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= 0001.2616.p (345 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 137 2e-33 gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC fami... 135 5e-33 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 130 1e-31 gi|300313395|ref|YP_003777487.1| porin transmembrane protein [He... 124 1e-29 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 123 2e-29 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 137 bits (344), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 112/313 (35%), Positives = 157/313 (50%), Gaps = 34/313 (10%) Query: 20 SAAAQSSVAVYGVVDAGLTWESERHRAGSSTS----LVSGGNSASRLGFRGSEELGQGWK 75 +A AQSSV++YG++D GLT+ S ++G + + SG SR+GF+G+E+LG G Sbjct: 17 TAHAQSSVSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQGSRIGFKGTEDLGGGMN 76 Query: 76 ALFVLESGFSLDDGALGQGGLLWGRKSLVGL-SGPYGTLTLGRQDSPLYDYAA------P 128 A F LE+GF DDG+LGQGGLL+GR+S VGL S +G+L++GRQ YD+ A Sbjct: 77 AFFTLETGFGADDGSLGQGGLLFGRQSFVGLGSTQWGSLSVGRQ----YDFMANIGGQYA 132 Query: 129 MDPLSGALAF-----------TRIFTQANKYRRDNNTIKYASPTLGGFKGQLAYSFGETA 177 M LS A +F T + R NN+IKY S GGF GETA Sbjct: 133 MGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGFSFGAMVGLGETA 192 Query: 178 GASASGRLLSAGLNYTRGASSSSLSMQNINSQAVGNNGIKTIRLVNLGTRYDF-KVAAVS 236 G + +GR +SA Y G S +L+ +I + G + R+ G RY Sbjct: 193 GNNNAGRTVSATGQYDNGPFSGALAYTDIKD----STGSFSTRIYGGGARYQIGAFTPFG 248 Query: 237 LMMQTNKSNEGAKAMDSRDFLAGVSVPLGAHKISASVIVHKDRKQASGDARQLALGYTYG 296 ++ Q +N AKA PL ++A+ K R Q G+A+ L Y Sbjct: 249 VVTQVKNTNTSAKATTYELGTVYALTPL--WDLAAAYQFQK-RNQGVGNAQALVATVDYK 305 Query: 297 LSPRTHLYGGMAH 309 +S RT LY G + Sbjct: 306 ISKRTDLYVGAVY 318 >gi|300310663|ref|YP_003774755.1| outer membrane porin, OmpC family protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 135 bits (340), Expect = 5e-33, Method: Compositional matrix adjust. Identities = 125/349 (35%), Positives = 169/349 (48%), Gaps = 29/349 (8%) Query: 13 TLLCLCGSAAAQSSVAVYGVVDAGLTWESERHRAGSSTSLVSGGNSASRLGFRGSEELGQ 72 +LLC G A AQS+V +YGV+D + + + + GS SL SGG ASR+GF+GSE+LG Sbjct: 11 SLLC-AGGALAQSNVTLYGVIDTYMGYTNATGK-GSVASLDSGGYQASRVGFKGSEDLGG 68 Query: 73 GWKALFVLESGFSLDDGALGQGGLLWGRKSLVGLSGPYGTLTLGRQDSPLYDYAAPMDPL 132 G +A F +E+GF+ D GA+ L+ R+S VGL G L LGRQ+SP + A +D Sbjct: 69 GLRANFQMENGFASDSGAMHDSTRLFNRQSWVGLGNELGELRLGRQNSPGFLMIARLDAF 128 Query: 133 SGALAFTRIFTQANKYR-RDNNTIKYASPTLGGFKGQLAYSFGE-TAGASASGRLLSAGL 190 +GA + + Y R +N I Y SP + GF+ Q Y GE TA + + AG Sbjct: 129 AGA-TYASFLNNVSAYTPRYDNVIGYLSPVMRGFRVQAYYGLGEQTAPRNGLSTAMLAG- 186 Query: 191 NYTRGASSSSLSMQNINSQAVGNNGIKTIRLVNLGTRYDFKVAAVSL-MMQTNKSNEGAK 249 Y G +S NS N+ I TIR G YD+ V L + N A Sbjct: 