Align Probable 2-dehydro-3-deoxygalactonokinase DgoK1; 2-keto-3-deoxy-galactonokinase; 2-oxo-3-deoxygalactonate kinase; EC 2.7.1.58 (characterized)
to candidate WP_160148006.1 RSPH17029_RS18270 2-dehydro-3-deoxygalactonokinase
Query= SwissProt::Q92RN7 (306 letters) >NCBI__GCF_000015985.1:WP_160148006.1 Length = 306 Score = 204 bits (519), Expect = 2e-57 Identities = 129/298 (43%), Positives = 159/298 (53%), Gaps = 14/298 (4%) Query: 10 VDWGTSSFRLWIIGEDGAVLAERRSAE-GMTTAAKTGFHTILDGHLAAVSAPAHLPIIIC 68 VDWGTS R WI G L+ S + GM T + + +L A++ APA P++IC Sbjct: 18 VDWGTSRMRAWI-WRGGRDLSPMHSDDRGMKTLTQADYPAVLAQATASLGAPAGTPVLIC 76 Query: 69 GMAGARQGWKEAGYIETPAALAEIAGRATAIPDVDRDIRILPGLAQRDRRHPDVMRGEET 128 GMAGAR GW EAGY+ P L ++ A + DRD+RILPG++ PDVMRGEET Sbjct: 77 GMAGARGGWLEAGYLAAPTDLGDLHRHARRVGLPDRDVRILPGVSCSGTA-PDVMRGEET 135 Query: 129 QLLGAAAHLGAGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGELFDTIARHTILSHAVAE 188 QL G G L C+PGTHSKW R + GF+TFMTGELF+ I RH+IL+ + E Sbjct: 136 QLAGLLDDPAPG--LTCLPGTHSKWARRDGSVLSGFTTFMTGELFEVIGRHSILARTLGE 193 Query: 189 ADTFAAGSAAFTDAVSRTRENPALATNLLFSVRAGQLLHGTAAADARAQLSGTLIGLEIA 248 AAF +A P L F +RA LL ARA+LSG LIG E A Sbjct: 194 ----GWDDAAFLEAAEEALSAPELVWRAFFGLRASALLEEGRPVSARARLSGLLIGAECA 249 Query: 249 GA--LAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAVRAGLSAAARAIW 304 A L G+G V LV SG + Y AL + G V D +E GL AA IW Sbjct: 250 AARRLYGAGP---VTLVASGAMERAYGRALAAAGFAVTLRDGEEITCRGLIRAAEQIW 304 Lambda K H 0.319 0.133 0.394 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: 263 Number of extensions: 17 Number of successful extensions: 5 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. 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