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= 0001.1303.p (361 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313395|ref|YP_003777487.1| porin transmembrane protein [He... 173 2e-44 gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 143 3e-35 gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) ... 138 6e-34 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 129 5e-31 gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC fami... 129 5e-31 >gi|300313395|ref|YP_003777487.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 173 bits (439), Expect = 2e-44, Method: Compositional matrix adjust. Identities = 132/377 (35%), Positives = 189/377 (50%), Gaps = 40/377 (10%) Query: 19 AQSSVTIYGSLDAGVAYINNLNGGSVARLDQGTMQPDRIGFRGSEDLGGNLKAVFQLEAG 78 AQSSVT+YG++D G+AY +N G S ++ G + ++G G+EDLGG A+F+LE G Sbjct: 33 AQSSVTLYGTVDLGLAYSSNQGGASNTYMNSGALAASKLGLTGTEDLGGGNMALFRLENG 92 Query: 79 FYTDTGATPNASKLFNRYSTVGLAG-DFGALTLGHMPDVVFDYVGKLSNGFQLTNWYLFH 137 F DTGA A LFNR S VGL+ D+G +T+G F YVG L LT H Sbjct: 93 FNADTGAQSTAGVLFNRQSYVGLSSKDYGQVTVGRQYTPYFQYVGALGPTNVLTGATGAH 152 Query: 138 PGNLDSLANTYQFDNAVRYTSPTLGGFQGSVMVGFGEVAGDSSNGRNISAGGTYTNGPWR 197 PG++D+L T + +N++ YT PTLGG Q V G GE AG ++NG ++SA Y + Sbjct: 153 PGDIDALDTTLRMNNSITYTLPTLGGLQAGVQYGMGEQAGSAANGSSVSAALRYDYQAFS 212 Query: 198 AALAYSKLNNRAAG-YAGTFLTSVGLGNAGTVFNSLTTTAG------------GLGYTIG 244 + Y++L N A G AG+F GN G+ N+ AG YT G Sbjct: 213 WSAGYTRLKNLANGNTAGSF------GNVGSFANNSPVNAGYASADSTQLLATAARYTRG 266 Query: 245 SVRLNTAYTQVKLALPSGATPKQ----KNLDLGAAWRYATLDTINLGYGFSKLQG----- 295 + L Y+ V+ + + Q + L ++ + + GY ++ + Sbjct: 267 DLMLGLNYSNVQYKAGALSAFSQTAVFNTIGLIGSYNVSPALVLAAGYSYTAEKARNGIS 326 Query: 296 --ARWNTLSLSHVHEFSKRTQWYVQAAYQRAGGDARFA------VMNGTGASGATG---V 344 A++N LSL V+ SKRT Y AYQRA G A ++N + G + Sbjct: 327 SPAKYNQLSLEEVYSLSKRTALYAIQAYQRASGQTLRAGGVGSSIVNAVASVGDSQNGTP 386 Query: 345 SGGRGQMVTTIGMHHSF 361 S G GQ V +G+ HSF Sbjct: 387 SSGSGQFVAMLGIRHSF 403 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 143 bits (360), Expect = 3e-35, Method: Compositional matrix adjust. Identities = 125/379 (32%), Positives = 177/379 (46%), Gaps = 45/379 (11%) Query: 1 MKK-LMMAAAASCLSASALAQSSVTIYGSLDAGVAYINNL-----NGGSVARLDQGTMQP 54 MKK L++AA + + +A AQSSV+IYG +D G+ Y ++ G + R+D G Q Sbjct: 1 MKKTLLVAAMLAGGATTAHAQSSVSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQG 60 Query: 55 DRIGFRGSEDLGGNLKAVFQLEAGFYTDTGATPNASKLFNRYSTVGLAG-DFGALTLGHM 113 RIGF+G+EDLGG + A F LE GF D G+ LF R S VGL +G+L++G Sbjct: 61 SRIGFKGTEDLGGGMNAFFTLETGFGADDGSLGQGGLLFGRQSFVGLGSTQWGSLSVGRQ 120 Query: 114 PDVVFDYVGKLSNGFQLT----NWYLFHPGNLDSLANTYQF-----DNAVRYTSPTLGGF 164 D + + G+ + G W L + N + + +N+++Y S GGF Sbjct: 121 YDFMANIGGQYAMGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGF 180 Query: 165 QGSVMVGFGEVAGDSSNGRNISAGGTYTNGPWRAALAYSKLNNRAAGYAGTFLTSVGLGN 224 MVG GE AG+++ GR +SA G Y NGP+ ALAY+ + + G+F T + Sbjct: 181 SFGAMVGLGETAGNNNAGRTVSATGQYDNGPFSGALAYTDIKDS----TGSFSTRI---- 232 Query: 225 AGTVFNSLTTTAGGLGYTIGSVRLNTAYTQVKLALPSGATPKQKNLDLGAAWRYATLDTI 284 GG Y IG+ TQVK + + K +LG + L + Sbjct: 233 ----------YGGGARYQIGAFTPFGVVTQVK---NTNTSAKATTYELGTVYALTPLWDL 279 Query: 285 NLGYGFSKLQGARWNTLSLSHV--HEFSKRTQWYVQAAYQRAGGDARFAVMNGTGASGAT 342 Y F K N +L ++ SKRT YV A Y R G + V G G AT Sbjct: 280 AAAYQFQKRNQGVGNAQALVATVDYKISKRTDLYVGAVYDRDKGYNAYPVFGG-GIQSAT 338 Query: 343 GVSGGRGQMVTTIGMHHSF 361 G Q +GM H F Sbjct: 339 G-----NQTALRLGMRHRF 352 >gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 390 Score = 138 bits (348), Expect = 6e-34, Method: Compositional matrix adjust. Identities = 135/408 (33%), Positives = 189/408 (46%), Gaps = 65/408 (15%) Query: 1 MKKLMMAAAA-SCLSASALAQSSVTIYGSLDAGVAYINNL-----NGGSVARLDQGTMQP 54 MKK ++A A + +A AQSSVTIYG +D GV Y + + GS L+ G +Q Sbjct: 1 MKKSLLALAVLGAFAGAAQAQSSVTIYGIVDTGVVYQSKVATPTGGTGSKFSLNSGVIQG 60 Query: 55 DRIGFRGSEDLGGNLKAVFQLEAGFYTDTGA---TPNASKLFNRYSTVGLAGDFGALTLG 111 RIGF+G+EDLGG L AVF LEAGF DTGA + ++ LF R S VGLAG+FG++ LG Sbjct: 61 SRIGFKGTEDLGGGLSAVFNLEAGFSNDTGALDDSKTSNTLFRRKSVVGLAGNFGSVLLG 120 Query: 112 HMPDVVFDYVGKLSNGFQLTNWYLFHPGNLDSLANTYQFDNAVRYTSPTLGGFQGSVMVG 171 D D + ++ W NLD L T + +N++ YT+ L GF G++M G Sbjct: 121 RQTDFA-DTISSYTSVQDFGGWTGAAGHNLDRLEGT-RTNNSISYTTANLNGFTGNLMYG 178 Query: 172 FGEVAGDSSNGRNISAGGTYTNGPWRAALAY--SKLNNRAAGYA-----GTFLTSVGLGN 224 FGE AG +S G+ GG Y NGP + Y SK + A + GT + G N Sbjct: 179 FGETAGQTSAGQAFGVGGKYDNGPLGLGINYYQSKAGSTPADASLLAATGTNQFTNGTNN 238 Query: 225 AGTVFNSLTTTAGGLGYTIGSVRLNTAYTQVKLALPSGATPKQKNLDLGAAWRYATL--- 281 T L A Y G R+ +++VK L + Q NL AT+ Sbjct: 239 GSTAQKVLNVAA---SYQFGPARVYGNWSRVKQDLNT-----QANLTAAGVGSLATISNR 290 Query: 282 --------DTINLGYGFS----------------KLQG----ARWNTLSLSHVHEFSKRT 313 D +G +S + G A+ +SL + SKRT Sbjct: 291 TLAASNKADIYEIGTAYSLSPSLKLLAAVDHTRAQFDGVSGKAKLTQVSLGTDYWLSKRT 350 Query: 314 QWYVQAAYQRAGGDARFAVMNGTGASGATGVSGGRGQMVTTIGMHHSF 361 Y AY +A +N G + ++G G +G + +G+ H F Sbjct: 351 DLYAFLAYSKA------TDLNNPGVADSSGTDGNQGAVA--VGIRHKF 390 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 129 bits (323), Expect = 5e-31, Method: Compositional matrix adjust. Identities = 103/296 (34%), Positives = 151/296 (51%), Gaps = 22/296 (7%) Query: 1 MKKLMMAAAA-SCLSASALAQSS-VTIYGSLDAGVAYINNL-----NGGSVARLDQGTMQ 53 MKK ++A A + +A AQSS +TIYG++DA + Y N + N GS+ ++ G ++ Sbjct: 1 MKKSLLALAVLGAFAGAAHAQSSSITIYGAIDASLTYTNKIATDGKNTGSLTAVESGLVK 60 Query: 54 PDRIGFRGSEDLGGNLKAVFQLEAGFYTDTGATPNASKLFNRYSTVGLAGDFGALTLGHM 113 R+G +GSEDLGG