Align lysine-specific permease (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= CharProtDB::CH_091040 (611 letters) >FitnessBrowser__Keio:14712 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:
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