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= 0002.0604.p (323 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspir... 404 e-114 gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein ... 212 4e-56 gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein ... 202 3e-53 gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-de... 194 7e-51 gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein... 183 1e-47 >gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspirillum seropedicae SmR1] Length = 431 Score = 404 bits (1038), Expect = e-114, Method: Compositional matrix adjust. Identities = 190/323 (58%), Positives = 237/323 (73%), Gaps = 1/323 (0%) Query: 1 LHHGKSKDGSFLYPAFPYTNYTKVTREDSNALFAYMQTVTPVRQPSQEHALRFPYNNRIL 60 LHHG+ K+G FLYPAFPYT+YT+++R DS+ALFAY+Q++ PV + +Q H LRFPY+ R+L Sbjct: 110 LHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFAYLQSLPPVARANQAHTLRFPYDQRML 169 Query: 61 LAGWRALYFTPGAYRADSKQSVEWNRGAYLVQGLGHCSACHTTRNAFGATVAKSDLGGGL 120 L WRALYFTP +Y+ D +Q +WNRGAYLVQG GHCSACH+ RN GA++ L GG+ Sbjct: 170 LGLWRALYFTPQSYQPDPRQDAQWNRGAYLVQGAGHCSACHSARNRLGASIEPLALAGGV 229 Query: 121 IPIMNWYAPSLTSDAEAGLGNWELQHITALLKTGVSPRSTVFGPMAEVVSRSLQHLNDSD 180 IP + WYAP L A+ GL +W I ALLKTGVSP + GPM+E+V RSLQ+LND+D Sbjct: 230 IPALQWYAPPLHGGAD-GLQDWSTADIAALLKTGVSPHAVTLGPMSEIVGRSLQYLNDAD 288 Query: 181 IQAMAVYLKSLPQNDPPPAFDTPQPDKATADRVMQAGAKIYEQHCAECHKAGGQGIAPAY 240 + AMAVYLKSLP + A + A A+R+M+ G ++Y C +CH GQG AP Y Sbjct: 289 VSAMAVYLKSLPASAADDAARPASVEPAEAERIMKQGKQLYGTLCVDCHGGKGQGSAPDY 348 Query: 241 PPMNGNRALTMGSAVNPIRMVLNGGFPPSTQGNPRPYGMPPFGQLLNDQEVAAVVSYIRN 300 PP+ GNRA+ N +R VLNGGFPPST GNP P+GMPPFG L+DQEVAAVVSY+RN Sbjct: 349 PPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQLSDQEVAAVVSYVRN 408 Query: 301 SWDNRAGFVSPQEVNRYRSIPLD 323 SW N+ G VS EVNRYRS+PLD Sbjct: 409 SWGNQGGLVSAAEVNRYRSVPLD 431 >gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 482 Score = 212 bits (539), Expect = 4e-56, Method: Compositional matrix adjust. Identities = 121/327 (37%), Positives = 176/327 (53%), Gaps = 9/327 (2%) Query: 1 LHHGKSKDGSFLYPAFPYTNYTKVTREDSNALFAYM-QTVTPVRQPSQEHALRFPYNNRI 59 + G +K G +YPA PY +Y+++T ED AL+AY + V P Q ++ + + +P + R Sbjct: 145 MRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFSKAVPPSAQENRANDIPWPLSMRW 204 Query: 60 LLAGWRALYF-TPGAYRADSKQSVEWNRGAYLVQGLGHCSACHTTRNAFGATVAKSDLGG 118 LA WR ++ TP Y + E RGAYLV+GLGHC +CH+ R A + GG Sbjct: 205 PLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLGHCGSCHSPRAVTMQEKALKEDGG 264 Query: 119 GLI-----PIMNWYAPSLTSDAEAGLGNWELQHITALLKTGVSPRSTVFGPMAEVVSRSL 173 L + W PSL ++ G+ W + L+TG + + FG M +V+ S+ Sbjct: 265 RLFLSGGQVVDGWSVPSLRNEHGGGIAGWSQADLVEFLRTGRNQYTASFGAMNDVIEDSM 324 Query: 174 QHLNDSDIQAMAVYLKSLP--QNDPPPAFDTPQPDKATADRVMQAGAKIYEQHCAECHKA 231 Q+++D+D+ AMA YL SLP Q P +D+ A R GA+IY CA CH++ Sbjct: 325 