LKAVF LE GF DTG ++ R +TVGL+G+FG + +G Sbjct: 61 GSRLGIKGSEDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGLSGNFGTVLVGRQ 120 Query: 114 PDVVFDYVGKLS-NGFQLTNWYLFHPGNLDSLANTYQFDNAVRYTSPTLGGFQGSVMVGF 172 D + D G S GF + H LD + + +N++RY SP G S + GF Sbjct: 121 NDPLNDIGGIASAGGFGVPG--TVHSKGLDR-TDGQRLNNSIRYNSPNFNGLSFSGIYGF 177 Query: 173 GEVAGDSSNGRNISAGGTYTNGPWRAALAY--SKLNNRAAGYAGTFLTSVGLG-----NA 225 GE G + GR+I G Y NGP L Y SK+ + G + + G +A Sbjct: 178 GEQVGRAVGGRSIGLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVNAKAACNGAGEKDHA 237 Query: 226 G-TVFNSLTTTAGGLGYTIGSVRLNTAYTQVKLALPSGATPKQKNLDLGAAWRYAT 280 G T + T A Y G ++ A++ V+L L T +K+ + GA + T Sbjct: 238 GDTCLKTWTLAA---AYQFGPAKVYGAFSHVRLPLAKLHTKVRKDNNFGAMYDAKT 290 >gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC family protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 129 bits (323), Expect = 5e-31, Method: Compositional matrix adjust. Identities = 121/370 (32%), Positives = 170/370 (45%), Gaps = 33/370 (8%) Query: 1 MKKLMMAAAASCLSAS-ALAQSSVTIYGSLDAGVAYINNLNGGSVARLDQGTMQPDRIGF 59 MKK AS L A ALAQS+VT+YG +D + Y N GSVA LD G Q R+GF Sbjct: 1 MKKAWAVGVASLLCAGGALAQSNVTLYGVIDTYMGYTNATGKGSVASLDSGGYQASRVGF 60 Query: 60 RGSEDLGGNLKAVFQLEAGFYTDTGATPNASKLFNRYSTVGLAGDFGALTLGHMPDVVFD 119 +GSEDLGG L+A FQ+E GF +D+GA ++++LFNR S VGL + G L LG F Sbjct: 61 KGSEDLGGGLRANFQMENGFASDSGAMHDSTRLFNRQSWVGLGNELGELRLGRQNSPGFL 120 Query: 120 YVGKLSNGFQLTNWYLFHPGNLDSL-ANTYQFDNAVRYTSPTLGGFQGSVMVGFGEVAGD 178 + +L + F + F L+++ A T ++DN + Y SP + GF+ G GE Sbjct: 121 MIARL-DAFAGATYASF----LNNVSAYTPRYDNVIGYLSPVMRGFRVQAYYGLGEQTAP 175 Query: 179 SSNGRNISAGGTYTNGPWRAALAYSKLNNRAAGYAGTFLTSVGLGNAGTVFNSLTTTAGG 238 + G Y +GP ++ S N +A +T AGG Sbjct: 176 RNGLSTAMLAGEYESGPLYLGVSSSAQN-----------------SANDNITIRSTFAGG 218 Query: 239 LGYTIGSVRLNTAYTQVKL--ALPSGATPKQ--KNLDLGAAWRYATLDTINLGYGFSKLQ 294 Y GS ++ Y + A S TP L A +R T+ GYG++K Sbjct: 219 -AYDYGSGKVFLGYYRGNNLGAAASANTPGSYYSAYSLSANYRLTGQATLGAGYGWAKDS 277 Query: 295 ---GARWNTLSLSHVHEFSKRTQWYVQAAYQRAGGDARFAVMNGTGASGATGVSGGRGQM 351 G SL ++ S+RT Y A+ A F++ + VSGG Sbjct: 278 TGAGRNARQFSLIGTYDLSRRTMLYATYAHLANNNGASFSLAGAAPITKNAPVSGGTVNG 337 Query: 352 VTTIGMHHSF 361 V +G+ H F Sbjct: 338 V-QVGIRHLF 346 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 0.317 0.133 0.395 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: 1,112,070 Number of extensions: 49900 Number of successful extensions: 196 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 14 Length of query: 361 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 275 Effective length of database: 1,212,660 Effective search space: 333481500 Effective search space used: 333481500 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)