Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::ALD51314.1 (582 letters) >FitnessBrowser__Dyella79:N515DRAFT_2924 Length = 492 Score = 232 bits (592), Expect = 2e-65 Identities = 148/480 (30%), Positives = 248/480 (51%), Gaps = 36/480 (7%) Query: 44 ARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSA 103 A +KR+L LV G+G ++GAG+FV +G+A++ AGPA+VLS+ AG L+A Sbjct: 23 AHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAA 82 Query: 104 FCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG 163 CY EFA +PV+G A+SY T GE++A+ G +L+++Y+ + A VA ++GY L Sbjct: 83 LCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLA 142 Query: 164 IES-------KLRITVNGLP----DGFNE-----IDVVAVLVVLALTVIICYSTRESSVL 207 + S L T+ P DG + I++ AV ++ A+T + +S+ + Sbjct: 143 LISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFV 202 Query: 208 NMVLTVLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYI 267 N ++ + + I+ I + N+ ++ G +G +GV AA+V+ SYI Sbjct: 203 NSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASE--GASKYGWAGVGRAAAIVFFSYI 260 Query: 268 GYDAVSTMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAF 327 G+DAVST A E KNP +D+P+G+ GS+IL T+LY ++A ++ + + ++ P S A Sbjct: 261 GFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTAL 320 Query: 328 MGSDGWRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPV 387 W+ ++ +GA G+ + +LV ++GQ R + R ++PA F ++H K TP Sbjct: 321 DNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPH 380 Query: 388 NASAFLGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYV------SVGVTNP 441 + +G+ AA+ ++ +L +V++GTL F V V+ RY + V P Sbjct: 381 VGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVP 440 Query: 442 WPT--LSYLFCFSLTSILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARKP 499 W L L C +L F W++ + A AI + L+ Y + RKP Sbjct: 441 WIVCPLGALACMALFLQSFLEHWRW----------MLAWIAIGQAIYFLYGYSHSKLRKP 490 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: 708 Number of extensions: 36 Number of successful extensions: 2 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: 492 Length adjustment: 35 Effective length of query: 547 Effective length of database: 457 Effective search space: 249979 Effective search space used: 249979 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