Align Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components
Query= SwissProt::P69811 (376 letters) >FitnessBrowser__Marino:GFF3781 Length = 978 Score = 249 bits (637), Expect = 2e-70 Identities = 153/376 (40%), Positives = 219/376 (58%), Gaps = 15/376 (3%) Query: 1 MFQLSVQDIHPGEKAGDKEEAIRQVAAALVQAGNVAEGYVNGMLAREQQTSTFLGNGIAI 60 M L+ D+ G A D ++A++Q A L +AG + Y+ GM AREQQ+ST LGNGIAI Sbjct: 36 MLTLTANDVRLGATASDWQDALQQAARDLERAGRTSPEYLAGMNAREQQSSTVLGNGIAI 95 Query: 61 PHGTTDTRDQVLKTGVQVFQFPEGVTWGDGQVAYVAIGIAASSDEHLGLLRQLTHVLSDD 120 PHGT ++RD VL+TGV++ QFPEGV+W DG +V + IAA SDEHL +LR LT VL Sbjct: 96 PHGTPESRDAVLETGVRILQFPEGVSWHDGARVHVLVAIAAQSDEHLDILRHLTRVLDKP 155 Query: 121 SVAEQLKSATTAEELRALLMGEKQSEQLKLDNEMLTLDIVASDLLTLQALNAARLKEAGA 180 +AE+L AT A EL ALL K K D+E L L I AS L + AARL+ Sbjct: 156 GLAEKLGHATDATELVALL--SKAPAVAKCDSETLCLGIDASTPNELALIAAARLQSLRC 213 Query: 181 VDATFVTKAINEQPLNLGQGIWLSDSAEGNLRSAIAVSRAANAFDVDGETAAM--LVSVA 238 VD F+ + + P++LGQG WL+ G R ++++ A TA + + +A Sbjct: 214 VDTDFLASIVGQPPVDLGQGFWLTHHTVGARRPTLSLATPKRA------TAELRGVFCLA 267 Query: 239 MNDDQPIAVLKRLADLLLDNKADRLLKADAATLLALLTSDDAPTDDVLSAEFVVRNEHGL 298 D+ +L+R+ L ++ + L A+A LLA L+ + A D ++A+ + N HGL Sbjct: 268 GPGDECHDLLERIDTFLAGDEPIQGLSAEA--LLARLSGEAA---DAVTAKVTLLNTHGL 322 Query: 299 HARPGTMLVNTIKQFNSDITVTNLDGTGKPANGRSLMKVVALGVKKGHRLRFTAQGADAE 358 HARP LV ++ N+ I + L+G G + SL +V+ LG ++G L +A G DA Sbjct: 323 HARPAKQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLLSATGDDAS 382 Query: 359 QALKAIGDAIAAGLGE 374 QA++++ AI GLGE Sbjct: 383 QAIQSLTSAIEGGLGE 398 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: 715 Number of extensions: 34 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: 978 Length adjustment: 37 Effective length of query: 339 Effective length of database: 941 Effective search space: 318999 Effective search space used: 318999 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