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= 0001.0789.p (411 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 516 e-147 gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspir... 296 3e-81 gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) ... 273 1e-74 gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspir... 228 8e-61 gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspir... 159 4e-40 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 516 bits (1328), Expect = e-147, Method: Compositional matrix adjust. Identities = 267/417 (64%), Positives = 327/417 (78%), Gaps = 18/417 (4%) Query: 1 MKKSILALAVLGAFGGAAHAQSN-ITIYGAVDASLSYTNKIGISGKDAHGNDIAGKDTGG 59 MKKS+LALAVLGAF GAAHAQS+ ITIYGA+DASL+YTNKI GK+ TG Sbjct: 1 MKKSLLALAVLGAFAGAAHAQSSSITIYGAIDASLTYTNKIATDGKN----------TGS 50 Query: 60 QMALDSGLIKGSRLGIKGVEDLGGGLKAIFTIENGFNVDSGDAGQKGVLWGRQATVGLSG 119 A++SGL+KGSRLGIKG EDLGGGLKA+FT+ENGFNVD+G+AGQ ++WGRQ TVGLSG Sbjct: 51 LTAVESGLVKGSRLGIKGSEDLGGGLKAVFTLENGFNVDTGEAGQGKLMWGRQTTVGLSG 110 Query: 120 NFGTVLAGRQKDVLDDVGSITSPGDFGGVVSRVHSLNLDRTNGERVNNSIRYNTPDFNGF 179 NFGTVL GRQ D L+D+G I S G FG V VHS LDRT+G+R+NNSIRYN+P+FNG Sbjct: 111 NFGTVLVGRQNDPLNDIGGIASAGGFG-VPGTVHSKGLDRTDGQRLNNSIRYNSPNFNGL 169 Query: 180 IGSVIYGFGEQAGKTGSGQSFGLGGTYANGPLNVGLGYFQSKMGNAN--ASDVNGASACN 237 S IYGFGEQ G+ G+S GLG Y NGPL++GLGYFQSKMG + +SDVN +ACN Sbjct: 170 SFSGIYGFGEQVGRAVGGRSIGLGSQYVNGPLSLGLGYFQSKMGGGSDGSSDVNAKAACN 229 Query: 238 GPGKN---GDTCLKTWTLAASYQFGPAKVYGSYSHVRLPLTAPRTRFDSRFDSFAAFIDP 294 G G+ GDTCLKTWTLAA+YQFGPAKVYG++SHVRLPL T+ + ++F A D Sbjct: 230 GAGEKDHAGDTCLKTWTLAAAYQFGPAKVYGAFSHVRLPLAKLHTKV-RKDNNFGAMYDA 288 Query: 295 KKLGLYQPAAKGDYTIGGANNESSQTFDIGVNYRLSPALSLISSLQYTRAKFVRTSDGRL 354 K Y P+ ++IGGAN++SSQTFDIG++Y+L P+L+L+S++Q+TRAKFV + GRL Sbjct: 289 KTGTGYNPSDATAFSIGGANHKSSQTFDIGMSYQLMPSLTLMSAVQHTRAKFVGAASGRL 348 Query: 355 LQVNLGAKYELSKRTTTYAVLRNLRSSDMYNVGLSSDRVPGANRGQTGINAGLIHSF 411 LQ+NLGAKY+LSKRT+ YA++RNLRSSDMYNVGLS D+ PG +R QT I+ GLIH+F Sbjct: 349 LQLNLGAKYDLSKRTSAYALVRNLRSSDMYNVGLSKDQEPGIDRSQTAISTGLIHTF 405 >gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 387 Score = 296 bits (757), Expect = 3e-81, Method: Compositional matrix adjust. Identities = 190/424 (44%), Positives = 262/424 (61%), Gaps = 50/424 (11%) Query: 1 MKKSILALAVLGAFGGAAHAQSNITIYGAVDASLSYTNKIGISGKDAHGNDIAGKDTGGQ 60 MKKS+LALAVLGAF GAA AQS++TIYG VD ++Y++K+G + DA+GN TG + Sbjct: 1 MKKSLLALAVLGAFAGAAQAQSSVTIYGIVDTGIAYSSKVGYT--DANGN----AATGSK 54 Query: 61 MALDSGLIKGSRLGIKGVEDLGGGLKAIFTIENGFNVDSG-----DAGQKGVLWGRQATV 115 ++SG+I+GSR+G KGVEDLGGGL A+F +E GF D G DA L+ R++ V Sbjct: 55 FGINSGVIQGSRIGFKGVEDLGGGLSAVFNLETGFTSDDGGLQGSDAVTSSNLFRRKSVV 114 Query: 116 GLSGNFGTVLAGRQKDVLDDVGSITSPGDFGGVVSRVHSLNLDRTNGERVNNSIRYNTPD 175 GLSG FGTVL GRQ D D + + T+ DFGGVV+ S +L+R G R NNS+ Y T + Sbjct: 115 GLSGGFGTVLLGRQTDFADTISAYTAVADFGGVVANSGS-SLNRLQGTRTNNSVSYTTAN 173 Query: 176 FNGFIGSVIYGFGEQAGKTGSGQSFGLGGTYANGPLNVGLGYFQSKMGNANASDVN---- 231 +GF G++IYGFGEQAGKT +GQ++G+GG Y NGPL +G+ Y+QSK G + SD + Sbjct: 174 LSGFTGNLIYGFGEQAGKTSAGQAYGIGGKYDNGPLGLGINYYQSKAG-STPSDTSLIPA 232 Query: 232 --GASACNGPGKNGDTCLKTWTLAASYQFGPAKVYGSYSHVRLPLTAPRTRFDSRFDSFA 289 +A G G+T LK+ + ASYQFGPA+VY +YS V+ L T + Sbjct: 233 AGATNANTALGVAGNTALKSLNVVASYQFGPARVYANYSRVKQDLKGTPTVATATL---- 288 Query: 290 AFIDPKKLGLYQPAAKGDYTIGGANNESSQTFDIGVNYRLSPALSLISSLQYTRAKF--V 347 AN + + T++IG Y LSP+L L++++ ++RA F V Sbjct: 289 -----------------------ANAQKADTYEIGTAYSLSPSLKLLAAVDHSRATFNGV 325 Query: 348 RTSDGRLLQVNLGAKYELSKRTTTYAVLRNLRSSDMYNVGLSSDRVPGANRGQTGINAGL 407 T G+L Q++LGA Y LSKRT YA + N+R+SD+ N G++ G++ QT I G+ Sbjct: 326 NT-KGKLTQISLGADYFLSKRTDLYAFVSNMRASDIQNPGVTGG-ATGSDASQTAIITGI 383 Query: 408 IHSF 411 H F Sbjct: 384 RHKF 387 >gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 390 Score = 273 bits (699), Expect = 1e-74, Method: Compositional matrix adjust. Identities = 182/419 (43%), Positives = 253/419 (60%), Gaps = 37/419 (8%) Query: 1 MKKSILALAVLGAFGGAAHAQSNITIYGAVDASLSYTNKIGISGKDAHGNDIAGKDTGGQ 60 MKKS+LALAVLGAF GAA AQS++TIYG VD + Y +K+ TG + Sbjct: 1 MKKSLLALAVLGAFAGAAQAQSSVTIYGIVDTGVVYQSKVAT----------PTGGTGSK 50 Query: 61 MALDSGLIKGSRLGIKGVEDLGGGLKAIFTIENGFNVDSG---DAGQKGVLWGRQATVGL 117 +L+SG+I+GSR+G KG EDLGGGL A+F +E GF+ D+G D+ L+ R++ VGL Sbjct: 51 FSLNSGVIQGSRIGFKGTEDLGGGLSAVFNLEAGFSNDTGALDDSKTSNTLFRRKSVVGL 110 Query: 118 SGNFGTVLAGRQKDVLDDVGSITSPGDFGGVVSRVHSLNLDRTNGERVNNSIRYNTPDFN 177 +GNFG+VL GRQ D D + S TS DFGG NLDR G R NNSI Y T + N Sbjct: 111 