Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate WP_058857461.1 AS188_RS02160 amino acid permease
Query= TCDB::P24207 (458 letters) >NCBI__GCF_001482365.1:WP_058857461.1 Length = 498 Score = 315 bits (807), Expect = 2e-90 Identities = 171/437 (39%), Positives = 252/437 (57%), Gaps = 19/437 (4%) Query: 9 EDTASNQEPT-------LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGY 60 + TA + PT L R L RH+ +IA+GGAIGTGLF+ G I AGP L Y Sbjct: 8 QTTAPTRPPTPAEAHARLRRSLKPRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALAAY 67 Query: 61 GVAGIIAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 120 G++ FL+M+ LGEM PVSG+F ++ ++ P GF GWNYW + + AEL Sbjct: 68 VAIGLMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELV 127 Query: 121 AAGIYMQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGL 180 AA + M+YW PDVP+WIW+A F I+ +N ++ R YGE+EFWF+LIKV ++ + G+ Sbjct: 128 AAALIMRYWLPDVPSWIWSALFLAILFGLNALSTRAYGESEFWFSLIKVATVVIFLVLGV 187 Query: 181 WLLFSGHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEK 240 ++ GGE DN F G G++ V FSF G EL+G+ A EA DPEK Sbjct: 188 LMIVGILGGESPGFDNWTTGEAPFVGGGAGILAIFMVAGFSFQGTELVGVAAGEAEDPEK 247 Query: 241 SIPKAVNQVVYRILLFYIGSLVVLLALYPWVE-------VKSNS-SPFVMIFHNLDSNVV 292 ++P+A+ V RILLFY+G++ ++ L P+ V+ S SPF ++F N Sbjct: 248 NVPRAIRTVFVRILLFYVGAITIVGFLIPYTSPHLLGSGVEDISISPFTLVFENAGVLAA 307 Query: 293 ASALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAIT 352 AS +N VIL A LS NSG+Y+++RML+ L+ G APKFL +V+RRGVP+N+L+ + + Sbjct: 308 ASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPKFLAKVNRRGVPMNALLATTTVG 367 Query: 353 SLVVLINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGR---ETQFKALL 409 + L + A+ L++ + W+ I +H RFR A QG+ + +KA Sbjct: 368 AACFLTTLIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRKAYTAQGKDLGDLPYKARF 427 Query: 410 YPFGNYLCIAFLGMILL 426 +P G + +A +++L Sbjct: 428 FPLGPMIALALCAVVIL 444 Lambda K H 0.329 0.143 0.447 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: 582 Number of extensions: 38 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: 458 Length of database: 498 Length adjustment: 34 Effective length of query: 424 Effective length of database: 464 Effective search space: 196736 Effective search space used: 196736 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 (21.8 bits) S2: 51 (24.3 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