187 EYESGPLYLGVSSSAQNSA---NDNI-TIRSTFAGGAYDYGSGKVFLGYYRGNNLGAAAS 242 Query: 250 AMDSRDFLAGVSVP-----LGAHKISASVIVHKDRKQASGDARQLALGYTYGLSPRTHLY 304 A + + S+ G + A KD A +ARQ +L TY LS RT LY Sbjct: 243 ANTPGSYYSAYSLSANYRLTGQATLGAGYGWAKDSTGAGRNARQFSLIGTYDLSRRTMLY 302 Query: 305 GGMAHISNNKSARFGLASLA--------EGGAPDGSDPMLYTAGVKHTF 345 AH++NN A F LA A GG +G G++H F Sbjct: 303 ATYAHLANNNGASFSLAGAAPITKNAPVSGGTVNGVQ-----VGIRHLF 346 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 130 bits (327), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 127/405 (31%), Positives = 173/405 (42%), Gaps = 81/405 (20%) Query: 13 TLLCLCGSAAAQSS-VAVYGVVDAGLTWE----SERHRAGSSTSLVSGGNSASRLGFRGS 67 L G+A AQSS + +YG +DA LT+ ++ GS T++ SG SRLG +GS Sbjct: 10 VLGAFAGAAHAQSSSITIYGAIDASLTYTNKIATDGKNTGSLTAVESGLVKGSRLGIKGS 69 Query: 68 EELGQGWKALFVLESGFSLDDGALGQGGLLWGRKSLVGLSGPYGTLTLGRQDSPLYD--- 124 E+LG G KA+F LE+GF++D G GQG L+WGR++ VGLSG +GT+ +GRQ+ PL D Sbjct: 70 EDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGLSGNFGTVLVGRQNDPLNDIGG 129 Query: 125 ------YAAPMDPLSGALAFTRIFTQANKYRRDNNTIKYASPTLGGFKGQLAYSFGETAG 178 + P S L T +R NN+I+Y SP G Y FGE G Sbjct: 130 IASAGGFGVPGTVHSKGLDRT-------DGQRLNNSIRYNSPNFNGLSFSGIYGFGEQVG 182 Query: 179 ASASGRLLSAGLNYTRGASSSSLSM------------QNINSQAVGNN-------GIKTI 219 + GR + G Y G S L ++N++A N G + Sbjct: 183 RAVGGRSIGLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVNAKAACNGAGEKDHAGDTCL 242 Query: 220 RLVNLGTRYDFKVAAV------------SLMMQTNKSNE--------------------- 246 + L Y F A V L + K N Sbjct: 243 KTWTLAAAYQFGPAKVYGAFSHVRLPLAKLHTKVRKDNNFGAMYDAKTGTGYNPSDATAF 302 Query: 247 ---GAKAMDSRDFLAGVSVPLGAHKISASVIVHKDRK---QASGDARQLALGYTYGLSPR 300 GA S+ F G+S L S + H K ASG QL LG Y LS R Sbjct: 303 SIGGANHKSSQTFDIGMSYQLMPSLTLMSAVQHTRAKFVGAASGRLLQLNLGAKYDLSKR 362 Query: 301 THLYGGMAHISNNKSARFGLASLAEGGAPDGSDPMLYTAGVKHTF 345 T Y + ++ ++ GL+ E G D S + T G+ HTF Sbjct: 363 TSAYALVRNLRSSDMYNVGLSKDQEPGI-DRSQTAIST-GLIHTF 405 >gi|300313395|ref|YP_003777487.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 403 Score = 124 bits (310), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 123/376 (32%), Positives = 183/376 (48%), Gaps = 58/376 (15%) Query: 23 AQSSVAVYGVVDAGLTWESERHRAGSSTSLVSGGNSASRLGFRGSEELGQGWKALFVLES 82 AQSSV +YG VD GL + S + A S+T + SG +AS+LG G+E+LG G ALF LE+ Sbjct: 33 AQSSVTLYGTVDLGLAYSSNQGGA-SNTYMNSGALAASKLGLTGTEDLGGGNMALFRLEN 91 Query: 83 GFSLDDGALGQGGLLWGRKSLVGLSGP-YGTLTLGRQDSPLYDYAAPMDP---LSGAL-A 137 GF+ D GA G+L+ R+S VGLS YG +T+GRQ +P + Y + P L+GA A Sbjct: 92 GFNADTGAQSTAGVLFNRQSYVGLSSKDYGQVTVGRQYTPYFQYVGALGPTNVLTGATGA 151 Query: 138 FTRIFTQANKYRRDNNTIKYASPTLGGFKGQLAYSFGETAGASASGRLLSAGLNYTRGAS 