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= 0003.0070.p (369 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... 455 e-129 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 132 3e-32 gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspir... 115 4e-27 gi|300313545|ref|YP_003777637.1| porin precursor transmembrane p... 103 3e-23 gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 101 8e-23 >gi|300310376|ref|YP_003774468.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 355 Score = 455 bits (1170), Expect = e-129, Method: Compositional matrix adjust. Identities = 247/368 (67%), Positives = 285/368 (77%), Gaps = 31/368 (8%) Query: 20 FGACLASAQAE-DSVTIYGRVVAGIDVQSNVHQVNGN--TGTQVRAASNQWGTSMIGFKG 76 GA A AQA+ SVTIYGRVVAG+D+ +NV + +G+ TGT++RAASNQWGTSMIG KG Sbjct: 1 MGAFSAQAQAQTSSVTIYGRVVAGVDIMTNVPKTDGSGTTGTRIRAASNQWGTSMIGVKG 60 Query: 77 KEDLGGGLNSFFLLESGFGATTGKTNGPE-----LFNRRSYVGLNGS-AGSIKIGKNLFI 130 EDLGGG N+FFLLESGFG+TTG NG + LFNRRSYVGL+ + AGS+K+GKNLFI Sbjct: 61 TEDLGGGTNAFFLLESGFGSTTGGLNGTDINGTSLFNRRSYVGLSSANAGSLKLGKNLFI 120 Query: 131 DNDVWFLDPTGQQWIGTANLVKGRNWGGASNIIEYQTPTWGGFNATFQTSLGEKAGSTTK 190 +NDVWFLDPTGQQWIGTANLV+GRNW GASN+IEY TPT+GGF AT QTSLGE AGS +K Sbjct: 121 NNDVWFLDPTGQQWIGTANLVRGRNWPGASNVIEYTTPTFGGFGATVQTSLGEAAGSFSK 180 Query: 191 G-------RKDGVSLVYQNQGLELRAIYDLVRDANGKYGSIKTNQDGTTTVGDVFDTSKE 243 G RKDG+SLVYQN GLELR IYD++RDANG+Y DV+DTSKE Sbjct: 181 GGTSTKYGRKDGLSLVYQNNGLELRGIYDVIRDANGRYT-------------DVYDTSKE 227 Query: 244 LILGGTYTIDKLKMYVGYENLKAPDV--AAGTPDTVNHYWVGANYQISPALTLIGSVFHV 301 LILGGTY IDKLKM++GYENL+APD A+G PD VNHYW+GANY ++P L+GSVFHV Sbjct: 228 LILGGTYKIDKLKMFLGYENLRAPDANTASGVPDRVNHYWLGANYDVTPQFQLVGSVFHV 287 Query: 302 NVNNNGGSANLYMVGANYNLSKRTLLYVGAGTVRNKGNATFSLEADQAGPPLAGQGQNGG 361 N NN GSANL+M G NY LSKRTLLYVG GT+RN NA +SLEAD + G Q GG Sbjct: 288 NANNGNGSANLFMAGVNYFLSKRTLLYVGGGTMRNGNNANYSLEADSSTGGGKGTNQTGG 347 Query: 362 YVGIAHSF 369 Y GIAHSF Sbjct: 348 YFGIAHSF 355 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 132 bits (333), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 121/360 (33%), Positives = 165/360 (45%), Gaps = 39/360 (10%) Query: 26 SAQAEDSVTIYGRVVAGIDVQSNVHQVNGNTGTQVRAASNQWGTSMIGFKGKEDLGGGLN 85 S QA+ SVTIYG V G++ +N NG G+ R S TS IGF+G EDLGGGL Sbjct: 18 SVQAQSSVTIYGLVDTGVEYLNNAGP-NG-AGSVTRMTSGATNTSRIGFRGTEDLGGGLK 75 Query: 86 SFFLLESGFGATTGKTNGP--ELFNRRSYVGLNGSAGSIKIGKNLFIDNDVWFL---DPT 140 + F LE+GF G +G +LFNR+S VGL G G + G++ D FL DP Sbjct: 76 ALFQLENGFKLDNGSFDGDANQLFNRQSTVGLEGGFGRVVAGRSYSTTYD--FLGPFDPM 133 Query: 141 G----QQWIGTANLVKGRNWG---GASNIIEYQTPTWGGFNATFQTSLGEKAGSTTKGRK 193 G W TA R G G SN+++YQ + G GE AG T G K Sbjct: 