Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 422 bits (1084), Expect = e-122 Identities = 211/441 (47%), Positives = 294/441 (66%), Gaps = 6/441 (1%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 LHRGL +RH+Q+IAIGGAIG GLF+G+G+ I++AGP ++L YAI G +FF+MRA+GELL Sbjct: 11 LHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFVMRAMGELL 70 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 L S + +GP AGF TGW+YWF W+ TGMA+I A+ Y YW+P++P W+P Sbjct: 71 LANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWWPEIPLWLP 130 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIG--LAIIFFGVTPLGPTASF 196 + T+ VL+ +N AV +FGE+EFWFA+IK+V IVA+I +G + I FG P G TASF Sbjct: 131 GVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFG-APNGTTASF 189 Query: 197 SNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRIL 256 +NL HGGF P G G + QI +FA+ G+EL G A E ++PE LP A N + RI+ Sbjct: 190 NNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAINSIPIRIV 249 Query: 257 IFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFS 316 +FYV AL ++M + PWNE+ P SPFV +F G+P AA I+N VVIT+AASS NSGIFS Sbjct: 250 VFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASSANSGIFS 309 Query: 317 TGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALM--GIGVLLNYIVPEQVFVWVTS 374 T RMLY L+ G AP+ +G +S + VP+ +TFS + +G+L + F +T+ Sbjct: 310 TSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIEAFTLITT 369 Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434 +S V + WS I++A++ YR+ K+V F+MPG +V+ F +A+ +LSL+ Sbjct: 370 VSSVLFMVVWSYILVAYIVYRRRNPELHEKSV-FKMPGGVVMAVVVLVFFVAMLGVLSLE 428 Query: 435 PGTRVALYVAPVWFALLGIGY 455 TR AL PVWF +LG+G+ Sbjct: 429 TDTRTALLATPVWFIILGVGW 449 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: 747 Number of extensions: 34 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: 468 Length adjustment: 33 Effective length of query: 439 Effective length of database: 435 Effective search space: 190965 Effective search space used: 190965 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 24 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