QYMSDADLNAMARYLLSLPPRQQAAPYRYDSATAQAAYDGRPDGPGARIYLDRCAACHRS 384 Query: 232 GGQGIAPAYPPMNGNRALTMGSAVNPIRMVLNGGFPPSTQGNPRPYGMPPFGQLLNDQEV 291 G G A+P + GN L A + IR++L GG PST M P+ QLL+DQ+V Sbjct: 385 NGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGRQPSTASATAGLVMAPYAQLLDDQQV 444 Query: 292 AAVVSYIRNSWDNRAGFVSPQEVNRYR 318 A V SYI+ +W NR G + EV + R Sbjct: 445 AEVTSYIQTAWGNRGGTTTAAEVAKVR 471 Score = 57.4 bits (137), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 56/176 (31%), Positives = 77/176 (43%), Gaps = 45/176 (25%) Query: 86 RGAYLVQGLGHCSACHTTRNAFGATVAKSDLGGGLI---PIMNWYAPSLTSDAEAGLGNW 142 RGAYL + G C ACHT++ GA A GGL PI Y+ ++T D + G+G+W Sbjct: 85 RGAYLARA-GDCVACHTSKG--GAPFA-----GGLALASPIGAIYSTNITPDKQHGIGDW 136 Query: 143 ELQHITALLKTGVSPRSTVFGPMAEVVSRSLQHLNDSDIQAMAVYL-KSLP-------QN 194 + L++TGV+ P S S L D D+QA+ Y K++P N Sbjct: 137 SYEDFARLMRTGVTKAGYTVYPAMPYPSYS--RLTDEDMQALYAYFSKAVPPSAQENRAN 194 Query: 195 D-------------------PPPAFDTPQPDKATADRVMQAGAKIYE--QHCAECH 229 D P PA TP A +D+ + GA + E HC CH Sbjct: 195 DIPWPLSMRWPLALWRKVFAPTPAPYTP---AAGSDQELARGAYLVEGLGHCGSCH 247 >gi|300312638|ref|YP_003776730.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 441 Score = 202 bits (514), Expect = 3e-53, Method: Compositional matrix adjust. Identities = 129/329 (39%), Positives = 176/329 (53%), Gaps = 16/329 (4%) Query: 1 LHHGKSKDGSFLYPAFPYTNYTKVTREDSNALFAY-MQTVTPVRQPSQEHALRFPYNNRI 59 L HG KDG+ LYPA PY +Y KV D AL+AY M V P++ + +P + R Sbjct: 99 LRHGIRKDGASLYPAMPYPSYAKVKPADVKALYAYFMHGVQADPAPNRGVDITWPLSMRW 158 Query: 60 LLAGWRALYFTPGAYRADSKQSVEWNRGAYLVQGLGHCSACHTTRNAFGATVAKSD---- 115 L+ WR + F P + + RG YLV+GLGHC ACHT R A S+ Sbjct: 159 PLSIWRKV-FAPAVAVDGPEDNSPLVRGQYLVEGLGHCGACHTPRGVGMQEKALSNDSSQ 217 Query: 116 -LGGGLIPIMNWYAPSLTSDAEAGLGNWELQHITALLKTGVSPRSTVFGPMAEVVSRSLQ 174 L GG+I + A +L D GLGNW I A LKTG + S FG MA+VV+ S Q Sbjct: 218 FLSGGVID--GYLANNLRGDGRDGLGNWSEADIVAFLKTGRNSHSAAFGGMADVVANSTQ 275 Query: 175 HLNDSDIQAMAVYLKSL-PQNDPPPAF----DTPQPDKATADRVMQAGAKIYEQHCAECH 229 ++ + D+ AMA YLKSL P D PA T Q + +D+ GA + +CA CH Sbjct: 276 YMTEEDLSAMAKYLKSLKPVKDGTPALAYDDKTHQALRKGSDQ--SPGAMAFLNNCAACH 333 Query: 230 KAGGQGIAPAYPPMNGNRALTMGSAVNPIRMVLNGGFPPSTQGNPRPYGMPPFGQLLNDQ 289 ++ G+G +P + + + + + IR+VL G P T P + MP FG L+DQ Sbjct: 334 RSSGKGYDETFPSLALSPTVNAENPASLIRIVLEGAEMPWTHKAPTQFAMPAFGSRLSDQ 393 Query: 290 EVAAVVSYIRNSWDNRAGFVSPQEVNRYR 318 EVA VV++IR+SW N+A VS +V + R Sbjct: 394 EVAEVVTFIRSSWGNQASSVSASDVAKVR 422 >gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-dehydrogenase cytochrome c subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 194 bits (493), Expect = 7e-51, Method: Compositional matrix adjust. Identities = 123/334 (36%), Positives = 172/334 (51%), Gaps = 25/334 (7%) Query: 1 LHHGKSKDGSFLYPAFPYTNYTKVTREDSNALFAY-MQTVTPVRQPSQEHALRFPYNNRI 59 + HG DG+ LYPA PY +Y KV+ ED +AL+ Y MQ V PV ++ FP+N R Sbjct: 94 