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= 0236.0009.p (283 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein... 247 8e-67 gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-de... 221 4e-59 gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspir... 204 8e-54 gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein ... 203 2e-53 gi|300310653|ref|YP_003774745.1| cytochrome protein [Herbaspiril... 202 2e-53 >gi|300311001|ref|YP_003775093.1| cytochrome c subunit II protein [Herbaspirillum seropedicae SmR1] Length = 453 Score = 247 bits (630), Expect = 8e-67, Method: Compositional matrix adjust. Identities = 110/170 (64%), Positives = 131/170 (77%) Query: 37 QQIQRGEYLARAGDCMACHTVKGKAPFSGGLPMNTPFGTIYSTNITPDKQTGIGDYSYDD 96 Q I+RGEYLA AGDC ACH+ KG+APFSGG P+++P GTIYSTNITP K GIG Y+ D Sbjct: 31 QLIKRGEYLAIAGDCAACHSQKGRAPFSGGHPISSPLGTIYSTNITPSKTAGIGSYTRDQ 90 Query: 97 FASALRKGKGRNGVRLYPAMPYTSFAKLSDEDVSALYAYFMQGVKPVQQDNPKTALPFPF 156 FA+ALR+G +G +LYPAMPYT++A+L+DEDV+ALY YFMQGV V Q P T LPFPF Sbjct: 91 FAAALRQGVRADGSQLYPAMPYTAYARLNDEDVTALYTYFMQGVAAVDQAAPATDLPFPF 150 Query: 157 NMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQSLGHCGACHTPXN 206 N+R+ M WN LF + KPF+ D +QS WNRGAYLVQ L HC CHTP N Sbjct: 151 NIRLSMKAWNWLFLDKKPFEPDPSQSAQWNRGAYLVQGLAHCSTCHTPRN 200 >gi|300313847|ref|YP_003777939.1| membrane-bound D-gluconate 2-dehydrogenase cytochrome c subunit [Herbaspirillum seropedicae SmR1] Length = 423 Score = 221 bits (564), Expect = 4e-59, Method: Compositional matrix adjust. Identities = 119/270 (44%), Positives = 160/270 (59%), Gaps = 13/270 (4%) Query: 9 AVLATAALSLAAVAVAQTVNPTPSTPQPQQIQRGEYLARAGDCMACHTVKGKAPFSGGLP 68 ++ A A SL A+ T + RG+YLARAGDCMACH+ GK +SGGL Sbjct: 6 SLFAALAWSLGALGTLTTAQAA----DQDLVARGQYLARAGDCMACHSAAGKPAYSGGLA 61 Query: 69 MNTPFGTIYSTNITPDKQTGIGDYSYDDFASALRKGKGRNGVRLYPAMPYTSFAKLSDED 128 +++ G IYSTNITPDK+ GIG+YS F++A+R G +G +LYPAMPY S+AK+SDED Sbjct: 62 IDSGHGIIYSTNITPDKEHGIGNYSEAQFSAAVRHGVRADGTQLYPAMPYPSYAKVSDED 121 Query: 129 VSALYAYFMQGVKPVQQDNPKTALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRG 188 + ALY YFMQGV+PV P +++ FPFN+R M WN+ F +KPF+ S RG Sbjct: 122 IHALYTYFMQGVQPVASTPPASSMSFPFNIRWGMKLWNVFFANDKPFREQDGWSAEIKRG 181 Query: 189 AYLVQSLGHCGACHTPXNAVVNVADPTSLIHVVLAGSAMPSTKSDPSAMGMPAFGWRLSD 248 AYLV+ LGHCG+CHTP +N S L+G + + + PS GMP + S Sbjct: 182 AYLVEGLGHCGSCHTPRGVAMNEKASDSSQAQFLSGGDL-NGWAVPSLRGMPHW----SA 236 Query: 249 QEVAEVVSFIRGNWGNHAAAVTAEQVAVVR 278 Q++ + + R N A+V E VV Sbjct: 237 QDIVDYLQTGR----NKTASVAGEMSLVVE 262 Score = 93.2 bits (230), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 73/273 (26%), Positives = 116/273 (42%), Gaps = 55/273 (20%) Query: 38 QIQRGEYLARA-GDCMACHTVKG-----------KAPFSGGLPMNTPFGTIYSTNITPDK 85 +I+RG YL G C +CHT +G +A F G +N Sbjct: 177 EIKRGAYLVEGLGHCGSCHTPRGVAMNEKASDSSQAQFLSGGDLN---------GWAVPS 227 Query: 86 QTGIGDYSYDDFASALRKGKGRNG--VRLYPAMPYTSFAKLSDEDVSALYAYFMQGVKPV 143 G+ +S D L+ G+ + + S + L ED+ A+ AY ++ + PV Sbjct: 228 LRGMPHWSAQDIVDYLQTGRNKTASVAGEMSLVVEHSTSHLKREDLQAMAAY-LKTLSPV 