Align L-glutamine and L-histidine transporter (characterized)
to candidate Ga0059261_1577 Ga0059261_1577 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Korea:Ga0059261_1577 Length = 470 Score = 915 bits (2365), Expect = 0.0 Identities = 470/470 (100%), Positives = 470/470 (100%) Query: 1 MAGGLFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAV 60 MAGGLFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAV Sbjct: 1 MAGGLFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAV 60 Query: 61 IMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVS 120 IMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVS Sbjct: 61 IMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVS 120 Query: 121 TVAVGWSGYAAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLN 180 TVAVGWSGYAAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLN Sbjct: 121 TVAVGWSGYAAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLN 180 Query: 181 AALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFY 240 AALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFY Sbjct: 181 AALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFY 240 Query: 241 GFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALI 300 GFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALI Sbjct: 241 GFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALI 300 Query: 301 LRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKRGSPVR 360 LRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKRGSPVR Sbjct: 301 LRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKRGSPVR 360 Query: 361 ITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWW 420 ITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWW Sbjct: 361 ITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWW 420 Query: 421 LVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE 470 LVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE Sbjct: 421 LVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE 470 Lambda K H 0.327 0.140 0.426 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: 982 Number of extensions: 31 Number of successful extensions: 1 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: 470 Length of database: 470 Length adjustment: 33 Effective length of query: 437 Effective length of database: 437 Effective search space: 190969 Effective search space used: 190969 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: 51 (24.3 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