Align PTS system, IIA component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate 206413 DVU0981 multiphosphoryl transfer protein, putative
Query= TCDB::Q82ZC8 (150 letters) >MicrobesOnline__882:206413 Length = 854 Score = 47.8 bits (112), Expect = 4e-10 Identities = 47/142 (33%), Positives = 69/142 (48%), Gaps = 16/142 (11%) Query: 1 MLGIVIATHGA-LSDGAKDAAT------VIMGATENIETVNLNSGDDVQALGGQIKTAIE 53 M+GIV+ TH A L G ++ A V + I+ + G D ++ TAIE Sbjct: 1 MVGIVVVTHSAVLGQGLRELAEQMTQGRVPLAVAGGIDDPDHPIGTDPV----RVMTAIE 56 Query: 54 NVQQGDGVLVMVDLLSASPYNQAVLVINELEPALQKKIF---VVSGTNLPMVLEAINHQL 110 VQQGDGVLV++DL SA + L + E A Q ++ +V G VL + L Sbjct: 57 EVQQGDGVLVLMDLGSALMSAETALDLLPPEVASQVRLSAAPLVEGLMAAAVLASTGADL 116 Query: 111 LGTPIAEAAQAIVAQGKESVQA 132 +AE AQ+ +A +E + A Sbjct: 117 --GAVAEEAQSALAAKRELLGA 136 Lambda K H 0.312 0.130 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: 251 Number of extensions: 15 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: 150 Length of database: 854 Length adjustment: 29 Effective length of query: 121 Effective length of database: 825 Effective search space: 99825 Effective search space used: 99825 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 (21.9 bits) S2: 49 (23.5 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