AGNFGSVLLGRQTDFADTISSYTSVQDFGGWTGAAGH-NLDRLEGTRTNNSISYTTANLN 169 Query: 178 GFIGSVIYGFGEQAGKTGSGQSFGLGGTYANGPLNVGLGYFQSKMGN--ANAS--DVNGA 233 GF G+++YGFGE AG+T +GQ+FG+GG Y NGPL +G+ Y+QSK G+ A+AS G Sbjct: 170 GFTGNLMYGFGETAGQTSAGQAFGVGGKYDNGPLGLGINYYQSKAGSTPADASLLAATGT 229 Query: 234 SACNGPGKNGDTCLKTWTLAASYQFGPAKVYGSYSHVRLPLTAPRTRFDSRFDSFAAFID 293 + NG T K +AASYQFGPA+VYG++S V+ L +++ + AA Sbjct: 230 NQFTNGTNNGSTAQKVLNVAASYQFGPARVYGNWSRVKQDL-------NTQANLTAA--- 279 Query: 294 PKKLGLYQPAAKGDYTIGGANNESSQTFDIGVNYRLSPALSLISSLQYTRAKFVRTS-DG 352 G+ A + T+ +N + ++IG Y LSP+L L++++ +TRA+F S Sbjct: 280 ----GVGSLATISNRTLAASNK--ADIYEIGTAYSLSPSLKLLAAVDHTRAQFDGVSGKA 333 Query: 353 RLLQVNLGAKYELSKRTTTYAVLRNLRSSDMYNVGLSSDRVPGANRGQTGINAGLIHSF 411 +L QV+LG Y LSKRT YA L +++D+ N G++ N+G + G+ H F Sbjct: 334 KLTQVSLGTDYWLSKRTDLYAFLAYSKATDLNNPGVADSSGTDGNQGAVAV--GIRHKF 390 >gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 372 Score = 228 bits (581), Expect = 8e-61, Method: Compositional matrix adjust. Identities = 153/397 (38%), Positives = 206/397 (51%), Gaps = 59/397 (14%) Query: 24 ITIYGAVDASLSYTNKIGISGKDAHGNDIAGKDTGGQMALDSGLIKGSRLGIKGVEDLGG 83 +T+YG +D SL YT+K+G D G + +LDSG SR+G++G E+LG Sbjct: 26 VTVYGVIDMSLVYTSKVG-------------PDNGSRASLDSGDAMASRIGLRGREELGD 72 Query: 84 GLKAIFTIENGFNVDSGDAGQKGVLWGRQATVGLSGNFGTVLAGRQKDVLDDVG-SITSP 142 GL AIF +E GF D G G L+ R++ VGL+G FGT+ GRQ D L+++G TS Sbjct: 73 GLAAIFQLETGFAGDDGAMATPGTLFDRKSVVGLAGRFGTLTVGRQTDYLEEIGQQYTSF 132 Query: 143 GDF-GGVVSRVHSLNLDRTNGERVNNSIRYNTPDFNGFIGSVIYGFGEQAGKTGSGQSFG 201 F GG V H +LDR G R NNS+R++T ++ G GS YG GE AG T SGQS G Sbjct: 133 QIFGGGGVRAAHFNSLDRITGARSNNSLRFDTAEYGGLRGSFYYGAGEVAGSTRSGQSLG 192 Query: 202 LGGTYANGPLNVGLGYFQSKMGNANASDVNGASACNGPGKNGDTCLKTWTLAASYQFGPA 261 +GG + G + VG YFQSK+ ASD P + GDT LKT+TL ASYQ GPA Sbjct: 193 VGGNFRRGNVGVGAAYFQSKL----ASDAL-------PARAGDTELKTFTLGASYQAGPA 241 Query: 262 KVYGSYSHVRLPLTAPRTRFDSRFDSFAAFIDPKKLGLYQPAAKGDYTIGGANNESSQTF 321 K++ ++S +R P P A+ G I A + Sbjct: 242 KLFAAWSQIRRPTQQP------------------------LASSGLVAITSATR--ANVL 275 Query: 322 DIGVNYRLSPALSLISSLQYTRAKFVR----TSDGRLLQVNLGAKYELSKRTTTYAVLRN 377 D+GV+Y L L L++S+ + RA R + G QVNLG LSKRT YA+ Sbjct: 276 DVGVDYALDSKLHLLASVIHDRADLSRAAGGATRGSTTQVNLGVDLLLSKRTDVYAMASR 335 Query: 378 LRSSDMYNVGLSS---DRVPGANRGQTGINAGLIHSF 411 ++ D+ N G+ S P + Q + GL H F Sbjct: 336 QQARDVLNPGIISAAYSSAPADDSSQNVLRVGLRHKF 372 >gi|300311557|ref|YP_003775649.