Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= TCDB::P24207 (458 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 817 bits (2111), Expect = 0.0 Identities = 406/457 (88%), Positives = 432/457 (94%), Gaps = 1/457 (0%) Query: 1 MKNASTVSEDTASNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGY 60 MK+AST SE T PTLHRGL NRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGY Sbjct: 1 MKDASTSSE-TIEESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGY 59 Query: 61 GVAGIIAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 120 VAGI+AFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT Sbjct: 60 AVAGIVAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 119 Query: 121 AAGIYMQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGL 180 AAGIYMQYW PDVPTWIWAAAFF+IINAVNLVNVRLYGE EFWFALIKVLAIIGMIGFGL Sbjct: 120 AAGIYMQYWLPDVPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGL 179 Query: 181 WLLFSGHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEK 240 W+LF GHGG KA IDNLW++GGFFATGW+GLI+SLAVIMFSFGGLELIGITAAEA++PEK Sbjct: 180 WMLFGGHGGSKAGIDNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEK 239 Query: 241 SIPKAVNQVVYRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVI 300 SIPKAVNQVVYRILLFYIGSLVVLLALYPWVE++S+SSPFVMIFHNLDSNVVASALNFVI Sbjct: 240 SIPKAVNQVVYRILLFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVI 299 Query: 301 LVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINY 360 LVASLSVYNSGVYSNSRMLFGLSVQGNAPKFL RVS+RGVP+NSL+LSG ITSLVV++NY Sbjct: 300 LVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVVVLNY 359 Query: 361 LLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAF 420 LLPQKA GLLMALVVATLLLNWIMICLAHL+FRAA RR+GRE +FKALL P NY+CIAF Sbjct: 360 LLPQKALGLLMALVVATLLLNWIMICLAHLKFRAAQRRKGREPKFKALLSPASNYICIAF 419 Query: 421 LGMILLLMCTMDDMRLSAILLPVWIVFLFMAFKTLRR 457 L +IL+LMCT+D MRLSAILLPVWI+FLF AFKTLRR Sbjct: 420 LALILVLMCTIDGMRLSAILLPVWILFLFAAFKTLRR 456 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: 804 Number of extensions: 34 Number of successful extensions: 1 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: 458 Length adjustment: 33 Effective length of query: 425 Effective length of database: 425 Effective search space: 180625 Effective search space used: 180625 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 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