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= 0001.0837.p (354 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310376|ref|YP_003774468.1| outer membrane porin [Herbaspir... 654 0.0 gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 114 9e-27 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 111 9e-26 gi|300313291|ref|YP_003777383.1| porin transmembrane protein [He... 98 8e-22 gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspir... 96 3e-21 >gi|300310376|ref|YP_003774468.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 355 Score = 654 bits (1687), Expect = 0.0, Method: Compositional matrix adjust. Identities = 338/355 (95%), Positives = 345/355 (97%), Gaps = 1/355 (0%) Query: 1 MGAFSAQAQAQ-SSVTIYGRVVAGVDIMTNVPKNDGSGTTGTRIRSASNQWGTSMIGFKG 59 MGAFSAQAQAQ SSVTIYGRVVAGVDIMTNVPK DGSGTTGTRIR+ASNQWGTSMIG KG Sbjct: 1 MGAFSAQAQAQTSSVTIYGRVVAGVDIMTNVPKTDGSGTTGTRIRAASNQWGTSMIGVKG 60 Query: 60 TEDLGGGTNAFFLLESGFGSTTGGLNGTDVNGTSLFNRRSYVGLSSANAGTLKLGKNLFI 119 TEDLGGGTNAFFLLESGFGSTTGGLNGTD+NGTSLFNRRSYVGLSSANAG+LKLGKNLFI Sbjct: 61 TEDLGGGTNAFFLLESGFGSTTGGLNGTDINGTSLFNRRSYVGLSSANAGSLKLGKNLFI 120 Query: 120 NNDVWFLDPTGQQWIGTANLVRGRNWPGASNVIEYTTPTYGGFGATLQTSLGEAAGSFSK 179 NNDVWFLDPTGQQWIGTANLVRGRNWPGASNVIEYTTPT+GGFGAT+QTSLGEAAGSFSK Sbjct: 121 NNDVWFLDPTGQQWIGTANLVRGRNWPGASNVIEYTTPTFGGFGATVQTSLGEAAGSFSK 180 Query: 180 GGTSTKYGRKDGLSLVYQNNGLELRGIYDVVRDPNGRYTDVYDTSKELILGGTYKIDKLK 239 GGTSTKYGRKDGLSLVYQNNGLELRGIYDV+RD NGRYTDVYDTSKELILGGTYKIDKLK Sbjct: 181 GGTSTKYGRKDGLSLVYQNNGLELRGIYDVIRDANGRYTDVYDTSKELILGGTYKIDKLK 240 Query: 240 LFLGYENLRAPDVNPASGAPDRVNHYWLGANYDVTSQLQLVGSVFHVNANNGNGSANLFM 299 +FLGYENLRAPD N ASG PDRVNHYWLGANYDVT Q QLVGSVFHVNANNGNGSANLFM Sbjct: 241 MFLGYENLRAPDANTASGVPDRVNHYWLGANYDVTPQFQLVGSVFHVNANNGNGSANLFM 300 Query: 300 AGVNYFLSKRTLLYVGAGTMRNGNNANYSLEADSSTGGGKGTNQTGGYFGIAHSF 354 AGVNYFLSKRTLLYVG GTMRNGNNANYSLEADSSTGGGKGTNQTGGYFGIAHSF Sbjct: 301 AGVNYFLSKRTLLYVGGGTMRNGNNANYSLEADSSTGGGKGTNQTGGYFGIAHSF 355 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 114 bits (286), Expect = 9e-27, Method: Compositional matrix adjust. Identities = 120/365 (32%), Positives = 166/365 (45%), Gaps = 48/365 (13%) Query: 8 AQAQSSVTIYGRVVAGVDIMTNVPKNDGSGTTGTRIRSASNQWGTSMIGFKGTEDLGGGT 67 A AQSSV+IYG + G+ ++ PK+ G G R+ S Q S IGFKGTEDLGGG Sbjct: 18 AHAQSSVSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQ--GSRIGFKGTEDLGGGM 75 Query: 68 NAFFLLESGFGSTTGGLNGTDVNGTSLFNRRSYVGLSSANAGTLKLGKNL-FINN----- 121 NAFF LE+GFG+ G L G LF R+S+VGL S G+L +G+ F+ N Sbjct: 76 NAFFTLETGFGADDGSLG----QGGLLFGRQSFVGLGSTQWGSLSVGRQYDFMANIGGQY 131 Query: 122 DVWFLDPTGQ-QWIGTANLVRG-----RNWPG--ASNVIEYTTPTYGGFGATLQTSLGEA 173 + L P G W A+ G + G +N I+Y + +GGF LGE Sbjct: 132 AMGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGFSFGAMVGLGET 191 Query: 174 AGSFSKGGTSTKYGRKDGLSLVYQNNGLELRGIYDVVRDPNGRY-TDVYDTSKELILGGT 232 AG+ + G T + G+ Y N Y ++D G + T +Y G Sbjct: 192 AGNNNAGRTVSATGQ-------YDNGPFSGALAYTDIKDSTGSFSTRIYGG------GAR 238 Query: 233 YKIDKLKLFLGYENLRAPDVNPASGAPDRVNHYWLGANYDVTSQLQLVGSVFHVNANNGN 292 Y+I F ++ + + + Y LG Y +T L + N G Sbjct: 239 YQIGAFTPFGVVTQVKNTNTSA------KATTYELGTVYALTPLWDLAAAYQFQKRNQGV 292 Query: 293 GSANLFMAGVNYFLSKRTLLYVGAGTMRNGNNANYSLEA---DSSTGGGKGTNQTGGYFG 349 G+A +A V+Y +SKRT LYVGA R+ Y + S+TG NQT G Sbjct: 293 GNAQALVATVDYKISKRTDLYVGAVYDRDKGYNAYPVFGGGIQSATG-----NQTALRLG 347 Query: 350 IAHSF 354 + H F Sbjct: 348 MRHRF 352 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 111 bits (278), Expect = 9e-26, Method: Compositional matrix adjust. Identities = 123/361 (34%), Positives = 170/361 (47%), Gaps = 41/361 (11%) Query: 9 QAQSSVTIYGRVVAGVDIMTNVPKNDGSGTTGTRIRSASNQWGTSMIGFKGTEDLGGGTN 68 QAQSSVTIYG V GV+ + N N G+G+ TR+ S + TS IGF+GTEDLGGG Sbjct: 20 QAQSSVTIYGLVDTGVEYLNNAGPN-GAGSV-TRMTSGATN--TSRIGFRGTEDLGGGLK 75 Query: 69 AFFLLESGFGSTTGGLNGTDVNGTSLFNRRSYVGLSSANAGTLKLGKNLFINNDVWFL-- 126 A F LE+GF G +G D N LFNR+S VGL G + G++ D FL Sbjct: 76 ALFQLENGFKLDNGSFDG-DAN--QLFNRQSTVGL-EGGFGRVVAGRSYSTTYD--FLGP 129 Query: 127 -DPTG----QQWIGTANLV--RGRNWP-GASNVIEYTTPTYGGFGATLQTSLGEAAGSFS 178 DP G W TA R P G SN+++Y + G GE AG Sbjct: 130 FDPMGYSANYSWATTAGATGNRKDGMPTGVSNLVKYQGE-FSGVKIGAMYGFGEVAG--- 185 Query: 179 KGGTSTKYGRKDGLSLVYQNNGLELRGIYDVVRDPNGRYTDV-YDTSKELILGGTYKI-D 236 T+ G K G+ L + + YD R+ + T+ YD + L Y+ + Sbjct: 186 ----ETRNGAKYGVGLGWGTGPFSVVATYD--RNNSATATNTPYDRATSAHLAAGYQPSE 239 Query: 237 KLKLFLGYENLRAPDVNPASGAPD-RVNHYWLGANYDVTSQLQLVGSVFHVNANNGNGSA 295 K LGY + + A+GA D R + +W GA Y T + L+G++++ N N A Sbjct: 240 AWKFNLGYRYYKK---SLATGAADLRSDFFWGGAAYKFTPAMTLIGAIYYQNIKNVANDA 296 Query: 296 NLFMAG--VNYFLSKRTLLYVGAGTMRNGNNANYSLEADSSTGGGKGTNQTGGYFGIAHS 353 + M + Y +SKRT LY+ + N L D + G G++Q G G+ H Sbjct: 297 DPIMYSLRLKYAMSKRTDLYLSTAYAKAKNGQLVGLSRDDA---GYGSSQFGMTLGMQHR 353 Query: 354 F 354 F Sbjct: 354 F 354 >gi|300313291|ref|YP_003777383.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 98.2 bits (243), Expect = 8e-22, Method: Compositional matrix adjust. Identities = 115/368 (31%), Positives = 166/368 (45%), Gaps = 50/368 (13%) Query: 11 QSSVTIYGRVVAGVDIMTNVPKNDGSGTTGTRIRSASNQWGTSMIGFKGTEDLGGGTNAF 70 QSSVTIYG + GV TN N G + ++ S + + S IGFKGTEDLGGG A Sbjct: 24 QSSVTIYGIIDTGVVYTTNANAN---GNSVFKMPSLTGSF-PSRIGFKGTEDLGGGLQAM 79 Query: 71 FLLESGFGSTTGGLNGTDVNGTSLFNRRSYVGLSSANAGTLKLGKNLFINNDVWFLDPTG 130 F+LESGF TG + G LF R+SYVGL ++ G L LG+ + ++ +L Sbjct: 80 FVLESGFAPDTGAMG----QGGRLFGRQSYVGLKNS-WGQLMLGRQV----NMTYLSQLK 130 Query: 131 QQWIGTANLVRGR---NWPGA--SNVIEYTTPTYGGF--GATLQ--------------TS 