Align PTS system galactose-specific EIIB component; Galactose-specific phosphotransferase enzyme IIB component; EC 2.7.1.204 (characterized)
to candidate BWI76_RS22400 BWI76_RS22400 PTS sugar transporter subunit IIB
Query= SwissProt::A2RIE6 (108 letters) >FitnessBrowser__Koxy:BWI76_RS22400 Length = 104 Score = 74.3 bits (181), Expect = 4e-19 Identities = 44/105 (41%), Positives = 62/105 (59%), Gaps = 5/105 (4%) Query: 4 KVIALACAAGMSTSLLVSKMQKAAAENGKDYEIFAKSTADIDNMLAGTGSPKPDVLLLGP 63 K I L C+AGMSTSLLV KM A + G EI A A+ D + V+LLGP Sbjct: 2 KKIMLCCSAGMSTSLLVKKMIAEAEQRGLPVEINAFGVAEFDRQVGHY-----QVVLLGP 56 Query: 64 QVAFMKGEVAKKAEIAGVPMDVIKMQDYGMMRGDKVLAAAENLMN 108 QV +M+ ++ K+A+ G+ ++ I M DYGM +G VL A +L++ Sbjct: 57 QVKYMQKDLQKQADKYGIRVEPINMMDYGMQKGGAVLDFALSLID 101 Lambda K H 0.315 0.129 0.350 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: 43 Number of extensions: 2 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: 108 Length of database: 104 Length adjustment: 11 Effective length of query: 97 Effective length of database: 93 Effective search space: 9021 Effective search space used: 9021 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: 40 (21.1 bits) S2: 40 (20.0 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