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= 0013.0004.p (344 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 259 2e-70 gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 130 1e-31 gi|300313291|ref|YP_003777383.1| porin transmembrane protein [He... 116 3e-27 gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) ... 110 1e-25 gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspir... 104 9e-24 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 259 bits (662), Expect = 2e-70, Method: Compositional matrix adjust. Identities = 155/337 (45%), Positives = 212/337 (62%), Gaps = 14/337 (4%) Query: 16 SATIYGVIDVGMEYFNNAGRRG-GSLLRLQSGGASTSRIGFKGVEDLGGGMQSFFQLEGG 74 S TIYG++D G+EY NNAG G GS+ R+ SG +TSRIGF+G EDLGGG+++ FQLE G Sbjct: 24 SVTIYGLVDTGVEYLNNAGPNGAGSVTRMTSGATNTSRIGFRGTEDLGGGLKALFQLENG 83 Query: 75 FLADSG--DGSDPHSFFNRQANVGLAGSYGKVLIGRSESTTGDF-SINDPL--SNHYSWS 129 F D+G DG D + FNRQ+ VGL G +G+V+ GRS STT DF DP+ S +YSW+ Sbjct: 84 FKLDNGSFDG-DANQLFNRQSTVGLEGGFGRVVAGRSYSTTYDFLGPFDPMGYSANYSWA 142 Query: 130 GASTHMRGDRKDGILGRISNVVKYEGKFGAYRLGGSYGLGESAGSHASNARYSAGVQYLG 189 + G+RKDG+ +SN+VKY+G+F ++G YG GE AG + A+Y G+ + Sbjct: 143 -TTAGATGNRKDGMPTGVSNLVKYQGEFSGVKIGAMYGFGEVAGETRNGAKYGVGLGWGT 201 Query: 190 GSVTGVLTFDRQNSKLAF-PGYDQASNIQVSGSYAQALA-KFFAGYRRYARHALTASKDV 247 G + V T+DR NS A YD+A++ ++ Y + A KF GYR Y + T + D+ Sbjct: 202 GPFSVVATYDRNNSATATNTPYDRATSAHLAAGYQPSEAWKFNLGYRYYKKSLATGAADL 261 Query: 248 RSDFVWIGASYLMWPATTVSGAVYHVDLRNDPKGNNGTPTMYAVRLSYAMSARTTFYATG 307 RSDF W GA+Y PA T+ GA+Y+ +++N N+ P MY++RL YAMS RT Y + Sbjct: 262 RSDFFWGGAAYKFTPAMTLIGAIYYQNIKN--VANDADPIMYSLRLKYAMSKRTDLYLST 319 Query: 308 AYAAASNSQPVGVSNAVNSYSESGAQAGINIGATHRF 344 AYA A N Q VG+S Y S Q G+ +G HRF Sbjct: 320 AYAKAKNGQLVGLSRDDAGYGSS--QFGMTLGMQHRF 354 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 130 bits (328), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 116/362 (32%), Positives = 170/362 (46%), Gaps = 59/362 (16%) Query: 6 TSAQGASSGGSATIYGVIDVGMEYFNNAGRRGGSLLRLQSGGASTSRIGFKGVEDLGGGM 65 TS A + + TIYG++D + Y +NA +G S +R+ +G + SRIGFKG EDLGGG+ Sbjct: 14 TSGGAAFAQSNVTIYGIVDTSIHYLSNANAQGNSNVRMDNGAIANSRIGFKGTEDLGGGL 73 Query: 66 QSFFQLEGGFLADSGDGSDPHSFFNRQANVGLAGSYGKVLIGRSESTTGDFSIN--DPLS 123 ++ FQLE GF +D+G S F RQ+ VGL G +GKV +GR + D + DPL+ Sbjct: 74 KAMFQLENGFSSDTGAMQQGGSLFGRQSWVGLQGGFGKVRVGRQNTPLFDLLADHFDPLT 133 Query: 124 -NHY---SWSGASTHMRGDRKDGILGRISNVVKYEGKFGAYRLGGSYGLGESAGS----- 174 +Y SW A+ L R N+++Y+G FG S+ GE AGS Sbjct: 134 VGNYASNSWLPAAAS---------LVRSPNMLRYDGDFGPVAASASWAFGEKAGSVRTGS 184 Query: 175 -HASNARYSAGVQYLGGSVTGVLTFDRQNSKLAFPGYDQASNIQVSGSYAQALAKFFAGY 233 +S RY+AG LGG T NS L ++ +S SY +AK F G+ Sbjct: 185 QFSSALRYTAGPLALGGGYQ--QTVSSTNSSLKHTTWN------LSASYDFGVAKVFGGW 236 Query: 234 RRYARHA------LTASKDV-------------------RSDFVWIGASYLMWPATTVSG 268 + + A DV + + ++G+SY A T++G Sbjct: 237 LNIKDDSGLTGSVMAADGDVSNGWTTAGAANNGSTGVKRKDNGFFLGSSYKATNALTLTG 296 Query: 269 AVYHVDLRN---DPKGNNGTPTMYAV--RLSYAMSARTTFYATGAYAAASNSQPVGVSNA 323 A Y+ +N GN G Y + YA+S RT Y T Y A ++ ++N+ Sbjct: 297 AFYYDRSKNVSYVSTGNVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAVYELTNS 356 Query: 324 VN 325 N Sbjct: 357 AN 358 >gi|300313291|ref|YP_003777383.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 99/364 (27%), Positives = 157/364 (43%), Gaps = 59/364 (16%) Query: 16 SATIYGVIDVGMEYFNNAGRRGGSLLRLQS-GGASTSRIGFKGVEDLGGGMQSFFQLEGG 74 S TIYG+ID G+ Y NA G S+ ++ S G+ SRIGFKG EDLGGG+Q+ F LE G Sbjct: 26 SVTIYGIIDTGVVYTTNANANGNSVFKMPSLTGSFPSRIGFKGTEDLGGGLQAMFVLESG 85 Query: 75 FLADSGDGSDPHSFFNRQANVGLAGSYGKVLIGRSESTTGDFSINDPL--SNHYSWSGAS 132 F D+G F RQ+ VGL S+G++++GR + T + + N ++ Sbjct: 86 FAPDTGAMGQGGRLFGRQSYVGLKNSWGQLMLGRQVNMTYLSQLKTDVMGPNLFAIGSID 145 Query: 133 THMRGDRKDGILGRISNVVKYEGKFGAYRLGGSYGL----------------GESAGSHA 176 ++ R D N + Y G F + +G +Y GE AG+ Sbjct: 146 AYLPNARSD-------NAIGYLGNFSGFTVGATYSFGRDAAGPAGPAATNCPGEVAGNSK 198 Query: 177 SNARYSAGVQYLG----------------GSVTGVLTFDRQNSKLAFPGYDQASNIQVSG 220 + + +A + Y G G+ G+ + D + ++ GY ++++ G Sbjct: 199 ACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGMTSSDNTDQRVTLNGYFMLGDVKIGG 258 Query: 221 SYAQALAKFFAGYRRYARHALTASKDVRSDFVWIGASYLMWPATTVSGAVYHVDLRNDPK 280 R R A + D SD ++G SY + A + V +D++N P Sbjct: 259 GVVD----------RRTRAAANTNTD--SDLYYLGVSYPLSVALVLDAQVSRLDVKNSPN 306 Query: 281 GNNGTPTMYAVRLSYAMSARTTFYATGAYAAASNSQPVGVSNAVNSYSESGAQAGINIGA 340 T+ RL+Y +S RT Y + Y + V + +A + Q G+ G Sbjct: 307 ----DVTLSVARLTYNLSKRTAVYGSLGYIKNGGTSSVAL-DAGGTVGAGKNQLGVMTGI 361 Query: 341 THRF 344 H F Sbjct: 362 RHTF 365 >gi|300310676|ref|YP_003774768.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 110 bits (275), Expect = 1e-25, Method: Compositional matrix adjust. Identities = 119/366 (32%), Positives = 170/366 (46%), Gaps = 52/366 (14%) Query: 4 GVTSAQGASSGGSATIYGVIDVGMEYFNNAGRRGG---SLLRLQSGGASTSRIGFKGVED 60 G T+A SS +IYG+ID+G+ Y+++A + GG LLR+ SG A SRIGFKG ED Sbjct: 14 GATTAHAQSS---VSIYGLIDLGLTYYSSAPKSGGGGARLLRMDSGIAQGSRIGFKGTED 70 Query: 61 LGGGMQSFFQLEGGFLADSGDGSDPHSFFNRQANVGLAGS-YGKVLIGRSESTTGDFSIN 119 LGGGM +FF LE GF AD G F RQ+ VGL + +G + +GR DF N Sbjct: 71 LGGGMNAFFTLETGFGADDGSLGQGGLLFGRQSFVGLGSTQWGSLSVGRQY----DFMAN 126 Query: 120 DPLSNHY---SWSGASTHMRGDRKDGILG-----------RISNVVKYE-GKFGAYRLGG 164 + Y + S A + G D G R +N +KY KFG + G Sbjct: 127 --IGGQYAMGALSPAGSFGWGLHADAAHGTALNNHIYAGDRTNNSIKYNSAKFGGFSFGA 184 Query: 165 SYGLGESAGSHASNARYSAGVQYLGGSVTGVLTF-DRQNSKLAFPGYDQASNIQVSGSYA 223 GLGE+AG++ + SA QY G +G L + D ++S +F ++ I G+ Sbjct: 185 MVGLGETAGNNNAGRTVSATGQYDNGPFSGALAYTDIKDSTGSF-----STRIYGGGARY 239 Query: 224 QALAKFFAGYRRYARHALTASKDVRSDFVWIGASYLMWPATTVSGAVYHVDLRNDPKGNN 283 Q A G ++ T++K + +G Y + P ++ A Y RN GN Sbjct: 240 QIGAFTPFGVVTQVKNTNTSAKATTYE---LGTVYALTPLWDLA-AAYQFQKRNQGVGN- 294 Query: 284 GTPTMYAVRLSYAMSARTTFYATGAY--AAASNSQPV---GVSNAVNSYSESGAQAGINI 338 + Y +S RT Y Y N+ PV G+ +A +G Q + + Sbjct: 295 --AQALVATVDYKISKRTDLYVGAVYDRDKGYNAYPVFGGGIQSA------TGNQTALRL 346 Query: 339 GATHRF 344 G HRF Sbjct: 347 GMRHRF 352 >gi|300310614|ref|YP_003774706.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 369 Score = 104 bits (260), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 108/369 (29%), Positives = 167/369 (45%), Gaps = 52/369 (14%) Query: 5 VTSAQGASSGGSATIYGVIDVGMEYFNN-----AGRRGGSLLRLQSGGAST-SRIGFKGV 58 +T + S S T+YG+ID G+EY +N AG++G LLR+ + A+T SRIG +G Sbjct: 12 LTMSATLSQAQSVTLYGIIDTGVEYVSNVSNVGAGQQG--LLRVPNLTATTPSRIGLRGS 69 Query: 59 EDLGGGMQSFFQLEGGFLADSGDGSDPHSFFNRQANVGLAGSYGKVLIGRSESTTGDFSI 118 EDLGGG++S F LE GF DSG + F R A VGL+ +G+V GR + ++ Sbjct: 70 EDLGGGLRSVFMLESGFAPDSGALNQGGRMFGRIAYVGLSDHWGQVSFGRQATMLLWATL 129 Query: 119 NDPL--SNHYSWSGASTHMRGDRKDGILGRISNVVKYEGKFGAYRLGGSYGL-------- 168 + + +N Y + + R D N + Y G FGA+ LGG+Y Sbjct: 130 DSDILGANVYGANALDNYRPNARAD-------NSIAYRGSFGAFTLGGTYSFGRDTVNAG 182 Query: 169 ---------GESAGSHASNARYSAGVQYLGGSVTGVLTFDR----QNSKLAFPGYDQASN 215 GE AG + +S V+Y + L +D + + + + Sbjct: 183 QNPAGTNCAGEQAGDSLACREWSLMVKYDTAAWGASLAYDTLRGGKGAAAGLSSSQLSDS 242 Query: 216 IQVSGSYAQALAKFFAGYRRYARHALTASKDVRSDFVWIGASYLMWPATTVSGAVYHVDL 275 + G+Y +A + G RH S +S + G SY + P ++G +Y+ L Sbjct: 243 RMLLGAYIKA-DRLKVGIGGSLRHN-QGSALSKSQLYYAGLSYDLTPTLNLAGQLYY--L 298 Query: 276 RNDPKGNNGTPTMYAVRLSYAMSARTTFYATGAYA--------AASNSQPVGVSNAVNSY 327 D N + A+R +Y++SART Y TG + + S VG +N Sbjct: 299 HYDDSANK--AWLGALRATYSLSARTALYLTGGFIDNRGQSNLSVSAGGSVGTANPAPGG 356 Query: 328 SESGAQAGI 336 ++ G AGI Sbjct: 357 NQFGMMAGI 365 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 0.132 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: 1,018,542 Number of extensions: 43226 Number of successful extensions: 158 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 128 Number of HSP's successfully gapped: 14 Length of query: 344 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 258 Effective length of database: 1,212,660 Effective search space: 312866280 Effective search space used: 312866280 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)