134 GYSANYSWATTAGATGNRKDGMPTGVSNLVKYQGE-FSGVKIGAMYGFGEVAGETRNGAK 192 Query: 194 DGVSLVYQNQGLELRAIYDLVRDANGKYGSIKTNQDGTTTVGDVFDTSKELILGGTYTI- 252 GV L + + A YD + T +D + L Y Sbjct: 193 YGVGLGWGTGPFSVVATYD--------------RNNSATATNTPYDRATSAHLAAGYQPS 238 Query: 253 DKLKMYVGYENLKAPDVAAGTPD-TVNHYWVGANYQISPALTLIGSVFHVNVNNNGGSAN 311 + K +GY K +A G D + +W GA Y+ +PA+TLIG++++ N+ N A+ Sbjct: 239 EAWKFNLGYRYYK-KSLATGAADLRSDFFWGGAAYKFTPAMTLIGAIYYQNIKNVANDAD 297 Query: 312 --LYMVGANYNLSKRTLLYVGAGTVRNKGNATFSLEADQAGPPLAGQGQNGGYVGIAHSF 369 +Y + Y +SKRT LY+ + K L D AG G Q G +G+ H F Sbjct: 298 PIMYSLRLKYAMSKRTDLYLSTAYAKAKNGQLVGLSRDDAG---YGSSQFGMTLGMQHRF 354 >gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 369 Score = 115 bits (289), Expect = 4e-27, Method: Compositional matrix adjust. Identities = 115/389 (29%), Positives = 177/389 (45%), Gaps = 51/389 (13%) Query: 8 KTILKALGTASLFGACLASAQAEDSVTIYGRVVAGIDVQSNVHQVNGNTGTQVRAASNQW 67 K I+ AL T S A L+ AQ SVT+YG + G++ SNV V +R + Sbjct: 5 KAIIAALLTMS---ATLSQAQ---SVTLYGIIDTGVEYVSNVSNVGAGQQGLLRVPNLTA 58 Query: 68 GT-SMIGFKGKEDLGGGLNSFFLLESGFGATTGKTN-GPELFNRRSYVGLNGSAGSIKIG 125 T S IG +G EDLGGGL S F+LESGF +G N G +F R +YVGL+ G + G Sbjct: 59 TTPSRIGLRGSEDLGGGLRSVFMLESGFAPDSGALNQGGRMFGRIAYVGLSDHWGQVSFG 118 Query: 126 KNLF------IDNDVWFLDPTGQQWIGTANLVKGRNWGGASNIIEYQ----------TPT 169 + +D+D+ G G L R A N I Y+ T + Sbjct: 119 RQATMLLWATLDSDI-----LGANVYGANALDNYRPNARADNSIAYRGSFGAFTLGGTYS 173 Query: 170 WG------GFNATFQTSLGEKAGSTTKGRKDGVSLVYQNQGLELRAIYDLVRDANGKYGS 223 +G G N GE+AG + R+ + + Y YD +R G Sbjct: 174 FGRDTVNAGQNPAGTNCAGEQAGDSLACREWSLMVKYDTAAWGASLAYDTLRGGKGAAAG 233 Query: 224 IKTNQDGTTTVGDVFDTSKELILGGTYTIDKLKMYVGYENLKAPDVAAGTPDTVNHYWVG 283 + ++Q + ++LG D+LK+ +G +L+ +A + + Y+ G Sbjct: 234 LSSSQL----------SDSRMLLGAYIKADRLKVGIG-GSLRHNQGSALSKSQL--YYAG 280 Query: 284 ANYQISPALTLIGSVFHVNVNNNGGSANLYMVGANYNLSKRTLLYVGAGTVRNKGNATFS 343 +Y ++P L L G +++++ +++ A L + A Y+LS RT LY+ G + N+G + S Sbjct: 281 LSYDLTPTLNLAGQLYYLHYDDSANKAWLGALRATYSLSARTALYLTGGFIDNRGQSNLS 340 Query: 344 LEADQA---GPPLAGQGQNGGYVGIAHSF 369 + A + P G Q G GI HSF Sbjct: 341 VSAGGSVGTANPAPGGNQFGMMAGIRHSF 369 >gi|300313545|ref|YP_003777637.1| porin precursor transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 360 Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 110/347 (31%), Positives = 159/347 (45%), Gaps = 41/347 (11%) Query: 11 LKALGTASLFGACLA--SAQAEDSVTIYGRVVAGIDVQSNVHQVNGNTGTQVRAASNQWG 68 +K A +C+ SA A+ SVT+ G V A + N +G+TG++ S Sbjct: 1 MKKTRLALALASCMVAGSAMAQSSVTVSGLVDAYVGSMKN----SGDTGSKATVGSGGMT 56 Query: 69 TSMIGFKGKEDLGGGLNSFFLLESGFGATT---GKTNGPELFNRRSYVGLNGSAGSIKIG 125 TS IGFKG EDLGGGL + F L S F A T G+ G LF+R + VGL G G + +G Sbjct: 57 TSWIGFKGIEDLGGGLRAEFALTSFFQADTGAYGRFGGDNLFSRDANVGLAGDFGRVSLG 116 Query: 126 KNL---FIDNDVWFLDPTGQQWIGTANLVK---------GRNW-------GGASNIIEYQ 166 + L F+ ++ +P G + + ++ R W G SN + Y Sbjct: 117 RGLAPSFLPTVLF--NPFGDSFTFSPLVLHVYTPSGNFGSRTWTQANAADSGWSNQVIYT 174 Query: 167 TPTWGGFNATFQTSLGEKAGSTTKGRKDGVSLVYQNQGLELRAIYDLVRDANGKYGSIKT 226 TP +GG A GE AG + K + GV+ +Y N GL L +Y + +N G+ Sbjct: 175 TPKFGGLQANVHYQFGEVAGQSGK-KNIGVNALYFNGGLALTGLYFDAQVSNPNSGAAII 233 Query: 227 NQDGTTTVGDVFDTSKELILGGTYTIDKLKMYVGYENLKAPDVAAGTPDTVNHYW-VGAN 285 D T+ + K +LG TY +K+Y Y+N K D AG P + + +G + Sbjct: 234 --DATSPFSSI-TRQKTWMLGATYDFQVVKLYGTYQNSK--DTTAGNPQAKDKLFSLGLS 288 Query: 286 YQISPALTLIGSVFHVNVNN--NGG--SANLYMVGANYNLSKRTLLY 328 + L G + GG S N VG +Y +SKRT LY Sbjct: 289 APVGNGSILAGFARTKRTGDLLAGGDVSRNTTSVGYDYFMSKRTDLY 335 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 101 bits (252), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 103/344 (29%), Positives = 151/344 (43%), Gaps = 40/344 (11%) Query: 12 KALGTASLFGACLASAQAEDSVTIYGRVVAGIDVQSNVHQVNGNTGTQVRAASNQWGTSM 71 K L A++ +A A+ SV+IYG + G+ S+ + G +R S S Sbjct: 3 KTLLVAAMLAGGATTAHAQSSVSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQGSR 62 Query: 72 IGFKGKEDLGGGLNSFFLLESGFGATTGKT-NGPELFNRRSYVGLNGSA-GSIKIGKNL- 128 IGFKG EDLGGG+N+FF LE+GFGA G G LF R+S+VGL + GS+ +G+ Sbjct: 63 IGFKGTEDLGGGMNAFFTLETGFGADDGSLGQGGLLFGRQSFVGLGSTQWGSLSVGRQYD 122 Query: 129 FIDN-----DVWFLDPTGQ-QWIGTANLVKG-----RNWGG--ASNIIEYQTPTWGGFNA 175 F+ N + L P G W A+ G + G +N I+Y + +GGF+ Sbjct: 123 FMANIGGQYAMGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGFSF 182 Query: 176 TFQTSLGEKAGSTTKGRKDGVSLVYQNQGLELRAIYDLVRDANGKYGSIKTNQDGTTTVG 235 LGE AG+ GR + Y N Y ++D+ G + Sbjct: 183 GAMVGLGETAGNNNAGRTVSATGQYDNGPFSGALAYTDIKDSTGSF-------------- 228 Query: 236 DVFDTSKELILGGT-YTIDKLKMYVGYENLKAPDVAAGTPDTVNHYWVGANYQISPALTL 294 S + GG Y I + +K + +A Y +G Y ++P L Sbjct: 229 -----STRIYGGGARYQIGAFTPFGVVTQVKNTNTSA----KATTYELGTVYALTPLWDL 279 Query: 295 IGSVFHVNVNNNGGSANLYMVGANYNLSKRTLLYVGAGTVRNKG 338 + N G+A + +Y +SKRT LYVGA R+KG Sbjct: 280 AAAYQFQKRNQGVGNAQALVATVDYKISKRTDLYVGAVYDRDKG 323 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 0.133 0.393 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: 1,182,914 Number of extensions: 52386 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 124 Number of HSP's successfully gapped: 15 Length of query: 369 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 282 Effective length of database: 1,207,925 Effective search space: 340634850 Effective search space used: 340634850 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)