Align Amino acid transporter (characterized, see rationale)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= uniprot:A0A0H3C3Q5 (483 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 325 bits (834), Expect = 2e-93 Identities = 179/483 (37%), Positives = 276/483 (57%), Gaps = 21/483 (4%) Query: 14 RKAIDTITAGHADSHQ--LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILS 70 +K+I +I A +S + LK+TL +L+ +GVG +G G++++TG+ A +GP V LS Sbjct: 2 KKSIASIVAEANESGEGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLS 61 Query: 71 FLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVA 130 F+IA C AALCYAE ++MIP +GSAYTYSYA MGE AW +GW L+LEY++ CA VA Sbjct: 62 FVIAALGCGFAALCYAEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVA 121 Query: 131 VGWSAHAHGLFKM--IGFPDALLAGPHQ----------GGLINMPAVFISMAVAGLLALG 178 + WS + I P L P + G+IN+PA + + + +L G Sbjct: 122 ISWSQYLTKFLASLHIYLPPQLTLSPFETAKLADGSTVNGIINIPAALVVVLMTAILIRG 181 Query: 179 TRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGV 238 T+ SA VN ++VF+K+ ++VF+ L + A++ P++P G GV Sbjct: 182 TKGSAIVNGIIVFLKVGVVLVFIALGWQYIDPANYHPYIPEN------TGTFGQFGWSGV 235 Query: 239 MAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTE 298 + A L+FF F GFDAV+ +A+ETKNP RDL IGI+GS+ VCT ++ + V G + + Sbjct: 236 LRGAGLVFFVFIGFDAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYK 295 Query: 299 VFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRA 358 F+ S AP+ +E + ++Q + LA +I +VIL + QSR+F+ +++DGLLP+ Sbjct: 296 EFANSGAPVAIAIEKTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKM 355 Query: 359 LSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLRE 418 S V+AK TP ++ V + + + + + E+ + GTL AF+ V +++LR Sbjct: 356 FSDVHAKFKTPYKSNIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILRKTN 415 Query: 419 PNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLA 478 P R F P P++ GIL C+ + + LP +T L +IG +Y YG + S L Sbjct: 416 PEAKRPFKVPFVPLIPILGILTCIAMMVFLPWETWLRLAVWLIIGLAIYFWYGKKNSKLK 475 Query: 479 QQE 481 QE Sbjct: 476 AQE 478 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: 665 Number of extensions: 47 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: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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