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= 0001.3893.p (371 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313291|ref|YP_003777383.1| porin transmembrane protein [He... 623 e-180 gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspir... 325 4e-90 gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 158 8e-40 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 156 2e-39 gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 137 2e-33 >gi|300313291|ref|YP_003777383.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 623 bits (1606), Expect = e-180, Method: Compositional matrix adjust. Identities = 316/342 (92%), Positives = 334/342 (97%) Query: 30 QSSVTIYGIIDTGVVYTTNANANGDSVFKMPSLTGTFPSRIGFKGTEDLGGGLQALFVLE 89 QSSVTIYGIIDTGVVYTTNANANG+SVFKMPSLTG+FPSRIGFKGTEDLGGGLQA+FVLE Sbjct: 24 QSSVTIYGIIDTGVVYTTNANANGNSVFKMPSLTGSFPSRIGFKGTEDLGGGLQAMFVLE 83 Query: 90 NGFAPDTGAMGQGNRLFGRQSYVGLKGNWGQISLGRQVNMTYLSQLKTDVLGPNIFAIGS 149 +GFAPDTGAMGQG RLFGRQSYVGLK +WGQ+ LGRQVNMTYLSQLKTDV+GPN+FAIGS Sbjct: 84 SGFAPDTGAMGQGGRLFGRQSYVGLKNSWGQLMLGRQVNMTYLSQLKTDVMGPNLFAIGS 143 Query: 150 IDNYLPNARSDNAIGYLGSFSGFTLGATYSFGRDAAGPAGPAATNCPGEVAGNSKACRQV 209 ID YLPNARSDNAIGYLG+FSGFT+GATYSFGRDAAGPAGPAATNCPGEVAGNSKACRQV Sbjct: 144 IDAYLPNARSDNAIGYLGNFSGFTVGATYSFGRDAAGPAGPAATNCPGEVAGNSKACRQV 203 Query: 210 TALLGYDGKGWGVTSSYDILYGNTGASNGLTSSDNKDQRVTLNGYFMIGDVKIGGGVVDR 269 TALLGYDGKGWGVTSSYDILYGNTGASNG+TSSDN DQRVTLNGYFM+GDVKIGGGVVDR Sbjct: 204 TALLGYDGKGWGVTSSYDILYGNTGASNGMTSSDNTDQRVTLNGYFMLGDVKIGGGVVDR 263 Query: 270 RTRAAANTNTDSDLYYLGVSYPLSTALVLDAQVSRLDVKNSPNDVTLSVARLTYSLSKRT 329 RTRAAANTNTDSDLYYLGVSYPLS ALVLDAQVSRLDVKNSPNDVTLSVARLTY+LSKRT Sbjct: 264 RTRAAANTNTDSDLYYLGVSYPLSVALVLDAQVSRLDVKNSPNDVTLSVARLTYNLSKRT 323 Query: 330 ALYTSLGYIKNSGTSAIAIDAGGSVGAGKNQLGVMTGIRHTF 371 A+Y SLGYIKN GTS++A+DAGG+VGAGKNQLGVMTGIRHTF Sbjct: 324 AVYGSLGYIKNGGTSSVALDAGGTVGAGKNQLGVMTGIRHTF 365 >gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 369 Score = 325 bits (833), Expect = 4e-90, Method: Compositional matrix adjust. Identities = 175/356 (49%), Positives = 232/356 (65%), Gaps = 12/356 (3%) Query: 26 AALAQS-SVTIYGIIDTGVVYTTNAN---ANGDSVFKMPSLTGTFPSRIGFKGTEDLGGG 81 A L+Q+ SVT+YGIIDTGV Y +N + A + ++P+LT T PSRIG +G+EDLGGG Sbjct: 16 ATLSQAQSVTLYGIIDTGVEYVSNVSNVGAGQQGLLRVPNLTATTPSRIGLRGSEDLGGG 75 Query: 82 LQALFVLENGFAPDTGAMGQGNRLFGRQSYVGLKGNWGQISLGRQVNMTYLSQLKTDVLG 141 L+++F+LE+GFAPD+GA+ QG R+FGR +YVGL +WGQ+S GRQ M + L +D+LG Sbjct: 76 LRSVFMLESGFAPDSGALNQGGRMFGRIAYVGLSDHWGQVSFGRQATMLLWATLDSDILG 135 Query: 142 PNIFAIGSIDNYLPNARSDNAIGYLGSFSGFTLGATYSFGRDAAGPA-GPAATNCPGEVA 200 N++ ++DNY PNAR+DN+I Y GSF FTLG TYSFGRD PA TNC GE A Sbjct: 136 ANVYGANALDNYRPNARADNSIAYRGSFGAFTLGGTYSFGRDTVNAGQNPAGTNCAGEQA 195 Query: 201 GNSKACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGLTSSDNKDQRVTLNGYFMIGDV 260 G+S ACR+ + ++ YD WG + +YD L G GA+ GL+SS D R+ L Y + Sbjct: 196 GDSLACREWSLMVKYDTAAWGASLAYDTLRGGKGAAAGLSSSQLSDSRMLLGAYIKADRL 255 Query: 261 KIGGGVVDRRTRAAANTNTDSDLYYLGVSYPLSTALVLDAQVSRLDVKNSPNDVTLSVAR 320 K+G G R + +A + S LYY G+SY L+ L L Q+ L +S N L R Sbjct: 256 KVGIGGSLRHNQGSALSK--SQLYYAGLSYDLTPTLNLAGQLYYLHYDDSANKAWLGALR 313 Query: 321 LTYSLSKRTALYTSLGYIKNSGTSAIAIDAGGSVGA-----GKNQLGVMTGIRHTF 371 TYSLS RTALY + G+I N G S +++ AGGSVG G NQ G+M GIRH+F Sbjct: 314 ATYSLSARTALYLTGGFIDNRGQSNLSVSAGGSVGTANPAPGGNQFGMMAGIRHSF 369 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 158 bits (399), Expect = 8e-40, Method: Compositional matrix adjust. Identities = 139/383 (36%), Positives = 185/383 (48%), Gaps = 61/383 (15%) Query: 25 GAALAQSSVTIYGIIDTGVVYTTNANANGDSVFKMPSLTGTFPSRIGFKGTEDLGGGLQA 84 GAA AQS+VTIYGI+DT + Y +NANA G+S +M + SRIGFKGTEDLGGGL+A Sbjct: 17 GAAFAQSNVTIYGIVDTSIHYLSNANAQGNSNVRMDN-GAIANSRIGFKGTEDLGGGLKA 75 Query: 85 LFVLENGFAPDTGAMGQGNRLFGRQSYVGLKGNWGQISLGRQVNMTYLSQLKTDVLGPNI 144 +F LENGF+ DTGAM QG LFGRQS+VGL+G +G++ +GRQ T L L D P Sbjct: 76 MFQLENGFSSDTGAMQQGGSLFGRQSWVGLQGGFGKVRVGRQ--NTPLFDLLADHFDPLT 133 Query: 145 FAIGSIDNYLPNA----RSDNAIGYLGSFSGFTLGATYSFGRDAAG-------------P 187 + +++LP A RS N + Y G F A+++FG A Sbjct: 134 VGNYASNSWLPAAASLVRSPNMLRYDGDFGPVAASASWAFGEKAGSVRTGSQFSSALRYT 193 Query: 188 AGPAAT--NCPGEVAGNSKACRQVTALLGYDGKGWGVTSSYDI----LYG---NTGASNG 238 AGP A V+ + + + T W +++SYD ++G N +G Sbjct: 194 AGPLALGGGYQQTVSSTNSSLKHTT---------WNLSASYDFGVAKVFGGWLNIKDDSG 244 Query: 239 LTSSDNKDQRVTLNGYFMIGDVKIGGGVVDRRTRAAANTNTDSDLYYLGVSYPLSTALVL 298 LT S NG+ G G V R+ ++LG SY + AL L Sbjct: 245 LTGSVMAADGDVSNGWTTAGAANNGSTGVKRKDNG----------FFLGSSYKATNALTL 294 Query: 299 DAQVSRLDVKNSPNDVTLSV---ARLT------YSLSKRTALYTSLGYIKNSGTSAIAID 349 KN T +V R T Y+LSKRT LYT++ Y K + + Sbjct: 295 TGAFYYDRSKNVSYVSTGNVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAVYELT 354 Query: 350 AGGSVGAGKNQL-GVMTGIRHTF 371 + GKN L V GIRH F Sbjct: 355 NSAN---GKNSLTTVGVGIRHIF 374 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 156 bits (395), Expect = 2e-39, Method: Compositional matrix adjust. Identities = 131/367 (35%), Positives = 177/367 (48%), Gaps = 49/367 (13%) Query: 25 GAALAQSSVTIYGIIDTGVVYTTNANANG-DSVFKMPSLTGTFPSRIGFKGTEDLGGGLQ 83 G+ AQSSVTIYG++DTGV Y NA NG SV +M S T SRIGF+GTEDLGGGL+ Sbjct: 17 GSVQAQSSVTIYGLVDTGVEYLNNAGPNGAGSVTRMTS-GATNTSRIGFRGTEDLGGGLK 75 Query: 84 ALFVLENGFAPDTGAM-GQGNRLFGRQSYVGLKGNWGQISLGRQVNMTYLSQLKTDVLGP 142 ALF LENGF D G+ G N+LF RQS VGL+G +G++ GR + TY D LGP Sbjct: 76 ALFQLENGFKLDNGSFDGDANQLFNRQSTVGLEGGFGRVVAGRSYSTTY------DFLGP 129 Query: 143 NIFAIGSIDNY---------------LPNARSDNAIGYLGSFSGFTLGATYSFGRDAAGP 187 +G NY +P S N + Y G