Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 228 bits (580), Expect = 5e-64 Identities = 140/441 (31%), Positives = 223/441 (50%), Gaps = 16/441 (3%) Query: 26 GEVKNGG-LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLC 84 GE GG LK++L RH++++A+G IG GLF+GS A++ GPA +++ Y+I G+ +L Sbjct: 10 GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPA-IMLSYIIGGLAILV 68 Query: 85 TCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFW 144 AL EMAV PV G+F Y ++ P GF GW Y WL E+ A ++ + W Sbjct: 69 IMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVW 128 Query: 145 REDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGD 204 D +W L+ + I + V+ +GE EF ++IKI + +I G+ I G G+ Sbjct: 129 FPDTPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN 188 Query: 205 QGY-IGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASK 261 G +G+ G F +G + F++ G EM+GL A E+ NP+K+IP A Sbjct: 189 DGVALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIG 248 Query: 262 QVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAV 321 VFWRI +FY+ LF++ I P N+ T+ SPFV+ + GIK I+N V Sbjct: 249 SVFWRILLFYVGALFVILSIYPWNE--------IGTQGSPFVMTFERLGIKTAAGIINFV 300 Query: 322 ITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGA 381 + A LS N F + R + ++A+ AP F S G P ++L I LL + Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLN 360 Query: 382 APQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM---KAQGINLGLIPYKTPFGVAG 438 ++F W+ ++ G ++ W I LA ++ R + + G+ + Y +A Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLAL 420 Query: 439 SYLGLGLNILALIASFYTALF 459 ++L L + ++A AL+ Sbjct: 421 AFLLLVVGLMAYFPDTRIALY 441 Lambda K H 0.327 0.142 0.442 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: 674 Number of extensions: 38 Number of successful extensions: 5 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: 536 Length of database: 472 Length adjustment: 34 Effective length of query: 502 Effective length of database: 438 Effective search space: 219876 Effective search space used: 219876 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