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= 0004.0011.p (379 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 138 6e-34 gi|300313813|ref|YP_003777905.1| transmembrane outer membrane po... 114 1e-26 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 102 4e-23 gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) ... 99 8e-22 gi|300313291|ref|YP_003777383.1| porin transmembrane protein [He... 98 1e-21 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 138 bits (348), Expect = 6e-34, Method: Compositional matrix adjust. Identities = 127/383 (33%), Positives = 184/383 (48%), Gaps = 46/383 (12%) Query: 18 GNASAQSSVTVYGLIDATISTTNNANANGARLTGISTAWFSGNRLGFQGKEDLGGGTGAI 77 G A AQS+VT+YG++D +I +NANA G + + +R+GF+G EDLGGG A+ Sbjct: 17 GAAFAQSNVTIYGIVDTSIHYLSNANAQGNSNVRMDNGAIANSRIGFKGTEDLGGGLKAM 76 Query: 78 FKLEAEYLVATGAMDTPGVLFNRDSWVGLQNNETFGKVTIGRQNTLVRDFSQIYGDAYGS 137 F+LE + TGAM G LF R SWVGLQ FGKV +GRQNT + D + D + Sbjct: 77 FQLENGFSSDTGAMQQGGSLFGRQSWVGLQGG--FGKVRVGRQNTPLFD---LLADHFDP 131 Query: 138 SKLGYEEGGFTNNNNFKQLIFYSGSATGTRYDNGVVWKKVFNNGIVVGAGYQFGEVAGAM 197 +G N+ + +A+ R N + + F + A + FGE AG++ Sbjct: 132 LTVG----------NYASNSWLPAAASLVRSPNMLRYDGDFGP-VAASASWAFGEKAGSV 180 Query: 198 NSGTTKAFALGYNGSNYVISGFYNE--ANTNNKLNSSTEKHKAYSLGGSYIMDLVRLNAG 255 +G+ + AL Y + G Y + ++TN+ L KH ++L SY + ++ G Sbjct: 181 RTGSQFSSALRYTAGPLALGGGYQQTVSSTNSSL-----KHTTWNLSASYDFGVAKVFGG 235 Query: 256 YFHYTAEQGALGT------RTDNAWTV--SAKLTPQGVMDYELGY---QVMKAKNA---- 300 + + + G G+ N WT +A GV + G+ KA NA Sbjct: 236 WLNIKDDSGLTGSVMAADGDVSNGWTTAGAANNGSTGVKRKDNGFFLGSSYKATNALTLT 295 Query: 301 -AISSDGSSTLNAFSDATNSTVTGSGKKATLYASAFYHLSKRTELYVAADYMKLTDN--Y 357 A D S ++ S G GK+ TL A Y LSKRT+LY DY K D Y Sbjct: 296 GAFYYDRSKNVSYVSTGN----VGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKDAAVY 351 Query: 358 RV-GSANGFKNQTELAVGMRTRF 379 + SANG + T + VG+R F Sbjct: 352 ELTNSANGKNSLTTVGVGIRHIF 374 >gi|300313813|ref|YP_003777905.1| transmembrane outer membrane porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 354 Score = 114 bits (286), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 116/381 (30%), Positives = 181/381 (47%), Gaps = 62/381 (16%) Query: 18 GNASAQSSVTVYGLIDATISTTNNANANGA-RLTGISTAWFSGNRLGFQGKEDLGGGTGA 76 G+ AQSSVT+YGL+D + NNA NGA +T +++ + +R+GF+G EDLGGG A Sbjct: 17 GSVQAQSSVTIYGLVDTGVEYLNNAGPNGAGSVTRMTSGATNTSRIGFRGTEDLGGGLKA 76 Query: 77 IFKLEAEYLVATGAMD-TPGVLFNRDSWVGLQNNETFGKVTIGRQNTLVRDFSQIYGDAY 135 +F+LE + + G+ D LFNR S VGL+ FG+V GR + DF Sbjct: 77 LFQLENGFKLDNGSFDGDANQLFNRQSTVGLEGG--FGRVVAGRSYSTTYDF-------- 126 Query: 136 GSSKLG-YEEGGFTNNNNFKQLIFYSGSATGTRYD-------NGVVWKKVFNNGIVVGAG 187 LG ++ G++ N ++ + ATG R D N V ++ F +G+ +GA Sbjct: 127 ----LGPFDPMGYSANYSWAT----TAGATGNRKDGMPTGVSNLVKYQGEF-SGVKIGAM 177 Query: 188 YQFGEVAGAMNSGTTKAFALGYNGSNYVISGFYNEANTNNKLNSSTEKHKAYSLGGSY-I 246 Y FGEVAG +G LG+ + + Y+ N+ N+ ++ + L Y Sbjct: 178 YGFGEVAGETRNGAKYGVGLGWGTGPFSVVATYDRNNSATATNTPYDRATSAHLAAGYQP 237 Query: 247 MDLVRLNAGYFHY--TAEQGALGTRTDNAWTVSA-KLTPQGVMDYELGYQVMKAKNAAIS 303 + + N GY +Y + GA R+D W +A K TP + + YQ + KN A Sbjct: 238 SEAWKFNLGYRYYKKSLATGAADLRSDFFWGGAAYKFTPAMTLIGAIYYQNI--KNVAND 295 Query: 304 SDGSSTLNAFSDATNSTVTGSGKKATLYASAF-YHLSKRTELYVAADYMKLTDNYRVGSA 362 +D +Y+ Y +SKRT+LY++ Y K + VG + Sbjct: 296 AD----------------------PIMYSLRLKYAMSKRTDLYLSTAYAKAKNGQLVGLS 333 Query: 363 N---GF-KNQTELAVGMRTRF 379 G+ +Q + +GM+ RF Sbjct: 334 RDDAGYGSSQFGMTLGMQHRF 354 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 102 bits (255), Expect = 4e-23, Method: Compositional matrix adjust. Identities = 117/408 (28%), Positives = 171/408 (41%), Gaps = 75/408 (18%) Query: 1 MKKSLLSIAMLGAVASYGNASAQSS-VTVYGLIDATISTTNNANANG---ARLTGISTAW 56 MKKSLL++A+LGA A G A AQSS +T+YG IDA+++ TN +G LT + + Sbjct: 1 MKKSLLALAVLGAFA--GAAHAQSSSITIYGAIDASLTYTNKIATDGKNTGSLTAVESGL 58 Query: 57 FSGNRLGFQGKEDLGGGTGAIFKLEAEYLVATGAMDTPGVLFNRDSWVGLQNNETFGKVT 116 G+RLG +G EDLGGG A+F LE + V TG +++ R + VGL N FG V Sbjct: 59 VKGSRLGIKGSEDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGLSGN--FGTVL 116 Query: 117 IGRQNTLVRDFSQIYGDAYGSSKLGYEEGGFTNNNNFKQLIFYSGSATGTRYDNGVVWKK 176 +GRQN + D I +S G+ G ++ + G R +N + + Sbjct: 117 VGRQNDPLNDIGGI------ASAGGFGVPGTVHSKGLDR-------TDGQRLNNSIRYNS 163 Query: 177 VFNNGIVVGAGYQFGEVAGAMNSGTTKAFALGY-NGSNYVISGFY-----------NEAN 224 NG+ Y FGE G G + Y NG + G++ ++ N Sbjct: 164 PNFNGLSFSGIYGFGEQVGRAVGGRSIGLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVN 223 Query: 225 TNNKLNSSTEKH-------KAYSLGGSYIMDLVRLNAGYFHYTAEQGALGT--RTDN--- 272 N + EK K ++L +Y ++ + H L T R DN Sbjct: 224 AKAACNGAGEKDHAGDTCLKTWTLAAAYQFGPAKVYGAFSHVRLPLAKLHTKVRKDNNFG 283 Query: 273 -----------------AWTV-SAKLTPQGVMDYELGYQVMKAKNAAISSDGSSTLNAFS 314 A+++ A D + YQ+M S TL + Sbjct: 284 AMYDAKTGTGYNPSDATAFSIGGANHKSSQTFDIGMSYQLMP----------SLTLMSAV 333 Query: 315 DATNSTVTG--SGKKATLYASAFYHLSKRTELYVAADYMKLTDNYRVG 360 T + G SG+ L A Y LSKRT Y ++ +D Y VG Sbjct: 334 QHTRAKFVGAASGRLLQLNLGAKYDLSKRTSAYALVRNLRSSDMYNVG 381 >gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 390 Score = 98.6 bits (244), Expect = 8e-22, Method: Compositional matrix adjust. Identities = 133/421 (31%), Positives = 182/421 (43%), Gaps = 73/421 (17%) Query: 1 MKKSLLSIAMLGAVASYGNASAQSSVTVYGLIDATI----STTNNANANGARLTGISTAW 56 MKKSLL++A+LGA A A AQSSVT+YG++D + G++ + +++ Sbjct: 1 MKKSLLALAVLGAFAG--AAQAQSSVTIYGIVDTGVVYQSKVATPTGGTGSKFS-LNSGV 57 Query: 57 FSGNRLGFQGKEDLGGGTGAIFKLEAEYLVATGAMD---TPGVLFNRDSWVGLQNNETFG 113 G+R+GF+G EDLGGG A+F LEA + TGA+D T LF R S VGL N FG Sbjct: 58 IQGSRIGFKGTEDLGGGLSAVFNLEAGFSNDTGALDDSKTSNTLFRRKSVVGLAGN--FG 115 Query: 114 KVTIGRQNTLVRDFSQIYGDAYGSSKLGYEEGGFTN--NNNFKQLIFYSGSATGTRYDNG 171 V +GRQ DF+ D S + GG+T +N +L GTR +N Sbjct: 116 SVLLGRQT----DFA----DTISSYTSVQDFGGWTGAAGHNLDRL-------EGTRTNNS 