286 Query: 144 QQDNPKTALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQSLGHCGACH- 202 +P + + K + + ++ YL +C ACH Sbjct: 287 ASSGSGRVIPQGVDATV--------------SKLTAAKDLTLGERLYL----DNCAACHF 328 Query: 203 ------------TPXNAVVNVADPTSLIHVVLAGSAMPSTKSDPSAMGMPAFGWRLSDQE 250 VVN +P++L+HV+LAG+ PST+ PS + MP F RLSD+E Sbjct: 329 VTGRGAPGIFPVLDGATVVNAENPSALLHVILAGARTPSTEKAPSILVMPGFAHRLSDEE 388 Query: 251 VAEVVSFIRGNWGNHAAAVTAEQVAVVRKGVEK 283 A + +F+R WGNHA V+ +V +R G++K Sbjct: 389 AAALATFVRQGWGNHAGKVSEREVGKLRAGMDK 421 >gi|300310719|ref|YP_003774811.1| cytochrome c protein [Herbaspirillum seropedicae SmR1] Length = 431 Score = 204 bits (518), Expect = 8e-54, Method: Compositional matrix adjust. Identities = 102/240 (42%), Positives = 147/240 (61%), Gaps = 8/240 (3%) Query: 30 TPSTPQPQQIQRGEYLARAGDCMACHTVKGKAPFSGGLPMNTPFGTIYSTNITPDKQTGI 89 TP+ +Q+ +G+YLARAG+CMACHT +G AP++GG + +PFGT+Y++NITPDK TGI Sbjct: 39 TPAPDPTRQLAQGQYLARAGNCMACHTARGGAPYAGGRAIASPFGTLYTSNITPDKTTGI 98 Query: 90 GDYSYDDFASALRKGKGRNGVRLYPAMPYTSFAKLSDEDVSALYAYFMQGVKPVQQDNPK 149 G +S DDF AL G+G+ G LYPA PYTS+ +LS D AL+AY +Q + PV + N Sbjct: 99 GQWSADDFWRALHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFAY-LQSLPPVARANQA 157 Query: 150 TALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQSLGHCGACHTPXNAVV 209 L FP++ R+L+ W L+F + ++ D Q WNRGAYLVQ GHC ACH+ N + Sbjct: 158 HTLRFPYDQRMLLGLWRALYFTPQSYQPDPRQDAQWNRGAYLVQGAGHCSACHSARNRLG 217 Query: 210 NVADPTSLIHVVLAGSAMPSTKSDPSAMGMPAFGWRLSDQEVAEVVSFIRGNWGNHAAAV 269 +P + LAG +P+ + + A G L D A++ + ++ HA + Sbjct: 218 ASIEP-----LALAGGVIPALQWYAPPLHGGADG--LQDWSTADIAALLKTGVSPHAVTL 270 Score = 83.2 bits (204), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 79/270 (29%), Positives = 108/270 (40%), Gaps = 40/270 (14%) Query: 25 QTVNPTPSTPQPQQIQRGEYLAR-AGDCMACHTVKGKA-------PFSGGLPMNTPFGTI 76 Q+ P P Q Q RG YL + AG C ACH+ + + +GG+ P Sbjct: 181 QSYQPDPR--QDAQWNRGAYLVQGAGHCSACHSARNRLGASIEPLALAGGV---IPALQW 235 Query: 77 YSTNITPDKQTGIGDYSYDDFASALRKGKGRNGVRLYPAMPYT--SFAKLSDEDVSALYA 134 Y+ + G+ D+S D A+ L+ G + V L P S L+D DVSA+ Sbjct: 236 YAPPLH-GGADGLQDWSTADIAALLKTGVSPHAVTLGPMSEIVGRSLQYLNDADVSAMAV 294 Query: 135 YFMQGVKPVQQDNPKTALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQS 194 Y D + A P +M L+ G V Sbjct: 295 YLKSLPASAADDAARPASVEPAEAERIMKQGKQLY------------------GTLCVDC 336 Query: 195 LGHCGACHTPX------NAVVNVADPTSLIHVVLAGSAMPSTKSDPSAMGMPAFGWRLSD 248 G G P N + P + + VL G PST +P GMP FG +LSD Sbjct: 337 HGGKGQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQLSD 396 Query: 249 QEVAEVVSFIRGNWGNHAAAVTAEQVAVVR 278 QEVA VVS++R +WGN V+A +V R Sbjct: 397 QEVAAVVSYVRNSWGNQGGLVSAAEVNRYR 426 >gi|300313762|ref|YP_003777854.1| cytochrome c precursor protein [Herbaspirillum seropedicae SmR1] Length = 482 Score = 203 bits (516), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 98/188 (52%), Positives = 128/188 (68%), Gaps = 2/188 (1%) Query: 19 AAVAVAQTVNPTPS-TPQPQQIQRGEYLARAGDCMACHTVKGKAPFSGGLPMNTPFGTIY 77 A A+AQ + S + + QQI RG YLARAGDC+ACHT KG APF+GGL + +P G IY Sbjct: 