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= 0001.1027.p (144 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ... 282 9e-78 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 64 5e-12 gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR ... 59 2e-10 gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ... 57 6e-10 gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 53 9e-09 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 282 bits (721), Expect = 9e-78, Method: Compositional matrix adjust. Identities = 138/144 (95%), Positives = 144/144 (100%) Query: 1 MAGSSMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSD 60 MAGSSMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSD Sbjct: 1 MAGSSMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSD 60 Query: 61 YIEIALKPNAQATIRINGPKSGGKKAETVTGKTDLAERLRQLHEDNPDLAVMISADKDIK 120 YIEIALKPN+QATIRINGPKSGGKKAETVTGKTDL+ERLR+LH+DNP+LAVMISADKDIK Sbjct: 61 YIEIALKPNSQATIRINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIK 120 Query: 121 YDDVVQVISEAKKQGIARVGLATK 144 YD+VVQVISEAKKQGIARVGLATK Sbjct: 121 YDEVVQVISEAKKQGIARVGLATK 144 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 63.9 bits (154), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 45/132 (34%), Positives = 69/132 (52%), Gaps = 13/132 (9%) Query: 14 FKSEINVVPYIDVMLVLLIIFMVATPITNPSV-INLPTAGKSTQPPSDYIE-IALKPNAQ 71 F EIN P +DVMLVLLIIF++ P+ N +V I+LP A S+QP E I L +A Sbjct: 13 FNPEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKA--SSQPDQVKPESINLSIDAS 70 Query: 72 ATIRINGPKSGGKKAETVTGKTDLAERLRQLHEDNPDLAVMISADKDIKYDDVVQVISEA 131 + N E +L+ R+ + P + + A++ +Y+ V QV+S A Sbjct: 71 GNVFWN---------EEKIDSGELSVRIAAAAQKQPQPELHLRAERTTQYEKVAQVMSAA 121 Query: 132 KKQGIARVGLAT 143 + G+A++G T Sbjct: 122 QSGGLAKIGFVT 133 >gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 135 Score = 58.5 bits (140), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 40/134 (29%), Positives = 67/134 (50%), Gaps = 7/134 (5%) Query: 11 PRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSDYIEIALKPNA 70 P+K K+ + ++P IDVM+ LL+ F++ S+ +P G TQ PS LKP Sbjct: 7 PKKRKARVEIIPMIDVMMFLLVFFVLI------SLNVIPALGLKTQLPSSSTAQDLKPQT 60 Query: 71 QATIRINGPKSGGKKAETVTGKTDLAERLRQLHEDNPDLAVMISADKDIKYDDVVQVISE 130 +A I I + E T L RL +L + L ++I++D+ ++ +V V+ Sbjct: 61 KAVITIAKDEVIQVDGENTTLDA-LTARLDKLRHEGEKLNLIINSDRGVEVQRLVDVMDT 119 Query: 131 AKKQGIARVGLATK 144 KK G + +AT+ Sbjct: 120 LKKGGFDSISIATR 133 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 57.0 bits (136), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 39/129 (30%), Positives = 65/129 (50%), Gaps = 11/129 (8%) Query: 16 SEINVVPYIDVMLVLLIIFMVATPI-TNPSVINLPTAGKSTQPPSDYIEIALKPNAQATI 74 ++INV P +DVMLVLL+IF++ P+ T+ ++LPTA +S P I L +A + Sbjct: 16 ADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTA-QSAPAPEKPETITLGIDAAGKL 74 Query: 75 RINGPKSGGKKAETVTGKTDLAERLRQLHEDNPDLAVMISADKDIKYDDVVQVISEAKKQ 134 N + +L RL P + + ADK +Y + +V+S A+ Sbjct: 75 YWN---------DQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGA 125 Query: 135 GIARVGLAT 143 G++++G T Sbjct: 126 GLSKLGFVT 134 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 53.1 bits (126), Expect = 9e-09, Method: Compositional matrix adjust. Identities = 40/144 (27%), Positives = 73/144 (50%), Gaps = 11/144 (7%) Query: 5 SMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVIN--LPTAG--KSTQPPSD 60 + R GRPR+ EIN++P+IDV+LV++I MV T + + + LPTA K+ + P Sbjct: 2 NFRKGRPRE-DLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQLTLPTADAPKALEQP-- 58 Query: 61 YIEIALKPNAQATIRINGPKSGGKKAETVTGKTDLAERLRQLHEDNPDLAVMISADKDIK 120 E+ + +A +N + + A+ G ++ + + + D ++I+AD Sbjct: 59 -FELNIAVDANGRYALNNKRISARDAQ---GLSEEMQAVVRASASKLDPVIIINADALAT 114 Query: 121 YDDVVQVISEAKKQGIARVGLATK 144 + VV V+ A+ G +V A + Sbjct: 115 HQTVVNVLEAARMAGYPKVTFAAQ 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 0.315 0.133 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: 430,763 Number of extensions: 15939 Number of successful extensions: 49 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 49 Number of HSP's successfully gapped: 5 Length of query: 144 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 67 Effective length of database: 1,255,275 Effective search space: 84103425 Effective search space used: 84103425 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)