Align Amino acid transporter (characterized, see rationale)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Pedo557:CA265_RS15000 Length = 491 Score = 304 bits (779), Expect = 4e-87 Identities = 183/467 (39%), Positives = 270/467 (57%), Gaps = 21/467 (4%) Query: 30 LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILSFLIAGAVCACAALCYAEL 88 LK+TLS LVALGVGAI+G G++ T A AGP V + F+IA CA A LCYAEL Sbjct: 23 LKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSVTIGFIIAAIGCALAGLCYAEL 82 Query: 89 STMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAVGWSAHAHGLFKMI---- 144 S+ IP SGSAYTY+YA MGE +AW +GW L+LEY + A V + WS + + L + Sbjct: 83 SSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAATVGIAWSEYLNKLLVEVLHTS 142 Query: 145 GFPDALLAGPHQ-------GGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIAL 197 P P Q G++N+PA+FI ++ LL GT ESA VN ++V K+ + Sbjct: 143 PIPYEWCHSPFQSHPDGTVNGIMNLPALFIVGLLSLLLIKGTSESAFVNGLIVITKVGIV 202 Query: 198 IVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADA--AKVGVMAAASLIFFAFYGFDAV 255 I+ +VL N ++ P++P +V + + GV+ AA +FFAF GFDAV Sbjct: 203 ILIIVLGWGFINESNHHPYIP-AATTYVDHAGISHSFGGFWGVIGAAGTVFFAFIGFDAV 261 Query: 256 STAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVF--SKSEAPLVFILES 313 STAA+ETKNPK + IGI+GS+AVCT +Y++ A V G + E F EA +V + Sbjct: 262 STAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGIAPVEFFRTKGGEASVVAAISE 321 Query: 314 LNHGK--IAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVM 371 G +++LV +A + +VIL + GQSR+F+ M++DGLLP+ S ++ K TP Sbjct: 322 YMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMSKDGLLPKMFSDLHPKFKTPYK 381 Query: 372 MTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWP 431 L+ ++ + + + + ++ + GTL+AF+ V +VI+LR +P+ PR F TP P Sbjct: 382 ANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVAVIILRKTDPDLPRQFKTPWVP 441 Query: 432 IVAPAGILGCLYLFLSLPGKTQLYFLYAHL-IGAVVYLAYGMRKSVL 477 ++ G++ C + L L G T L+ L +G ++Y Y + S L Sbjct: 442 LIPILGVVACGLMILGL-GWTNWLRLFGWLALGFIIYFGYSKKNSHL 487 Lambda K H 0.326 0.138 0.415 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: 673 Number of extensions: 31 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: 483 Length of database: 491 Length adjustment: 34 Effective length of query: 449 Effective length of database: 457 Effective search space: 205193 Effective search space used: 205193 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: 52 (24.6 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