VRHGVRADGTQLYPAMPYPSYAKVSDEDIHALYTYFMQGVQPVASTPPASSMSFPFNIRW 153 Query: 60 LLAGWRALYFTPGAYRADSKQSVEWNRGAYLVQGLGHCSACHTTRN-AFGATVAKSD--- 115 + W + +R S E RGAYLV+GLGHC +CHT R A + S Sbjct: 154 GMKLWNVFFANDKPFREQDGWSAEIKRGAYLVEGLGHCGSCHTPRGVAMNEKASDSSQAQ 213 Query: 116 -LGGGLIPIMNWYAPSLTSDAEAGLGNWELQHITALLKTGVSPRSTVFGPMAEVVSRSLQ 174 L GG + W PSL G+ +W Q I L+TG + ++V G M+ VV S Sbjct: 214 FLSGG--DLNGWAVPSLR-----GMPHWSAQDIVDYLQTGRNKTASVAGEMSLVVEHSTS 266 Query: 175 HLNDSDIQAMAVYLKSL-PQNDPPPAFDTPQPDKATADRVMQA-----GAKIYEQHCAEC 228 HL D+QAMA YLK+L P PQ AT ++ A G ++Y +CA C Sbjct: 267 HLKREDLQAMAAYLKTLSPVASSGSGRVIPQGVDATVSKLTAAKDLTLGERLYLDNCAAC 326 Query: 229 HKAGGQGIAPAYPPMNGNRALTMGSAVNP---IRMVLNGGFPPSTQGNPRPYGMPPFGQL 285 H G+G +P ++G T+ +A NP + ++L G PST+ P MP F Sbjct: 327 HFVTGRGAPGIFPVLDGA---TVVNAENPSALLHVILAGARTPSTEKAPSILVMPGFAHR 383 Query: 286 LNDQEVAAVVSYIRNSWDNRAGFVSPQEVNRYRS 319 L+D+E AA+ +++R W N AG VS +EV + R+ Sbjct: 384 LSDEEAAALATFVRQGWGNHAGKVSEREVGKLRA 417 >gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein [Herbaspirillum seropedicae SmR1] Length = 453 Score = 183 bits (465), Expect = 1e-47, Method: Compositional matrix adjust. Identities = 117/329 (35%), Positives = 155/329 (47%), Gaps = 19/329 (5%) Query: 1 LHHGKSKDGSFLYPAFPYTNYTKVTREDSNALFAY-MQTVTPVRQPSQEHALRFPYNNRI 59 L G DGS LYPA PYT Y ++ ED AL+ Y MQ V V Q + L FP+N R+ Sbjct: 95 LRQGVRADGSQLYPAMPYTAYARLNDEDVTALYTYFMQGVAAVDQAAPATDLPFPFNIRL 154 Query: 60 LLAGWRALYFTPGAYRADSKQSVEWNRGAYLVQGLGHCSACHTTRNAFGATVAKSDLGGG 119 + W L+ + D QS +WNRGAYLVQGL HCS CHT RN A + L GG Sbjct: 155 SMKAWNWLFLDKKPFEPDPSQSAQWNRGAYLVQGLAHCSTCHTPRNFLMAEQLERRLQGG 214 Query: 120 LIPIMNWYAPSLTSDAEAGLGNWELQHITALLKTG-VSPRSTVFGPMAEVVSRSLQHLND 178 + WYAP +T A W + + L +G + +T GPM E + S L Sbjct: 215 --SLGTWYAPDITPAALQAKPAWTREMLADYLASGHAANGATAAGPMLEAIEMSFSRLRR 272 Query: 179 SDIQAMAVYL-------KSLPQNDPPPAFDTPQPDKA-TADRVMQAGAKIYEQHCAECHK 230 D++AMA YL + N PP Q D A + GA++Y +CA CH Sbjct: 273 EDLEAMASYLLPPTAATAAPAVNKPPAGLTPVQGDDTPQALAALSPGARVYMNNCASCHN 332 Query: 231 AGGQGIAPAYPPMNGNRALTMGSAVNPIRMVLNGGFPPSTQGNPRPYGMPPFGQLLNDQE 290 GQG+ PP+ + L + N + +L G P Q GM F LND++ Sbjct: 333 TAGQGLN-GLPPLQSHPVLRQPNGDNVVMAILEGVLPEHGQ------GMIGFAHTLNDEQ 385 Query: 291 VAAVVSYIRNSWDNRAGFVSPQEVNRYRS 319 VAAV +Y+ V+ Q V R+ Sbjct: 386 VAAVTNYLLQDIGGSKVSVTTQRVATLRA 414 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 0.317 0.133 0.416 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: 1,145,928 Number of extensions: 51137 Number of successful extensions: 181 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 154 Number of HSP's successfully gapped: 9 Length of query: 323 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 238 Effective length of database: 1,217,395 Effective search space: 289740010 Effective search space used: 289740010 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)