Align L-alanine and D-alanine permease (characterized)
to candidate PfGW456L13_4790 D-serine/D-alanine/glycine transporter
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4790 Length = 473 Score = 905 bits (2340), Expect = 0.0 Identities = 454/473 (95%), Positives = 458/473 (96%) Query: 1 MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60 MPVGNHLP GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI Sbjct: 1 MPVGNHLPQGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60 Query: 61 IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120 IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA Sbjct: 61 IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120 Query: 121 VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG 180 VAVYMGIWFPDVPRWIWALAAL+SMGSINLIAVKAFGEFEFWFALIKIVTIIAMV+GG+G Sbjct: 121 VAVYMGIWFPDVPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIG 180 Query: 181 IIAFGFGNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ 240 IIAFGFGNDGVALGISNLW HGGFMPNGV GVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ Sbjct: 181 IIAFGFGNDGVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ 240 Query: 241 KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV 300 KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV Sbjct: 241 KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV 300 Query: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLN 360 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTS NGVPRRALLLSI ALLLGVLLN Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLN 360 Query: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420 YLVPEKVFVWVT+IATFGAIWTWVMILLAQLKFRK LSASE A LKYRMWLYPVSSYLAL Sbjct: 361 YLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLAL 420 Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPTGDVQRAVRSAS 473 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFY FKLQPT Q A RS S Sbjct: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTNVSQGAARSVS 473 Lambda K H 0.328 0.142 0.444 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: 978 Number of extensions: 39 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: 473 Length of database: 473 Length adjustment: 33 Effective length of query: 440 Effective length of database: 440 Effective search space: 193600 Effective search space used: 193600 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