Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_034528196.1 LOSG293_RS05960 amino acid permease
Query= TCDB::Q2VQZ4 (536 letters) >NCBI__GCF_000740055.1:WP_034528196.1 Length = 498 Score = 309 bits (792), Expect = 1e-88 Identities = 176/472 (37%), Positives = 257/472 (54%), Gaps = 9/472 (1%) Query: 20 TRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIG 79 + V+ E++N +K+ LK RH+ MIA+GG IG GLFV SG A+ GP L+ Y+ +G Sbjct: 4 SEQVQDTELENHEVKRGLKTRHVSMIALGGCIGTGLFVASGSAISSAGPGGALVAYIAMG 63 Query: 80 IMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASI 139 +M+ +L EMA P++G+F Y ++VDP+ GFAMGW Y W + ++ A++ Sbjct: 64 MMVYFLMTSLGEMATNMPISGSFAAYSAKYVDPALGFAMGWNYWFNWAITVAVDISTAAL 123 Query: 140 TIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINC 199 I+FW + +W +V LV+L I VR YGE EF LS+IKI V F+++G++ Sbjct: 124 VIKFWLPGVPGWIWSAVALVILFVINALSVRTYGETEFWLSLIKIVTIVVFLVVGLLTIF 183 Query: 200 GGVGDQ--GYIGVKYWRDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIP 257 G +G G Y + P F +VFVVA FSF GTE+VG+ A ES +P KS+P Sbjct: 184 GIMGGHATGLENFTYKKAP-FVGGFPAILSVFVVAGFSFQGTELVGITAGESEDPHKSVP 242 Query: 258 MASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSI 317 A QVFWRI +FYIL + ++ LI+P L+G+S + SPF L Q AG+ SI Sbjct: 243 KAINQVFWRIILFYILAIAVIALIIPYTSHDLLGSSATDVAISPFTLVFQRAGLAAAASI 302 Query: 318 MNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLA 377 MNAVI +VLS ANS + STR + ++A AP F G P+ ++ + Sbjct: 303 MNAVILTSVLSSANSGMYASTRMLYSLAHEGYAPKAFGRTTKNGIPMLALVGTTLIAAVT 362 Query: 378 YIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVA 437 +I + G +++ WL+A +GL W I ++H R R QG +L + Y + Sbjct: 363 FISSI-AGPQLYLWLVAASGLTGFIAWIGIAISHFRFRRAFIKQGHDLSELKYHAKWFPI 421 Query: 438 GSYLGLGLNILALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYK 489 G L L L I +I PAS A+ +Y++ V +LY+ YK Sbjct: 422 GPILALILCIGVIIGQ-----DPASFANFNWTQILVTYISVPLVLVLYIVYK 468 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: 628 Number of extensions: 23 Number of successful extensions: 3 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: 498 Length adjustment: 35 Effective length of query: 501 Effective length of database: 463 Effective search space: 231963 Effective search space used: 231963 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