Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_001484605.1:WP_058929813.1 Length = 470 Score = 217 bits (553), Expect = 7e-61 Identities = 138/444 (31%), Positives = 224/444 (50%), Gaps = 31/444 (6%) Query: 37 LKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEMAVLY 96 LK R + M+ +G AIGAGLF+GSG +Q GPA +LI YL+ G +++ AL EMA Sbjct: 16 LKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPA-VLISYLVAGTLIILVMWALGEMAAAN 74 Query: 97 PVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAVWVSV 156 P +GAF Y + P G +GW + L + V+ E + A+ + + + + V Sbjct: 75 PDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPALPVWLMAFV 134 Query: 157 FLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCG---GVGDQGYIGVKYW 213 F+VVL + + V+ +GE EF +++K+ A VGF+++G + G GV G + Sbjct: 135 FIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQSPGL--ANFT 192 Query: 214 RDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIFYIL 273 D A F G V AF+FGGTE+V +AAAE+A P +S+ A + V WRI +FYI Sbjct: 193 GDGFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLWRILVFYIG 252 Query: 274 NLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVANSC 333 +F++ ++P +G++G SPF ++ AG+ + + V A+LS N+ Sbjct: 253 AIFVIAAVVP------VGSAGLK---SPFAAVLEAAGMPGAATAITLVAVAALLSALNAN 303 Query: 334 TFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLL 393 +G++R ++A+R AP + P+ V+ +AFG++ + ++ LL Sbjct: 304 LYGASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFPEKVLPVLL 363 Query: 394 ALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGL----IPYKTPFGVAGSYLGLGLNILA 449 + G L VW S LA + +R +G L L P+ T FG L Sbjct: 364 NIVGSTCLLVWTSALLAQLALRLRANREGTELPLRMPGFPWLTCFG------------LL 411 Query: 450 LIASFYTALFPASGASPTAEAFFS 473 ++A+ +T F + P + F+ Sbjct: 412 ILAAIFTVGFIGEDSRPQLLSTFA 435 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: 618 Number of extensions: 36 Number of successful extensions: 4 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: 470 Length adjustment: 34 Effective length of query: 502 Effective length of database: 436 Effective search space: 218872 Effective search space used: 218872 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 Apr 09 2024. 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