Align L-alanine and D-alanine permease (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 410 bits (1054), Expect = e-119 Identities = 204/455 (44%), Positives = 296/455 (65%), Gaps = 5/455 (1%) Query: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y IGG+ +IMR LGEM Sbjct: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIAFMIMRQLGEMV 69 Query: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 PVAGSFS +A Y G GFL+GWNYW L+++ +AE+TAV Y+ W+P P W+ Sbjct: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTWVS 129 Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197 AL + +INL VKA+GE EFWFA+IK+V +I M++ G ++ G G G I+N Sbjct: 130 ALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHG--GPQASITN 187 Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257 LW+HGGF P+G G+ M L ++MF++ G+E+IG+TA EA PQK+IP A+ V +RIL+F Sbjct: 188 LWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIF 247 Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317 Y+ +L V+LS+YPWNE+ GSPFVM F ++G A ++N VV+TAALS N G+++ Sbjct: 248 YICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307 Query: 318 RMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSIATF 377 RMLY LA+ G AP K GVP A+ LS A V++NYL+P + + ++ Sbjct: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVA 367 Query: 378 GAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFPDTR 437 + W +I L LK RK++ A + L ++ + +PVS+++ LAF+ L++ ++A P Sbjct: 368 ALVLNWALISLTHLKSRKAMVAAGET-LVFKSFWFPVSNWICLAFMALILVILAMTPGLS 426 Query: 438 IALYVGPVFLVLLTVLFYVFKLQPTQVAQGEARPV 472 +++++ P +LV++ YVFK + V QG AR V Sbjct: 427 VSVWLVPAWLVVMWA-GYVFKRRRAAV-QGGARVV 459 Lambda K H 0.328 0.142 0.447 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: 665 Number of extensions: 30 Number of successful extensions: 2 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: 461 Length adjustment: 33 Effective length of query: 439 Effective length of database: 428 Effective search space: 187892 Effective search space used: 187892 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 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