Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= uniprot:Q4KIP0 (466 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 347 bits (890), Expect = e-100 Identities = 187/467 (40%), Positives = 274/467 (58%), Gaps = 15/467 (3%) Query: 2 DQTLKQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 61 D L RGL NRH+QLIA+GGAIGTGLF+GS + AGPS+IL YAI GF+ F + Sbjct: 3 DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62 Query: 62 MRQLGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWW 121 MR +GE+++ S G GF+ GW YW ++ GMA++ A+ Y Q+WW Sbjct: 63 MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122 Query: 122 PEIPTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGS 178 PEIP W+ + +++ +N+ V+ FGE EFWFAIIK+VAIV +I +G +M+ F Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182 Query: 179 GGSQASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAIN 238 G+ AS +NL HGGFFPNG TG L +F+F G+EL G AAE +P +P+AIN Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242 Query: 239 QVVYRVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNF 298 + R+++FYV ALAV++ + PW+E+ + +SPFV++F+L G AAA I+NF Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEV---------SPDNSPFVQMFALAGIPAAAGIINF 293 Query: 299 VVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLV 358 VV+T+A S NSG++ SRMLYGL+ +G APK L+K+ VP L S L + V + Sbjct: 294 VVITSAASSANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGL 353 Query: 359 NYLAPH--EALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYL 416 Y EA L+ + M+ W+ I + ++ +R+ E FK + + Sbjct: 354 LYAGGTVIEAFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVV 413 Query: 417 CLAFMVMIVGVMWMIPGIRASVYAIPVWVLVIW-GFYLLSRAKKASQ 462 L F V ++GV+ + R ++ A PVW +++ G++ AK A + Sbjct: 414 VLVFFVAMLGVLSLETDTRTALLATPVWFIILGVGWFATGGAKGAQR 460 Lambda K H 0.327 0.141 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: 654 Number of extensions: 40 Number of successful extensions: 5 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: 466 Length of database: 468 Length adjustment: 33 Effective length of query: 433 Effective length of database: 435 Effective search space: 188355 Effective search space used: 188355 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