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= 0011.0121.p (148 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ... 303 4e-84 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 162 7e-42 gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR ... 94 5e-21 gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 70 9e-14 gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ... 59 2e-10 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 303 bits (776), Expect = 4e-84, Method: Compositional matrix adjust. Identities = 148/148 (100%), Positives = 148/148 (100%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK 60 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK Sbjct: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK 60 Query: 61 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS 120 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS Sbjct: 61 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS 120 Query: 121 AAQGAGLSKLGFVTDPKTPAHVQEKKEN 148 AAQGAGLSKLGFVTDPKTPAHVQEKKEN Sbjct: 121 AAQGAGLSKLGFVTDPKTPAHVQEKKEN 148 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 162 bits (411), Expect = 7e-42, Method: Compositional matrix adjust. Identities = 76/136 (55%), Positives = 103/136 (75%), Gaps = 1/136 (0%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK 60 M+ G +D+ + +IN TP+VDVMLVLL+IFIIT P+ HA+K+DLP A S P K Sbjct: 1 MAMGSLSDSDDDFN-PEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKASSQPDQVK 59 Query: 61 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS 120 PE+I L IDA+G ++WN++ + S EL R+ AAA KQPQPEL LRA+++T+Y+ +A+VMS Sbjct: 60 PESINLSIDASGNVFWNEEKIDSGELSVRIAAAAQKQPQPELHLRAERTTQYEKVAQVMS 119 Query: 121 AAQGAGLSKLGFVTDP 136 AAQ GL+K+GFVTDP Sbjct: 120 AAQSGGLAKIGFVTDP 135 >gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 139 Score = 94.0 bits (232), Expect = 5e-21, Method: Compositional matrix adjust. Identities = 51/131 (38%), Positives = 77/131 (58%) Query: 6 FNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEKPETIT 65 ND +IN+TP++DVMLVLL+IFI+T P A+K+ LP A + P + I Sbjct: 4 MNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASKDID 63 Query: 66 LGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGA 125 + I A G + WN P + +EL A + AAA P + + AD+ Y ++A+V++ Q Sbjct: 64 ISIQADGTVLWNRVPANLDELRAHVVAAAAAAVPPAVNVYADEQVPYGSVAKVLAGVQAG 123 Query: 126 GLSKLGFVTDP 136 GLS++ FVT+P Sbjct: 124 GLSRINFVTEP 134 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 69.7 bits (169), Expect = 9e-14, Method: Compositional matrix adjust. Identities = 44/125 (35%), Positives = 73/125 (58%), Gaps = 11/125 (8%) Query: 17 DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSAPAPEKPETITLGIDAAGKL 74 +IN+ P +DV+LV+++ ++T FT AL+L LPTA + A E+P + + +DA G+ Sbjct: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQLTLPTADAPKALEQPFELNIAVDANGRY 71 Query: 75 YWNDQPVS-------SEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGAGL 127 N++ +S SEE+ A + A+A K P + + AD +QT+ V+ AA+ AG Sbjct: 72 ALNNKRISARDAQGLSEEMQAVVRASASKL-DPVIIINADALATHQTVVNVLEAARMAGY 130 Query: 128 SKLGF 132 K+ F Sbjct: 131 PKVTF 135 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 58.5 bits (140), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 38/129 (29%), Positives = 66/129 (51%), Gaps = 11/129 (8%) Query: 16 ADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTA-QSAPAPEKPETITLGIDAAGKL 74 ++INV P +DVMLVLL+IF++ P+ T+ ++LPTA +S P I L ++ + Sbjct: 16 SEINVVPYIDVMLVLLIIFMVATPI-TNPSVINLPTAGKSTQPPSDYIEIALKPNSQATI 74 Query: 75 YWN---------DQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGA 125 N + +L RL P+ + + ADK +Y + +V+S A+ Sbjct: 75 RINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIKYDEVVQVISEAKKQ 134 Query: 126 GLSKLGFVT 134 G++++G T Sbjct: 135 GIARVGLAT 143 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 0.314 0.129 0.364 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: 485,428 Number of extensions: 19719 Number of successful extensions: 59 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 59 Number of HSP's successfully gapped: 6 Length of query: 148 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 71 Effective length of database: 1,255,275 Effective search space: 89124525 Effective search space used: 89124525 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 (22.0 bits) S2: 126 (53.1 bits)