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= 0003.0006.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|300313057|ref|YP_003777149.1| porin signal peptide protein [H... 665 0.0 gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC fami... 188 6e-49 gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 112 5e-26 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 110 2e-25 gi|300313395|ref|YP_003777487.1| porin transmembrane protein [He... 105 8e-24 >gi|300313057|ref|YP_003777149.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 380 Score = 665 bits (1717), Expect = 0.0, Method: Compositional matrix adjust. Identities = 338/369 (91%), Positives = 351/369 (95%) Query: 1 MGLLLAASTTALAQSTSNVTLYGTVDQYLGYMHSSSGKSLWALNDGAILRSRIGLKGYED 60 MGLLLAAS +ALAQS SNVTLYGT+DQYLGYM SSSGKSLWALNDGAILRSRIGLKGYED Sbjct: 12 MGLLLAASGSALAQSASNVTLYGTLDQYLGYMRSSSGKSLWALNDGAILRSRIGLKGYED 71 Query: 61 LGGGYAATFTLENGFAGDTGGLADSTRLFDRQSWVGIKTPGAGEFRVGRQNSVPFFIGGA 120 LGGGYA TFTLENGF+ DTG AD TRLFDRQSWVGIKTP AGEFR+GRQNSVPFFIGGA Sbjct: 72 LGGGYATTFTLENGFSADTGAQADGTRLFDRQSWVGIKTPAAGEFRIGRQNSVPFFIGGA 131 Query: 121 IDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAGFQFDIHYAMPETAGEGLGRRGVYQF 180 IDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAG Q D+HYAMPETAGEGLGRRGVYQ Sbjct: 132 IDYTERTTYGSIINTFGVPSRFDNDLSWKSPRWAGLQIDLHYAMPETAGEGLGRRGVYQL 191 Query: 181 GLDYTNGPYRAGYAGLVAKPNAGGLYSNTVQYHNVYADYDYGPGKIYLAYVRSNNTTANA 240 G+DY NGPYRAGYAGL+AKPNAGGLY N VQYHNVY +YDYGPGK+YLAYVRSNNTTAN Sbjct: 192 GIDYINGPYRAGYAGLMAKPNAGGLYDNAVQYHNVYLNYDYGPGKVYLAYVRSNNTTANT 251 Query: 241 NGNNAATILNNVSNPNNFFAGNDPNIQRFYNVYQVSADYRLTPQLRIGALYGVMVDTSHK 300 NGNNAATILNNVSNPNNFFAGND N+QRFYNVYQ+SADYRLTPQLRIGALYGVMVDTSHK Sbjct: 252 NGNNAATILNNVSNPNNFFAGNDANVQRFYNVYQISADYRLTPQLRIGALYGVMVDTSHK 311 Query: 301 DGGAQGGNVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADINGKSLIG 360 +GGAQGGNVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADINGKSL+G Sbjct: 312 EGGAQGGNVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADINGKSLVG 371 Query: 361 LQMGILHRF 369 LQMGILHRF Sbjct: 372 LQMGILHRF 380 >gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC family protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 188 bits (478), Expect = 6e-49, Method: Compositional matrix adjust. Identities = 132/362 (36%), Positives = 190/362 (52%), Gaps = 36/362 (9%) Query: 11 ALAQSTSNVTLYGTVDQYLGYMHSSSGKSLWALNDGAILRSRIGLKGYEDLGGGYAATFT 70 ALAQS NVTLYG +D Y+GY +++ S+ +L+ G SR+G KG EDLGGG A F Sbjct: 18 ALAQS--NVTLYGVIDTYMGYTNATGKGSVASLDSGGYQASRVGFKGSEDLGGGLRANFQ 75 Query: 71 LENGFAGDTGGLADSTRLFDRQSWVGIKTPGAGEFRVGRQNSVPFFIGGAIDYTERTTYG 