Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_057508922.1 ABB28_RS12355 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_001431535.1:WP_057508922.1 Length = 491 Score = 233 bits (595), Expect = 1e-65 Identities = 138/437 (31%), Positives = 229/437 (52%), Gaps = 30/437 (6%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +KR+L L+ G+G ++GAG+FV +G+A++ AGPAV LS+ +AG L+ CY EF Sbjct: 33 LKRTLTAKHLILLGIGAVIGAGIFVMTGQAAAFHAGPAVTLSFVLAGLACALAGLCYAEF 92 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALGIESKLR 169 A MPV+G A+SY T GE +A+ G L+++Y+ ++A+VA +++ YL + + L Sbjct: 93 AAMMPVSGSAYSYSYATLGEGMAWFIGWCLVLEYLFASASVAVAWSAYLLSFVTTTLHLP 152 Query: 170 ITVNGLPDGFNEIDVV----------------AVLVVLALTVIICYSTRESSVLNMVLTV 213 PD + + AVL+V A+T ++ +S+ +N ++ Sbjct: 153 F-----PDALSSAPIAWEGGQFIASGQLFNLPAVLIVAAVTGLLYVGISQSTFVNGIIVA 207 Query: 214 LHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVS 273 + + I I G + DT N+ N + F FG SGV ++V+ ++IG+DAVS Sbjct: 208 IKVSVICLFIGFGASHIDTANWQPFIPENTGT-FGEFGWSGVLRAGSIVFFAFIGFDAVS 266 Query: 274 TMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGW 333 T A E K+P +++P+G+ GS+ + T++Y ++ ++ LLPY + P + A Sbjct: 267 TAAGETKDPQRNMPIGLLGSLAICTIIYVIVCLVLTGLLPYQQLGTAKPVATALEAYPQL 326 Query: 334 RWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFL 393 W+ + +GA G+ + +LV M+GQ R I R ++P + KVH + TP A+ + Sbjct: 327 AWLKTAVEIGAIAGLSSVVLVMMMGQTRIAYTISRDGLLPRFLGKVHARFKTPYVATIIV 386 Query: 394 GICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWPT--------L 445 G+ AA+A L +L LVS+GTL F V V+ RY + P+ L Sbjct: 387 GVIAAALAGMMPLNVLGELVSMGTLLAFATVCIGVLVLRYTRPELVRPFRVPMAWLICPL 446 Query: 446 SYLFCFSLTSILFTLLW 462 L C +L ++ F W Sbjct: 447 GALACLTLFAMAFREHW 463 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: 696 Number of extensions: 32 Number of successful extensions: 2 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: 491 Length adjustment: 35 Effective length of query: 547 Effective length of database: 456 Effective search space: 249432 Effective search space used: 249432 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 24 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