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 374 Score = 159 bits (401), Expect = 4e-40, Method: Compositional matrix adjust. Identities = 139/395 (35%), Positives = 184/395 (46%), Gaps = 90/395 (22%) Query: 15 GGAAHAQSNITIYGAVDASLSYTNKIGISGKDAHGNDIAGKDTGGQMALDSGLIKGSRLG 74 GGAA AQSN+TIYG VD S+ Y +S +A GN + +D+G I SR+G Sbjct: 16 GGAAFAQSNVTIYGIVDTSIHY-----LSNANAQGNS--------NVRMDNGAIANSRIG 62 Query: 75 IKGVEDLGGGLKAIFTIENGFNVDSGDAGQKGVLWGRQATVGLSGNFGTVLAGRQK---- 130 KG EDLGGGLKA+F +ENGF+ D+G Q G L+GRQ+ VGL G FG V GRQ Sbjct: 63 FKGTEDLGGGLKAMFQLENGFSSDTGAMQQGGSLFGRQSWVGLQGGFGKVRVGRQNTPLF 122 Query: 131 DVLDD------VGSITSPGDFGGVVSRVHSLNLDRTNGERVNNSIRYNTPDFNGFIGSVI 184 D+L D VG+ S S V S N+ R +G DF S Sbjct: 123 DLLADHFDPLTVGNYASNSWLPAAASLVRSPNMLRYDG------------DFGPVAASAS 170 Query: 185 YGFGEQAGKTGSGQSFGLGGTYANGPLNVGLGYFQSKMGNANASDVNGASACNGPGKNGD 244 + FGE+AG +G F Y GPL +G GY Q+ S+ N K+ Sbjct: 171 WAFGEKAGSVRTGSQFSSALRYTAGPLALGGGYQQT------------VSSTNSSLKH-- 216 Query: 245 TCLKTWTLAASYQFGPAKVYGSYSHVRLPLTAPRTRFDSRFDSFAAFIDPKKLGLYQPAA 304 TW L+ASY FG AKV+G + +++ D L AA Sbjct: 217 ---TTWNLSASYDFGVAKVFGGWLNIK---------------------DDSGLTGSVMAA 252 Query: 305 KGDY-----TIGGANNESSQT------FDIGVNYRLSPALSLISSLQYTRAK---FVRT- 349 GD T G ANN S+ F +G +Y+ + AL+L + Y R+K +V T Sbjct: 253 DGDVSNGWTTAGAANNGSTGVKRKDNGFFLGSSYKATNALTLTGAFYYDRSKNVSYVSTG 312 Query: 350 --SDGRLLQVNLGAKYELSKRTTTYAVLRNLRSSD 382 DG+ + A Y LSKRT Y + ++ D Sbjct: 313 NVGDGKRYTLVGWADYALSKRTQLYTTIDYNKAKD 347 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 0.135 0.393 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: 1,362,053 Number of extensions: 65247 Number of successful extensions: 201 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 147 Number of HSP's successfully gapped: 16 Length of query: 411 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 323 Effective length of database: 1,203,190 Effective search space: 388630370 Effective search space used: 388630370 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: 132 (55.5 bits)