130 +ENGFA D+G + DSTRLF+RQSWVG+ GE R+GRQNS F + +D TY Sbjct: 76 MENGFASDSGAMHDSTRLFNRQSWVGLGNE-LGELRLGRQNSPGFLMIARLDAFAGATYA 134 Query: 131 SIINTFGV-PSRFDNDLSWKSPRWAGFQFDIHYAMPETAGEGLGRRGVYQFGL--DYTNG 187 S +N R+DN + + SP GF+ +Y + E R G+ L +Y +G Sbjct: 135 SFLNNVSAYTPRYDNVIGYLSPVMRGFRVQAYYGLGEQTAP---RNGLSTAMLAGEYESG 191 Query: 188 PYRAGYAGLVAKPNAGGLYSNTVQYHNVYADYDYGPGKIYLAYVRSNNTTANANGNNAAT 247 P Y G+ + + T++ YDYG GK++L Y R NN A A+ N + Sbjct: 192 PL---YLGVSSSAQNSANDNITIRSTFAGGAYDYGSGKVFLGYYRGNNLGAAASANTPGS 248 Query: 248 ILNNVSNPNNFFAGNDPNIQRFYNVYQVSADYRLTPQLRIGALYGVMVDTSHKDGGAQGG 307 +Y+ Y +SA+YRLT Q +GA YG D++ A+ Sbjct: 249 ---------------------YYSAYSLSANYRLTGQATLGAGYGWAKDSTGAGRNARQF 287 Query: 308 NVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADINGKSLIGLQMGILH 367 ++ YDLS+RT LY ++ N A + +G+A N A ++G ++ G+Q+GI H Sbjct: 288 SLIGTYDLSRRTMLYATYAHLANNNGASFSLAGAAPITKN---APVSGGTVNGVQVGIRH 344 Query: 368 RF 369 F Sbjct: 345 LF 346 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 112 bits (280), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 132/395 (33%), Positives = 182/395 (46%), Gaps = 75/395 (18%) Query: 11 ALAQSTSNVTLYGTVDQYLGYMHSSS--GKSLWALNDGAILRSRIGLKGYEDLGGGYAAT 68 A AQS NVT+YG VD + Y+ +++ G S +++GAI SRIG KG EDLGGG A Sbjct: 19 AFAQS--NVTIYGIVDTSIHYLSNANAQGNSNVRMDNGAIANSRIGFKGTEDLGGGLKAM 76 Query: 69 FTLENGFAGDTGGLADSTRLFDRQSWVGIKTPGAGEFRVGRQNSVPFFIGGAIDYTERTT 128 F LENGF+ DTG + LF RQSWVG++ G G+ RVGRQN+ F + D+ + T Sbjct: 77 FQLENGFSSDTGAMQQGGSLFGRQSWVGLQ-GGFGKVRVGRQNTPLFDL--LADHFDPLT 133 Query: 129 YGSIINTFGVPS-----------RFDNDLSWKSPRWAGFQFDIHYAMPETAGEGLGRRGV 177 G+ + +P+ R+D D P A +A E AG R Sbjct: 134 VGNYASNSWLPAAASLVRSPNMLRYDGDF---GPVAA----SASWAFGEKAGS---VRTG 183 Query: 178 YQF--GLDYTNGPYR--AGYAGLVAKPNAGGLYSNTVQYHNVYADYDYGPGKIYLAYVRS 233 QF L YT GP GY V+ N+ ++ N+ A YD+G K++ ++ Sbjct: 184 SQFSSALRYTAGPLALGGGYQQTVSSTNSSLKHTT----WNLSASYDFGVAKVFGGWLNI 239 Query: 234 NNTTANANGNNAATILNNVSN-------PNNFFAGNDPNIQRFYNVYQVSADYRLTPQLR 286 + + AA +VSN NN G ++R N + + + Y+ T L Sbjct: 240 KDDSGLTGSVMAAD--GDVSNGWTTAGAANNGSTG----VKRKDNGFFLGSSYKATNALT 293 Query: 287 I-GALYGVMVDTSHKDGGAQGGNVG----------AYYDLSKRTTLYGFANYMKNQANAG 335 + GA Y D S GNVG A Y LSKRT LY +Y K + A Sbjct: 294 LTGAFY---YDRSKNVSYVSTGNVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAV 350 Query: 336 WRFSGSAGPGSNLAGADINGK-SLIGLQMGILHRF 369 + + SA NGK SL + +GI H F Sbjct: 351 YELTNSA-----------NGKNSLTTVGVGIRHIF 374 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 110 bits (275), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 123/430 (28%), Positives = 169/430 (39%), Gaps = 93/430 (21%) Query: 1 MGLLLAASTTALAQSTSNVTLYGTVDQYLGYMH--SSSGK---SLWALNDGAILRSRIGL 55 + +L A + A AQS+S +T+YG +D L Y + ++ GK SL A+ G + SR+G+ Sbjct: 8 LAVLGAFAGAAHAQSSS-ITIYGAIDASLTYTNKIATDGKNTGSLTAVESGLVKGSRLGI 66 Query: 56 KGYEDLGGGYAATFTLENGFAGDTGGLADSTRLFDRQSWVGIKTPGAGEFRVGRQNSVPF 115 KG EDLGGG A FTLENGF DTG ++ RQ+ VG+ + G VGRQN Sbjct: 67 KGSEDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGL-SGNFGTVLVGRQNDPLN 125 Query: 116 FIGGAIDYTERTTYGSIINTFGVP-------------SRFDNDLSWKSPRWAGFQFDIHY 162 IGG FGVP R +N + + SP + G F Y Sbjct: 126 DIGGIAS----------AGGFGVPGTVHSKGLDRTDGQRLNNSIRYNSPNFNGLSFSGIY 175 Query: 163 AMPETAGEGLGRRGVYQFGLDYTNGPYRAGYAGLVAKPNAGGLYSNTVQYH--------- 213 E G +G R + G Y NGP G +K G S+ V Sbjct: 176 GFGEQVGRAVGGRSI-GLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVNAKAACNGAGEK 234 Query: 214 -----------NVYADYDYGPGKIYLAYVRSNNTTANANGNNAATILNNVSNPNNFFAGN 262 + A Y +GP K+Y A+ A + V NNF A Sbjct: 235 DHAGDTCLKTWTLAAAYQFGPAKVYGAFSHVRLPLAK--------LHTKVRKDNNFGAMY 286 Query: 263 DPNIQRFYN------------------VYQVSADYRLTPQLRIGALYGVMVDTSHKDGGA 304 D YN + + Y+L P L L + T K GA Sbjct: 287 DAKTGTGYNPSDATAFSIGGANHKSSQTFDIGMSYQLMPSL---TLMSAVQHTRAKFVGA 343 Query: 305 QGG-----NVGAYYDLSKRTTLYGFANYMKNQANAGWRFSGSAGPGSNLAGADINGKSLI 359 G N+GA YDLSKRT+ Y +++ S PG + +S Sbjct: 344 ASGRLLQLNLGAKYDLSKRTSAYALVRNLRSSDMYNVGLSKDQEPGID--------RSQT 395 Query: 360 GLQMGILHRF 369 + G++H F Sbjct: 396 AISTGLIHTF 405 >gi|300313395|ref|YP_003777487.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 105 bits (261), Expect = 8e-24, Method: Compositional matrix adjust. Identities = 76/206 (36%), Positives = 102/206 (49%), Gaps = 8/206 (3%) Query: 17 SNVTLYGTVDQYLGYMHSSSGKSLWALNDGAILRSRIGLKGYEDLGGGYAATFTLENGFA 76 S+VTLYGTVD L Y + G S +N GA+ S++GL G EDLGGG A F LENGF Sbjct: 35 SSVTLYGTVDLGLAYSSNQGGASNTYMNSGALAASKLGLTGTEDLGGGNMALFRLENGFN 94 Query: 77 GDTGGLADSTRLFDRQSWVGIKTPGAGEFRVGRQNSVPFFIGGAIDYTERTT-----YGS 131 DTG + + LF+RQS+VG+ + G+ VGRQ + F GA+ T T + Sbjct: 95 ADTGAQSTAGVLFNRQSYVGLSSKDYGQVTVGRQYTPYFQYVGALGPTNVLTGATGAHPG 154 Query: 132 IINTFGVPSRFDNDLSWKSPRWAGFQFDIHYAMPETAGEGLGRRGVY-QFGLDYTNGPYR 190 I+ R +N +++ P G Q + Y M E AG V DY + Sbjct: 155 DIDALDTTLRMNNSITYTLPTLGGLQAGVQYGMGEQAGSAANGSSVSAALRYDYQAFSWS 214 Query: 191 AGYAGL--VAKPNAGGLYSNTVQYHN 214 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 0.415 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: 1,271,702 Number of extensions: 59425 Number of successful extensions: 175 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 143 Number of HSP's successfully gapped: 14 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 131 (55.1 bits)