Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 228 bits (581), Expect = 4e-64 Identities = 142/429 (33%), Positives = 219/429 (51%), Gaps = 24/429 (5%) Query: 30 NGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLAL 89 N L++ L+ RH++++A+G AIG GLF+GS A++ GPA +L+ YL+ G+ + AL Sbjct: 4 NDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPA-ILLSYLLGGVAIFIIMRAL 62 Query: 90 AEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDIN 149 EMAV PV G+F Y ++ P G+ GW Y WL E+ A + + W D+ Sbjct: 63 GEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVP 122 Query: 150 MAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGY-I 208 +W LV + + + V+ YGE EF ++IK+ V I+ G + G+G+QG Sbjct: 123 QWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPT 182 Query: 209 GVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWR 266 G+ G F KG + F++ G EM+GL A E+ NP+KSIP A VFWR Sbjct: 183 GISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWR 242 Query: 267 IAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAV 326 I IFY+ LF++ I P N+ T SPFV+ + GIK I+N V+ A Sbjct: 243 ILIFYVGALFVIMSIYPWNE--------LGTHGSPFVMTFERLGIKSAAGIINFVVLTAA 294 Query: 327 LSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIA---FG-LLAYIGAA 382 LS N + + R + +A++ AP F G P V++ + FG LL Y+ A Sbjct: 295 LSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPA 354 Query: 383 PQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM-KAQGINLGLIPYKTPFGVAGSYL 441 ++F W+ + G ++ WG + + ++ R G+ +AQ L ++ PF SYL Sbjct: 355 ----KVFVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQL---VFRMPFFPYASYL 407 Query: 442 GLGLNILAL 450 L +L + Sbjct: 408 ALAFLVLVV 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: 638 Number of extensions: 36 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: 454 Length adjustment: 34 Effective length of query: 502 Effective length of database: 420 Effective search space: 210840 Effective search space used: 210840 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