RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780472|ref|YP_003064885.1| cytochrome o ubiquinol oxidase subunit III [Candidatus Liberibacter asiaticus str. psy62] (210 letters) >gnl|CDD|131889 TIGR02842, CyoC, cytochrome o ubiquinol oxidase, subunit III. Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. Length = 180 Score = 234 bits (598), Expect = 2e-62 Identities = 103/181 (56%), Positives = 130/181 (71%), Gaps = 1/181 (0%) Query: 30 TYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCS 89 T GFW+YLMSDC++FA F TYAVL N A GP+ ++FD+ + V T +LLLSS++ Sbjct: 1 TIFGFWLYLMSDCILFATLFATYAVLSNNTAGGPSGKEIFDLPFVLVETFLLLLSSITFG 60 Query: 90 FAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALV 149 FAMLA K + WL +T G+ FI MEIYEF HLI+ P RSAFLS+FF LV Sbjct: 61 FAMLAMNKKNKK-MVILWLAITFLLGLGFIGMEIYEFYHLIAEGNGPDRSAFLSAFFTLV 119 Query: 150 GLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGV 209 G HGLHV GLIW+ V++IQ+ K GL N+RRL CLS+FWHFLD++WICVF+FVYL+GV Sbjct: 120 GTHGLHVTSGLIWIIVMIIQVYKYGLTKINRRRLACLSLFWHFLDIVWICVFTFVYLLGV 179 Query: 210 V 210 + Sbjct: 180 L 180 >gnl|CDD|182628 PRK10663, PRK10663, cytochrome o ubiquinol oxidase subunit III; Provisional. Length = 204 Score = 208 bits (530), Expect = 1e-54 Identities = 96/178 (53%), Positives = 126/178 (70%), Gaps = 1/178 (0%) Query: 33 GFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAM 92 GFWIYLMSDC++F++ F TYAVL A GP D+F++ + V T +LL SS++ A Sbjct: 28 GFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAA 87 Query: 93 LASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVGLH 152 +A K + +SWL +T FG FI MEIYEF HLI P RS FLS+FFALVG H Sbjct: 88 IA-MYKNNKSQVISWLALTFLFGAGFIGMEIYEFHHLIVEGMGPDRSGFLSAFFALVGTH 146 Query: 153 GLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGVV 210 GLHV GLIW+ VL++Q+ ++GL S N+ R++CLS+FWHFLD++WICVF+ VYLMG + Sbjct: 147 GLHVTSGLIWMAVLMVQVARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM 204 >gnl|CDD|131943 TIGR02897, QoxC, cytochrome aa3 quinol oxidase, subunit III. This family (QoxC) encodes subunit III of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. Length = 190 Score = 137 bits (346), Expect = 2e-33 Identities = 70/180 (38%), Positives = 108/180 (60%), Gaps = 2/180 (1%) Query: 32 LGFWIYLMSDCLMFAVFFVTYAVL-GKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSF 90 LGFWI+L ++ +FA F TY VL AG P ++F++ + + T +LL SS +C Sbjct: 12 LGFWIFLGAEIALFATLFATYLVLQHGGDYAGKMPAELFELPLVLIMTFLLLFSSFTCGI 71 Query: 91 AMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVG 150 A + K + W+++T G F+ EIYEFAH S PQ ++ SSFF L+G Sbjct: 72 A-IYEMRKENQKLMMFWMIITLLLGAGFVGFEIYEFAHYASEGVTPQIGSYWSSFFVLLG 130 Query: 151 LHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGVV 210 HG HV G++W L+IQI ++GL ++ +S++WHFLD++W+ +F+ VYL+G+V Sbjct: 131 THGCHVTLGIVWAICLLIQIQRRGLTPYTAPKVFIVSLYWHFLDVVWVFIFTAVYLIGMV 190 >gnl|CDD|177845 PLN02194, PLN02194, cytochrome-c oxidase. Length = 265 Score = 50.4 bits (120), Expect = 3e-07 Identities = 52/190 (27%), Positives = 90/190 (47%), Gaps = 17/190 (8%) Query: 29 GTYLGFWIYLMSDCLMFAVFF--VTYAVLGKNYAAG----PAPIDVFDISGI-FVSTIVL 81 G G ++++S+ + F FF +++ L G P I+V D I F++T +L Sbjct: 81 GPRYGSILFIVSEVMFFFAFFWASSHSSLAPAVEIGGIWPPKGIEVLDPWEIPFLNTPIL 140 Query: 82 LLSSLSCSFA---MLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQR 138 S + ++A +LA KR ++ V+ +L+ F F ME Y+ IS Sbjct: 141 PSSGAAVTWAHHAILAGKEKRAVYALVATVLLALVFTG-FQGMEYYQAPFTIS------D 193 Query: 139 SAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWI 198 S + S+FF G HG HV G ++L + I+ L + + +WHF+D++W+ Sbjct: 194 SIYGSTFFLATGFHGFHVIIGTLFLIICGIRQYLGHLTKEHHVGFEAAAWYWHFVDVVWL 253 Query: 199 CVFSFVYLMG 208 +F +Y G Sbjct: 254 FLFVSIYWWG 263 >gnl|CDD|180549 PRK06381, PRK06381, threonine synthase; Validated. Length = 319 Score = 28.1 bits (63), Expect = 1.5 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%) Query: 122 EIYEFAHLI-SMEAVPQRSAFLSSFFALVGLHGLHVFFGLIWLFVLVI 168 E+ ++A L+ ME + +A +S AL L G+ V VI Sbjct: 270 EMVKYAELLRRMEGL---NALPASASALAALVKYLKKNGVNDNVVAVI 314 >gnl|CDD|180094 PRK05454, PRK05454, glucosyltransferase MdoH; Provisional. Length = 696 Score = 28.0 bits (63), Expect = 2.0 Identities = 21/108 (19%), Positives = 39/108 (36%), Gaps = 15/108 (13%) Query: 73 GIFVSTIVLLLSS--LSCSFAMLASATKR-----LIHKTVSWLLVTAFFGMIFIIMEIYE 125 +F +T+VLL L +L +R + +S LL T F ++ I ++ Sbjct: 455 ALFAATMVLLFLPKLLGL-LLVLLDPKRRRAFGGALRLLLSVLLETLFSALLAPIRMLFH 513 Query: 126 FAHLISMEA-------VPQRSAFLSSFFALVGLHGLHVFFGLIWLFVL 166 ++S+ +R + + HG H GL+ Sbjct: 514 TRFVVSILLGRDVGWNSQRRDDGSTPWGEAFRRHGWHTLLGLVLAAGA 561 >gnl|CDD|181596 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional. Length = 861 Score = 27.7 bits (62), Expect = 2.0 Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%) Query: 129 LISMEAVP--QRSAFLSSFFALVGLHGLHV 156 L+SME + Q+ FL+ F L HGL V Sbjct: 324 LVSMETIGMWQQVGFLADVFTLFKKHGLSV 353 >gnl|CDD|130176 TIGR01106, ATPase-IIC_X-K, sodium or proton efflux -- potassium uptake antiporter, P-type ATPase, alpha subunit. Sequences from Blastocladiella emersonii (GP|6636502, GP|6636502 and PIR|T43025), C. elegans (GP|2315419, GP|6671808 and PIR|T31763) and Drosophila melanogaster (GP|7291424) score below trusted cutoff, apparently due to long branch length (excessive divergence from the last common ancestor) as evidenced by a phylogenetic tree. Experimental evidence is needed to determine whether these sequences represent ATPases with conserved function. Aside from fragments, other sequences between trusted and noise appear to be bacterial ATPases of unclear lineage, but most likely calcium pumps. Length = 997 Score = 27.8 bits (62), Expect = 2.2 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%) Query: 119 IIMEIYEFAHLISMEAVPQRSAFLS-SFFALVGLHGLHVFFGLIWLFVLVIQILKKGLIS 177 I +EI F H+I+ AV FL SFF L + G +I+L +++ + +GL++ Sbjct: 258 IAIEIEHFIHIITGVAV-----FLGVSFFILSLILGYTWLEAVIFLIGIIVANVPEGLLA 312 Query: 178 GNQRRLICLSM 188 +CL++ Sbjct: 313 ---TVTVCLTL 320 >gnl|CDD|178648 PLN03100, PLN03100, Permease subunit of ER-derived-lipid transporter; Provisional. Length = 292 Score = 25.5 bits (56), Expect = 9.8 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 108 LLVTAFFGMIFIIMEIYEFAHL 129 LL ++F GM+F I + EF L Sbjct: 93 LLTSSFVGMVFTIQFVREFTKL 114 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.335 0.146 0.465 Gapped Lambda K H 0.267 0.0744 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,431,024 Number of extensions: 214926 Number of successful extensions: 921 Number of sequences better than 10.0: 1 Number of HSP's gapped: 905 Number of HSP's successfully gapped: 95 Length of query: 210 Length of database: 5,994,473 Length adjustment: 89 Effective length of query: 121 Effective length of database: 4,071,361 Effective search space: 492634681 Effective search space used: 492634681 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: 55 (24.9 bits)