Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__BFirm:BPHYT_RS33230 Length = 486 Score = 256 bits (655), Expect = 1e-72 Identities = 147/438 (33%), Positives = 240/438 (54%), Gaps = 21/438 (4%) Query: 44 ARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSA 103 A G + +SL + G+G ++GAG+FV +G A++ AGP++VLS+ + G Sbjct: 21 ADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPSIVLSFVLGGIACAFVG 80 Query: 104 FCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTAL- 162 CY+E A +PV G +++Y T GE A++ G +LI++Y + A VA ++GY+ + L Sbjct: 81 LCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGAATVAVGWSGYIVSLLH 140 Query: 163 --GIE-----SKLRITVNGLPDGFNEIDVV---AVLVVLALTVIICYSTRESSVLNMVLT 212 GI + TV L DG +V A++++ LT ++ T+ES+ LN ++ Sbjct: 141 NVGISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTMLVLGTKESARLNNIMV 200 Query: 213 VLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAV 272 + +V +V I +G N+ +N F FG SG+ G+A+V+ ++IG+DAV Sbjct: 201 AVKLVVVVAFIALGVFFIKPANWHPFIPAN-TGEFGNFGMSGILRGSAVVFFAFIGFDAV 259 Query: 273 STMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDG 332 ST A+E K P +D+P+G+ GS+I+ T+LY L+A ++ L+PY ++ P + + + G Sbjct: 260 STAAQEAKKPQRDMPIGILGSLIICTILYILVAGVLTGLVPYAELNVPDPIAKG-VDAIG 318 Query: 333 WRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAF 392 W S +I +GA G+ T +LV + GQ+R + ++P FA+VHP+ TP + Sbjct: 319 LNWFSILIKIGALTGLTTVILVLLYGQSRIFFTMSTDGLLPPLFARVHPRLQTPYLSQIL 378 Query: 393 LGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW--------PT 444 +G A +A T + +L +VSIGTLF F +V AVIY R + P+ P Sbjct: 379 IGSVVAIVAALTPISVLGEMVSIGTLFAFILVCGAVIYLRRSDSDASRPFRVPGVPVVPV 438 Query: 445 LSYLFCFSLTSILFTLLW 462 L LFC L + L + W Sbjct: 439 LGILFCLLLMAGLPLVTW 456 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: 714 Number of extensions: 40 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: 582 Length of database: 486 Length adjustment: 35 Effective length of query: 547 Effective length of database: 451 Effective search space: 246697 Effective search space used: 246697 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