Align Sugar hosphotransferase system IIA component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)
Query= TCDB::Q5V5X4 (158 letters) >FitnessBrowser__Keio:1937187 Length = 833 Score = 73.6 bits (179), Expect = 7e-18 Identities = 46/146 (31%), Positives = 80/146 (54%), Gaps = 4/146 (2%) Query: 13 LIPANHISLSEPPAEKEACIESLLDLLVDSGRVEDRDRALEA-LLERESETTTGVGMGIG 71 L+ A I+L KE ++ + D L+ +GR R LEA L RE+ +TG+G Sbjct: 689 LVTAECITLESDWRSKEEVLKGMTDNLLLAGRCR-YPRKLEADLWAREAVFSTGLGFSFA 747 Query: 72 IPHAKTDAVSRPSLAFARSQEGVDFGSMDGEPATLVFMILVPEAGGEEHLNILSSLSRAL 131 IPH+K++ + + +++ AR Q V +G D E ++ + L A G++H+ I S L+R + Sbjct: 748 IPHSKSEHIEQSTISVARLQAPVRWG--DDEAQFIIMLTLNKHAAGDQHMRIFSRLARRI 805 Query: 132 MHDDVRDRLHAAADEATVQDVLREAI 157 MH++ R+ L AA + +L+ + Sbjct: 806 MHEEFRNALVNAASADAIASLLQHEL 831 Lambda K H 0.314 0.131 0.357 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: 234 Number of extensions: 10 Number of successful extensions: 2 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: 158 Length of database: 833 Length adjustment: 29 Effective length of query: 129 Effective length of database: 804 Effective search space: 103716 Effective search space used: 103716 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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