Align arginine permease (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= CharProtDB::CH_091699 (590 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 269 bits (687), Expect = 2e-76 Identities = 168/479 (35%), Positives = 249/479 (51%), Gaps = 34/479 (7%) Query: 67 MEDGIGDEDEGEVQNAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISY 126 M+D + E + R L+ RHI +IALGG IGTGLF+G+ + AGP L+ Y Sbjct: 1 MKDASTSSETIEESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGY 59 Query: 127 LFMGSLAYSVTQSLGEMATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELS 186 G +A+ + + LGEM PV+ SF F+ ++ P G +G+ YW + + EL+ Sbjct: 60 AVAGIVAFLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELT 119 Query: 187 VVGQVIQFWTYKVPLAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCF 246 G +Q+W VP W + F++II +NL V+ YGE EFW A IKVLAIIG + + Sbjct: 120 AAGIYMQYWLPDVPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGL 179 Query: 247 CMVCGAGVTGPVGF-RYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGI 305 M+ G G W++ G + G + G + SL F+F G EL+GI Sbjct: 180 WMLFGGHGGSKAGIDNLWKHGGFFATG----------WHGLIMSLAVIMFSFGGLELIGI 229 Query: 306 TAGEAANPRKSVPRAIKKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIA 365 TA EA NP KS+P+A+ +VV+RIL FYIGSL+ + L P+ + QS S SPF++ Sbjct: 230 TAAEAQNPEKSIPKAVNQVVYRILLFYIGSLVVLLALYPWVE---IQSDS----SPFVMI 282 Query: 366 IENSGTKVLPHIFNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYI 425 N + V+ N VIL +S NS +Y SR+LFGLS APKFL+R +K GVP Sbjct: 283 FHNLDSNVVASALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLARVSKRGVPVN 342 Query: 426 AVFVTAAFGALAYMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISR 485 ++ ++ +L + K L+ + W+ I ++H++F A + +G Sbjct: 343 SLLLSGIITSLVVVLNYLLPQKALGLLMALVVATLLLNWIMICLAHLKFRAAQRRKG--- 399 Query: 486 DELPFKAKLMPGLAYYAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILF 544 E FKA L P Y F+ +I+++ +G+ +A + L VWILF Sbjct: 400 REPKFKALLSPASNYICIAFLALILVLM------CTIDGMRLSA------ILLPVWILF 446 Lambda K H 0.325 0.140 0.438 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: 723 Number of extensions: 33 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: 590 Length of database: 458 Length adjustment: 35 Effective length of query: 555 Effective length of database: 423 Effective search space: 234765 Effective search space used: 234765 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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