Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_084937109.1 HA51_RS22655 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_002095475.1:WP_084937109.1 Length = 488 Score = 303 bits (777), Expect = 7e-87 Identities = 166/480 (34%), Positives = 257/480 (53%), Gaps = 15/480 (3%) Query: 32 GLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAE 91 GL+++LK RH+ MIAIGG+IG GLFV SG + + GP L+ Y +IG+M+ +L E Sbjct: 12 GLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYALIGLMVYFLMTSLGE 71 Query: 92 MAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMA 151 +A PV+G+F TY ++V+ +GFA+GW Y W + +L+A+ + + +W D Sbjct: 72 LAAFMPVSGSFATYGSKYVEEGFGFALGWNYWYNWAVTIAVDLVASQLVMNYWFPDTPGW 131 Query: 152 VWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVK 211 +W ++FL ++ + V+G+GE E+ S+IK+ V FI++G+++ G + G Sbjct: 132 IWSALFLCLMFLLNYISVKGFGEAEYWFSLIKVVTVVIFIVVGVLMITGIMRGAENAGWH 191 Query: 212 YWR--DPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269 W D F V ++ FSF GTE++G+AA ES +P K+IP A +QVFWRI + Sbjct: 192 NWTVGDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESQDPAKNIPRAVRQVFWRILL 251 Query: 270 FYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSV 329 FYI + I+ LILP DP+L+ + SPF L Q+AG+ ++MNAVI AVLS Sbjct: 252 FYIFAILIISLILPYTDPKLLHNDVTDIAISPFTLVFQNAGLLSAAAVMNAVILTAVLSA 311 Query: 330 ANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIF 389 NS + STR + +A AP F + G P +I L ++ + E++ Sbjct: 312 GNSGMYASTRMLFNLAREGKAPRIFGKLSKGGVPRNALIATTVVAGLCFLSSKFGNQEVY 371 Query: 390 GWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGLGLNILA 449 WLL +G+ W I ++H R R G AQG+NL +PY++ F G L ++ Sbjct: 372 LWLLNTSGMTGFIAWLGIAISHYRFRRGYVAQGLNLADLPYRSGFFPLGPIFAFVLCLII 431 Query: 450 LIASFYTALFPAS----GASPTAEAFFSSYLAFFSVTLLYLGYKACTRKRQMYVRPAEMD 505 + Y A G + T Y+ L++LGYK R +V+ +EM+ Sbjct: 432 TLGQNYQAFLQDRIDWYGVAAT-------YIGIPLFLLIWLGYKLVRGSR--WVKYSEME 482 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: 643 Number of extensions: 26 Number of successful extensions: 2 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: 488 Length adjustment: 35 Effective length of query: 501 Effective length of database: 453 Effective search space: 226953 Effective search space used: 226953 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