Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_000566685.1:WP_025765060.1 Length = 484 Score = 226 bits (577), Expect = 1e-63 Identities = 151/512 (29%), Positives = 255/512 (49%), Gaps = 77/512 (15%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +KRSL LV G+G ++GAG+F +G A++ +GPAV +S+ +A + CY EF Sbjct: 25 LKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSGPAVTISFIVAAVGCGFAGLCYAEF 84 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG------ 163 A +P+AG A++Y T GEF+A++ G +L+++Y L A V+ S++ YL L Sbjct: 85 ASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYALGAATVSVSWSRYLLEFLSKFDIHL 144 Query: 164 ----IESKLRITVNGLPDGF----NEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLH 215 + S + L DG I++ A+L+V L++++ T S+ LN L +L Sbjct: 145 PTQLVSSPFEVLT--LSDGTIIDNGIINLPAILIVWMLSLLLIRGTEGSAYLNNFLVILK 202 Query: 216 IVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTM 275 + ++ I +G++ + +N+ N + FG SG+ GAA+V+ ++IG+DAVST Sbjct: 203 VAVVLIFIGLGWSHINPENYVPYIPEN-TGNYENFGWSGIATGAAVVFFAFIGFDAVSTA 261 Query: 276 AEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRW 335 A+E KNP K +P+G+ GS+I+ T+LY L A M+ L+ Y DA + + G+ Sbjct: 262 AQEAKNPQKGMPIGILGSLIVCTILYVLFAHVMTGLVNYKEFANDAKPAATAFAATGYDS 321 Query: 336 VSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGI 395 + + V G + +LV +LGQ+R + + ++P +F+++HPK STP + F + Sbjct: 322 LQTGLIVAILAGYTSVMLVMLLGQSRVFYSMSKDGLLPKFFSEIHPKFSTPWKTNIFFML 381 Query: 396 CTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWPTLSYLFCFSLTS 455 + A F + L ++VSIGTLF F +V VGV W Sbjct: 382 FVSIFAGFVPVSDLGHMVSIGTLFAFSLVC----------VGV---W------------- 415 Query: 456 ILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARKPEFWGVPLMPWIPSISI 515 + + P P++F PL+P++P + I Sbjct: 416 -----MLRVKRPDLPRSFR-----------------------------TPLVPFVPLMGI 441 Query: 516 FLNIFLLGSLDKPSYVRFGFFSALAVLVYVLY 547 + ++L+ SL S+ R + AL + +Y Y Sbjct: 442 IVCVYLMYSLPIESWYRLAIWLALGLAIYFFY 473 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: 662 Number of extensions: 40 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 582 Length of database: 484 Length adjustment: 35 Effective length of query: 547 Effective length of database: 449 Effective search space: 245603 Effective search space used: 245603 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