Align lysine-specific permease (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= CharProtDB::CH_091040 (611 letters) >lcl|FitnessBrowser__Keio:14712 b0576 phenylalanine transporter (NCBI) Length = 458 Score = 262 bits (670), Expect = 2e-74 Identities = 157/441 (35%), Positives = 239/441 (54%), Gaps = 24/441 (5%) Query: 96 EEEAHYEDKHVKRALKQRHIGMIALGGTIGTGLFVGISTPLSNAGPVGSLIAYIFMGTIV 155 E+ A ++ + R L RHI +IALGG IGTGLF+GI + AGP L+ Y G I Sbjct: 9 EDTASNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGYGVAGIIA 67 Query: 156 YFVTQSLGEMATFIPVTSSITVFSKRFLSPAFGVSNGYMYWFNWAITYAVEVSVIGQVIE 215 + + + LGEM PV+ S F+ ++ P G +G+ YW + + E++ G ++ Sbjct: 68 FLIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQ 127 Query: 216 YWTDKVPLAAWIAIFWVIITLMNFFPVKVYGEFEFWVASVKVLAIMGYLIYALIIVCGGS 275 YW VP W A F++II +N V++YGE EFW A +KVLAI+G + + L ++ G Sbjct: 128 YWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSG- 186 Query: 276 HQGPIGF--RYWRNPGAWGPGIISSDKSEGRFLGWVSSLINAAFTYQGTELVGITAGEAA 333 H G WR G + G + G + SL F++ G EL+GITA EA Sbjct: 187 HGGEKASIDNLWRYGGFFATG----------WNGLILSLAVIMFSFGGLELIGITAAEAR 236 Query: 334 NPRKTVPRAINKVVFRIVLFYIMSLFFIGLLVPYNDSRLSASSAVIASSPFVISIQNAGT 393 +P K++P+A+N+VV+RI+LFYI SL + L P+ + + + SSPFV+ N + Sbjct: 237 DPEKSIPKAVNQVVYRILLFYIGSLVVLLALYPWVEVKSN-------SSPFVMIFHNLDS 289 Query: 394 YALPDIFNAVVLITVVSAANSNVYVGSRVLYSLARTGNAPKQFGYVTRQGVPYLGVVCTA 453 + N V+L+ +S NS VY SR+L+ L+ GNAPK V+R+GVP ++ + Sbjct: 290 NVVASALNFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSG 349 Query: 454 ALGLLAFLVVNNNANTAFNWLINISTLAGLCAWLFISLAHIRFMQALKHRGISRDDLPFK 513 A+ L L+ AF L+ + L W+ I LAH+RF A++ +G + FK Sbjct: 350 AITSLVVLINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQG---RETQFK 406 Query: 514 AKLMPYGAYYAAFFVTVIIFI 534 A L P+G Y F+ +I+ + Sbjct: 407 ALLYPFGNYLCIAFLGMILLL 427 Lambda K H 0.324 0.138 0.426 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: 733 Number of extensions: 49 Number of successful extensions: 5 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: 611 Length of database: 458 Length adjustment: 35 Effective length of query: 576 Effective length of database: 423 Effective search space: 243648 Effective search space used: 243648 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 (21.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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