Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate BPHYT_RS01785 BPHYT_RS01785 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__BFirm:BPHYT_RS01785 Length = 463 Score = 219 bits (558), Expect = 2e-61 Identities = 131/389 (33%), Positives = 221/389 (56%), Gaps = 17/389 (4%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +K++L DL GVG ++G G+FV +G + AGPA+++S+ IA +A Y EF Sbjct: 22 LKKALGALDLTFLGVGAIIGTGIFVLTGTGAVQ-AGPALMISFLIAAIACGFAALAYAEF 80 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTAL---GIES 166 A +PVAG ++Y T GE A++ G +L+++Y L+ +AV+ ++GYL + L G+ Sbjct: 81 ASTIPVAGSIYTYSYATLGELAAWIIGWDLMLEYGLATSAVSVGWSGYLQSLLSGFGVSL 140 Query: 167 KLRITV--NGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVFIVFVIV 224 + +T LP ++ A LV++A+T ++ RES+ +N V+ + +V ++ VI Sbjct: 141 PVALTAAPGALPGHDTLFNLPAFLVMMAITALLSVGVRESARINNVMVAIKVVVVLLVIG 200 Query: 225 IGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVK 284 +G N+ F P G +GVF AA+++ ++IG+D+VS+ AEEVK+P + Sbjct: 201 VGVFHVTPANWHP---------FMPNGWNGVFGAAAVMFFAFIGFDSVSSAAEEVKDPKR 251 Query: 285 DIPVGVSGSVILVTVLYCLMAASMSMLLPY-DMIDPDAPFSGAFMGSDGWRWVSNVIGVG 343 D+P+G+ S+ + VLY +AA ++ ++P + P S A + G +WV+ I +G Sbjct: 252 DLPIGIIASLGVCAVLYVAVAAVVTGIVPSAQFANISHPVSYALQVA-GEKWVAGFIDLG 310 Query: 344 AGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICTAAIALF 403 A G+LT +LV GQ R + + R ++P ++VHP+ +TP + +GI I Sbjct: 311 AVLGMLTVILVMAYGQTRVIFAMSRDGLLPERLSRVHPRFATPFFTTWLVGIFFGLIGAL 370 Query: 404 TDLQILLNLVSIGTLFVFYMVANAVIYKR 432 L +L L++IGTL F MV+ AV+ R Sbjct: 371 VPLNVLAELINIGTLAAFSMVSIAVLVLR 399 Lambda K H 0.326 0.139 0.423 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: 653 Number of extensions: 44 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: 582 Length of database: 463 Length adjustment: 35 Effective length of query: 547 Effective length of database: 428 Effective search space: 234116 Effective search space used: 234116 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