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= 0001.4028.p (386 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... 728 0.0 gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptid... 87 3e-18 gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-de... 69 9e-13 gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspir... 62 6e-11 gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein ... 59 6e-10 >gi|300313447|ref|YP_003777539.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 386 Score = 728 bits (1880), Expect = 0.0, Method: Compositional matrix adjust. Identities = 361/386 (93%), Positives = 379/386 (98%) Query: 1 MKLAKRLQTLSLGASLLAAGLPAWAVVDSPGGPAVLQTNFQPPVTKIAEQIYDLHIMMLV 60 MKLAKRLQ+L LGASLLAAGLPAWAVVDSPGGPAVLQ NFQPPVTKIAEQIYDLHI+ML+ Sbjct: 1 MKLAKRLQSLILGASLLAAGLPAWAVVDSPGGPAVLQMNFQPPVTKIAEQIYDLHILMLI 60 Query: 61 ICLLIFVAVFGVMFYSIIKHRKSVGHKAASFHESTTVEIAWTVVPFLIVIGMALPATKTV 120 ICL+IFVAVFGVMFYSIIKHRKSVGHKA++FHEST VEIAWTVVPFLIVIGMALPATKTV Sbjct: 61 ICLVIFVAVFGVMFYSIIKHRKSVGHKASTFHESTAVEIAWTVVPFLIVIGMALPATKTV 120 Query: 121 VAMKDTSNADLTIKVTGMQWKWGYDYLKGEGEGISFLSSLATPREQITDPALKKNDNYLI 180 VAMKDTSNADLTIKVTGMQWKWGYDYLKGEGEGISFLS+LATPREQ+TDP+LKKNDNYLI Sbjct: 121 VAMKDTSNADLTIKVTGMQWKWGYDYLKGEGEGISFLSNLATPREQVTDPSLKKNDNYLI 180 Query: 181 EVDNPVVVPVNKKVRLVTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQC 240 EVDNPVVVPVNKKVR+VTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQC Sbjct: 181 EVDNPVVVPVNKKVRIVTTANDVIHSWTIPAFGVKQDAIPGFVRDTWFRAEKIGTYRGQC 240 Query: 241 VELCGKDHAFMPIVVNVVSDDDYKKWVEGKKKEMAAKADDPSKVWTVDELKQRGEKVYAA 300 VELCGKDHAFMPIVVNVVS+DDYK+WV+GKKKEMAAKADDP+K WTVDELKQRGEKVYAA Sbjct: 241 VELCGKDHAFMPIVVNVVSEDDYKQWVDGKKKEMAAKADDPNKTWTVDELKQRGEKVYAA 300 Query: 301 NCVVCHQANGKGVPGAFPALDGSAVVNGPKDGQIHILLNGKNAMPAWKGILNDTEIAAVI 360 NCV CHQANGKGVPGAFPALDGS VVNGPKDGQIH++LNGKNAMP WKG+LNDTEIAAVI Sbjct: 301 NCVTCHQANGKGVPGAFPALDGSPVVNGPKDGQIHLVLNGKNAMPPWKGVLNDTEIAAVI 360 Query: 361 TYTRNNWSNKAQENIVQPAEVLAARK 386 TYTRN+WSNKAQENIVQPAEVLAARK Sbjct: 361 TYTRNSWSNKAQENIVQPAEVLAARK 386 >gi|300311627|ref|YP_003775719.1| cytochrome c oxidase polypeptide II precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 344 Score = 86.7 bits (213), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 65/239 (27%), Positives = 96/239 (40%), Gaps = 38/239 (15%) Query: 39 NFQPPVTKIAEQIYDLHIMMLVICLLIFVAVFGVMFYSIIKHRKSVGHKAASFHESTTVE 98 + Q P A I L + L +C ++F+ ++ + R+ AA+ T Sbjct: 34 DVQQPAGPQAATIASLWHVTLGLCTVVFLLTLLACAVALFRRRRYSAEAAAAT-PRLTWA 92 Query: 99 IAWTVVPFLIVIGMALPATKTVVAMKDT----SNADLTIKVTGMQWKWGYDY---LKGEG 151 I W + L G+ VVA + + L +K+T QW W Y L G+G Sbjct: 93 IGWAL--GLSATGLLALFAADVVASRALDQLPTAGALQVKLTARQWWWQAQYHDPLTGQG 150 Query: 152 