Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 421 bits (1083), Expect = e-122 Identities = 204/455 (44%), Positives = 301/455 (66%), Gaps = 5/455 (1%) Query: 9 NEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIF 68 N + ++ L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAIGGV F Sbjct: 45 NLDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAF 104 Query: 69 FIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHY 128 IMR LGE++ PV+GSF+ +A ++ G F GF +GW+YW ++V+ MAE+TAV YVHY Sbjct: 105 MIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHY 164 Query: 129 WFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT 188 W+P VP W+ AL A + +N V +GE EFWFA+IKVV ++ MI+ G ++ G Sbjct: 165 WWPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHG 224 Query: 189 PLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHAT 248 GP AS SNLW+HGGF P G G+ L ++MF++ G+ELIG+TA EA P+K +P A Sbjct: 225 --GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAV 282 Query: 249 NGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAAS 308 N V++RILIFY+ +L ++++L PWNE+ G SPFV +F +IG A ++N+VV+TAA S Sbjct: 283 NQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALS 342 Query: 309 SCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQV 368 NSG+++ RMLY LA+ G APRA +V + VP +AI SA V++NY++P + Sbjct: 343 VYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEA 402 Query: 369 FVWVTSISLVGSLWTWSIIMIAHLGYRKA-IAAGRVKAVAFRMPGAPYANWLVVAFMIAV 427 + ++ + + W++I + HL R+A +AAG + + F+ P +NW+ +AFM + Sbjct: 403 LGLLMALVVAALVLNWALISLTHLKSRRAMVAAG--ETLVFKSFWFPVSNWICLAFMALI 460 Query: 428 AVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462 V+L++ PG V++ + PVW ++ GY F + RA Sbjct: 461 LVILAMTPGLSVSVLLVPVWLVVMWAGYAFKRRRA 495 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: 780 Number of extensions: 33 Number of successful extensions: 4 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: 506 Length adjustment: 34 Effective length of query: 438 Effective length of database: 472 Effective search space: 206736 Effective search space used: 206736 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: 52 (24.6 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