197 + R NN+I Y PTLGG + + Y GE AG++A+G +SA L Y A Sbjct: 152 HPGDIDALDTTLRMNNSITYTLPTLGGLQAGVQYGMGEQAGSAANGSSVSAALRYDYQAF 211 Query: 198 SSSLSMQNINSQAVGNNG---------------------IKTIRLVNLGTRYDFKVAAVS 236 S S + + A GN + +L+ RY Sbjct: 212 SWSAGYTRLKNLANGNTAGSFGNVGSFANNSPVNAGYASADSTQLLATAARYTRG----D 267 Query: 237 LMMQTNKSN----EGAKAMDSRDFLAGVSVPLGAHKISASVIV--------HKDRKQASG 284 LM+ N SN GA + S+ + +G++ +S ++++ K R S Sbjct: 268 LMLGLNYSNVQYKAGALSAFSQTAVFNTIGLIGSYNVSPALVLAAGYSYTAEKARNGISS 327 Query: 285 DAR--QLALGYTYGLSPRTHLYGGMAHI-SNNKSARFG---------LASL--AEGGAP- 329 A+ QL+L Y LS RT LY A+ ++ ++ R G +AS+ ++ G P Sbjct: 328 PAKYNQLSLEEVYSLSKRTALYAIQAYQRASGQTLRAGGVGSSIVNAVASVGDSQNGTPS 387 Query: 330 DGSDPMLYTAGVKHTF 345 GS + G++H+F Sbjct: 388 SGSGQFVAMLGIRHSF 403 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 123 bits (308), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 114/346 (32%), Positives = 165/346 (47%), Gaps = 27/346 (7%) Query: 19 GSAAAQSSVAVYGVVDAGLTW--ESERHRAGSSTSLVSGGNSASRLGFRGSEELGQGWKA 76 GS AQSSV +YG+VD G+ + + + AGS T + SG + SR+GFRG+E+LG G KA Sbjct: 17 GSVQAQSSVTIYGLVDTGVEYLNNAGPNGAGSVTRMTSGATNTSRIGFRGTEDLGGGLKA 76 Query: 77 LFVLESGFSLDDGAL-GQGGLLWGRKSLVGLSGPYGTLTLGRQDSPLYDYAAPMDPLSGA 135 LF LE+GF LD+G+ G L+ R+S VGL G +G + GR S YD+ P DP+ + Sbjct: 77 LFQLENGFKLDNGSFDGDANQLFNRQSTVGLEGGFGRVVAGRSYSTTYDFLGPFDPMGYS 136 Query: 136 LAFTRIFTQ-ANKYRRD------NNTIKYASPTLGGFKGQLAYSFGETAGASASGRLLSA 188 ++ T A R+D +N +KY G K Y FGE AG + +G Sbjct: 137 ANYSWATTAGATGNRKDGMPTGVSNLVKYQGE-FSGVKIGAMYGFGEVAGETRNGAKYGV 195 Query: 189 GLNYTRGASSSSLSMQNINSQAVGNNGIKTIRLVNLGTRYDFKVA-AVSLMMQTNKSNEG 247 GL + G S + NS N +L Y A +L + K + Sbjct: 196 GLGWGTGPFSVVATYDRNNSATATNTPYDRATSAHLAAGYQPSEAWKFNLGYRYYKKSLA 255 Query: 248 AKAMDSR-DFLAGVSVPLGAHKISASV-----IVHKDRKQASGDARQL--ALGYTYGLSP 299 A D R DF G + A+K + ++ I +++ K + DA + +L Y +S Sbjct: 256 TGAADLRSDFFWGGA----AYKFTPAMTLIGAIYYQNIKNVANDADPIMYSLRLKYAMSK 311 Query: 300 RTHLYGGMAHISNNKSARFGLASLAEGGAPDGSDPMLYTAGVKHTF 345 RT LY A+ K+ L L+ A GS T G++H F Sbjct: 312 RTDLYLSTAYA---KAKNGQLVGLSRDDAGYGSSQFGMTLGMQHRF 354 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 0.131 0.374 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: 989,958 Number of extensions: 38510 Number of successful extensions: 131 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 97 Number of HSP's successfully gapped: 14 Length of query: 345 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 259 Effective length of database: 1,212,660 Effective search space: 314078940 Effective search space used: 314078940 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: 42 (22.0 bits) S2: 131 (55.1 bits)