Align Glucosamine-6-phosphate deaminase; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase; EC 3.5.99.6 (characterized)
to candidate WP_072784433.1 BUA36_RS11225 hypothetical protein
Query= SwissProt::Q9K487 (261 letters) >NCBI__GCF_900143065.1:WP_072784433.1 Length = 276 Score = 106 bits (264), Expect = 6e-28 Identities = 71/224 (31%), Positives = 115/224 (51%), Gaps = 13/224 (5%) Query: 16 IAEAMAQLLRRKPDALLGVATGSTPLPVYEALAAKVRSGAVDTAQARIAQLDEYVGLPAE 75 + +A +LR+KP A+L + G T + +++ L + R+ ++D + Q+DEY +P+ Sbjct: 40 LVSELADVLRQKPYAVLTPSVGRTMVGIFDVLRDQHRN-SIDWQRVICVQMDEYAHMPSS 98 Query: 76 HPESYRSVLRREVLEPLGIDMDAFMGPDGTAADVQAACEAYDTALGGSGGVDLQLLGIGT 135 P+S+ LRR+++EPLGI D AA V + Y+ L GG+D L G+G Sbjct: 99 DPDSFALTLRRDLVEPLGIGRFIHFYDDEGAAIVSP--KQYEEDLYKLGGIDCALHGVGR 156 Query: 136 DGHIGFNEPCSSLASRTRIKTLTEQTRIDNARFFDGDIEQVPH-HVITQGIGTILEARHV 194 + HIGFNEP I L++ TRI N VP+ H ++ G+G + A+ Sbjct: 157 NSHIGFNEPRQRTRLTGGIVRLSQATRIANG---------VPYRHGVSLGLGVLRAAQSS 207 Query: 195 VLLATGEGKADAVAASVEGPVAAVCPASALQLHPHATVVVDEAA 238 +L+ GE K DA + G P + L+ P ++ +D AA Sbjct: 208 ILVLLGEHKRDASYQLLFGSSGPHVPVTQLRHCPRVSICLDHAA 251 Lambda K H 0.317 0.134 0.387 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: 184 Number of extensions: 8 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: 261 Length of database: 276 Length adjustment: 25 Effective length of query: 236 Effective length of database: 251 Effective search space: 59236 Effective search space used: 59236 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: 41 (21.7 bits) S2: 47 (22.7 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