Align high affinity cationic amino acid transporter 1 (characterized)
to candidate Ga0059261_1577 Ga0059261_1577 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Korea:Ga0059261_1577 Length = 470 Score = 221 bits (562), Expect = 7e-62 Identities = 153/436 (35%), Positives = 233/436 (53%), Gaps = 50/436 (11%) Query: 16 RKVVDCSRE--ESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIA 73 ++V D + + E RL+ L+ LVALGVG+ +G G+ L G V AGPA+++SF+IA Sbjct: 9 KRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIG-VGAGKAGPAVIMSFVIA 67 Query: 74 ALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWS 133 A L Y E +P +GSAY YSY +GE+ A++ GW+LIL Y + S+VA WS Sbjct: 68 GAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWS 127 Query: 134 ATFDELI----GKPIGEFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMV 189 L+ G P+ + H A G++ ++ A+ II ++ GLL LG KESA + Sbjct: 128 GYAAPLLHAWTGMPLELMAGPH----ANGIV----NLPAIFIIAVVAGLLCLGTKESATL 179 Query: 190 NKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFS--- 246 N + ++ L FV ++ + N N++ F PFGF+ Sbjct: 180 NAALVVVKIIALAV-----FVAVALPYF-----------NGANLE----PFAPFGFAKTI 219 Query: 247 -------GVLSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSA 299 GV++ AA F+AF GFD I+T EE KNP + + +GIV S++ C Y V+ Sbjct: 220 SPDGVERGVMAAAAIIFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAV 279 Query: 300 ALTLMMPYFCLDIDSPLPGAFKHQGWEEAKYA--VAIGSLCALSTSLLGSMFPMPRVIYA 357 A P F +SP P A + +A +A+ ++ AL T LLG +F R+ + Sbjct: 280 AAVGATP-FTHFANSPEPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFT 338 Query: 358 MAEDGLLFKFLAKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVA 417 MA DG+L LAK++ R +PV T+ + AI AV+A L + ++ L + GTL A++ VA Sbjct: 339 MARDGMLPIGLAKVSKR-GSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVA 397 Query: 418 ACVLVLRYQ-PEQPNL 432 C++VLR + P+ P + Sbjct: 398 VCMMVLRVRAPDMPRM 413 Lambda K H 0.324 0.138 0.417 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: 760 Number of extensions: 46 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 470 Length adjustment: 35 Effective length of query: 587 Effective length of database: 435 Effective search space: 255345 Effective search space used: 255345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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