EGISFLSSLATPREQITDPALKKNDNYLIEVDNPVVVPVNKKVRLVTTANDVIHSWTIPA 211 N + +PV + V + + DVIHS +P Sbjct: 151 ----------------------------FTTANELHLPVGRAVIIDLDSEDVIHSLWLPN 182 Query: 212 FGVKQDAIPGFVRDTWFRAEKIGTYRGQCVELCGKDHAFMPIVVNVVSDDDYKKWVEGK 270 K D IPG RA++ GTYRGQC E CG +HA M ++V S DY +W G+ Sbjct: 183 LHGKLDLIPGKPAQLRLRADQAGTYRGQCAEFCGLEHARMALLVTAESPADYARWASGQ 241 >gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-dehydrogenase cytochrome c subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 68.6 bits (166), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 34/90 (37%), Positives = 45/90 (50%), Gaps = 12/90 (13%) Query: 294 GEKVYAANCVVCHQANGKGVPGAFPALDGSAVVNGPK-DGQIHILLNGKNA--------- 343 GE++Y NC CH G+G PG FP LDG+ VVN +H++L G Sbjct: 315 GERLYLDNCAACHFVTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTEKAPSI 374 Query: 344 --MPAWKGILNDTEIAAVITYTRNNWSNKA 371 MP + L+D E AA+ T+ R W N A Sbjct: 375 LVMPGFAHRLSDEEAAALATFVRQGWGNHA 404 >gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspirillum seropedicae SmR1] Length = 431 Score = 62.4 bits (150), Expect = 6e-11, Method: Compositional matrix adjust. Identities = 42/144 (29%), Positives = 69/144 (47%), Gaps = 19/144 (13%) Query: 255 VNVVSDDDYKKWVEGKKKEMAAKADDPSKVWTVD-----ELKQRGEKVYAANCVVCHQAN 309 + ++D D K A+ ADD ++ +V+ + ++G+++Y CV CH Sbjct: 281 LQYLNDADVSAMAVYLKSLPASAADDAARPASVEPAEAERIMKQGKQLYGTLCVDCHGGK 340 Query: 310 GKGVPGAFPALDGSAVVNGPKDGQ-IHILLNG-----------KNAMPAWKGILNDTEIA 357 G+G +P L G+ + GP + +LNG MP + L+D E+A Sbjct: 341 GQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQLSDQEVA 400 Query: 358 AVITYTRNNWSNKAQENIVQPAEV 381 AV++Y RN+W N Q +V AEV Sbjct: 401 AVVSYVRNSWGN--QGGLVSAAEV 422 >gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 441 Score = 58.9 bits (141), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 36/105 (34%), Positives = 52/105 (49%), Gaps = 14/105 (13%) Query: 294 GEKVYAANCVVCHQANGKGVPGAFPALDGSAVVNGPKDGQ-IHILLNGKN---------- 342 G + NC CH+++GKG FP+L S VN I I+L G Sbjct: 321 GAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNAENPASLIRIVLEGAEMPWTHKAPTQ 380 Query: 343 -AMPAWKGILNDTEIAAVITYTRNNWSNKAQENIVQPAEVLAARK 386 AMPA+ L+D E+A V+T+ R++W 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 0.319 0.134 0.410 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: 1,159,143 Number of extensions: 46155 Number of successful extensions: 152 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 152 Number of HSP's successfully gapped: 5 Length of query: 386 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 299 Effective length of database: 1,207,925 Effective search space: 361169575 Effective search space used: 361169575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 131 (55.1 bits)