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= 0001.0566.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 ... 263 3e-72 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 162 1e-41 gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR ... 89 2e-19 gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 67 9e-13 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 = 263 bits (673), Expect = 3e-72, Method: Compositional matrix adjust. Identities = 130/144 (90%), Positives = 135/144 (93%), Gaps = 4/144 (2%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSSPAPEK 60 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQS+PAPEK Sbjct: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEK 60 Query: 61 PETITLGIDAAGKLYWNDQPVSQAEMDTRLAAAAEKKPQPELQLRADKSTRYQTIAELMS 120 PETITLGIDAAGKLYWNDQPVS E+D RL AAA K+PQPELQLRADKSTRYQTIAE+MS Sbjct: 61 PETITLGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMS 120 Query: 121 AAQGAGLTKLGFVTDPQASSKTPA 144 AAQGAGL+KLGFVTDP KTPA Sbjct: 121 AAQGAGLSKLGFVTDP----KTPA 140 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 162 bits (409), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 73/136 (53%), Positives = 103/136 (75%), Gaps = 1/136 (0%) Query: 1 MSFGGFNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSSPAPEK 60 M+ G +D+ + +IN TP+VDVMLVLL+IFIIT P+ HA+K+DLP A S P K Sbjct: 1 MAMGSLSDSDDDFN-PEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKASSQPDQVK 59 Query: 61 PETITLGIDAAGKLYWNDQPVSQAEMDTRLAAAAEKKPQPELQLRADKSTRYQTIAELMS 120 PE+I L IDA+G ++WN++ + E+ R+AAAA+K+PQPEL LRA+++T+Y+ +A++MS 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 = 88.6 bits (218), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 47/131 (35%), Positives = 75/131 (57%) Query: 6 FNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSSPAPEKPETIT 65 ND +IN+TP++DVMLVLL+IFI+T P A+K+ LP A + P + I Sbjct: 4 MNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASKDID 63 Query: 66 LGIDAAGKLYWNDQPVSQAEMDTRLAAAAEKKPQPELQLRADKSTRYQTIAELMSAAQGA 125 + I A G + WN P + E+ + AAA P + + AD+ Y ++A++++ 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 = 66.6 bits (161), Expect = 9e-13, Method: Compositional matrix adjust. Identities = 46/134 (34%), Positives = 75/134 (55%), Gaps = 13/134 (9%) Query: 17 DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSSPAPEKPETITLGIDAAGKL 74 +IN+ P +DV+LV+++ ++T FT AL+L LPTA + A E+P + + +DA G+ Sbjct: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQLTLPTADAPKALEQPFELNIAVDANGRY 71 Query: 75 YWNDQPVS-------QAEMDTRLAAAAEKKPQPELQLRADKSTRYQTIAELMSAAQGAGL 127 N++ +S EM + A+A K P + + AD +QT+ ++ AA+ AG Sbjct: 72 ALNNKRISARDAQGLSEEMQAVVRASASKL-DPVIIINADALATHQTVVNVLEAARMAGY 130 Query: 128 TKLGFVTDPQASSK 141 K+ F QASSK Sbjct: 131 PKVTFAA--QASSK 142 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 58.9 bits (141), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 40/131 (30%), Positives = 69/131 (52%), Gaps = 15/131 (11%) Query: 16 ADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSSPAPE--------KPE---TI 64 ++INV P +DVMLVLL+IF++ P+ T+ ++LPTA S P KP TI Sbjct: 16 SEINVVPYIDVMLVLLIIFMVATPI-TNPSVINLPTAGKSTQPPSDYIEIALKPNSQATI 74 Query: 65 TL-GIDAAGKLYWNDQPVSQAEMDTRLAAAAEKKPQPELQLRADKSTRYQTIAELMSAAQ 123 + G + GK + + ++ RL + P+ + + ADK +Y + +++S A+ Sbjct: 75 RINGPKSGGK--KAETVTGKTDLSERLRKLHDDNPELAVMISADKDIKYDEVVQVISEAK 132 Query: 124 GAGLTKLGFVT 134 G+ ++G T Sbjct: 133 KQGIARVGLAT 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 0.127 0.357 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: 465,703 Number of extensions: 18522 Number of successful extensions: 59 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 60 Number of HSP's successfully gapped: 5 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 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 126 (53.1 bits)