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= 0012.0020.p (149 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... 226 9e-61 gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ... 65 2e-12 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 58 3e-10 gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR ... 57 8e-10 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 226 bits (575), Expect = 9e-61, Method: Compositional matrix adjust. Identities = 112/149 (75%), Positives = 126/149 (84%), Gaps = 7/149 (4%) Query: 1 MNFRKGRAREELEINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTANAEKALEQPFE 60 MNFRKGR RE+LEINLIPFIDVLLVIVIFLMVTTTYSKFTALQ+TLPTA+A KALEQPFE Sbjct: 1 MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQLTLPTADAPKALEQPFE 60 Query: 61 LNVAVDAQGRYAINNVQIAARDAAGLARELQSAVQANSANTDTSGGKPDPVVIINADALA 120 LN+AVDA GRYA+NN +I+ARDA GL+ E+Q+ V+A S K DPV+IINADALA Sbjct: 61 LNIAVDANGRYALNNKRISARDAQGLSEEMQAVVRA-------SASKLDPVIIINADALA 113 Query: 121 AHQTVINVLEAARTAGFAKVTFAAQTGGK 149 HQTV+NVLEAAR AG+ KVTFAAQ K Sbjct: 114 THQTVVNVLEAARMAGYPKVTFAAQASSK 142 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 65.5 bits (158), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 40/131 (30%), Positives = 73/131 (55%), Gaps = 16/131 (12%) Query: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQITLPTANAEKALEQPFELNVAVDAQGRY 71 +IN+ P +DV+LV+++ ++T FT AL++ LPTA + A E+P + + +DA G+ Sbjct: 17 DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSAPAPEKPETITLGIDAAGKL 74 Query: 72 AINNVQIAARDAAGLARELQSAVQANSANTDTSGGKPDPVVIINADALAAHQTVINVLEA 131 N+ +++ EL + + A +G +P P + + AD +QT+ V+ A Sbjct: 75 YWNDQPVSSE-------ELDARLTA------AAGKQPQPELQLRADKSTRYQTIAEVMSA 121 Query: 132 ARTAGFAKVTF 142 A+ AG +K+ F Sbjct: 122 AQGAGLSKLGF 132 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 58.2 bits (139), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 38/137 (27%), Positives = 69/137 (50%), Gaps = 14/137 (10%) Query: 13 EINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTANAEKALEQPFELNVAVDAQGRYA 72 EIN P +DV+LV++I ++T A++I LP A+++ +P +N+++DA G Sbjct: 16 EINTTPLVDVMLVLLIIFIITIPVMNH-AVKIDLPKASSQPDQVKPESINLSIDASGNVF 74 Query: 73 INNVQIAARDAAGLARELQSAVQANSANTDTSGGKPDPVVIINADALAAHQTVINVLEAA 132 N +I D+ L+ + +A Q +P P + + A+ ++ V V+ AA Sbjct: 75 WNEEKI---DSGELSVRIAAAAQK----------QPQPELHLRAERTTQYEKVAQVMSAA 121 Query: 133 RTAGFAKVTFAAQTGGK 149 ++ G AK+ F K Sbjct: 122 QSGGLAKIGFVTDPDKK 138 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 56.6 bits (135), Expect = 8e-10, Method: Compositional matrix adjust. Identities = 42/148 (28%), Positives = 75/148 (50%), Gaps = 12/148 (8%) Query: 2 NFRKGRARE-ELEINLIPFIDVLLVIVIFLMVTTTYSKFTALQITLPTANAEKALEQP-- 58 + R GR R+ + EIN++P+IDV+LV++I MV T + + I LPTA K+ + P Sbjct: 5 SMRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSV--INLPTAG--KSTQPPSD 60 Query: 59 -FELNVAVDAQGRYAINNVQIAARDAAGLARELQSAVQANSANTDTSGGKPDPVVIINAD 117 E+ + ++Q IN + + A + + + + + D P+ V+I+AD Sbjct: 61 YIEIALKPNSQATIRINGPKSGGKKAETVTGKTDLSERLRKLHDDN----PELAVMISAD 116 Query: 118 ALAAHQTVINVLEAARTAGFAKVTFAAQ 145 + V+ V+ A+ G A+V A + Sbjct: 117 KDIKYDEVVQVISEAKKQGIARVGLATK 144 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 0.318 0.131 0.350 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: 405,328 Number of extensions: 14009 Number of successful extensions: 85 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 83 Number of HSP's successfully gapped: 4 Length of query: 149 Length of database: 1,619,870 Length adjustment: 77 Effective length of query: 72 Effective length of database: 1,255,275 Effective search space: 90379800 Effective search space used: 90379800 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: 41 (21.8 bits) S2: 126 (53.1 bits)