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= 0001.3663.p (380 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313057|ref|YP_003777149.1| porin signal peptide protein [H... 693 0.0 gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC fami... 188 7e-49 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 117 1e-27 gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 111 9e-26 gi|300313395|ref|YP_003777487.1| porin transmembrane protein [He... 107 1e-24 >gi|300313057|ref|YP_003777149.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 693 bits (1788), Expect = 0.0, Method: Compositional matrix adjust. Identities = 353/380 (92%), Positives = 365/380 (96%) Query: 1 MKQLSLRTPVAMGLLLAASGTALAQSASNVTLYGTVDQYLGYMRSSSGKSLWALNDGAIL 60 M + S+RTPVAMGLLLAASG+ALAQSASNVTLYGT+DQYLGYMRSSSGKSLWALNDGAIL Sbjct: 1 MTKPSIRTPVAMGLLLAASGSALAQSASNVTLYGTLDQYLGYMRSSSGKSLWALNDGAIL 60 Query: 61 RSRIGLKGYEDLGAGYAATFTLENGFSGDTGGLADSSRLFDRQSWVGIKTPAAGEFRIGR 120 RSRIGLKGYEDLG GYA TFTLENGFS DTG AD +RLFDRQSWVGIKTPAAGEFRIGR Sbjct: 61 RSRIGLKGYEDLGGGYATTFTLENGFSADTGAQADGTRLFDRQSWVGIKTPAAGEFRIGR 120 Query: 121 QNSVPFFIGGAIDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAGIQFDLHYAMPETAG 180 QNSVPFFIGGAIDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAG+Q DLHYAMPETAG Sbjct: 121 QNSVPFFIGGAIDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAGLQIDLHYAMPETAG 180 Query: 181 EGLGRRGVYQLGVDYTSGPYRAGYAGLMAKPNAGGRYDNTVQYHNVYADYDYGPGKIYLA 240 EGLGRRGVYQLG+DY +GPYRAGYAGLMAKPNAGG YDN VQYHNVY +YDYGPGK+YLA Sbjct: 181 EGLGRRGVYQLGIDYINGPYRAGYAGLMAKPNAGGLYDNAVQYHNVYLNYDYGPGKVYLA 240 Query: 241 YVRSNNTTANANGNNAATILNNVSNPNNFFAGNDPNIQRFYNVYQISADYRLTPQLRIGA 300 YVRSNNTTAN NGNNAATILNNVSNPNNFFAGND N+QRFYNVYQISADYRLTPQLRIGA Sbjct: 241 YVRSNNTTANTNGNNAATILNNVSNPNNFFAGNDANVQRFYNVYQISADYRLTPQLRIGA 300 Query: 301 LYGVMVDTSHKEGGAQGGNIGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLA 360 LYGVMVDTSHKEGGAQGGN+GAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLA Sbjct: 301 LYGVMVDTSHKEGGAQGGNVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLA 360 Query: 361 GADINGKSLVGLQMGILHRF 380 GADINGKSLVGLQMGILHRF Sbjct: 361 GADINGKSLVGLQMGILHRF 380 >gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC family protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 188 bits (477), Expect = 7e-49, Method: Compositional matrix adjust. Identities = 134/374 (35%), Positives = 193/374 (51%), Gaps = 37/374 (9%) Query: 10 VAMGLLLAASGTALAQSASNVTLYGTVDQYLGYMRSSSGKSLWALNDGAILRSRIGLKGY 69 V + LL A G ALAQS NVTLYG +D Y+GY ++ S+ +L+ G SR+G KG Sbjct: 7 VGVASLLCAGG-ALAQS--NVTLYGVIDTYMGYTNATGKGSVASLDSGGYQASRVGFKGS 63 Query: 70 EDLGAGYAATFTLENGFSGDTGGLADSSRLFDRQSWVGIKTPAAGEFRIGRQNSVPFFIG 129 EDLG G A F +ENGF+ D+G + DS+RLF+RQSWVG+ GE R+GRQNS F + Sbjct: 64 EDLGGGLRANFQMENGFASDSGAMHDSTRLFNRQSWVGLGNE-LGELRLGRQNSPGFLMI 122 Query: 130 GAIDYTERTTYGSIINTFGV-PSRFDNDLSWKSPRWAGIQFDLHYAMPETAGEGLGRRGV 188 +D TY S +N R+DN + + SP G + +Y + E R G+ Sbjct: 123 ARLDAFAGATYASFLNNVSAYTPRYDNVIGYLSPVMRGFRVQAYYGLGEQTAP---RNGL 179 Query: 189 Y--QLGVDYTSGPYRAGYAGLMAKPNAGGRYDNTVQYHNVYADYDYGPGKIYLAYVRSNN 246 L +Y SGP Y G+ + + T++ YDYG GK++L Y R NN Sbjct: 180 STAMLAGEYESGPL---YLGVSSSAQNSANDNITIRSTFAGGAYDYGSGKVFLGYYRGNN 236 Query: 247 TTANANGNNAATILNNVSNPNNFFAGNDPNIQRFYNVYQISADYRLTPQLRIGALYGVMV 306 A A+ N + +Y+ Y +SA+YRLT Q +GA YG Sbjct: 237 LGAAASANTPGS---------------------YYSAYSLSANYRLTGQATLGAGYGWAK 275 Query: 307 DTSHKEGGAQGGNIGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADING 366 D++ A+ ++ YDLS+RT LY ++ N A + +G+A N A ++G Sbjct: 276 DSTGAGRNARQFSLIGTYDLSRRTMLYATYAHLANNNGASFSLAGAAPITKN---APVSG 332 Query: 367 KSLVGLQMGILHRF 380 ++ G+Q+GI H F Sbjct: 333 GTVNGVQVGIRHLF 346 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 117 bits (294), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 124/435 (28%), Positives = 177/435 (40%), Gaps = 93/435 (21%) Query: 7 RTPVAMGLLLAASGTALAQSASNVTLYGTVDQYLGYMR--SSSGK---SLWALNDGAILR 61 ++ +A+ +L A +G A AQS+S +T+YG +D L Y ++ GK SL A+ G + Sbjct: 3 KSLLALAVLGAFAGAAHAQSSS-ITIYGAIDASLTYTNKIATDGKNTGSLTAVESGLVKG 61 Query: 62 SRIGLKGYEDLGAGYAATFTLENGFSGDTGGLADSSRLFDRQSWVGIKTPAAGEFRIGRQ 121 SR+G+KG EDLG G A FTLENGF+ DTG ++ RQ+ VG+ + G +GRQ Sbjct: 62 SRLGIKGSEDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGL-SGNFGTVLVGRQ 120 Query: 122 NSVPFFIGGAIDYTERTTYGSIINTFGVP-------------SRFDNDLSWKSPRWAGIQ 168 N IGG FGVP R +N + + SP + G+ Sbjct: 121 NDPLNDIGGIAS----------AGGFGVPGTVHSKGLDRTDGQRLNNSIRYNSPNFNGLS 170 Query: 169 FDLHYAMPETAGEGLGRRGVYQLGVDYTSGPYRAGYAGLMAK----------------PN 212 F Y E G +G R + LG Y +GP G +K N Sbjct: 171 FSGIYGFGEQVGRAVGGRSI-GLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVNAKAACN 229 Query: 213 AGGRYDN----TVQYHNVYADYDYGPGKIYLAYVRSNNTTANANGNNAATILNNVSNPNN 268 G D+ ++ + A Y +GP K+Y A+ A + V NN Sbjct: 230 GAGEKDHAGDTCLKTWTLAAAYQFGPAKVYGAFSHVRLPLAK--------LHTKVRKDNN 281 Query: 269 FFAGNDPNIQRFYN------------------VYQISADYRLTPQLRIGALYGVMVDTSH 310 F A D YN + I Y+L P L L + T Sbjct: 282 FGAMYDAKTGTGYNPSDATAFSIGGANHKSSQTFDIGMSYQLMPSL---TLMSAVQHTRA 338 Query: 311 KEGGAQGG-----NIGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADIN 365 K GA G N+GA YDLSKRT+ Y +++ S PG + Sbjct: 339 KFVGAASGRLLQLNLGAKYDLSKRTSAYALVRNLRSSDMYNVGLSKDQEPGID------- 391 Query: 366 GKSLVGLQMGILHRF 380 +S + G++H F Sbjct: 392 -RSQTAISTGLIHTF 405 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 111 bits (278), Expect = 9e-26, Method: Compositional matrix adjust. Identities = 124/395 (31%), Positives = 