Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__BFirm:BPHYT_RS15500 Length = 461 Score = 226 bits (575), Expect = 2e-63 Identities = 144/422 (34%), Positives = 210/422 (49%), Gaps = 12/422 (2%) Query: 32 GLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAE 91 GLK+ LKNRH+Q+IA+GGAIG GLF+GS LQ GP+ +++GY I GI+ L E Sbjct: 9 GLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGIIAFMIMRQLGE 67 Query: 92 MAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMA 151 M PV G+F + ++ GF GW Y + ++ V EL A I +W + Sbjct: 68 MVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIHYWWPGVPTW 127 Query: 152 VWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVK 211 V V ++ I + V+ YGE EF +IIK+ A +G I+ G + G G Sbjct: 128 VSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGHGGPQASITN 187 Query: 212 YWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIF 270 W G F F G + V FSFGG E++G+ AAE+ P+KSIP A QV +RI IF Sbjct: 188 LWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKAVNQVIYRILIF 247 Query: 271 YILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVA 330 YI +L ++ + P N+ + A G SPFV+ G + +++N V+ A LSV Sbjct: 248 YICSLTVLLSLYPWNE---VAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAALSVY 299 Query: 331 NSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFG 390 NS + ++R + +AE+ AP +D +G P + L I E G Sbjct: 300 NSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALG 359 Query: 391 WLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLGLNIL 448 L+AL + W I L H++ R M A G L + P + +++ L L IL Sbjct: 360 LLMALVVAALVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSNWICLAFMALILVIL 419 Query: 449 AL 450 A+ Sbjct: 420 AM 421 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: 582 Number of extensions: 26 Number of successful extensions: 5 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: 461 Length adjustment: 34 Effective length of query: 502 Effective length of database: 427 Effective search space: 214354 Effective search space used: 214354 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 17 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