Align PTS system, galactitol-specific, IIC component, component of Pentitol [arabitol (arabinitol, lyxitol)/xylitol] PTS permease, IICBA (encoded within an operon that also encodes a polyol-P dehydrogenase, a ribose-5-P isomerase, a ribulose 5-P-3-epimerase, and a BlgG-type PTS antiterminator) (Saklani-Jusforgues et al., 2001; Kentache T et al., 2016, in press) (characterized)
to candidate 353633 BT4107 putative phosphotransferase enzyme II, C component (NCBI ptt file)
Query= TCDB::Q71WA6 (423 letters) >FitnessBrowser__Btheta:353633 Length = 465 Score = 302 bits (774), Expect = 1e-86 Identities = 159/421 (37%), Positives = 246/421 (58%), Gaps = 19/421 (4%) Query: 9 QYVLNLGPTVILPIMIFFIALIFRVPAKKALRSAITIGIGFVGINLVISLLSSNLGPAAQ 68 +Y++ LG V++PI+ + + + KAL+S + +G+GFVG+++V +LL+S+LGPA Sbjct: 6 KYIIGLGAAVMMPIIFTILGVCIGIKLPKALKSGLLVGVGFVGLSVVTALLTSSLGPALS 65 Query: 69 QMVERFGLNLTIIDAGWPAAAAASWASPVAAILIPICLVVNLALIFFKVTKTLDIDIWNY 128 +MVE +GL L I D GWP+AAA ++ + V A +IP+CL VNL ++ K T+T++ID+WNY Sbjct: 66 KMVEIYGLELGIFDMGWPSAAAVAYNTSVGAFIIPVCLGVNLLMLLTKTTRTVNIDLWNY 125 Query: 129 WHFIAAGATGYIVTGGNWWFAILCAIIYEVAVLWMADRTQPMVEEFYG-LKGISLPTGST 187 WHF GA Y + +W AII + L MAD T P ++FY + GIS+P Sbjct: 126 WHFAFIGAIVYFASDSIFW-GFFAAIICYIITLVMADMTAPAFQKFYDKMDGISIPQPFC 184 Query: 188 AAFGFIGIPVGWLIAKIPGIKNIHVDPETIQKRFGIFGEPMMMGLILGIAIGILAGYD-- 245 +F I + L+ KIPG +++D E ++K+FG+ GEP+ +G+++G IG L Sbjct: 185 QSFVPFAIVINKLLDKIPGFDKLNIDSEGMKKKFGLMGEPLFLGIVIGCGIGALGCASWK 244 Query: 246 -----VGAVAQLGMSMGAVMFLMPRMVKILMEGLIPISESAREFMKSRFKGRE-LYIGLD 299 + + LG+ MGAVM L+PR+ + +EGL PIS++ RE + ++K L IG+ Sbjct: 245 EVLDGIPGILGLGIKMGAVMELIPRITSLFIEGLKPISDATRELIAKKYKSNTGLSIGMS 304 Query: 300 AALSIGHPANISTGLILVPITLFLAVIIPGNKVLPFGDLATIPFYVSFVVASRKGNILHS 359 AL IGHP + L+L+P+T+FLAVI+PGN+ LP LA + + ++ KGN++ S Sbjct: 305 PALVIGHPTTLVVSLLLIPVTIFLAVILPGNRFLPLASLAGMFYLFPMILPITKGNVVKS 364 Query: 360 VLAGTVVIALALLMATDFGLVHTEMMKGVY--------EFPKGATQVSTLDMGGNFFNWV 411 + G V + + L T+ T K VY P G + LD + F W Sbjct: 365 FIIGLVALIVGLYFVTELAGFFTMAAKDVYAATGDPTVNIPAG-FEGGALDFASSLFCWG 423 Query: 412 I 412 I Sbjct: 424 I 424 Lambda K H 0.328 0.143 0.441 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: 542 Number of extensions: 34 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: 423 Length of database: 465 Length adjustment: 32 Effective length of query: 391 Effective length of database: 433 Effective search space: 169303 Effective search space used: 169303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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