGKRRPIADNGSPIGKDKNRRVVISL 267 >3ldt_A Outer membrane protein, OMPA family protein; OMPA-like domain, PSI-II, NYSGXRC, structural genomics, protein structure initiative; 2.30A {Legionella pneumophila} Length = 169 Score = 95.4 bits (237), Expect = 5e-21 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 1/103 (0%) Query: 47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105 + +F SS + L+N+ L + + G D +GSR+ L + Sbjct: 51 IIPTDKYFMFSSPRLNEICYPGLNNVIRLLNFYPQSTIYVAGFTDNVGSRSHKRKLSQAQ 110 Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148 A + + A GI+A R+K YG + A+NRR Sbjct: 111 AETMMTFLWANGIAAKRLKAEGYGDKNAISDNAIIHGSAQNRR 153 >1r1m_A Outer membrane protein class 4; 1.90A {Neisseria meningitidis} SCOP: d.79.7.1 Length = 164 Score = 95.2 bits (236), Expect = 6e-21 Identities = 31/113 (27%), Positives = 43/113 (38%), Gaps = 1/113 (0%) Query: 47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105 S+ F S+R L L L + +EGH D +GS + AL RR Sbjct: 12 SLSAKTLFGFDKDSLRAEAQDNLKVLAQRLSRTNIQSVRVEGHTDFMGSDKYNQALSERR 71 Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKGCRA 158 AY V N V+ G+ SR+ G+ + E AK + K A Sbjct: 72 AYVVANNLVSNGVPVSRISAVGLGESQAQMTQVCEAEVAKLGAKVSKAKKREA 124 >3oon_A Outer membrane protein (TPN50); protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG; 1.79A {Borrelia burgdorferi} Length = 123 Score = 84.8 bits (210), Expect = 8e-18 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 3/104 (2%) Query: 47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105 ++ + F +S+ I + + + + LEK + LIEGH ++ G L +R Sbjct: 14 NLSFDIEFYPNSFQILQKEYKKIDLIAKLLEKFKKNNILIEGHTEQFGLEEEMHELSEKR 73 Query: 106 AYAVFNYFVARGISA-SRMKVTSYGKEMPSVYGHDEDAYAKNRR 148 A A+ NY + + ++ +G + P Y AKNRR Sbjct: 74 ARAIGNYLIKMKVKDKDQILFKGWGSQKP-KYPKSSPLKAKNRR 116 >3cyp_B Chemotaxis protein MOTB; bacterial flagellar motor, peptidoglycan binding, bacterial flagellum, flagellar rotation, inner membrane, membrane; 1.60A {Helicobacter pylori} PDB: 3cyq_B* Length = 138 Score = 82.6 bits (204), Expect = 4e-17 Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 7/112 (6%) Query: 50 DSVFFDT-SSYSIRPADIQVLSNLGSWLEKH--DCDFLIEGHADELGSRNSSIA----LG 102 D F+ +S +I + + + ++K + G D+ + L Sbjct: 3 DPFTFENATSDAINQDMMLYIERIAKIIQKLPKRVHINVRGFTDDTPLVKTRFKSHYELA 62 Query: 103 LRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK 154 RAY V + G++ +++ +SYG P + KN R +F Sbjct: 63 ANRAYRVMKVLIQYGVNPNQLSFSSYGSTNPIAPNDSLENRMKNNRVEIFFS 114 >2zov_A Chemotaxis protein MOTB; 2-layer sandwich, bacterial flagellum, cell projection, flagellar rotation, inner membrane, membrane; 2.00A {Salmonella typhimurium} Length = 210 Score = 75.1 bits (184), Expect = 7e-15 Identities = 24/112 (21%), Positives = 36/112 (32%), Gaps = 9/112 (8%) Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSS-----IALGLR 104 + F T S + P +L + L + GH D+ N L Sbjct: 71 NRPMFKTGSAEVEPYMRDILRAIAPVLNGIPNRISLAGHTDDFPYANGEKGYSNWELSAD 130 Query: 105 RAYAVFNYFVARGISASR-MKVTSYGKEMPSVYGHDEDAYAKNRRA-IVFLK 154 RA A VA G+ + ++V M A NRR ++ L Sbjct: 131 RANASRRELVAGGLDNGKVLRVVGMAATMRLS--DRGPDDAINRRISLLVLN 180 >2k1s_A Inner membrane lipoprotein YIAD; abbababab, OMPA, alpha beta, palmitate, transmembrane, structural genomics, PSI-2; NMR {Escherichia coli K12} Length = 149 Score = 67.9 bits (165), Expect = 9e-13 Identities = 27/108 (25%), Positives = 56/108 (51%), Gaps = 1/108 (0%) Query: 47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105 ++ ++V FD+SS +++PA L+ + L+++ + G+ D G + ++ L +R Sbjct: 31 NMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQR 90 Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153 A +V + + +G+ ASR++ G P + A+NRR + L Sbjct: 91 ADSVASALITQGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITL 138 >2hqs_H Peptidoglycan-associated lipoprotein; TOLB, PAL, TOL, transport protein/lipoprotein complex; 1.50A {Escherichia coli} SCOP: d.79.7.1 PDB: 2w8b_C 1oap_A Length = 118 Score = 67.2 bits (163), Expect = 2e-12 Identities = 48/107 (44%), Positives = 68/107 (63%), Gaps = 2/107 (1%) Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYA 108 + V+FD Y IR Q+L ++L + +EGHADE G+ +I+LG RRA A Sbjct: 6 NIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANA 65 Query: 109 VFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA-IVFLK 154 V Y +G+SA ++ + SYGKE P+V GHDE AY+KNRRA +V+L+ Sbjct: 66 VKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYLE 112 >2zvy_A Chemotaxis protein MOTB; 2-layer sandwich, bacterial flagellum, cell inner membrane, cell membrane, flagellar rotation, membrane; 1.75A {Salmonella typhimurium} PDB: 2zvz_A Length = 183 Score = 64.0 bits (155), Expect = 2e-11 Identities = 22/110 (20%), Positives = 33/110 (30%), Gaps = 8/110 (7%) Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSS-----IALGLR 104 + F T S + P +L + L + GH D+ N L Sbjct: 60 NRPMFKTGSAEVEPYMRDILRAIAPVLNGIPNRISLAGHTDDFPYANGEKGYSNWELSAD 119 Query: 105 RAYAVFNYFVA-RGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153 RA A VA + ++V M A NRR + + Sbjct: 120 RANASRRELVAGGLDNGKVLRVVGMAATMRLS--DRGPDDAINRRISLLV 167 >2aiz_P Outer membrane protein P6; alpha-beta sandwich; HET: UDP AMU DGL 6CL DAL; NMR {Haemophilus influenzae} SCOP: d.79.7.1 Length = 134 Score = 58.8 bits (141), Expect = 5e-10 Identities = 44/120 (36%), Positives = 69/120 (57%), Gaps = 7/120 (5%) Query: 35 LNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELG 93 + + LQ+++ ++V+F Y I +Q+L ++L L+EG+ DE G Sbjct: 20 YSVADLQQRY-----NTVYFGFDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERG 74 Query: 94 SRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA-IVF 152 + +IALG RRA AV Y +G+ A ++ SYG+E P+V GHDE AY+KNRRA + + Sbjct: 75 TPEYNIALGQRRADAVKGYLAGKGVDAGKLGTVSYGEEKPAVLGHDEAAYSKNRRAVLAY 134 >3khn_A MOTB protein, putative; structural genomics, OMPA-like domain, PSI-2, protein structure initiative; 2.03A {Desulfovibrio vulgaris str} Length = 174 Score = 56.0 bits (134), Expect = 4e-09 Identities = 23/114 (20%), Positives = 40/114 (35%), Gaps = 6/114 (5%) Query: 47 SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH------DCDFLIEGHADELGSRNSSIA 100 V V F + + P +VL+ L + F + + Sbjct: 48 RVPSEVLFAPGAVELAPGADRVLATLKDLFIRRREQNINIKGFTDDVQPSANARFKDNWE 