Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate CCNA_00435 CCNA_00435 amino acid transporter
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Caulo:CCNA_00435 Length = 483 Score = 191 bits (484), Expect = 8e-53 Identities = 139/460 (30%), Positives = 229/460 (49%), Gaps = 41/460 (8%) Query: 50 MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109 +K++L W LV GVG +VG G++ +G + AGP V+LS+ IAG +A CY E Sbjct: 30 LKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSFLIAGAVCACAALCYAEL 88 Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALGIESKLR 169 + +P +G A++Y GE +A+ G +LI++Y L AAVA G+ A G+ + Sbjct: 89 STMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVA---VGWSAHAHGLFKMI- 144 Query: 170 ITVNGLPDGF-------NEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVFIVFV 222 G PD I++ AV + +A+ ++ TRES+ +NMVL + I+ ++ Sbjct: 145 ----GFPDALLAGPHQGGLINMPAVFISMAVAGLLALGTRESATVNMVLVFVKIIALIVF 200 Query: 223 IVIGFTRGDTKNFTKAGDSNHASGFFPFGAS------GVFNGAAMVYLSYIGYDAVSTMA 276 +V+ + +FT N P GA+ GV A++++ ++ G+DAVST A Sbjct: 201 VVLCLPAFNLAHFTPF-MPNGFQAHVPEGAAADAAKVGVMAAASLIFFAFYGFDAVSTAA 259 Query: 277 EEVKNPVKDIPVGVSGSVILVTVLYCLMAA-SMSMLLPYDMIDPDAPFSGAFMGSDGWRW 335 EE KNP +D+ +G+ GS+ + T +Y ++AA S+ +AP + S Sbjct: 260 EETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTEVFSKSEAPLV-FILESLNHGK 318 Query: 336 VSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGI 395 ++ ++ + A + T +L M GQ+R V+ R ++P +KV+ KT TPV + G+ Sbjct: 319 IAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRALSKVNAKTGTPVMMTLLTGV 378 Query: 396 CTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRY-----VSVGVTNPWPTLSYLFC 450 A I+ L+ + L + GTL+ F V +VI R V T WP + Sbjct: 379 LAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREPNRPRVFSTPLWPIV----- 433 Query: 451 FSLTSILFTLLWQFAPPGKPK-----AFMLGACTAIAIGV 485 + IL L + PGK + A ++GA +A G+ Sbjct: 434 -APAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGM 472 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: 620 Number of extensions: 30 Number of successful extensions: 6 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: 483 Length adjustment: 35 Effective length of query: 547 Effective length of database: 448 Effective search space: 245056 Effective search space used: 245056 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 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