Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 224 bits (570), Expect = 7e-63 Identities = 141/398 (35%), Positives = 211/398 (53%), Gaps = 9/398 (2%) Query: 31 GGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALA 90 G L++ LKNRH+Q+IA+GGAIG GLF+GS G L+ GP+ +++GY I G + L Sbjct: 9 GSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPS-MILGYAIGGFIAFLIMRQLG 67 Query: 91 EMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINM 150 EM V PV G+F + ++ GF GW Y + ++ V EL A ++FW ++ Sbjct: 68 EMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPT 127 Query: 151 AVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGV 210 + F V++ I + V+ +GE EF +I+K+ A VG I+LG+ + G G + Sbjct: 128 WATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKGGEQASIS 187 Query: 211 KYWRDPGAF-TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269 W G F F G + FSFGG E+VG+ AAE+A P+ IP A QV +RI I Sbjct: 188 NLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILI 247 Query: 270 FYILNLFIVGLILPANDPRL-MGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLS 328 FYI L ++ + P + L +GA+G SPFV G ++N V+ A LS Sbjct: 248 FYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALS 307 Query: 329 VANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLL--AYIGAAPQG- 385 V NS + ++R + +AE+ AP I+S+G P+ V + LL A PQG Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGA 367 Query: 386 MEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGI 423 +E+ L++L + W I LAH++ R M+ QG+ Sbjct: 368 LEL---LMSLAVAALVINWAMISLAHLKFRRAMQQQGV 402 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: 627 Number of extensions: 33 Number of successful extensions: 6 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: 464 Length adjustment: 34 Effective length of query: 502 Effective length of database: 430 Effective search space: 215860 Effective search space used: 215860 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