Align Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate BWI76_RS17585 BWI76_RS17585 phosphoenolpyruvate-dependent PTS family enzyme IIA component
Query= TCDB::C0H3V2 (143 letters) >FitnessBrowser__Koxy:BWI76_RS17585 Length = 144 Score = 92.0 bits (227), Expect = 3e-24 Identities = 44/141 (31%), Positives = 77/141 (54%) Query: 1 MQVLAKENIKLNQTVSSKEEAIKLAGQTLIDNGYVTEDYISKMFEREETSSTFMGNFIAI 60 + + ++N+ L+ +K E + + G GYV+ED ++ + ERE STF+GN I + Sbjct: 2 IDTITQDNLHLSCRAKNKAEVLAMIGADFRSRGYVSEDCVAFLAERERQVSTFLGNGITL 61 Query: 61 PHGTEEAKSEVLHSGISIIQIPEGVEYGEGNTAKVVFGIAGKNNEHLDILSNIAIICSEE 120 PH + A S ++ +G+ I Q P+GV + N + G+ K +EH+D+L +A I S+E Sbjct: 62 PHLPKSATSIIVKTGVEIYQFPDGVIWDRNNVMFIAIGVIAKESEHIDVLREVASIFSDE 121 Query: 121 ENIERLISAKSEEDLIAIFNE 141 L ++ED + I + Sbjct: 122 VIARALSLIANKEDFLRILQQ 142 Lambda K H 0.310 0.130 0.342 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: 71 Number of extensions: 5 Number of successful extensions: 1 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: 143 Length of database: 144 Length adjustment: 16 Effective length of query: 127 Effective length of database: 128 Effective search space: 16256 Effective search space used: 16256 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 (21.8 bits) S2: 42 (20.8 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