Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate CA265_RS15145 CA265_RS15145 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Pedo557:CA265_RS15145 Length = 649 Score = 207 bits (527), Expect = 1e-57 Identities = 139/452 (30%), Positives = 224/452 (49%), Gaps = 61/452 (13%) Query: 28 RAGSVSTCFEETSRVRARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPA 87 R S+S ++ ++ + ++L DL FG+ ++GAG+F T G+AS+ GPA Sbjct: 7 RKKSISKILQDAAKGYGDHENTLHKTLGVRDLTAFGIAAIIGAGIFSTIGKASAD-GGPA 65 Query: 88 VVLSYAIAGFCALLSAFCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSN 147 V+ + +AF Y EFA +PV+G A++Y + FGE +A++ G +LI++Y + N Sbjct: 66 VIFLFIFTAVACSFAAFAYAEFASMVPVSGSAYTYSYVAFGELVAWIIGWSLIMEYSIGN 125 Query: 148 AAVARS----FTGYLCTA----LGIES----------------------KLRITVNGLPD 177 VA S FTG L T LGIE L L D Sbjct: 126 ITVAISWSDYFTGLLSTIKIPPLGIEGIHVPDWMTMDYLSAYNGHKHAEALLAAGKNLAD 185 Query: 178 -------------------GFNEI-DVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIV 217 F+ + D+ A+ +++ +T +I +ES + + V+ + Sbjct: 186 LDSATALANNAWLTAPKIGSFHLVADIPALGIIILITWLIYRGMKESRNASNAMVVVKLA 245 Query: 218 FIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAE 277 I+ V+ +G DTKN+ F P G SGV G + V+ +YIG+DA+ST AE Sbjct: 246 VILLVLAVGIFYVDTKNWDP---------FAPNGVSGVLKGVSAVFFAYIGFDAISTTAE 296 Query: 278 EVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVS 337 E KNP +D+P G+ ++I+ T+LY +A ++ ++ D + P + F + +S Sbjct: 297 ECKNPQRDLPRGMMWAIIICTILYVAIALVLTGIVKSDTLAVGDPLAFVF-DQINLKLMS 355 Query: 338 NVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICT 397 +I V A F + + LLV +GQ R + R ++P F+K+HPK TP A+ +G Sbjct: 356 GIIAVSAVFAMASVLLVFQMGQPRIWMSMSRDGLLPKSFSKIHPKYKTPSFATIVVGFVV 415 Query: 398 AAIALFTDLQILLNLVSIGTLFVFYMVANAVI 429 A +LF +L I+ +L SIGTLF F +V V+ Sbjct: 416 AVPSLFMNLTIVTDLCSIGTLFAFVLVCAGVL 447 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: 817 Number of extensions: 46 Number of successful extensions: 4 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: 649 Length adjustment: 37 Effective length of query: 545 Effective length of database: 612 Effective search space: 333540 Effective search space used: 333540 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: 53 (25.0 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