BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0025.0080.p (370 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptid... 664 0.0 gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptid... 90 3e-19 gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspir... 69 8e-13 gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-de... 67 2e-12 gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein ... 65 6e-12 >gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 386 Score = 664 bits (1713), Expect = 0.0, Method: Compositional matrix adjust. Identities = 334/370 (90%), Positives = 349/370 (94%), Gaps = 4/370 (1%) Query: 1 VPSWAWGDKVVDSQGGPAVLQTNFQPPVTQIAEQIYDLHHLMLIICLVIFVAVFGVMFYS 60 +P+WA VVDS GGPAVLQ NFQPPVT+IAEQIYDLH LMLIICLVIFVAVFGVMFYS Sbjct: 21 LPAWA----VVDSPGGPAVLQMNFQPPVTKIAEQIYDLHILMLIICLVIFVAVFGVMFYS 76 Query: 61 ILKHRKSLGHKSASFHESTTVEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIKAT 120 I+KHRKS+GHK+++FHEST VEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIK T Sbjct: 77 IIKHRKSVGHKASTFHESTAVEIAWTVVPFLIVIGMALPATKTVVAMKDTSNADLTIKVT 136 Query: 121 GMQWKWGYDYLKGEGEGISFLSNLATPREQITDASLKKNDNYLIEVDNPVVVPVNKKVRI 180 GMQWKWGYDYLKGEGEGISFLSNLATPREQ+TD SLKKNDNYLIEVDNPVVVPVNKKVRI Sbjct: 137 GMQWKWGYDYLKGEGEGISFLSNLATPREQVTDPSLKKNDNYLIEVDNPVVVPVNKKVRI 196 Query: 181 ITTANDVIHSWTIPAFGVKQDAIPGFVRDTWFKAEKIGTYRGQCVELCGKDHAFMPIVVN 240 +TTANDVIHSWTIPAFGVKQDAIPGFVRDTWF+AEKIGTYRGQCVELCGKDHAFMPIVVN Sbjct: 197 VTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQCVELCGKDHAFMPIVVN 256 Query: 241 VVSDADYKTWVDGKKKEMAAKADDPSKVWTIDELKQRGEKVYTANCVVCHQANGKGVPGA 300 VVS+ DYK WVDGKKKEMAAKADDP+K WT+DELKQRGEKVY ANCV CHQANGKGVPGA Sbjct: 257 VVSEDDYKQWVDGKKKEMAAKADDPNKTWTVDELKQRGEKVYAANCVTCHQANGKGVPGA 316 Query: 301 FPALDGDPVVNGPKAAQIAVVLNGKNAMPAWKSVLNDTEIAAVITYTRNSWSNKAQENIV 360 FPALDG PVVNGPK QI +VLNGKNAMP WK VLNDTEIAAVITYTRNSWSNKAQENIV Sbjct: 317 FPALDGSPVVNGPKDGQIHLVLNGKNAMPPWKGVLNDTEIAAVITYTRNSWSNKAQENIV 376 Query: 361 QPAEVLAARK 370 QPAEVLAARK Sbjct: 377 QPAEVLAARK 386 >gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 89.7 bits (221), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 67/239 (28%), Positives = 97/239 (40%), Gaps = 38/239 (15%) Query: 23 NFQPPVTQIAEQIYDLHHLMLIICLVIFVAVFGVMFYSILKHRKSLGHKSASFHESTTVE 82 + Q P A I L H+ L +C V+F+ ++ + R+ ++A+ T Sbjct: 34 DVQQPAGPQAATIASLWHVTLGLCTVVFLLTLLACAVALFRRRR-YSAEAAAATPRLTWA 92 Query: 83 IAWTVVPFLIVIGMALPATKTVVAMKDT----SNADLTIKATGMQWKWGYDY---LKGEG 135 I W + L G+ VVA + + L +K T QW W Y L G+G Sbjct: 93 IGWAL--GLSATGLLALFAADVVASRALDQLPTAGALQVKLTARQWWWQAQYHDPLTGQG 150 Query: 136 EGISFLSNLATPREQITDASLKKNDNYLIEVDNPVVVPVNKKVRIITTANDVIHSWTIPA 195 N + +PV + V I + DVIHS +P Sbjct: 151 ----------------------------FTTANELHLPVGRAVIIDLDSEDVIHSLWLPN 182 Query: 196 FGVKQDAIPGFVRDTWFKAEKIGTYRGQCVELCGKDHAFMPIVVNVVSDADYKTWVDGK 254 K D IPG +A++ GTYRGQC E CG +HA M ++V S ADY W G+ Sbjct: 183 LHGKLDLIPGKPAQLRLRADQAGTYRGQCAEFCGLEHARMALLVTAESPADYARWASGQ 241 >gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspirillum seropedicae SmR1] Length = 431 Score = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust. Identities = 45/144 (31%), Positives = 71/144 (49%), Gaps = 19/144 (13%) Query: 239 VNVVSDADYKTWVDGKKKEMAAKADDPSKVWTID-----ELKQRGEKVYTANCVVCHQAN 293 + ++DAD K A+ ADD ++ +++ + ++G+++Y CV CH Sbjct: 281 LQYLNDADVSAMAVYLKSLPASAADDAARPASVEPAEAERIMKQGKQLYGTLCVDCHGGK 340 Query: 294 GKGVPGAFPALDGDPVVNGPKAAQ-IAVVLNG-----------KNAMPAWKSVLNDTEIA 341 G+G +P L G+ + GP A + VLNG MP + L+D E+A Sbjct: 341 GQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQLSDQEVA 400 Query: 342 AVITYTRNSWSNKAQENIVQPAEV 365 AV++Y RNSW N Q +V AEV Sbjct: 401 AVVSYVRNSWGN--QGGLVSAAEV 422 >gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-dehydrogenase cytochrome c subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 35/90 (38%), Positives = 45/90 (50%), Gaps = 12/90 (13%) Query: 278 GEKVYTANCVVCHQANGKGVPGAFPALDGDPVVNGPK-AAQIAVVLNGKNA--------- 327 GE++Y NC CH G+G PG FP LDG VVN +A + V+L G Sbjct: 315 GERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTEKAPSI 374 Query: 328 --MPAWKSVLNDTEIAAVITYTRNSWSNKA 355 MP + L+D E AA+ T+ R W N A Sbjct: 375 LVMPGFAHRLSDEEAAALATFVRQGWGNHA 404 >gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 441 Score = 65.5 bits (158), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 39/105 (37%), Positives = 54/105 (51%), Gaps = 14/105 (13%) Query: 278 GEKVYTANCVVCHQANGKGVPGAFPALDGDPVVNGPKAAQ-IAVVLNGKN---------- 326 G + NC CH+++GKG FP+L P VN A I +VL G Sbjct: 321 GAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNAENPASLIRIVLEGAEMPWTHKAPTQ 380 Query: 327 -AMPAWKSVLNDTEIAAVITYTRNSWSNKAQENIVQPAEVLAARK 370 AMPA+ S L+D E+A V+T+ R+SW N+A V ++V RK Sbjct: 381 FAMPAFGSRLSDQEVAEVVTFIRSSWGNQASS--VSASDVAKVRK 423 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.318 0.133 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,171,819 Number of extensions: 46026 Number of successful extensions: 133 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 129 Number of HSP's successfully gapped: 6 Length of query: 370 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 283 Effective length of database: 1,207,925 Effective search space: 341842775 Effective search space used: 341842775 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 (21.7 bits) S2: 131 (55.1 bits)