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= 0001.0969.p (142 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 268 1e-73 gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ... 65 2e-12 gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ... 55 2e-09 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 55 3e-09 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 268 bits (685), Expect = 1e-73, Method: Compositional matrix adjust. Identities = 128/142 (90%), Positives = 138/142 (97%) Query: 1 MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTADAQKALEQPFE 60 MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQ+TLPTADA KALEQPFE Sbjct: 1 MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQLTLPTADAPKALEQPFE 60 Query: 61 ISIAVDANGRYAINNKRIAARDAQGLSDEMQAAVKGSGSKLDPVVIINADALATHQTVIN 120 ++IAVDANGRYA+NNKRI+ARDAQGLS+EMQA V+ S SKLDPV+IINADALATHQTV+N Sbjct: 61 LNIAVDANGRYALNNKRISARDAQGLSEEMQAVVRASASKLDPVIIINADALATHQTVVN 120 Query: 121 VLEAARMAGYPKVTFAAQSSSK 142 VLEAARMAGYPKVTFAAQ+SSK Sbjct: 121 VLEAARMAGYPKVTFAAQASSK 142 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 65.1 bits (157), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 40/125 (32%), Positives = 73/125 (58%), Gaps = 11/125 (8%) Query: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQITLPTADAQKALEQPFEISIAVDANGRY 71 +IN+ P +DV+LV+++ ++T FT AL++ LPTA + A E+P I++ +DA G+ Sbjct: 17 DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSAPAPEKPETITLGIDAAGKL 74 Query: 72 AINNKRIAARDAQGLSDEMQAAVK-GSGSKLDPVVIINADALATHQTVINVLEAARMAGY 130 N++ ++ S+E+ A + +G + P + + AD +QT+ V+ AA+ AG Sbjct: 75 YWNDQPVS-------SEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGAGL 127 Query: 131 PKVTF 135 K+ F Sbjct: 128 SKLGF 132 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 55.5 bits (132), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 43/144 (29%), Positives = 73/144 (50%), Gaps = 11/144 (7%) Query: 2 NFRKGRPRE-DLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTADAQKALEQP-- 58 + R GRPR+ EIN++P+IDV+LV++I MV T + + I LPTA K+ + P Sbjct: 5 SMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSV--INLPTAG--KSTQPPSD 60 Query: 59 -FEISIAVDANGRYAINNKRIAARDAQ---GLSDEMQAAVKGSGSKLDPVVIINADALAT 114 EI++ ++ IN + + A+ G +D + K + V+I+AD Sbjct: 61 YIEIALKPNSQATIRINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIK 120 Query: 115 HQTVINVLEAARMAGYPKVTFAAQ 138 + V+ V+ A+ G +V A + Sbjct: 121 YDEVVQVISEAKKQGIARVGLATK 144 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 54.7 bits (130), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 38/130 (29%), Positives = 67/130 (51%), Gaps = 7/130 (5%) Query: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTADAQKALEQPFEISIAVDANGRYA 72 EIN P +DV+LV++I ++T A++I LP A +Q +P I++++DA+G Sbjct: 16 EINTTPLVDVMLVLLIIFIITIPVMNH-AVKIDLPKASSQPDQVKPESINLSIDASGNVF 74 Query: 73 INNKRIAARDAQGLSDEMQAAVKGSGSKLDPVVIINADALATHQTVINVLEAARMAGYPK 132 N ++I D+ LS + AA + + P + + A+ ++ V V+ AA+ G K Sbjct: 75 WNEEKI---DSGELSVRIAAAAQ---KQPQPELHLRAERTTQYEKVAQVMSAAQSGGLAK 128 Query: 133 VTFAAQSSSK 142 + F K Sbjct: 129 IGFVTDPDKK 138 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 0.319 0.132 0.356 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: 379,042 Number of extensions: 13431 Number of successful extensions: 57 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 58 Number of HSP's successfully gapped: 5 Length of query: 142 Length of database: 1,619,870 Length adjustment: 76 Effective length of query: 66 Effective length of database: 1,260,010 Effective search space: 83160660 Effective search space used: 83160660 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 126 (53.1 bits)