Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_066600509.1 V473_RS03185 amino acid permease
Query= TCDB::ALD51314.1 (582 letters) >NCBI__GCF_001046645.1:WP_066600509.1 Length = 464 Score = 194 bits (493), Expect = 7e-54 Identities = 132/435 (30%), Positives = 213/435 (48%), Gaps = 24/435 (5%) Query: 46 SGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFC 105 +G + R+L W L+ GVG +VG G+ G + AGPAV+LS+AIAG +A Sbjct: 17 AGHQLARTLSWPHLLALGVGAIVGTGILTLIGVGADR-AGPAVLLSFAIAGAICACAALA 75 Query: 106 YTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY---LCTAL 162 Y E + MP AG A+SY + GE +A++ G +LI++Y L + VA ++GY L TA+ Sbjct: 76 YAELSTMMPAAGSAYSYSYVALGEGIAWVVGWSLILEYSLVVSTVAVGWSGYAAPLLTAI 135 Query: 163 GIESKLRITVNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIVFIVFV 222 G L G P+ I++ A+ ++ + ++ TRES+ LN +L ++ IV + Sbjct: 136 GFPKML---TQG-PELGGLINLPAIFIIAVVAGLLMLGTRESARLNTILVLIKIVTLSLF 191 Query: 223 IVIGFTRGDTKNFTKAGDSNHASGFFPFGAS-GVFNGAAMVYLSYIGYDAVSTMAEEVKN 281 + D +N A P G GV AA+++ ++ G+DA+ST AEE KN Sbjct: 192 VAYALPAFDAQNLEPFMPFGFAKHMGPDGVERGVMAAAAIIFFAFYGFDAISTAAEEAKN 251 Query: 282 PVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVSNVIG 341 P +D+ +G+ GS+I+ T++Y L+AA+ LP+ + G ++ ++ Sbjct: 252 PDRDLAIGIVGSLIICTLIYVLVAAAAIGALPFTRFADSPEPLALILREMGQGGIARIVA 311 Query: 342 VGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICTAAIA 401 + A + T LL + GQ+R V+ R +P AK+ K TP +A A IA Sbjct: 312 IAAVIALPTVLLGFLYGQSRIFLVMARDGFLPQSLAKI-SKRGTPARITAVTAALVAVIA 370 Query: 402 LFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWPT-------------LSYL 448 + + L + GTL F V ++ R S + P+ T +YL Sbjct: 371 GLLPIDEIAALANAGTLIAFTAVGWCLLVLRRRSPDLRRPFRTPAAWFVGVGAIGGCAYL 430 Query: 449 F-CFSLTSILFTLLW 462 F + +IL L+W Sbjct: 431 FVSLPMKTILACLVW 445 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: 623 Number of extensions: 28 Number of successful extensions: 4 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: 464 Length adjustment: 35 Effective length of query: 547 Effective length of database: 429 Effective search space: 234663 Effective search space used: 234663 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 24 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