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= 0030.0113.p (137 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 ... 215 1e-57 gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ... 63 7e-12 gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ... 61 4e-11 gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat... 55 2e-09 gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR ... 54 6e-09 >gi|300310551|ref|YP_003774643.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 144 Score = 215 bits (547), Expect = 1e-57, Method: Compositional matrix adjust. Identities = 104/139 (74%), Positives = 125/139 (89%), Gaps = 2/139 (1%) Query: 1 MRGGRPRKFKSEINVVPYIDVMLVLLIIFMVAAPVNDPSVINLPTAGKSTVPPSEYIEIA 60 MRGGRPRKFKSEINVVPYIDVMLVLLIIFMVA P+ +PSVINLPTAGKST PPS+YIEIA Sbjct: 6 MRGGRPRKFKSEINVVPYIDVMLVLLIIFMVATPITNPSVINLPTAGKSTQPPSDYIEIA 65 Query: 61 LKPDAKATIKVNGPKRG--ETQTASGRPDLAQKLQALHADSPDMPVMISADKEIKYDEVV 118 LKP+++ATI++NGPK G + +T +G+ DL+++L+ LH D+P++ VMISADK+IKYDEVV Sbjct: 66 LKPNSQATIRINGPKSGGKKAETVTGKTDLSERLRKLHDDNPELAVMISADKDIKYDEVV 125 Query: 119 QVIAAAKKLGIARVGLATK 137 QVI+ AKK GIARVGLATK Sbjct: 126 QVISEAKKQGIARVGLATK 144 >gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 138 Score = 63.2 bits (152), Expect = 7e-12, Method: Compositional matrix adjust. Identities = 46/131 (35%), Positives = 71/131 (54%), Gaps = 13/131 (9%) Query: 9 FKSEINVVPYIDVMLVLLIIFMVAAPVNDPSV-INLPTAGKS--TVPPSEYIEIALKPDA 65 F EIN P +DVMLVLLIIF++ PV + +V I+LP A V P I L DA Sbjct: 13 FNPEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKASSQPDQVKPE---SINLSIDA 69 Query: 66 KATIKVNGPKRGETQTASGRPDLAQKLQALHADSPDMPVMISADKEIKYDEVVQVIAAAK 125 + N E + SG +L+ ++ A P + + A++ +Y++V QV++AA+ Sbjct: 70 SGNVFWN-----EEKIDSG--ELSVRIAAAAQKQPQPELHLRAERTTQYEKVAQVMSAAQ 122 Query: 126 KLGIARVGLAT 136 G+A++G T Sbjct: 123 SGGLAKIGFVT 133 >gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 148 Score = 60.8 bits (146), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 42/127 (33%), Positives = 70/127 (55%), Gaps = 9/127 (7%) Query: 11 SEINVVPYIDVMLVLLIIFMVAAPVNDPSV-INLPTAGKSTVPPSEYIEIALKPDAKATI 69 ++INV P +DVMLVLL+IF++ AP+ ++ ++LPTA +S P + I L DA + Sbjct: 16 ADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTA-QSAPAPEKPETITLGIDAAGKL 74 Query: 70 KVNGPKRGETQTASGRPDLAQKLQALHADSPDMPVMISADKEIKYDEVVQVIAAAKKLGI 129 N Q S +L +L A P + + ADK +Y + +V++AA+ G+ Sbjct: 75 YWND------QPVSSE-ELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGAGL 127 Query: 130 ARVGLAT 136 +++G T Sbjct: 128 SKLGFVT 134 >gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 142 Score = 55.5 bits (132), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 45/141 (31%), Positives = 70/141 (49%), Gaps = 9/141 (6%) Query: 1 MRGGRPRKFKSEINVVPYIDVMLVLLIIFMVAAPVNDPSVIN--LPTAG--KSTVPPSEY 56 R GRPR+ EIN++P+IDV+LV++I MV + + + LPTA K+ P Sbjct: 3 FRKGRPRE-DLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQLTLPTADAPKALEQP--- 58 Query: 57 IEIALKPDAKATIKVNGPKRGETQTASGRPDLAQKLQALHADSPDMPVMISADKEIKYDE 116 E+ + DA +N KR + A G + Q + A D ++I+AD + Sbjct: 59 FELNIAVDANGRYALNN-KRISARDAQGLSEEMQAVVRASASKLDPVIIINADALATHQT 117 Query: 117 VVQVIAAAKKLGIARVGLATK 137 VV V+ AA+ G +V A + Sbjct: 118 VVNVLEAARMAGYPKVTFAAQ 138 >gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR protein [Herbaspirillum seropedicae SmR1] Length = 135 Score = 53.5 bits (127), Expect = 6e-09, Method: Compositional matrix adjust. Identities = 38/136 (27%), Positives = 66/136 (48%), Gaps = 13/136 (9%) Query: 6 PRKFKSEINVVPYIDVMLVLLIIFMVAAPVNDPSVINLPTAGKSTVPPSEYIEIALKPDA 65 P+K K+ + ++P IDVM+ LL+ F++ S+ +P G T PS LKP Sbjct: 7 PKKRKARVEIIPMIDVMMFLLVFFVLI------SLNVIPALGLKTQLPSSSTAQDLKPQT 60 Query: 66 KATIKVNGPK----RGETQTASGRPDLAQKLQALHADSPDMPVMISADKEIKYDEVVQVI 121 KA I + + GE T L +L L + + ++I++D+ ++ +V V+ Sbjct: 61 KAVITIAKDEVIQVDGENTTLDA---LTARLDKLRHEGEKLNLIINSDRGVEVQRLVDVM 117 Query: 122 AAAKKLGIARVGLATK 137 KK G + +AT+ Sbjct: 118 DTLKKGGFDSISIATR 133 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 0.316 0.134 0.370 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: 424,964 Number of extensions: 15696 Number of successful extensions: 65 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 65 Number of HSP's successfully gapped: 6 Length of query: 137 Length of database: 1,619,870 Length adjustment: 76 Effective length of query: 61 Effective length of database: 1,260,010 Effective search space: 76860610 Effective search space used: 76860610 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 (21.6 bits) S2: 126 (53.1 bits)