Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 230 bits (587), Expect = 8e-65 Identities = 141/429 (32%), Positives = 219/429 (51%), Gaps = 18/429 (4%) Query: 26 GEVKNGG-LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLC 84 G+ GG LK++L RH++++A+G IG GLF+GS A++ GPA +++ Y+I G+ +L Sbjct: 10 GQATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPA-IMLSYIIGGLAILV 68 Query: 85 TCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFW 144 AL EMAV PV G+F Y ++ P GF GW Y WL E+ A +I + W Sbjct: 69 IMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIW 128 Query: 145 REDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGD 204 D+ +W L + + + V+ +GE EF ++IKI + ++ GI I G G+ Sbjct: 129 FPDVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGN 188 Query: 205 QGY-IGVKYWRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASK 261 G +G+ G F G + F++ G EM+GL A E+ NP+K+IP A Sbjct: 189 DGVAVGISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIG 248 Query: 262 QVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAV 321 VFWRI +FY+ LF++ I P N+ +G+ G SPFV+ + GIK I+N V Sbjct: 249 SVFWRILLFYVGALFVILSIYPWNE---IGSQG-----SPFVMTFERLGIKTAAGIINFV 300 Query: 322 ITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGA 381 + A LS N F + R + ++A+ AP F G P ++L I LL + Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLAN 360 Query: 382 APQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGM-----KAQGINLGLIPYKTPFGV 436 ++F W+ ++ G ++ W I LA ++ RAG+ KA + L P + + Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLAL 420 Query: 437 AGSYLGLGL 445 A L +GL Sbjct: 421 AFLVLVVGL 429 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: 645 Number of extensions: 39 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: 472 Length adjustment: 34 Effective length of query: 502 Effective length of database: 438 Effective search space: 219876 Effective search space used: 219876 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