RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780472|ref|YP_003064885.1| cytochrome o ubiquinol oxidase subunit III [Candidatus Liberibacter asiaticus str. psy62] (210 letters) >1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: f.25.1.1 Length = 204 Score = 125 bits (315), Expect = 7e-30 Identities = 96/184 (52%), Positives = 125/184 (67%), Gaps = 1/184 (0%) Query: 27 HDGTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSL 86 GFWIYLMSDC++F++ F TYAVL A GP D+F++ + V T +LL SS+ Sbjct: 22 GGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSI 81 Query: 87 SCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFF 146 + A +A + +SWL +T FG FI MEIYEF HLI P RS FLS+FF Sbjct: 82 TYGMAAIAMYKNN-KSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFF 140 Query: 147 ALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYL 206 ALVG HGLHV GLIW+ VL++QI ++GL S N+ R++CLS+FWHFLD++WICVF+ VYL Sbjct: 141 ALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYL 200 Query: 207 MGVV 210 MG + Sbjct: 201 MGAM 204 >1qle_C Cytochrome C oxidase polypeptide III; oxidoreductase/immune system, complex (oxidoreductase/antibody), electron transport; HET: HEA PC1; 3.0A {Paracoccus denitrificans} SCOP: f.25.1.1 Length = 273 Score = 97.4 bits (242), Expect = 2e-21 Identities = 47/188 (25%), Positives = 90/188 (47%), Gaps = 14/188 (7%) Query: 32 LGFWIYLMSDCLMFAVFFVTYAVLGKNYAAG----------PAPIDVFDISGI-FVSTIV 80 GF +++MS+ + F +F + P I FD + ++T++ Sbjct: 88 YGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLI 147 Query: 81 LLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSA 140 LLLS ++ ++A A + T++ L+V G+ F ++ YE++H + Sbjct: 148 LLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFG---LADTV 204 Query: 141 FLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICV 200 + +F+ G HG HV G I+LFV +I++LK + + +WHF+D++W+ + Sbjct: 205 YAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFL 264 Query: 201 FSFVYLMG 208 F +Y+ G Sbjct: 265 FVVIYIWG 272 >1m56_C Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.25.1.1 PDB: 1m57_C* Length = 266 Score = 95.1 bits (236), Expect = 9e-21 Identities = 43/191 (22%), Positives = 86/191 (45%), Gaps = 14/191 (7%) Query: 29 GTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAP----------IDVFDISGI-FVS 77 G GF +++MS+ + F+ +F ++ +P I FD + ++ Sbjct: 78 GLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLIN 137 Query: 78 TIVLLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQ 137 T++LL S + ++A A + L + G +F + + YE++H Sbjct: 138 TLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSH---AAFGFA 194 Query: 138 RSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIW 197 + + ++FF G HG HV G I+L V +I++ + +WHF+D++W Sbjct: 195 GNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVW 254 Query: 198 ICVFSFVYLMG 208 + +F+ +Y+ G Sbjct: 255 LFLFASIYIWG 265 >1v54_C Cytochrome C oxidase polypeptide III; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.25.1.1 PDB: 1v55_C* 2dyr_C* 2eij_C* 2eik_C* 2eil_C* 2eim_C* 2ein_C* 2zxw_C* 2occ_C* 1oco_C* 1occ_C* 1ocz_C* 1ocr_C* 2dys_C* Length = 261 Score = 84.3 bits (208), Expect = 2e-17 Identities = 40/186 (21%), Positives = 72/186 (38%), Gaps = 9/186 (4%) Query: 29 GTYLGFWIYLMSDCLMFAVFF------VTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLL 82 G G ++++S+ L F FF P I + + + +L Sbjct: 78 GLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVL 137 Query: 83 LSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFL 142 L+S S + + L +T G+ F +++ E+ + Sbjct: 138 LASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYE---APFTISDGVYG 194 Query: 143 SSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFS 202 S+FF G HGLHV G +L V + LK S + + +WHF+D++W+ ++ Sbjct: 195 STFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYV 254 Query: 203 FVYLMG 208 +Y G Sbjct: 255 SIYWWG 260 >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 = 29.5 bits (66), Expect = 0.55 Identities = 20/136 (14%), Positives = 42/136 (30%), Gaps = 51/136 (37%) Query: 4 QKIGKSP-NFSLFYVK--------DKKESCVDHDGTYLGFWIYLMS---DC-----LMFA 46 ++ ++ + + + + + D