Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 335 bits (860), Expect = 1e-96 Identities = 169/447 (37%), Positives = 260/447 (58%), Gaps = 5/447 (1%) Query: 2 DNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMI 61 DNA L RGL NRH+QLIA+GGAIGTGLF+GS + AGPS+IL YAI G + F + Sbjct: 3 DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62 Query: 62 MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWW 121 MR +GE++ S G GF++GW YW ++ MA++ A+ Y YWW Sbjct: 63 MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122 Query: 122 PGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGP 181 P +P W+ ++ + A+NLA V+ +GE EFWFAIIK+VA++ +I G +++++ G P Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182 Query: 182 Q---ASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVN 238 AS +NL HGGFFP+G G + +F+F G+EL G AAE +P+ ++P+A+N Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242 Query: 239 QVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSV 298 + RI++FY+ +LAV++ + PWNEV+ SPFV +F+ G A ++N VV+T+A S Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASS 302 Query: 299 YNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYL--IPAE 356 NSG+++ SRMLYGL+ +G AP+ + +R VP + S L V + Y E Sbjct: 303 ANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIE 362 Query: 357 ALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALIL 416 A L+ + ++ W+ I + ++ RR E VFK V + L F +L Sbjct: 363 AFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAML 422 Query: 417 VILAMTPGLSVSVLLVPLWLVVMWAGY 443 +L++ ++L P+W +++ G+ Sbjct: 423 GVLSLETDTRTALLATPVWFIILGVGW 449 Lambda K H 0.327 0.140 0.440 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: 512 Number of extensions: 24 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: 461 Length of database: 468 Length adjustment: 33 Effective length of query: 428 Effective length of database: 435 Effective search space: 186180 Effective search space used: 186180 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 (21.7 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