Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_012400013.1 BPHY_RS03010 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_000020045.1:WP_012400013.1 Length = 466 Score = 224 bits (570), Expect = 7e-63 Identities = 144/425 (33%), Positives = 211/425 (49%), Gaps = 12/425 (2%) Query: 29 KNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLA 88 ++ GLK+ LKNRH+Q+IA+GGAIG GLF+GS G L+ GP+ +++GY I G + Sbjct: 10 QHDGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIGGFIAFLIMRQ 68 Query: 89 LAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDI 148 L EM PV G+F + ++ GF GW Y + ++ V EL A + FW + Sbjct: 69 LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHFWWPGV 128 Query: 149 NMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYI 208 + V VV+ I + V+ YGE EF +I+K+ A +G I+ G + G G Sbjct: 129 PAWLSALVCFVVINAINLANVKAYGETEFWFAIVKVVAVMGMIVFGGYLLLSGHGGPQAS 188 Query: 209 GVKYWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRI 267 W G F G + V FSFGG E++G+ AAE+ +P+KSIP A QV +RI Sbjct: 189 ISNLWSQGGFFPHGVHGLFMMLAVIMFSFGGLELIGITAAEADDPQKSIPKAVNQVIYRI 248 Query: 268 AIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVL 327 IFYI +L ++ + P N A G SPFV+ G + +++N V+ A L Sbjct: 249 LIFYICSLIVLLSLYPWNQV----AEG----GSPFVMIFSQIGAGLTANVLNVVVLTAAL 300 Query: 328 SVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGME 387 SV NS + ++R + +AE+ AP +D +G P + L I + Sbjct: 301 SVYNSGVYANSRMLYGLAEQGNAPRALLEVDRRGVPYMAIGLSAVATFACVIINYLMPAK 360 Query: 388 IFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLGL 445 L+AL + W I L H++ R M AQG L P G V +++ L L Sbjct: 361 ALDVLMALVVAALVLNWSLISLTHLKSRRAMLAQGDTLVFKSLWFPLGNWVCLAFMALIL 420 Query: 446 NILAL 450 ILAL Sbjct: 421 VILAL 425 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: 585 Number of extensions: 29 Number of successful extensions: 6 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: 466 Length adjustment: 34 Effective length of query: 502 Effective length of database: 432 Effective search space: 216864 Effective search space used: 216864 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