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 CCNA_00826 CCNA_00826 2-dehydro-3-deoxygalactonokinase
Query= SwissProt::Q92RN7 (306 letters) >FitnessBrowser__Caulo:CCNA_00826 Length = 306 Score = 181 bits (458), Expect = 2e-50 Identities = 122/299 (40%), Positives = 157/299 (52%), Gaps = 16/299 (5%) Query: 11 DWGTSSFRLWIIGEDGAVLAERRSAEGMTTAAKTGFHTILD--GHLAAVSAPAHLPIIIC 68 DWG S RLW+ G + RR G+T + T LD G + P + I+C Sbjct: 10 DWGGSRLRLWL--RQGKSVIHRRDGPGVTALTDSPEKTFLDLVGDWRE-AGPDYA--ILC 64 Query: 69 GMAGARQGWKEAGYIETPAALAEIAGRATAIPDVDRDIRILPGLA-QRDRRHPDVMRGEE 127 GM G+R GW EA Y PA +IA RA I +RI+PGL+ PDVMRGEE Sbjct: 65 GMVGSRMGWTEAPYAPCPATTGQIAARAVRIEAAGLPVRIVPGLSCVNPLGGPDVMRGEE 124 Query: 128 TQLLGAA---AHLGAGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGELFDTIARHTILSH 184 TQ+LGA A L +G HL+ +PGTH+KW + D ++ F T GE F + H+ L Sbjct: 125 TQILGALSLDAALRSGRHLLVLPGTHNKWAVVEDGQITTFLTAPIGETFALLKAHSTLG- 183 Query: 185 AVAEADTFAAGSAA-FTDAVSRTRENPA-LATNLLFSVRAGQLLHGTAAADARAQLSGTL 242 A + A GSAA F ++R E A T+L+F RA QLL ADA LSG L Sbjct: 184 --AGGGSLAEGSAAGFARGLTRIAEQGAGRLTHLMFETRARQLLEAMTPADAMGFLSGLL 241 Query: 243 IGLEIAGALAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAVRAGLSAAAR 301 IG ++A A G ++ V ++G G L LY AL + G+ AVD D AV AGLS R Sbjct: 242 IGADVAAARDWFGPMEAVTVIGDGPLAALYVQALAATGVTASAVDGDAAVLAGLSMITR 300 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: 260 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 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