Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_008537413.1 HMPREF9454_RS01155 PTS transporter subunit EIIC
Query= SwissProt::P0A283 (169 letters) >NCBI__GCF_000245775.1:WP_008537413.1 Length = 691 Score = 108 bits (271), Expect = 1e-28 Identities = 57/159 (35%), Positives = 96/159 (60%), Gaps = 10/159 (6%) Query: 8 KSLVSDDKKDTGTIEIVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGT 67 + LVS+ K + A +G++V+IE+VPD FA + +GDG+AI PT + AP +G+ Sbjct: 533 EELVSNTDKSPS---LKAFATGDLVSIENVPDEAFASRAMGDGVAIIPTEKYITAPANGS 589 Query: 68 IGKIFE-TNHAFSIESDSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLP 126 + + E T HA ++ D+ +E+ +H GIDTV +KG+GFK + + G VKVGD ++E D+ Sbjct: 590 VMMVMEETGHALGLKLDTDMEILIHIGIDTVNMKGDGFKVLVKAGDEVKVGDKLVEIDIE 649 Query: 127 LLEEKAKSTLTPVVISNMDEI------KELIKLSGSVTV 159 ++ + +T ++ +N D+ KE ++G TV Sbjct: 650 KIKRAGYNPITIMIATNFDQYSLLKFEKEQKVIAGKTTV 688 Lambda K H 0.315 0.139 0.377 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: 268 Number of extensions: 11 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: 169 Length of database: 691 Length adjustment: 28 Effective length of query: 141 Effective length of database: 663 Effective search space: 93483 Effective search space used: 93483 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 (21.9 bits) S2: 49 (23.5 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