62 ADTALAQRIAAQGSASAEDQQILRGAYLARAGDCVACHTSKGGAPFAGGLALASPIGAIY 121 Query: 78 STNITPDKQTGIGDYSYDDFASALRKGKGRNGVRLYPAMPYTSFAKLSDEDVSALYAYFM 137 STNITPDKQ GIGD+SY+DFA +R G + G +YPAMPY S+++L+DED+ ALYAYF Sbjct: 122 STNITPDKQHGIGDWSYEDFARLMRTGVTKAGYTVYPAMPYPSYSRLTDEDMQALYAYFS 181 Query: 138 QGVKPVQQDNPKTALPFPFNMRILMAGWNMLFFEN-KPFKADSTQSISWNRGAYLVQSLG 196 + V P Q+N +P+P +MR +A W +F P+ + RGAYLV+ LG Sbjct: 182 KAVPPSAQENRANDIPWPLSMRWPLALWRKVFAPTPAPYTPAAGSDQELARGAYLVEGLG 241 Query: 197 HCGACHTP 204 HCG+CH+P Sbjct: 242 HCGSCHSP 249 Score = 79.0 bits (193), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 78/276 (28%), Positives = 115/276 (41%), Gaps = 50/276 (18%) Query: 30 TPSTPQPQQIQRGEYLARA-GDCMACH-----TVKGKAPFSGGLPMNTPFGTIYSTNITP 83 TP+ Q++ RG YL G C +CH T++ KA G + G + P Sbjct: 221 TPAAGSDQELARGAYLVEGLGHCGSCHSPRAVTMQEKALKEDGGRLFLSGGQVVDGWSVP 280 Query: 84 DKQT----GIGDYSYDDFASALRKGKGRNGVRLYPAMP---YTSFAKLSDEDVSALYAYF 136 + GI +S D LR G+ + + AM S +SD D++A+ Y Sbjct: 281 SLRNEHGGGIAGWSQADLVEFLRTGRNQYTAS-FGAMNDVIEDSMQYMSDADLNAMARYL 339 Query: 137 MQGVKPVQQDNPKTALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQSLG 196 + + P QQ A P+ ++ A ++ +P GA + L Sbjct: 340 LS-LPPRQQ-----AAPYRYDSATAQAA-----YDGRPD----------GPGARIY--LD 376 Query: 197 HCGACHTPX-------------NAVVNVADPTSLIHVVLAGSAMPSTKSDPSAMGMPAFG 243 C ACH N V+ +D TS I ++L G PST S + + M + Sbjct: 377 RCAACHRSNGTGYGKAFPALAGNPVLQTSDATSAIRIILQGGRQPSTASATAGLVMAPYA 436 Query: 244 WRLSDQEVAEVVSFIRGNWGNHAAAVTAEQVAVVRK 279 L DQ+VAEV S+I+ WGN TA +VA VRK Sbjct: 437 QLLDDQQVAEVTSYIQTAWGNRGGTTTAAEVAKVRK 472 >gi|300310653|ref|YP_003774745.1| cytochrome protein [Herbaspirillum seropedicae SmR1] Length = 974 Score = 202 bits (515), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 96/187 (51%), Positives = 123/187 (65%), Gaps = 3/187 (1%) Query: 23 VAQTVNPTPSTPQPQQIQRGEYLARAGDCMACHTVKGKAPFSGGLPMNTPFGTIYSTNIT 82 +A P P I+RG +A AGDC CHT G A +GG + TPFGT+YSTNIT Sbjct: 571 IAPIARPDPDLYSAATIERGRRVALAGDCAVCHTAPGGATNAGGHALQTPFGTVYSTNIT 630 Query: 83 PDKQTGIGDYSYDDFASALRKGKGRNGVRLYPAMPYTSFAKLSDEDVSALYAYFMQGVKP 142 PD+ TGIG++SY F A+R+G R+G LYPA PYT+FAK+S+ D+ +LYAY M +P Sbjct: 631 PDEHTGIGNWSYAAFERAMREGIHRDGRHLYPAFPYTAFAKISEADMQSLYAYLM--AQP 688 Query: 143 -VQQDNPKTALPFPFNMRILMAGWNMLFFENKPFKADSTQSISWNRGAYLVQSLGHCGAC 201 V P L FPFN+R L+AGWN LF + + F+ D +S WNRGAYLV+ GHC AC Sbjct: 689 AVASTPPANDLRFPFNLRPLLAGWNTLFHDPQVFQPDPARSDLWNRGAYLVEGAGHCAAC 748 Query: 202 HTPXNAV 208 H+P NA+ Sbjct: 749 HSPRNAL 755 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 0.131 0.398 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: 765,538 Number of extensions: 30319 Number of successful extensions: 106 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 98 Number of HSP's successfully gapped: 12 Length of query: 283 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 199 Effective length of database: 1,222,130 Effective search space: 243203870 Effective search space used: 243203870 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: 130 (54.7 bits)