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 YP_002824985.1 NGR_c04360 2-dehydro-3-deoxygalactonokinase
Query= SwissProt::Q92RN7 (306 letters) >NCBI__GCF_000018545.1:YP_002824985.1 Length = 305 Score = 517 bits (1331), Expect = e-151 Identities = 258/304 (84%), Positives = 276/304 (90%) Query: 3 TAGYYAAVDWGTSSFRLWIIGEDGAVLAERRSAEGMTTAAKTGFHTILDGHLAAVSAPAH 62 TAGYYAAVDWGTSSFRLW+IGEDGA LAERRSAEGMTTAA+TGFH +LD HLAAVSAPAH Sbjct: 2 TAGYYAAVDWGTSSFRLWLIGEDGAALAERRSAEGMTTAARTGFHAVLDSHLAAVSAPAH 61 Query: 63 LPIIICGMAGARQGWKEAGYIETPAALAEIAGRATAIPDVDRDIRILPGLAQRDRRHPDV 122 LPIIICGMAGARQGWKEAGY+ETPAAL IAG A A+PDVDRDIRILPGLAQRD RHPDV Sbjct: 62 LPIIICGMAGARQGWKEAGYLETPAALGAIAGHAIAVPDVDRDIRILPGLAQRDGRHPDV 121 Query: 123 MRGEETQLLGAAAHLGAGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGELFDTIARHTIL 182 MRGEETQLLGAA L G HLVCMPGTHSKWVRL+ V+GFSTFMTGELFD I++HTIL Sbjct: 122 MRGEETQLLGAAGMLDHGRHLVCMPGTHSKWVRLSGQTVDGFSTFMTGELFDAISKHTIL 181 Query: 183 SHAVAEADTFAAGSAAFTDAVSRTRENPALATNLLFSVRAGQLLHGTAAADARAQLSGTL 242 SHAVAEAD AA SAAF DAV+R RENPALATNLLFSVRAGQLLHG +AADA+A+LSGTL Sbjct: 182 SHAVAEADAIAADSAAFADAVTRARENPALATNLLFSVRAGQLLHGLSAADAKARLSGTL 241 Query: 243 IGLEIAGALAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAVRAGLSAAARA 302 IGLEIAGALA +GSVDG+CLVGSG LG LYR+ALESQG+ VR VDADEAVRAGLSAAA+A Sbjct: 242 IGLEIAGALASAGSVDGICLVGSGRLGALYRSALESQGIAVRLVDADEAVRAGLSAAAQA 301 Query: 303 IWPL 306 IWPL Sbjct: 302 IWPL 305 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: 415 Number of extensions: 8 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: 306 Length of database: 305 Length adjustment: 27 Effective length of query: 279 Effective length of database: 278 Effective search space: 77562 Effective search space used: 77562 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 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