Align Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized)
to candidate WP_019614809.1 G327_RS0110890 fused PTS fructose transporter subunit IIA/HPr protein
Query= SwissProt::P69811 (376 letters) >NCBI__GCF_000381745.1:WP_019614809.1 Length = 373 Score = 323 bits (827), Expect = 6e-93 Identities = 173/374 (46%), Positives = 247/374 (66%), Gaps = 4/374 (1%) Query: 1 MFQLSVQDIHPGEKAGDKEEAIRQVAAALVQAGNVAEGYVNGMLAREQQTSTFLGNGIAI 60 M ++ DI + A +K++AI+ +A +LV+ V Y++GMLARE Q STFLGNGIAI Sbjct: 1 MLSINSSDIVLSQAAENKQQAIQSIANSLVEKTYVEAAYLDGMLAREAQNSTFLGNGIAI 60 Query: 61 PHGTTDTRDQVLKTGVQVFQFPEGVTWGDGQVAYVAIGIAASSDEHLGLLRQLTHVLSDD 120 PHGTT+TRD+V +TGV V FP+GV WG+ Y+AIGIAA SD+HL +L+QLT VLS + Sbjct: 61 PHGTTETRDKVKQTGVIVHHFPQGVDWGNDNTVYLAIGIAAQSDQHLAILKQLTKVLSAE 120 Query: 121 SVAEQLKSATTAEELRALLMGEKQSEQLKLDNEMLTLDIVASDLLTLQALNAARLKEAGA 180 + +QLK A+TA+ + +LL GE QSE L + +++ L+ ASDLL L A+ A +K GA Sbjct: 121 GIEQQLKEASTAQGIVSLLNGEMQSETL-FNADLIQLNFPASDLLQLTAVAAGLIKNQGA 179 Query: 181 VDATFVTKAINEQPLNLGQGIWLSDSAEGNLRSAIAVSRAANAFDVDGETAAMLVSVAMN 240 V ++F+ I +Q LGQG+WL+ S+ G ++A++ A+ +F + G+ L+ +A N Sbjct: 180 VQSSFIADVIAKQASYLGQGLWLNSSSTGISKTAVSFVSASESFQLQGKPVQGLLCIASN 239 Query: 241 DDQPIAVLKRLADLLLDNKADRLLKADAATLLALLTSDDAPTDDVLSAEFVVRNEHGLHA 300 + L L DL+ + ++L A ++ LLT + + F ++N HGLHA Sbjct: 240 SQLHLKNLNILIDLIHKQQIEQLFDASEEQVITLLTQEKLEGSQQI---FTIKNPHGLHA 296 Query: 301 RPGTMLVNTIKQFNSDITVTNLDGTGKPANGRSLMKVVALGVKKGHRLRFTAQGADAEQA 360 RPG MLV+ K+F + I +TNL+GTGK AN +SLMKV+ GV+ GH+L+F AQG DAE+A Sbjct: 297 RPGAMLVHVAKKFKAKIQMTNLNGTGKSANAKSLMKVMTQGVQFGHQLQFVAQGEDAEEA 356 Query: 361 LKAIGDAIAAGLGE 374 L AIG AI GLGE Sbjct: 357 LHAIGQAINEGLGE 370 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: 368 Number of extensions: 16 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: 373 Length adjustment: 30 Effective length of query: 346 Effective length of database: 343 Effective search space: 118678 Effective search space used: 118678 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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