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_011840127.1 RSPH17029_RS00195 2-dehydro-3-deoxygalactonokinase
Query= SwissProt::Q92RN7 (306 letters) >NCBI__GCF_000015985.1:WP_011840127.1 Length = 307 Score = 192 bits (487), Expect = 1e-53 Identities = 126/297 (42%), Positives = 163/297 (54%), Gaps = 13/297 (4%) Query: 7 YAAVDWGTSSFRLWIIGEDGAVLAERRSAEGMTTAAKTGFHTILDGHLAAV--SAPAHLP 64 + A DWGTS R+W +G +G VLAE RS EGM A GF L + PA +P Sbjct: 5 WIAADWGTSRLRVWAMGAEG-VLAEARSDEGMGQVAAGGFEAALLRLIGPWLGDGPA-VP 62 Query: 65 IIICGMAGARQGWKEAGYIETPAALAEIAGRATAIPDVDRDI--RILPGLAQRDRRHPDV 122 +++CGMAGARQGW+EA Y P A + +P D I RI+PGLAQ + DV Sbjct: 63 VVVCGMAGARQGWQEAPYRRLPCAPVDPQA-LVPVPSEDPRIAVRIVPGLAQA--KPADV 119 Query: 123 MRGEETQLLGAAAHLGAGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGELFDTIARHTIL 182 MRGEETQ+ GA A LG+ ++C+PGTHSKW +++ V F +F+TGELF ++ ++L Sbjct: 120 MRGEETQIAGALALLGSFDGVICLPGTHSKWAQVSAGEVVSFRSFLTGELFALLSERSVL 179 Query: 183 SHAVAEADTFAAGSAAFTDAVSRTRENPALATNLLFSVRAGQLLHGTAAADARAQLSGTL 242 H +A AF AVS +P LF +RA LL A ARA+LSG L Sbjct: 180 RHGLAAE---GWDDEAFLAAVSDGMSHPQKLGAKLFGLRAEALLQDLPPATARARLSGLL 236 Query: 243 IGLEIAGALAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAVRAGLSAA 299 IGLE+ GA V LVG L Y AL +QG+ R + A GL+AA Sbjct: 237 IGLELVGA-RSYWLGQPVVLVGEEALAARYGAALAAQGVQARLLPAAACTLGGLAAA 292 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: 274 Number of extensions: 15 Number of successful extensions: 7 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: 307 Length adjustment: 27 Effective length of query: 279 Effective length of database: 280 Effective search space: 78120 Effective search space used: 78120 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