Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 223 bits (568), Expect = 1e-62 Identities = 142/426 (33%), Positives = 211/426 (49%), Gaps = 12/426 (2%) Query: 28 VKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCL 87 ++ GLK+ LKNRH+Q+IA+GGAIG GLF+GS LQ GP+ +++GY I G++ Sbjct: 50 LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGVIAFMIMR 108 Query: 88 ALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWRED 147 L EM PV G+F + ++ GF GW Y + ++ V EL A + +W Sbjct: 109 QLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168 Query: 148 INMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGY 207 + V V + I + V+ YGE EF +IIK+ A +G I+ G + G G Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228 Query: 208 IGVKYWRDPGAFT-SFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWR 266 W G F F G + V FSFGG E++G+ AAE+ P+KSIP A QV +R Sbjct: 229 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 288 Query: 267 IAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAV 326 I IFYI +L ++ + P N+ + A G SPFV+ G + +++N V+ A Sbjct: 289 ILIFYICSLAVLLSLYPWNE---VAAGG-----SPFVMIFSQIGSTLTANVLNVVVLTAA 340 Query: 327 LSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGM 386 LSV NS + ++R + +AE+ AP +D +G P + L I Sbjct: 341 LSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPA 400 Query: 387 EIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG--VAGSYLGLG 444 E G L+AL + W I L H++ R M A G L + P + +++ L Sbjct: 401 EALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALI 460 Query: 445 LNILAL 450 L ILA+ Sbjct: 461 LVILAM 466 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: 615 Number of extensions: 27 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: 506 Length adjustment: 35 Effective length of query: 501 Effective length of database: 471 Effective search space: 235971 Effective search space used: 235971 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