169 +G G P A N I Y + GF GAT Sbjct: 131 TDVMGPNLFAIGSIDAYLPNARSDNAIGYL-GNFSGFTVGATYSFGRDAAGPAGPAATNC 189 Query: 170 LGEAAGSFSKGGTSTKYGRKDGLSLVYQNNGLELRGIYDVVRDPNGR---YTDVYDTSKE 226 GE AG+ +K R+ L Y G + YD++ G T +T + Sbjct: 190 PGEVAGN-------SKACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGMTSSDNTDQR 242 Query: 227 LILGGTYKIDKLKLFLGYENLRAPDVNPASGAPDRVNHYWLGANYDVTSQLQLVGSVFHV 286 + L G + + +K+ G + R A+ + Y+LG +Y ++ L L V + Sbjct: 243 VTLNGYFMLGDVKIGGGVVDRRT---RAAANTNTDSDLYYLGVSYPLSVALVLDAQVSRL 299 Query: 287 NANNGNGSANLFMAGVNYFLSKRTLLYVGAGTMRNGNNANYSLEADSSTGGGKGTNQTGG 346 + N L +A + Y LSKRT +Y G ++NG ++ +L+A + G GK NQ G Sbjct: 300 DVKNSPNDVTLSVARLTYNLSKRTAVYGSLGYIKNGGTSSVALDAGGTVGAGK--NQLGV 357 Query: 347 YFGIAHSF 354 GI H+F Sbjct: 358 MTGIRHTF 365 >gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 387 Score = 96.3 bits (238), Expect = 3e-21, Method: Compositional matrix adjust. Identities = 115/372 (30%), Positives = 160/372 (43%), Gaps = 35/372 (9%) Query: 12 SSVTIYGRVVAGVDIMTNVPKNDGSG--TTGTRIRSASNQWGTSMIGFKGTEDLGGGTNA 69 SSVTIYG V G+ + V D +G TG++ S S IGFKG EDLGGG +A Sbjct: 22 SSVTIYGIVDTGIAYSSKVGYTDANGNAATGSKFGINSGVIQGSRIGFKGVEDLGGGLSA 81 Query: 70 FFLLESGFGSTTGGLNGTD-VNGTSLFNRRSYVGLSSANAGTLKLGKNLFINNDVWFLDP 128 F LE+GF S GGL G+D V ++LF R+S VGLS GT+ LG+ + + Sbjct: 82 VFNLETGFTSDDGGLQGSDAVTSSNLFRRKSVVGLS-GGFGTVLLGRQTDFADTISAYTA 140 Query: 129 TGQQWIGTANLVRGRNWPGAS---NVIEYTTPTYGGFGATLQTSLGEAAGSFSKGGTSTK 185 AN N + N + YTT GF L GE AG S G Sbjct: 141 VADFGGVVANSGSSLNRLQGTRTNNSVSYTTANLSGFTGNLIYGFGEQAGKTSAGQAYGI 200 Query: 186 YGRKD----GLSL-VYQNNGLELRGIYDVVRDPNGRYTDVY------DTSKELILGGTYK 234 G+ D GL + YQ+ ++ + K L + +Y+ Sbjct: 201 GGKYDNGPLGLGINYYQSKAGSTPSDTSLIPAAGATNANTALGVAGNTALKSLNVVASYQ 260 Query: 235 IDKLKLFLGYENLR-----APDVNPASGA-PDRVNHYWLGANYDVTSQLQLVGSVFHVNA 288 +++ Y ++ P V A+ A + + Y +G Y ++ L+L+ +V H A Sbjct: 261 FGPARVYANYSRVKQDLKGTPTVATATLANAQKADTYEIGTAYSLSPSLKLLAAVDHSRA 320 Query: 289 N----NGNGSANLFMAGVNYFLSKRTLLYVGAGTMRNGNNANYSLEADSSTGGGKGTN-- 342 N G G +YFLSKRT LY MR + N + TGG G++ Sbjct: 321 TFNGVNTKGKLTQISLGADYFLSKRTDLYAFVSNMRASDIQNPGV-----TGGATGSDAS 375 Query: 343 QTGGYFGIAHSF 354 QT GI H F Sbjct: 376 QTAIITGIRHKF 387 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 0.314 0.134 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: 1,141,119 Number of extensions: 53853 Number of successful extensions: 146 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 111 Number of HSP's successfully gapped: 14 Length of query: 354 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 268 Effective length of database: 1,212,660 Effective search space: 324992880 Effective search space used: 324992880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 131 (55.1 bits)