D YL+S C + A Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD--------YLLSIPISCPLIGVIQLA 247 Query: 47 VFFVTYAVLGKNYAAGPAPIDVFD-IS-------GIFVSTIVLLLSSLSCSFAMLASATK 98 + VT +LG P ++ + G+ + + S SF + Sbjct: 248 HYVVTAKLLGFT------PGELRSYLKGATGHSQGLVTAVAIAETDSWE-SFFVSV---- 296 Query: 99 RLIHKTVSWLLVTAFF 114 K ++ L FF Sbjct: 297 ---RKAITVL----FF 305 Score = 29.1 bits (65), Expect = 0.80 Identities = 31/209 (14%), Positives = 55/209 (26%), Gaps = 96/209 (45%) Query: 1 MSRQKIGKSPNFSLF-YVKDKKESCVDHDGTYLGFWIYLMSDCLMFAVF----------- 48 M+++ K N +LF V + + A+F Sbjct: 132 MAKRPFDKKSNSALFRAVGEGNAQ--------------------LVAIFGGQGNTDDYFE 171 Query: 49 -----FVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKRLIHK 103 + TY VL V D + LS L +++ + Sbjct: 172 ELRDLYQTYHVL------------VGD----LIKFSAETLSELI----RTTLDAEKVFTQ 211 Query: 104 ---TVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSF---FALVGLHGL-HV 156 + WL + P + +L S L+G+ L H Sbjct: 212 GLNILEWL------------------ENP---SNTPDK-DYLLSIPISCPLIGVIQLAH- 248 Query: 157 FFGLIWLFVLVIQILKKGLISGNQRRLIC 185 +V+ ++L G G R + Sbjct: 249 -------YVVTAKLL--GFTPGELRSYLK 268 Score = 25.7 bits (56), Expect = 8.0 Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 11/33 (33%) Query: 94 ASATKRLI----HKTVSWLLVTAF-------FG 115 S ++R++ V W T F FG Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFG 505 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 27.5 bits (60), Expect = 2.4 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 162 WLFVLVIQILKKGLISGNQ 180 W+ +QIL G+I GN+ Sbjct: 1392 WMMNGALQILNSGIIPGNR 1410 >2r9r_B Paddle chimera voltage gated potassium channel KV1.2-KV2.1; voltage sensor, voltage dependent, ION channel, shaker, membrane protein; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB: 2a79_B* Length = 514 Score = 27.1 bits (59), Expect = 3.0 Identities = 19/143 (13%), Positives = 47/143 (32%), Gaps = 10/143 (6%) Query: 66 IDVFDISGIFVSTIVLLLSSLSC-----SFAMLASATKRLIHKTVSWLLVTAFFGMIFII 120 I + + I +S + L +L T ++ + F F I Sbjct: 184 IAIVSVMVILISIVSFCLETLPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPFFI 243 Query: 121 ME-----IYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGL 175 +E + F L+ A P ++ F ++ ++ + + ++ I+L +L+ Sbjct: 244 VETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQN 303 Query: 176 ISGNQRRLICLSMFWHFLDLIWI 198 + + + + F Sbjct: 304 VRRVVQIFRIMRILRIFKLSRHS 326 >1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Length = 114 Score = 26.4 bits (58), Expect = 5.4 Identities = 10/38 (26%), Positives = 17/38 (44%) Query: 62 GPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR 99 GP PI + GI + + L + + +A A K+ Sbjct: 21 GPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKK 58 >1mhs_A Proton pump, plasma membrane ATPase; ION transport, membrane protein, P-type ATPase, active transport, cryo-electron microscopy; 8.00A {Neurospora crassa} SCOP: i.18.1.1 Length = 920 Score = 25.8 bits (56), Expect = 6.5 Identities = 20/130 (15%), Positives = 40/130 (30%), Gaps = 25/130 (19%) Query: 43 LMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR-LI 101 ++ ++T + YA G V + + ++ L SL+ ++ + + Sbjct: 765 VLAVGTWITVTTM---YAQGENGGIVQNFGNM--DEVLFLQISLTENWLIFITRANGPFW 819 Query: 102 HKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLI 161 SW L A F + + F S ++V I Sbjct: 820 SSIPSWQLSGAIFLVDILAT------------CFTIWGWFEHSDTSIVA-------VVRI 860 Query: 162 WLFVLVIQIL 171 W+F I + Sbjct: 861 WIFSFGIFCI 870 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 0.335 0.146 0.465 Gapped Lambda K H 0.267 0.0455 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,792,869 Number of extensions: 74598 Number of successful extensions: 315 Number of sequences better than 10.0: 1 Number of HSP's gapped: 305 Number of HSP's successfully gapped: 42 Length of query: 210 Length of database: 5,693,230 Length adjustment: 88 Effective length of query: 122 Effective length of database: 3,559,758 Effective search space: 434290476 Effective search space used: 434290476 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.6 bits) S2: 54 (25.3 bits)