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= 0231.0076.p (258 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 366 e-103 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 70 1e-13 gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspir... 60 2e-10 gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) ... 60 2e-10 gi|300313395|ref|YP_003777487.1| porin transmembrane protein [He... 59 4e-10 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 366 bits (940), Expect = e-103, Method: Compositional matrix adjust. Identities = 180/263 (68%), Positives = 213/263 (80%), Gaps = 5/263 (1%) Query: 1 VSVGRQNTPLFDLMADHFDPLTVGNYESNAWLPAAATRIRSNNTLRYDGQFGPVAASVSY 60 V VGRQNTPLFDL+ADHFDPLTVGNY SN+WLPAAA+ +RS N LRYDG FGPVAAS S+ Sbjct: 112 VRVGRQNTPLFDLLADHFDPLTVGNYASNSWLPAAASLVRSPNMLRYDGDFGPVAASASW 171 Query: 61 AFGEQAGSARSGSQVSTALRYNAGGFAIGGGFQQTVDTLAAKNKATTYNLSASYDFGVAK 120 AFGE+AGS R+GSQ S+ALRY AG A+GGG+QQTV + + K TT+NLSASYDFGVAK Sbjct: 172 AFGEKAGSVRTGSQFSSALRYTAGPLALGGGYQQTVSSTNSSLKHTTWNLSASYDFGVAK 231 Query: 121 VFGGYFRLKDATGLNAAFMA-----TTSYSTANTLGGNVAGVERKDDGYFAGATFNATTA 175 VFGG+ +KD +GL + MA + ++TA GV+RKD+G+F G+++ AT A Sbjct: 232 VFGGWLNIKDDSGLTGSVMAADGDVSNGWTTAGAANNGSTGVKRKDNGFFLGSSYKATNA 291 Query: 176 LALTGAFYYDKSKNVAYTGLGNVGNGKRYAVVGVAEYALSKRTQLYTTVDYNKAKDAAVY 235 L LTGAFYYD+SKNV+Y GNVG+GKRY +VG A+YALSKRTQLYTT+DYNKAKDAAVY Sbjct: 292 LTLTGAFYYDRSKNVSYVSTGNVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAVY 351 Query: 236 EITNSTTGKNSLTTVGVGIRHIF 258 E+TNS GKNSLTTVGVGIRHIF Sbjct: 352 ELTNSANGKNSLTTVGVGIRHIF 374 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 70.5 bits (171), Expect = 1e-13, Method: Compositional matrix adjust. Identities = 76/272 (27%), Positives = 121/272 (44%), Gaps = 45/272 (16%) Query: 1 VSVGRQNTPLFDLMADHFDPLTVGNYESN-AW-LPAAATRIRSN-------NTLRYDGQF 51 V GR + +D + FDP+ Y +N +W A AT R + N ++Y G+F Sbjct: 114 VVAGRSYSTTYDFLGP-FDPM---GYSANYSWATTAGATGNRKDGMPTGVSNLVKYQGEF 169 Query: 52 GPVAASVSYAFGEQAGSARSGSQVSTALRYNAGGFAIGGGFQQTVDTLAAK---NKATTY 108 V Y FGE AG R+G++ L + G F++ + + A ++AT+ Sbjct: 170 SGVKIGAMYGFGEVAGETRNGAKYGVGLGWGTGPFSVVATYDRNNSATATNTPYDRATSA 229 Query: 109 NLSASYDFGVAKVFG-GYFRLKDATGLNAAFMATTSYSTANTLGGNVAGVERKDDGYFAG 167 +L+A Y A F GY K + AA + + D ++ G Sbjct: 230 HLAAGYQPSEAWKFNLGYRYYKKSLATGAA--------------------DLRSDFFWGG 269 Query: 168 ATFNATTALALTGAFYYDKSKNVAYTGLGNVGNGKRYAVVGVAEYALSKRTQLYTTVDYN 227 A + T A+ L GA YY KNVA N + Y++ +YA+SKRT LY + Y Sbjct: 270 AAYKFTPAMTLIGAIYYQNIKNVA-----NDADPIMYSL--RLKYAMSKRTDLYLSTAYA 322 Query: 228 KAKDAAVYEITNSTTG-KNSLTTVGVGIRHIF 258 KAK+ + ++ G +S + +G++H F Sbjct: 323 KAKNGQLVGLSRDDAGYGSSQFGMTLGMQHRF 354 >gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 372 Score = 60.1 bits (144), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 65/236 (27%), Positives = 105/236 (44%), Gaps = 35/236 (14%) Query: 40 RSNNTLRYD-GQFGPVAASVSYAFGEQAGSARSGSQVSTALRYNAGGFAIGGGFQQT--- 95 RSNN+LR+D ++G + S Y GE AGS RSG + + G +G + Q+ Sbjct: 155 RSNNSLRFDTAEYGGLRGSFYYGAGEVAGSTRSGQSLGVGGNFRRGNVGVGAAYFQSKLA 214 Query: 96 VDTLAAK---NKATTYNLSASYDFGVAKVFGGYFRLKDATGLNAA---FMATTSYSTANT 149 D L A+ + T+ L ASY G AK+F + +++ T A +A TS + AN Sbjct: 215 