Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_065399245.1 BBI00_RS13465 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_001684965.1:WP_065399245.1 Length = 473 Score = 220 bits (561), Expect = 8e-62 Identities = 136/426 (31%), Positives = 213/426 (50%), Gaps = 33/426 (7%) Query: 20 TRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIG 79 + + TGE N L + L NRH+Q+IA+GGAIG GLF+G G A GP+ +L GY + G Sbjct: 2 SNEKNTGE--NETLVRGLTNRHIQLIALGGAIGTGLFLGIGPAAVLAGPSVIL-GYALAG 58 Query: 80 IMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASI 139 I+ L EM V PV+G+F + ++ GFA GW Y + ++ V EL A Sbjct: 59 IIAFFIMRQLGEMVVQEPVSGSFSHFAYKYWGNFPGFASGWNYWILYILVSMAELTAIGH 118 Query: 140 TIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINC 199 I FW +I + V F VV+ + + V+ YGE EF SIIK+ A + I+ G+ + Sbjct: 119 YIHFWWPEIPLWVSSLFFFVVITALNLASVKVYGETEFWFSIIKVIAIIAMIVFGVYLLV 178 Query: 200 GGVGDQGYIGVKYWRDPGAF---------TSFKGFCAVFVVAAFSFGGTEMVGLAAAESA 250 G G + W D G F F G A + FSFGG E++G+ AAE+ Sbjct: 179 SGTGGEKATITNLWNDGGFFPKGLFNKTENGFSGLFAAMAMIMFSFGGLELIGITAAEAK 238 Query: 251 NPRKSIPMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDA- 309 NP K+IP A+ QV +RI IFY+ L I+ + P + +SPFV+ Q+ Sbjct: 239 NPEKTIPQATNQVIYRILIFYVGALVILFSLSPWRE--------ITEGSSPFVMVFQNLN 290 Query: 310 GIK------------VLPSIMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYI 357 G++ ++ +++N ++ A LSV NS + ++R + +A++ AP F K + Sbjct: 291 GLEFSLFGKVIQFNSLIANVLNLIVLTAALSVYNSSVYSNSRMLFGLAQQGNAPKFLKKL 350 Query: 358 DSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAG 417 + P +++ F + I + F +L+AL + W IC H++ + Sbjct: 351 NKNSVPTNAILISSCFAGICIIINKLVPEKAFQYLMALVVSTLIINWLMICYTHLKFKKA 410 Query: 418 MKAQGI 423 + +GI Sbjct: 411 ITREGI 416 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: 620 Number of extensions: 35 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: 473 Length adjustment: 34 Effective length of query: 502 Effective length of database: 439 Effective search space: 220378 Effective search space used: 220378 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