Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_053544618.1 CDES_RS05420 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_001277995.1:WP_053544618.1 Length = 468 Score = 217 bits (552), Expect = 9e-61 Identities = 133/410 (32%), Positives = 206/410 (50%), Gaps = 14/410 (3%) Query: 37 LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96 L+ RH+ IA+G AIG GLF GS GA+Q GP+ LL+ YL+ G ++ AL EM+V + Sbjct: 14 LRARHIHFIALGSAIGTGLFYGSAGAIQAAGPSVLLV-YLLGGAVVYFMLRALGEMSVHH 72 Query: 97 PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVSV 156 PV G+F Y + G+ GW +A L V +L A I + FW D VWV+ Sbjct: 73 PVRGSFAVYTRAHLGGWAGYITGWMFAFEMLIVCLADLTAIGIYMNFWFPDTPQWVWVAA 132 Query: 157 FLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIG--VKYWR 214 L+++ G + VR +GE+E V +I+K+ A + I+ G I G+G + W Sbjct: 133 TLLIVGGANLASVRWFGELEVVFTIVKVTAVIAMIVGGAAILAFGLGSNAEVAGISNLWE 192 Query: 215 DPGAF-TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIFYIL 273 G F +G A F++ F+FGGTE++G+A +E+ P KSIP A V RI +FY+ Sbjct: 193 HGGFFPNGIEGMIAAFILVLFAFGGTEIIGVAGSEAEEPEKSIPKAVNTVPVRILLFYVG 252 Query: 274 NLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVANSC 333 + ++ + P P + G + SPFV G+ ++N V+ A LS N+ Sbjct: 253 AILVILALNPW--PSITG------EESPFVQIFDTLGVNWAAGLLNLVVITAALSAINAD 304 Query: 334 TFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLL 393 FG+ R + +A+ N+AP I G P+ I+ I ++ I A +F + Sbjct: 305 LFGAGRVLTGLAKENLAPKAMGKIAKNGVPIMTTIIMIIVLIVGVILNAVLPERVFEIVA 364 Query: 394 ALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGL 443 +L ++VW I LA + R M A+ + + + PF G Y + Sbjct: 365 SLATFATVYVWLMILLAQVGSRRRMSAEEVE--TLKFPVPFYPFGQYFAI 412 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: 589 Number of extensions: 35 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 536 Length of database: 468 Length adjustment: 34 Effective length of query: 502 Effective length of database: 434 Effective search space: 217868 Effective search space used: 217868 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 24 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