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 18328 b4304 KpLE2 phage-like element; predicted phosphotransferase enzyme IIC component (NCBI)
Query= TCDB::Q71WA6 (423 letters) >FitnessBrowser__Keio:18328 Length = 437 Score = 336 bits (862), Expect = 7e-97 Identities = 163/404 (40%), Positives = 268/404 (66%), Gaps = 3/404 (0%) Query: 10 YVLNLGPTVILPIMIFFIALIFRVPAKKALRSAITIGIGFVGINLVISLLSSNLGPAAQQ 69 Y+L+LG TV +PI++ I LIFR+P +A+++ +T+GIGFVG+ LVI + +L P + Sbjct: 4 YILSLGGTVFVPIIMIVIGLIFRIPWLQAIKAGVTVGIGFVGMGLVIVMAIDSLSPPIKV 63 Query: 70 MVERFGLNLTIIDAGWPAAAAASWASPVAAILIPICLVVNLALIFFKVTKTLDIDIWNYW 129 M+ERFGL L + D G A+ +A+ + A++IP+ ++N+A++ ++TKT+++DI+NYW Sbjct: 64 MIERFGLALHVFDVGAGPASGVGYATAIGAMIIPVIFLLNVAMLVTRLTKTMNVDIYNYW 123 Query: 130 HFIAAGATGYIVTGGNWWFAILCAIIYEVAVLWMADRTQPMVEEFYGLKGISLPTGSTAA 189 H+ G ++TG + + +L AI + L MAD T V+ GL+GIS+P G ++ Sbjct: 124 HYAITGTVVQLMTG-SLIYGVLGAICHAALSLKMADWTAKRVQNIVGLEGISIPQGYGSS 182 Query: 190 FGFIGIPVGWLIAKIPGIKNIHVDPETIQKRFGIFGEPMMMGLILGIAIGILAGYDVGAV 249 + + + + KIP +K ++D + IQKR+G+ G+P+++G++LG+ G+ AG Sbjct: 183 SVPLFVLLDAIYEKIPFMKGRNIDAQEIQKRYGMVGDPVIIGVVLGLIFGLAAGEGFKGC 242 Query: 250 AQLGMSMGAVMFLMPRMVKILMEGLIPISESAREFMKSRFKGRELYIGLDAALSIGHPAN 309 A L +++ A+M L PRM+++++EGL+PIS+ AR+F + FKGRE+YIGLD A+++GHP Sbjct: 243 ASLMITVAAIMVLFPRMIRLIVEGLLPISDGARKFFQKYFKGREVYIGLDTAVTLGHPTT 302 Query: 310 ISTGLILVPITLFLAVIIPGNKVLPFGDLATIPFYVSFVVASRKGNILHSVLAGTVVIAL 369 I+ GL+L+PI L LA I+PGNKVLP DL PF++ +G+++ ++++G +V+ Sbjct: 303 IAVGLLLIPIMLILASILPGNKVLPLADLPVAPFFICMATVIHRGDLVRTLISGVIVMIT 362 Query: 370 ALLMATDFGLVHTEM-MKGVYEFPKGATQVSTLDMGGNFFNWVI 412 LL+AT F TEM +KG + F + Q+S L + GN F W I Sbjct: 363 VLLIATQFAPYFTEMALKGGFSFAGESAQISALSV-GNMFGWSI 405 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: 548 Number of extensions: 33 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 391 Effective length of database: 405 Effective search space: 158355 Effective search space used: 158355 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