FSG +GA Y F Sbjct: 130 -FDPMGYSANYSWATTAGATGNRKDGMPTGVS-NLVKYQGEFSGVKIGAMYGF------- 180 Query: 188 AGPAATNCPGEVAGNSKACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGLTSSDNKDQ 247 GEVAG ++ + LG+ + V ++YD N A+ T D Sbjct: 181 ---------GEVAGETRNGAKYGVGLGWGTGPFSVVATYDR---NNSATATNTPYDRATS 228 Query: 248 RVTLNGYFMIGDVKIGGGV-VDRRTRAAANTNTDSDLYYLGVSYPLSTALVLDAQVSRLD 306 GY K G +++ A + SD ++ G +Y + A+ L + + Sbjct: 229 AHLAAGYQPSEAWKFNLGYRYYKKSLATGAADLRSDFFWGGAAYKFTPAMTLIGAIYYQN 288 Query: 307 VKNSPNDV--TLSVARLTYSLSKRTALYTSLGYIKNSGTSAIAIDAGGSVGAGKNQLGVM 364 +KN ND + RL Y++SKRT LY S Y K + + G G +Q G+ Sbjct: 289 IKNVANDADPIMYSLRLKYAMSKRTDLYLSTAYAKAKNGQLVGLSR-DDAGYGSSQFGMT 347 Query: 365 TGIRHTF 371 G++H F Sbjct: 348 LGMQHRF 354 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 137 bits (345), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 128/378 (33%), Positives = 172/378 (45%), Gaps = 56/378 (14%) Query: 17 CATYAGGTGAALAQSSVTIYGIIDTGVVYTTNANANGDSVFKMPSLTGTFP--SRIGFKG 74 A AGG A AQSSV+IYG+ID G+ Y ++A +G ++ + SRIGFKG Sbjct: 8 AAMLAGGATTAHAQSSVSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQGSRIGFKG 67 Query: 75 TEDLGGGLQALFVLENGFAPDTGAMGQGNRLFGRQSYVGL-KGNWGQISLGRQVNM--TY 131 TEDLGGG+ A F LE GF D G++GQG LFGRQS+VGL WG +S+GRQ + Sbjct: 68 TEDLGGGMNAFFTLETGFGADDGSLGQGGLLFGRQSFVGLGSTQWGSLSVGRQYDFMANI 127 Query: 132 LSQLKTDVLGP-NIFAIG---------SIDNYL-PNARSDNAIGY-LGSFSGFTLGATYS 179 Q L P F G +++N++ R++N+I Y F GF+ GA Sbjct: 128 GGQYAMGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGFSFGAMVG 187 Query: 180 FGRDAAGPAGPAATNCPGEVAGNSKACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGL 239 GE AGN+ A R V+A T YD N S L Sbjct: 188 L----------------GETAGNNNAGRTVSA-----------TGQYD----NGPFSGAL 216 Query: 240 TSSDNKDQRVTLNGYFMIGDVK--IGG----GVVDRRTRAAANTNTDSDLYYLGVSYPLS 293 +D KD + + G + IG GVV + NT+ + Y LG Y L+ Sbjct: 217 AYTDIKDSTGSFSTRIYGGGARYQIGAFTPFGVVTQVKN--TNTSAKATTYELGTVYALT 274 Query: 294 TALVLDAQVSRLDVKNSPNDVTLSVARLTYSLSKRTALYTSLGYIKNSGTSAIAIDAGGS 353 L A + VA + Y +SKRT LY Y ++ G +A + GG Sbjct: 275 PLWDLAAAYQFQKRNQGVGNAQALVATVDYKISKRTDLYVGAVYDRDKGYNAYPVFGGGI 334 Query: 354 VGAGKNQLGVMTGIRHTF 371 A NQ + G+RH F Sbjct: 335 QSATGNQTALRLGMRHRF 352 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 0.133 0.385 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: 1,020,344 Number of extensions: 42369 Number of successful extensions: 202 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 161 Number of HSP's successfully gapped: 14 Length of query: 371 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 284 Effective length of database: 1,207,925 Effective search space: 343050700 Effective search space used: 343050700 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: 131 (55.1 bits)