Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate CCNA_01242 CCNA_01242 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Caulo:CCNA_01242 Length = 531 Score = 216 bits (550), Expect = 2e-60 Identities = 137/457 (29%), Positives = 239/457 (52%), Gaps = 42/457 (9%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +KR+L +L+ GVG ++GAG+FV +G+ +S AGPA++LS+ +AG L+ CY E Sbjct: 24 LKRTLGPINLMSLGVGAIIGAGIFVLTGQVASANAGPAIMLSFIVAGIACALAGLCYAEL 83 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCT---ALGIES 166 A MPV+G A++Y T GE A++ G L+++Y ++ + VA ++GY+ + ALGI Sbjct: 84 ASTMPVSGSAYTYAYGTLGEVFAWIMGWLLVLEYGVAASTVAVGWSGYVVSTLHALGINF 143 Query: 167 KL--------------RITVNGLPDG------FNEIDVVAVLVVLALTVIICYSTRESSV 206 + I P G +++VA + + ++ ++ ES+ Sbjct: 144 PMIQVAGADAPMWATPLIQAVAAPGGGTMFAMTGTLNLVAAIGIAMVSALLVVGVSESAN 203 Query: 207 LNMVLTVLHIVFIVFVIVIGFTRGDTKNFTK-AGDSNHASGFFPFGASGVFNGAAMVYLS 265 +N + V+ ++ +V I +G + N+ + G FG G+F GAA+++ + Sbjct: 204 VNNAIVVIKVIVLVTFIAVGAQYINPANWHPFIPEPTGQPG--EFGIGGIFRGAAIIFFA 261 Query: 266 YIGYDAVSTMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSG 325 Y+G++AVST A E KNP +D+P+G+ G++I+ T++Y +AA M+ ++P+ + AP + Sbjct: 262 YVGFEAVSTAAAEAKNPSRDVPIGILGALIICTLIYMAVAAVMTGVVPFRELASPAPIAV 321 Query: 326 A------------FMGSDGWR--WVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSV 371 A + ++G + +S I +GA G+ + +LV GQ R + R + Sbjct: 322 AIDRMGLEWADIPYAAAEGGKLNLLSFAIKIGAITGLSSVMLVLCYGQTRIFYTMARDGL 381 Query: 372 VPAWFAKVHPKTSTPVNASAFLGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYK 431 +P FA++HPK TP + LG+ A A F + +L +LVS+GT F +V +VIY Sbjct: 382 LPKVFAEIHPKFRTPWLGTILLGVVIAIAASFLPISLLGDLVSLGTAVAFSIVCLSVIYL 441 Query: 432 RYVSVGVTNPWPTLSYLF--CFSLTSILFTLLWQFAP 466 R + P+ +F + + LF F P Sbjct: 442 RIKHPDLPRPFKVPGGIFTAAAGIAACLFLPYQNFQP 478 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: 758 Number of extensions: 40 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: 531 Length adjustment: 36 Effective length of query: 546 Effective length of database: 495 Effective search space: 270270 Effective search space used: 270270 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