Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate N515DRAFT_2925 N515DRAFT_2925 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Dyella79:N515DRAFT_2925 Length = 480 Score = 254 bits (649), Expect = 6e-72 Identities = 146/438 (33%), Positives = 238/438 (54%), Gaps = 31/438 (7%) Query: 47 GGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCY 106 G ++R+L + + G+G ++G G+FV +G+A++ AGPAV++S+ +A C+ +A CY Sbjct: 21 GPSLRRTLGKWGITALGIGAVIGTGIFVVTGQAAAEHAGPAVLISFMLAAICSGFTALCY 80 Query: 107 TEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG-IE 165 EFA +P++G ++SY T GE +A+ G N++++Y +S +AVA S+TGY + L + Sbjct: 81 AEFATLIPISGSSYSYAYATLGELVAWFIGWNMVLEYGISASAVAASWTGYFTSLLDHVG 140 Query: 166 SKLRITVNGLPDGFNE---------IDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHI 216 L + + P F + +++ AV +VLALT + RESS LN+++ L + Sbjct: 141 IHLPVALTEAPLAFKDGHLVTTGHLLNLPAVAIVLALTWLCYVGIRESSGLNVLMVALKV 200 Query: 217 VFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMA 276 I+ V+V G+ D N+ + G +G SG+ GAAMV+ +YIG++A ST A Sbjct: 201 GLIIVVVVAGYRYVDPANWHPFIPAEQEPG--KYGWSGIMRGAAMVFFAYIGFEATSTAA 258 Query: 277 EEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWV 336 +E KNP KD+P G S+++ TVLY MAA ++ L+PY + P A W+ Sbjct: 259 QECKNPQKDLPFGTLVSLVICTVLYLAMAAVLTGLIPYTELGTSEPVVTAIRNHPELGWL 318 Query: 337 SNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGIC 396 V+ +GA G+ + +LV ++ Q R ++ R ++P F ++HPK TP + GI Sbjct: 319 RLVVEIGAMIGLSSVILVMIIAQPRIFMIMSRDGLLPPVFNRIHPKHRTPHLNTVITGIG 378 Query: 397 TAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPWPTLSYLF------- 449 A +A L +L +L S+GTL F V V+ RY + P L LF Sbjct: 379 IAILAAVFPLDLLADLTSMGTLIAFVAVCAGVLILRYTA-------PELPRLFRVPAAWF 431 Query: 450 -----CFSLTSILFTLLW 462 FS ++L+ + W Sbjct: 432 VCTAGVFSCLALLYFMAW 449 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: 647 Number of extensions: 36 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: 480 Length adjustment: 35 Effective length of query: 547 Effective length of database: 445 Effective search space: 243415 Effective search space used: 243415 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