160 Query: 172 VVWKKVFNNGIVVGAGYQFGEVAGAMNSGTT---------KAFALGYN------GSNYVI 216 + + NG Y FGE AG ++G LG N GS Sbjct: 161 ISYTTANLNGFTGNLMYGFGETAGQTSAGQAFGVGGKYDNGPLGLGINYYQSKAGSTPAD 220 Query: 217 SGFYNEANTN---NKLNSSTEKHKAYSLGGSYIMDLVRLNAGYFHYTAEQGALGTRTDNA 273 + TN N N+ + K ++ SY R+ + +R Sbjct: 221 ASLLAATGTNQFTNGTNNGSTAQKVLNVAASYQFGPARVYGNW-----------SRVKQD 269 Query: 274 WTVSAKLTPQGVMDYE-LGYQVMKAKN--------AAISSDGSSTLNAFSDATNSTVTGS 324 A LT GV + + + A N A S S L A D T + G Sbjct: 270 LNTQANLTAAGVGSLATISNRTLAASNKADIYEIGTAYSLSPSLKLLAAVDHTRAQFDGV 329 Query: 325 GKKATLYASAF---YHLSKRTELYVAADYMKLTD--NYRVGSANGFK-NQTELAVGMRTR 378 KA L + Y LSKRT+LY Y K TD N V ++G NQ +AVG+R + Sbjct: 330 SGKAKLTQVSLGTDYWLSKRTDLYAFLAYSKATDLNNPGVADSSGTDGNQGAVAVGIRHK 389 Query: 379 F 379 F Sbjct: 390 F 390 >gi|300313291|ref|YP_003777383.1| porin transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 365 Score = 98.2 bits (243), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 114/392 (29%), Positives = 171/392 (43%), Gaps = 85/392 (21%) Query: 23 QSSVTVYGLIDATISTTNNANANGA---RLTGISTAWFSGNRLGFQGKEDLGGGTGAIFK 79 QSSVT+YG+ID + T NANANG ++ ++ ++ S R+GF+G EDLGGG A+F Sbjct: 24 QSSVTIYGIIDTGVVYTTNANANGNSVFKMPSLTGSFPS--RIGFKGTEDLGGGLQAMFV 81 Query: 80 LEAEYLVATGAMDTPGVLFNRDSWVGLQNNETFGKVTIGRQNTLVRDFSQIYGDAYGSSK 139 LE+ + TGAM G LF R S+VGL+N ++G++ +GRQ + SQ+ D G + Sbjct: 82 LESGFAPDTGAMGQGGRLFGRQSYVGLKN--SWGQLMLGRQVNMTY-LSQLKTDVMGPN- 137 Query: 140 LGYEEGGFTNNNNFKQLIFYSGSA----TGTRYDNGVVWKKVFNNGIVVGAGYQF----- 190 +F GS R DN + + F +G VGA Y F Sbjct: 138 -----------------LFAIGSIDAYLPNARSDNAIGYLGNF-SGFTVGATYSFGRDAA 179 Query: 191 -----------GEVAGAMNSGTTKAFALGYNGSNYVISG----FYNEANTNNKLNSSTEK 235 GEVAG + LGY+G + ++ Y +N + SS Sbjct: 180 GPAGPAATNCPGEVAGNSKACRQVTALLGYDGKGWGVTSSYDILYGNTGASNGMTSSDNT 239 Query: 236 HKAYSLGGSYIMDLVRLNAGYFHYTAEQGALGTRTDNA---WTVSAKLTPQGVMDYELGY 292 + +L G +++ V++ G A T TD+ VS L+ V+D ++ Sbjct: 240 DQRVTLNGYFMLGDVKIGGGVVDRRTRAAA-NTNTDSDLYYLGVSYPLSVALVLDAQVSR 298 Query: 293 QVMKAKNAAISSDGSSTLNAFSDATNSTVTGSGKKATLYASAFYHLSKRTELYVAADYMK 352 +K N+ +D T S A Y+LSKRT +Y + Y+K Sbjct: 299 LDVK--------------NSPNDVTLSV-----------ARLTYNLSKRTAVYGSLGYIK 333 Query: 353 LTDNYRV-----GSANGFKNQTELAVGMRTRF 379 V G+ KNQ + G+R F Sbjct: 334 NGGTSSVALDAGGTVGAGKNQLGVMTGIRHTF 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 0.313 0.129 0.369 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: 1,136,456 Number of extensions: 48549 Number of successful extensions: 161 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 119 Number of HSP's successfully gapped: 14 Length of query: 379 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 292 Effective length of database: 1,207,925 Effective search space: 352714100 Effective search space used: 352714100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 131 (55.1 bits)