Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_057508921.1 ABB28_RS12350 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_001431535.1:WP_057508921.1 Length = 474 Score = 247 bits (631), Expect = 7e-70 Identities = 150/432 (34%), Positives = 231/432 (53%), Gaps = 17/432 (3%) Query: 46 SGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFC 105 +G + R+L + L G+G ++G G+FV +G+A+++ AGPA++LS+ +A C A Sbjct: 19 NGLSLTRTLGPWGLTALGIGAVIGGGIFVITGQAAANHAGPAIMLSFVLAAICCGFCALA 78 Query: 106 YTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG-I 164 Y EFA +PV+G A+SY TFGE A+ G L+++Y +S +AVA S+TGY + L Sbjct: 79 YAEFAAMVPVSGSAYSYTYATFGELAAWFIGWMLVLEYGVSASAVAVSWTGYFLSLLSHF 138 Query: 165 ESKLRITVNGLP-DGFNE-----IDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVF 218 + L + P DG +V A ++VL LT + R+SS +NM + +L Sbjct: 139 DIHLPAALVSAPLDGQLRPTGAIANVPAAILVLLLTWLCYVGIRKSSAMNMAMVILKTGL 198 Query: 219 IVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAEE 278 IV VI +G+ D N+ N G FG GV GAAMV+ +YIG++AVS A+E Sbjct: 199 IVLVIAVGWKYVDPANWQPFIPENTGPG--QFGMEGVLRGAAMVFFAYIGFEAVSVAAQE 256 Query: 279 VKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVSN 338 P +D+P+G+ S+++ T+LY MAA M+ L+PY ++ D P A W+ Sbjct: 257 SHRPQRDMPIGMMLSLVICTLLYIAMAAVMTGLVPYTLLGTDEPVVTAVAAHPSLGWLRV 316 Query: 339 VIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICTA 398 V+ +GA G+ + +LV ++GQ R ++GR ++P F K+HPK TP + GI A Sbjct: 317 VVEIGALVGLSSVVLVMIIGQPRIFMIMGRDGLLPPLFTKIHPKYRTPHINTVITGIGIA 376 Query: 399 AIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWP--------TLSYLFC 450 +A L +L L S+GTL F V V+ R + P+ +L L C Sbjct: 377 LLAALFPLDVLGELTSMGTLIAFAAVCAGVLVLRRTQPDLPRPFRIRGAWLVCSLGVLSC 436 Query: 451 FSLTSILFTLLW 462 +L S + W Sbjct: 437 MALLSAMTFHNW 448 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: 664 Number of extensions: 41 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: 474 Length adjustment: 35 Effective length of query: 547 Effective length of database: 439 Effective search space: 240133 Effective search space used: 240133 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