Align PTS system cellobiose-specific EIIB component; Cellobiose-specific phosphotransferase enzyme IIB component; EC 2.7.1.205 (characterized)
to candidate WP_038018225.1 HA49_RS13185 PTS sugar transporter subunit IIB
Query= SwissProt::Q9CIF0 (108 letters) >NCBI__GCF_000757425.2:WP_038018225.1 Length = 99 Score = 91.3 bits (225), Expect = 3e-24 Identities = 53/100 (53%), Positives = 65/100 (65%), Gaps = 5/100 (5%) Query: 4 KVIALACAAGMSTSLLVSKMQKAAADNGKDYEIFAKSTADIDNMLAGTGSPKPDVLLLGP 63 K I L CAAGMSTS+LVS+MQK AAD D EI A S ++D+ LA D LLGP Sbjct: 2 KNILLCCAAGMSTSMLVSRMQKYAADQAIDVEINAISINELDSHLANI-----DCCLLGP 56 Query: 64 QVAFMKGEVAKKAEIAGVPMDVIKMQDYGMMRGDKVLAAA 103 QV + EV +K +P+ VI ++DYGMMRGDKVL +A Sbjct: 57 QVKYKLAEVQQKLAPLNIPVAVIDIRDYGMMRGDKVLESA 96 Lambda K H 0.316 0.130 0.353 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: 50 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: 99 Length adjustment: 11 Effective length of query: 97 Effective length of database: 88 Effective search space: 8536 Effective search space used: 8536 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 (21.2 bits) S2: 40 (20.0 bits)
This GapMind analysis is from Sep 24 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