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= 0011.0001.p (129 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspir... 157 2e-40 gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) ... 152 1e-38 gi|300310328|ref|YP_003774420.1| porin signal peptide protein [H... 85 2e-18 gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspir... 80 8e-17 >gi|300313580|ref|YP_003777672.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 387 Score = 157 bits (398), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 84/130 (64%), Positives = 102/130 (78%), Gaps = 9/130 (6%) Query: 1 VYANYNRVKQDLNTASPTALPSKTLGSANKADIYEIGTAYSLTPTLKLLGAVTHTRADFN 60 VYANY+RVKQDL +PT + + TL +A KAD YEIGTAYSL+P+LKLL AV H+RA FN Sbjct: 266 VYANYSRVKQDLK-GTPT-VATATLANAQKADTYEIGTAYSLSPSLKLLAAVDHSRATFN 323 Query: 61 S-SSKGKLTQISLGTDYWLSKRTDLYAFLANIRASDMANSGVYGDATGNAATGGADASQT 119 ++KGKLTQISLG DY+LSKRTDLYAF++N+RASD+ N GV G AT G+DASQT Sbjct: 324 GVNTKGKLTQISLGADYFLSKRTDLYAFVSNMRASDIQNPGVTGGAT------GSDASQT 377 Query: 120 LVAVGVRHKF 129 + G+RHKF Sbjct: 378 AIITGIRHKF 387 >gi|300309527|ref|YP_003773619.1| outer membrane protein (porin) signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 390 Score = 152 bits (383), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 82/139 (58%), Positives = 99/139 (71%), Gaps = 17/139 (12%) Query: 1 VYANYNRVKQDLNT---------ASPTALPSKTLGSANKADIYEIGTAYSLTPTLKLLGA 51 VY N++RVKQDLNT S + ++TL ++NKADIYEIGTAYSL+P+LKLL A Sbjct: 259 VYGNWSRVKQDLNTQANLTAAGVGSLATISNRTLAASNKADIYEIGTAYSLSPSLKLLAA 318 Query: 52 VTHTRADFNS-SSKGKLTQISLGTDYWLSKRTDLYAFLANIRASDMANSGVYGDATGNAA 110 V HTRA F+ S K KLTQ+SLGTDYWLSKRTDLYAFLA +A+D+ N GV A Sbjct: 319 VDHTRAQFDGVSGKAKLTQVSLGTDYWLSKRTDLYAFLAYSKATDLNNPGV-------AD 371 Query: 111 TGGADASQTLVAVGVRHKF 129 + G D +Q VAVG+RHKF Sbjct: 372 SSGTDGNQGAVAVGIRHKF 390 >gi|300310328|ref|YP_003774420.1| porin signal peptide protein [Herbaspirillum seropedicae SmR1] Length = 405 Score = 84.7 bits (208), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 47/115 (40%), Positives = 69/115 (60%), Gaps = 7/115 (6%) Query: 17 PTALPSKTLGSANK--ADIYEIGTAYSLTPTLKLLGAVTHTRADFNSSSKGKLTQISLGT 74 P+ + ++G AN + ++IG +Y L P+L L+ AV HTRA F ++ G+L Q++LG Sbjct: 296 PSDATAFSIGGANHKSSQTFDIGMSYQLMPSLTLMSAVQHTRAKFVGAASGRLLQLNLGA 355 Query: 75 DYWLSKRTDLYAFLANIRASDMANSGVYGDATGNAATGGADASQTLVAVGVRHKF 129 Y LSKRT YA + N+R+SDM N G+ D G D SQT ++ G+ H F Sbjct: 356 KYDLSKRTSAYALVRNLRSSDMYNVGLSKD-----QEPGIDRSQTAISTGLIHTF 405 >gi|300312191|ref|YP_003776283.1| outer membrane porin [Herbaspirillum seropedicae SmR1] Length = 372 Score = 79.7 bits (195), Expect = 8e-17, Method: Compositional matrix adjust. Identities = 48/138 (34%), Positives = 80/138 (57%), Gaps = 17/138 (12%) Query: 1 VYANYNRVKQDLNTASPTALPSKTLG-----SANKADIYEIGTAYSLTPTLKLLGAVTHT 55 ++A ++++++ PT P + G SA +A++ ++G Y+L L LL +V H Sbjct: 243 LFAAWSQIRR------PTQQPLASSGLVAITSATRANVLDVGVDYALDSKLHLLASVIHD 296 Query: 56 RADFN----SSSKGKLTQISLGTDYWLSKRTDLYAFLANIRASDMANSGVYGDATGNAAT 111 RAD + +++G TQ++LG D LSKRTD+YA + +A D+ N G+ A +A Sbjct: 297 RADLSRAAGGATRGSTTQVNLGVDLLLSKRTDVYAMASRQQARDVLNPGIISAAYSSAPA 356 Query: 112 GGADASQTLVAVGVRHKF 129 D+SQ ++ VG+RHKF Sbjct: 357 --DDSSQNVLRVGLRHKF 372 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 0.312 0.126 0.354 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: 315,728 Number of extensions: 10116 Number of successful extensions: 50 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 46 Number of HSP's successfully gapped: 5 Length of query: 129 Length of database: 1,619,870 Length adjustment: 75 Effective length of query: 54 Effective length of database: 1,264,745 Effective search space: 68296230 Effective search space used: 68296230 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: 125 (52.8 bits)