Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 222 bits (565), Expect = 3e-62 Identities = 137/438 (31%), Positives = 226/438 (51%), Gaps = 23/438 (5%) Query: 38 ETSRVRARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGF 97 E+ + A G ++R+L + LVG G+GG++G G+FV +G ++ AGP V LS+ IAG Sbjct: 13 ESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVALSFLIAGV 72 Query: 98 CALLSAFCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY 157 + +A CY EFA +PVAG A++Y GE A++ G +L+++Y L A V+ ++GY Sbjct: 73 ASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVVSIGWSGY 132 Query: 158 LCTALGI----ESKLRITVNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTV 213 L L + + G DG + +D+ A+L + +++ + N + + Sbjct: 133 LRALLALFGVAPPEWAAGAPGTGDG-HILDLFAMLGAFGVALLLTLRVEWGARFNTAMVL 191 Query: 214 LHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVS 273 L I ++ VI+ + N+ F PFG GV GAA+V+ + GYD ++ Sbjct: 192 LKIAAVIVVILAAAPHINPANWRP---------FMPFGFGGVVEGAAVVFFAVFGYDTLT 242 Query: 274 TMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGW 333 T EE P +D+P V S+++ LY LM+ +++ + YD +D AP + AF + G Sbjct: 243 TAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNAAPVASAF-AALGM 301 Query: 334 RWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFL 393 W + V+ A GIL+ +L +LG AR + R ++PAWFA+ HP+ +TP + Sbjct: 302 GWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATPYRPTLIA 361 Query: 394 GICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW--------PTL 445 G A ++ F ++ + LV+IGTL F ++ AVI R+ V + P + Sbjct: 362 GGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRAPLSPYLPLI 421 Query: 446 SYLFCFSLTSILFTLLWQ 463 F L S L + W+ Sbjct: 422 GVGFSLWLLSKLPAIAWE 439 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: 643 Number of extensions: 42 Number of successful extensions: 6 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: 488 Length adjustment: 35 Effective length of query: 547 Effective length of database: 453 Effective search space: 247791 Effective search space used: 247791 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