SDALPARAGDTELKTFTLGASYQAGPAKLFAAWSQIRRPTQQPLASSGLVAITSATRANV 274 Query: 150 LGGNVAGVERKDDGYFAGATFNATTALALTGAFYYDKSKNVAYTGLGNVGNGKRYAVVGV 209 L G + + L L + +D++ G G+ + +GV Sbjct: 275 LD--------------VGVDYALDSKLHLLASVIHDRADLSRAAGGATRGSTTQVN-LGV 319 Query: 210 AEYALSKRTQLYTTVDYNKAKD-------AAVYEITNSTTGKNSLTTVGVGIRHIF 258 + LSKRT +Y +A+D +A Y +++ +S + VG+RH F Sbjct: 320 -DLLLSKRTDVYAMASRQQARDVLNPGIISAAY--SSAPADDSSQNVLRVGLRHKF 372 >gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 390 Score = 60.1 bits (144), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 67/241 (27%), Positives = 103/241 (42%), Gaps = 28/241 (11%) Query: 40 RSNNTLRYD-GQFGPVAASVSYAFGEQAGSARSGSQVSTALRYNAGGFAIGGGFQQT--- 95 R+NN++ Y ++ Y FGE AG +G +Y+ G +G + Q+ Sbjct: 156 RTNNSISYTTANLNGFTGNLMYGFGETAGQTSAGQAFGVGGKYDNGPLGLGINYYQSKAG 215 Query: 96 -----VDTLAAK---------NKATT----YNLSASYDFGVAKVFGGYFRLKDATGLNAA 137 LAA N +T N++ASY FG A+V+G + R+K A Sbjct: 216 STPADASLLAATGTNQFTNGTNNGSTAQKVLNVAASYQFGPARVYGNWSRVKQDLNTQAN 275 Query: 138 FMATTSYSTANTLGGNVAGVERKDDGYFAGATFNATTALALTGAFYYDKSKNVAYTGLGN 197 A S A T+ K D Y G ++ + +L L A + +++ + G+ Sbjct: 276 LTAAGVGSLA-TISNRTLAASNKADIYEIGTAYSLSPSLKLLAAVDHTRAQ---FDGVS- 330 Query: 198 VGNGKRYAVVGVAEYALSKRTQLYTTVDYNKAKDAAVYEITNSTTGKNSLTTVGVGIRHI 257 G K V +Y LSKRT LY + Y+KA D + +S+ + V VGIRH Sbjct: 331 -GKAKLTQVSLGTDYWLSKRTDLYAFLAYSKATDLNNPGVADSSGTDGNQGAVAVGIRHK 389 Query: 258 F 258 F Sbjct: 390 F 390 >gi|300313395|ref|YP_003777487.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 58.9 bits (141), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 85/299 (28%), Positives = 130/299 (43%), Gaps = 59/299 (19%) Query: 1 VSVGRQNTPLFDLMADHFDPLTVGNYESNAW---LPAAATRIRSNNTLRYD-GQFGPVAA 56 V+VGRQ TP F + P V + A + A T +R NN++ Y G + A Sbjct: 123 VTVGRQYTPYFQYVG-ALGPTNVLTGATGAHPGDIDALDTTLRMNNSITYTLPTLGGLQA 181 Query: 57 SVSYAFGEQAGSARSGSQVSTALRYNAGGFAIGGGFQQTVDTLAAKNKATTYNLSASYDF 116 V Y GEQAGSA +GS VS ALRY+ F+ G+ + + LA N A ++ S+ Sbjct: 182 GVQYGMGEQAGSAANGSSVSAALRYDYQAFSWSAGYTR-LKNLANGNTAGSFGNVGSFA- 239 Query: 117 GVAKVFGGYFRLKDATGLNAAFMATTSYSTANTLGGNVAGVERKDDGYFAGA-------- 168 + V GY D+T L +AT + T L + G+ + Y AGA Sbjct: 240 NNSPVNAGYAS-ADSTQL----LATAARYTRGDL---MLGLNYSNVQYKAGALSAFSQTA 291 Query: 169 ---------TFNATTALALTGAFYY--DKSKNVAYTGLGNVGNGKRYAVVGVAE-YALSK 216 ++N + AL L + Y +K++N + + +Y + + E Y+LSK Sbjct: 292 VFNTIGLIGSYNVSPALVLAAGYSYTAEKARN-------GISSPAKYNQLSLEEVYSLSK 344 Query: 217 RTQLYTTVDYNKAKDAAVYEITNSTTGKNSLTTVG-----------------VGIRHIF 258 RT LY Y +A + ++ N++ +VG +GIRH F Sbjct: 345 RTALYAIQAYQRASGQTLRAGGVGSSIVNAVASVGDSQNGTPSSGSGQFVAMLGIRHSF 403 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 0.315 0.130 0.371 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: 649,369 Number of extensions: 22185 Number of successful extensions: 119 Number of sequences better than 1.0e-08: 13 Number of HSP's gapped: 103 Number of HSP's successfully gapped: 13 Length of query: 258 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 175 Effective length of database: 1,226,865 Effective search space: 214701375 Effective search space used: 214701375 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 (21.6 bits) S2: 129 (54.3 bits)