Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate RR42_RS01585 RR42_RS01585 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Cup4G11:RR42_RS01585 Length = 464 Score = 237 bits (605), Expect = 7e-67 Identities = 148/439 (33%), Positives = 237/439 (53%), Gaps = 26/439 (5%) Query: 38 ETSRVRARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGF 97 E AR G +K+ L DL+ G+G ++G G+FV +G + AGPA+ +S+ IA Sbjct: 10 EAMLAAARDDG-LKKVLGPVDLILMGIGAIIGTGIFVLTGTGAL-TAGPALTVSFVIAAL 67 Query: 98 CALLSAFCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY 157 +A CY EFA +PV+G ++Y T GE +A++ G +L+++Y L+ +AV+ ++GY Sbjct: 68 ACGFAALCYAEFASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAVSVGWSGY 127 Query: 158 ---LCTALGIESKLRITV--NGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLT 212 L GI +T +P ++ A +++L +T ++ Y RES+ LN V+ Sbjct: 128 FQSLMAGFGIHLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESARLNNVMV 187 Query: 213 VLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAV 272 + I ++ I +G N+ F PFG GVFN AA+V+ ++IG+DAV Sbjct: 188 AVKIAVVLLFIGVGVWHVKPANWHP---------FAPFGLDGVFNAAALVFFAFIGFDAV 238 Query: 273 STMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPY-DMIDPDAPFSGAFMGSD 331 ++ AEEV+NP +D+P+G+ GS+ + TVLY +AA M+ ++P+ D P S A + Sbjct: 239 TSAAEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSLALQYA- 297 Query: 332 GWRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASA 391 G WV+ + +GA G+ T +LV GQ R + + R ++P + VHP +TP A+ Sbjct: 298 GENWVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATPFFATW 357 Query: 392 FLGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW--------P 443 +GI A IA F L +L L++IGTL F +++ AV+ R + + P Sbjct: 358 TVGIVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLPRAFRCPGVPVVP 417 Query: 444 TLSYLFCFSLTSILFTLLW 462 LS FC L + L L W Sbjct: 418 LLSVGFCLFLMAHLQALTW 436 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: 668 Number of extensions: 36 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: 464 Length adjustment: 35 Effective length of query: 547 Effective length of database: 429 Effective search space: 234663 Effective search space used: 234663 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