Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 213 bits (541), Expect = 2e-59 Identities = 137/441 (31%), Positives = 229/441 (51%), Gaps = 34/441 (7%) Query: 48 GDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYT 107 G +KR+L +L+ GVG +GAG+F +G A+++ +GPAV LS+ IA +A CY Sbjct: 18 GSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALCYA 77 Query: 108 EFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG---- 163 EFA +PVAG A++Y T GE A++ G +L+++Y + A VA S++ YL L Sbjct: 78 EFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASLHI 137 Query: 164 -IESKLRI------------TVNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMV 210 + +L + TVNG+ I++ A LVV+ +T I+ T+ S+++N + Sbjct: 138 YLPPQLTLSPFETAKLADGSTVNGI------INIPAALVVVLMTAILIRGTKGSAIVNGI 191 Query: 211 LTVLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYD 270 + L + ++ I +G+ D N+ N + F FG SGV GA +V+ +IG+D Sbjct: 192 IVFLKVGVVLVFIALGWQYIDPANYHPYIPENTGT-FGQFGWSGVLRGAGLVFFVFIGFD 250 Query: 271 AVSTMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPY-DMIDPDAPFSGAFMG 329 AV+ A+E KNP +D+P+G+ GS+++ TVL+ L M+ L Y + + AP + A + Sbjct: 251 AVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAPVAIA-IE 309 Query: 330 SDGWRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNA 389 + W+S I + G + +L+ ++ Q+R I + ++P F+ VH K TP + Sbjct: 310 KTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKFKTPYKS 369 Query: 390 SAFLGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW------- 442 + L + A F + ++ + SIGTL F MV ++ R + P+ Sbjct: 370 NIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILRKTNPEAKRPFKVPFVPL 429 Query: 443 -PTLSYLFCFSLTSILFTLLW 462 P L L C ++ L W Sbjct: 430 IPILGILTCIAMMVFLPWETW 450 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: 688 Number of extensions: 33 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: 483 Length adjustment: 35 Effective length of query: 547 Effective length of database: 448 Effective search space: 245056 Effective search space used: 245056 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