107 Query: 101 LGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK 154 + R+ V YF+ GI +R+ T G+ P ++ A+NRR L+ Sbjct: 108 VSALRSVNVLRYFLGAGIEPARLTATGLGELDPLFPNTSDENRARNRRVEFVLE 161 >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 = 36.1 bits (83), Expect = 0.004 Identities = 30/192 (15%), Positives = 56/192 (29%), Gaps = 67/192 (34%) Query: 10 LSAITMMSIS---GIDNLDTKISSPDTVL-NESSLQEQFSSS--------VGDSVFFDTS 57 + A + ++ G +L+ + P S LQEQF+ D + + Sbjct: 1 MDAYSTRPLTLSHG--SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADD---EPT 55 Query: 58 S----------YSIRPAD-------IQVLSNLGSWLEKHDCDFL--IEGHADELGSRNSS 98 + Y + QVL+ L + + +L + HA Sbjct: 56 TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLC---LTEFENCYLEGNDIHA-LAAKLLQE 111 Query: 99 IALGLRRAYAVF-NYFVARGISASRMKVTSYGKEMPSVYGH-------DEDA--YAKNRR 148 L + + NY AR ++ + + +A A Sbjct: 112 NDTTLVKTKELIKNYITARIMA---------KRPFDKKSNSALFRAVGEGNAQLVA---- 158 Query: 149 AIVFLKGCRANT 160 +F G + NT Sbjct: 159 --IF--GGQGNT 166 >2wvx_A Mannosidase, putative alpha-1,2-mannosidase; glycoside hydrolase family 92, GH92, hydrolase, BT3990; HET: MSE; 1.90A {Bacteroides thetaiotaomicron} PDB: 2wvx_B* Length = 744 Score = 27.7 bits (61), Expect = 1.4 Identities = 24/113 (21%), Positives = 39/113 (34%), Gaps = 4/113 (3%) Query: 1 MQYSTIFIILSAITMMSISGIDNLDTKISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYS 60 M + IL M + D + +++ + SS G + + Sbjct: 375 MVGNNSASILVDAYMKGVKVDDIKTLY----EGLIHGTENVHPEVSSTGRLGYEYYNKLG 430 Query: 61 IRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYF 113 P D+++ N LE D+ I A EL I+L +RA N F Sbjct: 431 YVPYDVKINENAARTLEYAYDDWCIYRLAKELKRPKKEISLFAKRAMNYKNLF 483 >2fcl_A Hypothetical protein TM1012; structural genomics, PSI, protein structure initiative, joint center for structural genomics, JCSG; HET: MLY; 1.20A {Thermotoga maritima} SCOP: d.218.1.11 PDB: 2ewr_A Length = 169 Score = 26.0 bits (57), Expect = 4.7 Identities = 7/27 (25%), Positives = 14/27 (51%) Query: 61 IRPADIQVLSNLGSWLEKHDCDFLIEG 87 IRP ++VL + L ++++ G Sbjct: 14 IRPEYLRVLRXIYDRLXNEXVNWVVTG 40 >1gxs_A HNL, hydroxynitrIle lyase; inhibitor complex, cyanogenesis mechanism; HET: NAG FUL FUC DKA; 2.3A {Sorghum bicolor} SCOP: c.69.1.5 Length = 270 Score = 25.4 bits (55), Expect = 6.9 Identities = 7/40 (17%), Positives = 16/40 (40%) Query: 45 SSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFL 84 SS+G + ++ + +L N +W + + F Sbjct: 66 CSSIGLGAMQELGAFRVHTNGESLLLNEYAWNKAANILFA 105 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 0.318 0.132 0.372 Gapped Lambda K H 0.267 0.0680 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,268,142 Number of extensions: 51598 Number of successful extensions: 118 Number of sequences better than 10.0: 1 Number of HSP's gapped: 106 Number of HSP's successfully gapped: 21 Length of query: 160 Length of database: 5,693,230 Length adjustment: 85 Effective length of query: 75 Effective length of database: 3,632,490 Effective search space: 272436750 Effective search space used: 272436750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (24.3 bits)