Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate BWI76_RS01140 BWI76_RS01140 amino acid permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Koxy:BWI76_RS01140 Length = 461 Score = 434 bits (1117), Expect = e-126 Identities = 209/448 (46%), Positives = 307/448 (68%), Gaps = 11/448 (2%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 ++ +L RGL+ RHI++IA+GG IGVGLF+GA + AGP ++L+Y I G+ +FFIMR++ Sbjct: 4 KKAELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSM 63 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GE+L PV+GSFA YA ++ PF G+ T WSYWFMW+ G++EITA+ VYV +WFP++ Sbjct: 64 GEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMA 123 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTA 194 QWIPAL + ++ L N AV ++GE+EFWFA+IKV TI+ MIV+GL +IFFG G Sbjct: 124 QWIPALIAVGLVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVVGLGVIFFGFGNGGHAI 183 Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254 F NL HGGF G G + L IV+ +YQGVELIG+TAGEA+NP+ L A V+WR Sbjct: 184 GFGNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWR 243 Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314 ILIFYVGA+ +++ + PW+++ SPFV F +IG+ AA I+N VV+TAA S CNSG+ Sbjct: 244 ILIFYVGAIFVIVTIFPWDQIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSGM 303 Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIV--PEQVFVWV 372 +S GRMLY LA+ Q P A +VS VPS + S ++ +G LNYI+ P++VFV+V Sbjct: 304 YSCGRMLYALARNRQLPAAIAKVSRNGVPSAGVALSILILLVGSCLNYIIPNPQRVFVYV 363 Query: 373 TSISLVGSLWTWSIIMIAHLGYR----KAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVA 428 S S++ + W +I+I+ L +R +A+A+ +++ F P+AN+L +AF++ V Sbjct: 364 YSASVLPGMVPWFVILISQLRFRLVHKEAMASHPFRSLLF-----PWANYLTMAFLVCVL 418 Query: 429 VLLSLDPGTRVALYVAPVWFALLGIGYR 456 + + + TR++L+V ++ A + + Y+ Sbjct: 419 IGMGFNDDTRMSLFVGIIFLAAVTLIYK 446 Lambda K H 0.328 0.142 0.445 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 787 Number of extensions: 41 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 461 Length adjustment: 33 Effective length of query: 439 Effective length of database: 428 Effective search space: 187892 Effective search space used: 187892 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory