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= 0038.0055.p (199 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, d... 318 2e-88 gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate tran... 266 1e-72 gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate tran... 77 1e-15 gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate tran... 55 4e-09 >gi|300310440|ref|YP_003774532.1| TrapT dctQ-M fusion permease, dicarboxylate transport protein [Herbaspirillum seropedicae SmR1] Length = 618 Score = 318 bits (814), Expect = 2e-88, Method: Compositional matrix adjust. Identities = 155/195 (79%), Positives = 178/195 (91%) Query: 4 RTAVVEGVATATEVSTIGIAYTIVVGILVYRRFDVKRLYPMLVETASLSGAILFIIGTAT 63 RTAVVEGVATATEVSTIGIAY++V G+LVYR+FD KRLYPMLV+TA+LSGAILFIIGTAT Sbjct: 424 RTAVVEGVATATEVSTIGIAYSVVAGLLVYRKFDWKRLYPMLVDTAALSGAILFIIGTAT 483 Query: 64 CMAWALTQSGFSHDLAHIMSLMPGGRWGFLLISIVTFIVLGSVLEGIPAMVLFGPLLFPI 123 M+WALTQSGFSH LA M+ +PGG++GFLL+SI FIVLGSVLEGIPAMVLF PLLFP+ Sbjct: 484 GMSWALTQSGFSHALAEAMTSVPGGKYGFLLVSIAAFIVLGSVLEGIPAMVLFAPLLFPV 543 Query: 124 ARQLGVHEVHYAMVVILAMGIGLFAPPFGLGYYSACTIGRVSPDAGMRKIWPYLGALLAG 183 A+ +GVHEVHYAMV+IL+MG+GLFAPPFGLGYY+ACTIGRV PD +++IWPYLGAL+ G Sbjct: 544 AKAIGVHEVHYAMVIILSMGVGLFAPPFGLGYYAACTIGRVHPDVAVKRIWPYLGALVVG 603 Query: 184 LLIVAAVPWISIGFL 198 LLIVA VPW SIGFL Sbjct: 604 LLIVAFVPWFSIGFL 618 >gi|300313111|ref|YP_003777203.1| TRAP-type C4-dicarboxylate transport system dctQ-M fusion permease large permease [Herbaspirillum seropedicae SmR1] Length = 627 Score = 266 bits (680), Expect = 1e-72, Method: Compositional matrix adjust. Identities = 143/201 (71%), Positives = 170/201 (84%), Gaps = 3/201 (1%) Query: 1 VLIRTAVVEGVATATEVSTIGIAYTIVVGILVY---RRFDVKRLYPMLVETASLSGAILF 57 +LIR AV+EGVATATEV+TIG+AYT+VVG++++ R KRLYPML+E+A+LSGAIL Sbjct: 427 MLIRVAVIEGVATATEVATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILL 486 Query: 58 IIGTATCMAWALTQSGFSHDLAHIMSLMPGGRWGFLLISIVTFIVLGSVLEGIPAMVLFG 117 IIG AT MAWALTQSGFS L +M +PGG GFLLI+IV FIVLGS+LEGIPA+VLFG Sbjct: 487 IIGMATAMAWALTQSGFSAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFG 546 Query: 118 PLLFPIARQLGVHEVHYAMVVILAMGIGLFAPPFGLGYYSACTIGRVSPDAGMRKIWPYL 177 PLLFP+AR LGVH+VHYAMVVILAMGIGLFAPPFG+G+Y+AC IG+VSPD ++W YL Sbjct: 547 PLLFPVARSLGVHDVHYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFNRVWGYL 606 Query: 178 GALLAGLLIVAAVPWISIGFL 198 AL+ LL+VA VPWISIGFL Sbjct: 607 AALVVALLVVAFVPWISIGFL 627 >gi|300310180|ref|YP_003774272.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 426 Score = 76.6 bits (187), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 52/195 (26%), Positives = 105/195 (53%) Query: 1 VLIRTAVVEGVATATEVSTIGIAYTIVVGILVYRRFDVKRLYPMLVETASLSGAILFIIG 60 V++ + GV T TE + + Y + + VY+ +K++ +L+++AS+S +L+II Sbjct: 224 VIVMGGIYTGVFTPTEAAAMAAVYAFFIAVFVYKDLTLKQVPKVLLDSASMSAMLLYIIT 283 Query: 61 TATCMAWALTQSGFSHDLAHIMSLMPGGRWGFLLISIVTFIVLGSVLEGIPAMVLFGPLL 120 A ++ +T +A ++ G FLL+ + ++ G+V+E +++ P+L Sbjct: 284 NAVLFSFLVTSENIPQAMAAWITDSGLGPITFLLVVNILLLLAGNVMEPSSIVLILAPIL 343 Query: 121 FPIARQLGVHEVHYAMVVILAMGIGLFAPPFGLGYYSACTIGRVSPDAGMRKIWPYLGAL 180 FP+A +LG+ VH+ +++++ M +G+ PP GL Y A I ++ + P+L + Sbjct: 344 FPVAMKLGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVMPWLLTM 403 Query: 181 LAGLLIVAAVPWISI 195 L L +V P +S+ Sbjct: 404 LGFLALVTYWPALSL 418 >gi|300311996|ref|YP_003776088.1| TRAP-type C4-dicarboxylate transport system large permease [Herbaspirillum seropedicae SmR1] Length = 449 Score = 54.7 bits (130), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 47/196 (23%), Positives = 94/196 (47%), Gaps = 7/196 (3%) Query: 3 IRTAVVEGVATATEVSTIGIAYTIVVGILVYRRFDVKRLYPMLVETASLSGAILFIIGTA 62 + A+ G+AT +E + +G +V+ +VYR + + + P L T SG +L IIG + Sbjct: 246 VMVALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMS 305 Query: 63 TCMAWALTQSGFSHDLAHIMSLMPGGRWGFLLISIVTFIVLGSVLEGIPAMVLFGPLLFP 122 ++ ++ S A + + +W L + + IVLG L + +++ P++ P Sbjct: 306 LLYSYVMSYLHISQSAAQWVVDLHLSKWLLLAVILGMVIVLGFFLPPVSIILMTAPIILP 365 Query: 123 IARQLGVHEVHYAMVVILAMGIGLFAPPFGLGYYSACTIGRVSPDAGM----RKIWPYLG 178 + G + + +V+ + M +GL PP GL + I ++PD + + P+L Sbjct: 366 PLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLF---VIKNIAPDIALGDVIKGTIPFLA 422 Query: 179 ALLAGLLIVAAVPWIS 194 + +L++ P I+ Sbjct: 423 LMFLAVLLLCMFPGIA 438 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 0.330 0.145 0.448 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: 559,169 Number of extensions: 22521 Number of successful extensions: 113 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 110 Number of HSP's successfully gapped: 4 Length of query: 199 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 118 Effective length of database: 1,236,335 Effective search space: 145887530 Effective search space used: 145887530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 128 (53.9 bits)