Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_002117405.1:WP_102938052.1 Length = 481 Score = 248 bits (633), Expect = 4e-70 Identities = 151/466 (32%), Positives = 241/466 (51%), Gaps = 31/466 (6%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +KR+L W L+ G+GG++GAG+FV +G+A++ AGP V +S+ ++G A CY E Sbjct: 29 LKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACTFVALCYAEL 88 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY---LCTALGIES 166 A +P AG ++Y +T GE A++ G NL+++Y A VA + GY + LGI Sbjct: 89 AALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNRVMQGLGIHL 148 Query: 167 KLRIT---------VNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIV 217 +T + G FN V A ++L LT ++ T ESS N ++ V+ ++ Sbjct: 149 PEALTSAYFANAHSIGGTHGVFN---VPAAAIILLLTALLMRGTSESSFFNNIIVVIKVM 205 Query: 218 FIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAE 277 ++ VI +G D N+T N F FG SGV GA++V+ +YIG+D VST A+ Sbjct: 206 VVLVVIFVGAAHVDAANWTPLIPEN-TDHFGHFGWSGVVRGASVVFFAYIGFDGVSTAAQ 264 Query: 278 EVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVS 337 E P +D+P+G+ GS+++ T+LY +AA + ++ Y + P + M G W+S Sbjct: 265 EAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKELGVPDPMA-LVMDRTGVAWLS 323 Query: 338 NVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICT 397 V+ +GA G+ T++L+ + GQ R + + ++P FA VHP TP + A +G+ Sbjct: 324 WVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPVWRTPAVSQALVGVFV 383 Query: 398 AAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW-----PTLSYLFCFS 452 A A + IL +VSIGTL F +V AV++ R + P+ P + L S Sbjct: 384 ALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPFRAPGIPAMPLLGIAS 443 Query: 453 LTSILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARK 498 +++ L P L AIG+ F Y V A++ Sbjct: 444 CLALMVAL---------PLETWLRLIVWTAIGMAIYFFYGVKHAKR 480 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: 660 Number of extensions: 36 Number of successful extensions: 4 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: 481 Length adjustment: 35 Effective length of query: 547 Effective length of database: 446 Effective search space: 243962 Effective search space used: 243962 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 Apr 09 2024. 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