Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__Keio:14712 Length = 458 Score = 246 bits (629), Expect = 1e-69 Identities = 151/434 (34%), Positives = 230/434 (52%), Gaps = 12/434 (2%) Query: 18 SETRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLI 77 + T +T + L + L NRH+Q+IA+GGAIG GLF+G G A+Q GPA LL GY + Sbjct: 4 ASTVSEDTASNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLL-GYGV 62 Query: 78 IGIMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAA 137 GI+ L EM V PV+G+F + ++ P GF GW Y + ++ V EL AA Sbjct: 63 AGIIAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAA 122 Query: 138 SITIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVI 197 I +++W D+ +W + F +++ + + VR YGE EF ++IK+ A +G I G+ + Sbjct: 123 GIYMQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWL 182 Query: 198 NCGGVGDQGYIGVKYWRDPGAF-TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSI 256 G G + WR G F T + G V FSFGG E++G+ AAE+ +P KSI Sbjct: 183 LFSGHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSI 242 Query: 257 PMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPS 316 P A QV +RI +FYI +L ++ + P + + +SPFV+ + V+ S Sbjct: 243 PKAVNQVVYRILLFYIGSLVVLLALYPWVE--------VKSNSSPFVMIFHNLDSNVVAS 294 Query: 317 IMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLL 376 +N VI VA LSV NS + ++R + ++ + AP F + +G P+ ++L A L Sbjct: 295 ALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSL 354 Query: 377 AYIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFG- 435 + + FG L+AL L W ICLAH+R RA M+ QG PFG Sbjct: 355 VVLINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGN 414 Query: 436 -VAGSYLGLGLNIL 448 + ++LG+ L ++ Sbjct: 415 YLCIAFLGMILLLM 428 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: 616 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 536 Length of database: 458 Length adjustment: 34 Effective length of query: 502 Effective length of database: 424 Effective search space: 212848 Effective search space used: 212848 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