Align Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized)
to candidate GFF780 PS417_03965 PTS fructose transporter subunit IIA
Query= SwissProt::P69811 (376 letters) >FitnessBrowser__WCS417:GFF780 Length = 952 Score = 243 bits (619), Expect = 2e-68 Identities = 148/374 (39%), Positives = 208/374 (55%), Gaps = 3/374 (0%) Query: 1 MFQLSVQDIHPGEKAGDKEEAIRQVAAALVQAGNVAEGYVNGMLAREQQTSTFLGNGIAI 60 M +L+V+ I G+ A DK A+ +A LV G VAEGY++G+ ARE Q STFLG GIAI Sbjct: 1 MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI 60 Query: 61 PHGTTDTRDQVLKTGVQVFQFPEGVTWGDGQVAYVAIGIAASSDEHLGLLRQLTHVLSDD 120 PHGT +TRDQV TGV++ QFPEGV WGDGQ+ Y+AIGIAA SDEHL LL+ LT L + Sbjct: 61 PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 Query: 121 SVAEQLKSATTAEELRALLMGEKQSEQLKLDNEMLTLDIVASDLLTLQALNAARLKEAGA 180 + + L+ A +AE L LL G Q +L LD +M+ L + A D L A L++A Sbjct: 121 DLGQALRRAGSAEALLKLLQGAPQ--ELALDAQMIGLGVSADDFEELVWRGARLLRQADC 178 Query: 181 VDATFVTKAINEQPLNLGQGIWLSDSAEGNLRSAIAVSRAANAFDVDGETAAMLVSVAMN 240 V F L LG G+W S + R +A G+ L +A Sbjct: 179 VSNGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASL 238 Query: 241 DDQPIAVLKRLADLLLDNKADRLLKADAATLLALLTSDDAPTDDVLSAEFVVRNEHGLHA 300 + +L+RL LL++ + L +A ++ + + + P D +A + N HGLHA Sbjct: 239 GEAHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELP-PDWPAARITLANAHGLHA 297 Query: 301 RPGTMLVNTIKQFNSDITVTNLDGTGKPANGRSLMKVVALGVKKGHRLRFTAQGADAEQA 360 RP +L K F+ D+ V +DG + +SL K+++LG ++G L F A+ + A A Sbjct: 298 RPAKILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDA 357 Query: 361 LKAIGDAIAAGLGE 374 L A+ A+ GLGE Sbjct: 358 LPALLAAVEEGLGE 371 Lambda K H 0.314 0.130 0.353 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: 711 Number of extensions: 42 Number of successful extensions: 3 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: 376 Length of database: 952 Length adjustment: 37 Effective length of query: 339 Effective length of database: 915 Effective search space: 310185 Effective search space used: 310185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 53 (25.0 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