Align PTS system, mannose-specific, IIAB component, component of The primary glucose /mannose uptake transporter, ManLMN (characterized)
to candidate BWI76_RS01735 BWI76_RS01735 PTS mannose/fructose/sorbose family transporter subunit IIB
Query= TCDB::E1UCI0 (321 letters) >FitnessBrowser__Koxy:BWI76_RS01735 Length = 164 Score = 137 bits (344), Expect = 2e-37 Identities = 65/164 (39%), Positives = 105/164 (64%), Gaps = 1/164 (0%) Query: 155 IEFVLTRVDSRLLHGQVATAWTKATHPTRIIVVSDAVAKDDLRKKLIEQAAPPGVKANVI 214 + L R+D RL+HGQV T W+K + RII+ +D V DD+R+ L+ QAAPPG+K NV+ Sbjct: 1 MNITLARIDDRLIHGQVTTVWSKVANAQRIIICNDDVYNDDVRRTLLRQAAPPGMKVNVV 60 Query: 215 PVQKMIEISKDPRFGNTKALLLFENPQDVLRAIEGGVEIEQVNVGSMAHSVGKVVVSKVL 274 ++K + + +P++ + LF NPQDVL ++ GV I +N+G MA GK ++K + Sbjct: 61 NLEKAVAVYHNPQYQDETVFYLFTNPQDVLTMVQQGVNIATLNIGGMAWRPGKKQLTKAV 120 Query: 275 SMGKDDVATFEKLKEKGVKFDVRKVPNDSSAN-MDEIIKKAKNE 317 S+ + D+ F++L + GV D+R V +D S N +D+I +++ E Sbjct: 121 SLDEADINAFQQLDKLGVNLDLRVVASDPSVNILDKIAEQSVTE 164 Lambda K H 0.315 0.132 0.365 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: 126 Number of extensions: 1 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: 321 Length of database: 164 Length adjustment: 23 Effective length of query: 298 Effective length of database: 141 Effective search space: 42018 Effective search space used: 42018 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: 46 (22.3 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