Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 359 bits (921), Expect = e-103 Identities = 178/458 (38%), Positives = 279/458 (60%), Gaps = 7/458 (1%) Query: 11 DQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFV 70 + A + L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I G + F + Sbjct: 2 NSAQQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMI 61 Query: 71 MRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWF 130 MR +GE++ SFS FA G + G+ +GW YW +V+ MA++ A+ Y +W+ Sbjct: 62 MRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWW 121 Query: 131 PGLSDWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVV-GLVMVAMHFQS 189 PG+ WV++L L+ +NLA VK +GE EFWFA+IK+VA++ +IV G ++++ H Sbjct: 122 PGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGH--- 178 Query: 190 PTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAI 249 G +AS +LW+ GG+FP G G F + +F+F G+EL+G TAAE P+KS+P+A+ Sbjct: 179 -GGPQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAV 237 Query: 250 NSIPIRIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAAS 309 N + RI++FY+ SL V++S+ PW+ V SPFV +F +G A+V+N VVLT+A S Sbjct: 238 NQVIYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALS 297 Query: 310 SANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVI 369 NSGV++ SRML+GLA++G AP+A K+ +R VP + S + V++ Y+ P+ Sbjct: 298 VYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEA 357 Query: 370 GAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFV 429 M V+A++ W +I ++L RK E ++K + W+C+AF + Sbjct: 358 LGLLMALVVAALVLN--WALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALI 415 Query: 430 LVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 LV+L + ++ + P W + + G++F ++ A + Sbjct: 416 LVILAMTPGLSVSVWLVPAWLVVMWAGYVFKRRRAAVQ 453 Lambda K H 0.329 0.141 0.441 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: 661 Number of extensions: 34 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: 470 Length of database: 461 Length adjustment: 33 Effective length of query: 437 Effective length of database: 428 Effective search space: 187036 Effective search space used: 187036 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