Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_900115975.1:WP_092483642.1 Length = 484 Score = 234 bits (598), Expect = 5e-66 Identities = 130/388 (33%), Positives = 221/388 (56%), Gaps = 15/388 (3%) Query: 58 DLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEFAVDMPVAG 117 DL GVG ++G G+FV +G A+++ AGP VV S+ ++G A L+A Y E +P AG Sbjct: 31 DLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAATLAAMVYAELGAAIPSAG 90 Query: 118 GAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVA---RSFTGYLCTALGIESKLRITVNG 174 A+++ ++ GE +A+L G NLI++Y+++ AV+ S+ G L ++GI T + Sbjct: 91 SAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGDLLQSVGITLPAAFTSSP 150 Query: 175 LPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVFIVFVIVIGFTRGDTKN 234 G +++ A L+VL +T +I T+ S+ N ++ V + I I +G + N Sbjct: 151 FDGGI--VNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLAAIALFIALGVQHINPAN 208 Query: 235 FTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAEEVKNPVKDIPVGVSGSV 294 + P+G SGVF+GAA+V+ +YIG+DAV+T +EEVKNP +D+P G+ ++ Sbjct: 209 WRPV---------LPYGISGVFHGAAIVFFAYIGFDAVATASEEVKNPQRDLPRGIIWTL 259 Query: 295 ILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVSNVIGVGAGFGILTSLLV 354 ++ T+LY ++A ++ ++ Y ++ +P + A + + G W S ++ VGA G+ + LLV Sbjct: 260 VISTLLYIVVAGILTGMVKYTNLNTASPVATALLRA-GIPWASALVSVGALAGLTSVLLV 318 Query: 355 AMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICTAAIALFTDLQILLNLVS 414 AM GQ+R + R ++P F +HP+ TPV S +G+ A I F + ++ L + Sbjct: 319 AMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVALIGAFLPIGLVAELAN 378 Query: 415 IGTLFVFYMVANAVIYKRYVSVGVTNPW 442 IGTL F V+ I R + + P+ Sbjct: 379 IGTLTAFIAVSTGAIILRRTNPDLRRPF 406 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: 640 Number of extensions: 31 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: 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 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