181/395 (45%), Gaps = 71/395 (17%) Query: 20 GTALAQSASNVTLYGTVDQYLGYMRSSS--GKSLWALNDGAILRSRIGLKGYEDLGAGYA 77 G A AQS NVT+YG VD + Y+ +++ G S +++GAI SRIG KG EDLG G Sbjct: 17 GAAFAQS--NVTIYGIVDTSIHYLSNANAQGNSNVRMDNGAIANSRIGFKGTEDLGGGLK 74 Query: 78 ATFTLENGFSGDTGGLADSSRLFDRQSWVGIKTPAAGEFRIGRQNSVPFFIGGAIDYTER 137 A F LENGFS DTG + LF RQSWVG++ G+ R+GRQN+ F + D+ + Sbjct: 75 AMFQLENGFSSDTGAMQQGGSLFGRQSWVGLQ-GGFGKVRVGRQNTPLFDL--LADHFDP 131 Query: 138 TTYGSIINTFGVPS-----------RFDNDLSWKSPRWAGIQFDLHYAMPETAGEGLGRR 186 T G+ + +P+ R+D D P + +A E AG + Sbjct: 132 LTVGNYASNSWLPAAASLVRSPNMLRYDGDF---GP----VAASASWAFGEKAGS-VRTG 183 Query: 187 GVYQLGVDYTSGPYR--AGYAGLMAKPNAGGRYDNTVQYHNVYADYDYGPGKIYLAYVRS 244 + + YT+GP GY ++ N+ ++ N+ A YD+G K++ ++ Sbjct: 184 SQFSSALRYTAGPLALGGGYQQTVSSTNSSLKHTT----WNLSASYDFGVAKVFGGWLNI 239 Query: 245 NNTTANANGNNAATILNNVSN-------PNNFFAGNDPNIQRFYNVYQISADYRLTPQLR 297 + + AA +VSN NN G ++R N + + + Y+ T L Sbjct: 240 KDDSGLTGSVMAAD--GDVSNGWTTAGAANNGSTG----VKRKDNGFFLGSSYKATNALT 293 Query: 298 I-GALYGVMVDTSHKEGGAQGGNIG----------AYYDLSKRTTLYGFANYMKNQANAG 346 + GA Y D S GN+G A Y LSKRT LY +Y K + A Sbjct: 294 LTGAFY---YDRSKNVSYVSTGNVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAV 350 Query: 347 WRFSGSAGPGSNLAGADINGK-SLVGLQMGILHRF 380 + + SA NGK SL + +GI H F Sbjct: 351 YELTNSA-----------NGKNSLTTVGVGIRHIF 374 >gi|300313395|ref|YP_003777487.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 107 bits (267), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 75/206 (36%), Positives = 105/206 (50%), Gaps = 8/206 (3%) Query: 28 SNVTLYGTVDQYLGYMRSSSGKSLWALNDGAILRSRIGLKGYEDLGAGYAATFTLENGFS 87 S+VTLYGTVD L Y + G S +N GA+ S++GL G EDLG G A F LENGF+ Sbjct: 35 SSVTLYGTVDLGLAYSSNQGGASNTYMNSGALAASKLGLTGTEDLGGGNMALFRLENGFN 94 Query: 88 GDTGGLADSSRLFDRQSWVGIKTPAAGEFRIGRQNSVPFFIGGAIDYTERTT-----YGS 142 DTG + + LF+RQS+VG+ + G+ +GRQ + F GA+ T T + Sbjct: 95 ADTGAQSTAGVLFNRQSYVGLSSKDYGQVTVGRQYTPYFQYVGALGPTNVLTGATGAHPG 154 Query: 143 IINTFGVPSRFDNDLSWKSPRWAGIQFDLHYAMPETAGEGLGRRGVY-QLGVDYTSGPYR 201 I+ R +N +++ P G+Q + Y M E AG V L DY + + Sbjct: 155 DIDALDTTLRMNNSITYTLPTLGGLQAGVQYGMGEQAGSAANGSSVSAALRYDYQAFSWS 214 Query: 202 AGYAGL--MAKPNAGGRYDNTVQYHN 225 AGY L +A N G + N + N Sbjct: 215 AGYTRLKNLANGNTAGSFGNVGSFAN 240 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 0.136 0.408 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: 1,267,491 Number of extensions: 57679 Number of successful extensions: 173 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 14 Length of query: 380 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 293 Effective length of database: 1,207,925 Effective search space: 353922025 Effective search space used: 353922025 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)