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= 0005.0002.p (147 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 ... 261 1e-71 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 158 2e-40 gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR ... 89 1e-19 gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 65 3e-12 gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ... 60 1e-10 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 261 bits (668), Expect = 1e-71, Method: Compositional matrix adjust. Identities = 126/137 (91%), Positives = 131/137 (95%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSNPAPEK 60 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQS PAPEK Sbjct: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK 60 Query: 61 PETITLGIDAAGKLYWNDQPVSEEDMDARLATAAAKKPQPELQLRADKSTRYEMIAEVMS 120 PETITLGIDAAGKLYWNDQPVS E++DARL AA K+PQPELQLRADKSTRY+ IAEVMS Sbjct: 61 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS 120 Query: 121 AAQGAGLTKLGFVTDPK 137 AAQGAGL+KLGFVTDPK Sbjct: 121 AAQGAGLSKLGFVTDPK 137 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 158 bits (400), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 73/136 (53%), Positives = 101/136 (74%), Gaps = 1/136 (0%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSNPAPEK 60 M+ G +D+ + +IN TP+VDVMLVLL+IFIIT P+ HA+K+DLP A S P K Sbjct: 1 MAMGSLSDSDDDF-NPEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKASSQPDQVK 59 Query: 61 PETITLGIDAAGKLYWNDQPVSEEDMDARLATAAAKKPQPELQLRADKSTRYEMIAEVMS 120 PE+I L IDA+G ++WN++ + ++ R+A AA K+PQPEL LRA+++T+YE +A+VMS Sbjct: 60 PESINLSIDASGNVFWNEEKIDSGELSVRIAAAAQKQPQPELHLRAERTTQYEKVAQVMS 119 Query: 121 AAQGAGLTKLGFVTDP 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 = 89.4 bits (220), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 48/131 (36%), Positives = 76/131 (58%) Query: 6 FNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSNPAPEKPETIT 65 ND +IN+TP++DVMLVLL+IFI+T P A+K+ LP A + P + I Sbjct: 4 MNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASKDID 63 Query: 66 LGIDAAGKLYWNDQPVSEEDMDARLATAAAKKPQPELQLRADKSTRYEMIAEVMSAAQGA 125 + I A G + WN P + +++ A + AAA P + + AD+ Y +A+V++ Q Sbjct: 64 ISIQADGTVLWNRVPANLDELRAHVVAAAAAAVPPAVNVYADEQVPYGSVAKVLAGVQAG 123 Query: 126 GLTKLGFVTDP 136 GL+++ FVT+P Sbjct: 124 GLSRINFVTEP 134 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 64.7 bits (156), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 41/125 (32%), Positives = 71/125 (56%), Gaps = 11/125 (8%) Query: 17 DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSNPAPEKPETITLGIDAAGKL 74 +IN+ P +DV+LV+++ ++T FT AL+L LPTA + A E+P + + +DA G+ Sbjct: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQLTLPTADAPKALEQPFELNIAVDANGRY 71 Query: 75 YWNDQPVS-------EEDMDARLATAAAKKPQPELQLRADKSTRYEMIAEVMSAAQGAGL 127 N++ +S E+M A + A+A K P + + AD ++ + V+ AA+ AG Sbjct: 72 ALNNKRISARDAQGLSEEMQA-VVRASASKLDPVIIINADALATHQTVVNVLEAARMAGY 130 Query: 128 TKLGF 132 K+ F Sbjct: 131 PKVTF 135 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 59.7 bits (143), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 38/129 (29%), Positives = 67/129 (51%), Gaps = 11/129 (8%) Query: 16 ADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTA-QSNPAPEKPETITLGIDAAGKL 74 ++INV P +DVMLVLL+IF++ P+ T+ ++LPTA +S P I L ++ + Sbjct: 16 SEINVVPYIDVMLVLLIIFMVATPI-TNPSVINLPTAGKSTQPPSDYIEIALKPNSQATI 74 Query: 75 YWN---------DQPVSEEDMDARLATAAAKKPQPELQLRADKSTRYEMIAEVMSAAQGA 125 N + + D+ RL P+ + + ADK +Y+ + +V+S A+ Sbjct: 75 RINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIKYDEVVQVISEAKKQ 134 Query: 126 GLTKLGFVT 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 0.130 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: 481,875 Number of extensions: 19559 Number of successful extensions: 56 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 54 Number of HSP's successfully gapped: 6 Length of query: 147 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 70 Effective length of database: 1,255,275 Effective search space: 87869250 Effective search space used: 87869250 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: 126 (53.1 bits)