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_011650658.1 RL_RS04785 2-dehydro-3-deoxygalactonokinase
Query= SwissProt::Q92RN7 (306 letters) >NCBI__GCF_000009265.1:WP_011650658.1 Length = 305 Score = 383 bits (984), Expect = e-111 Identities = 195/299 (65%), Positives = 224/299 (74%) Query: 7 YAAVDWGTSSFRLWIIGEDGAVLAERRSAEGMTTAAKTGFHTILDGHLAAVSAPAHLPII 66 Y AVDWGTSSFRLW+IG DG VLAERRS EGMT+AAKTGF +L GHL A+ AP +LP+I Sbjct: 6 YVAVDWGTSSFRLWLIGRDGTVLAERRSGEGMTSAAKTGFSAVLAGHLTAIEAPENLPVI 65 Query: 67 ICGMAGARQGWKEAGYIETPAALAEIAGRATAIPDVDRDIRILPGLAQRDRRHPDVMRGE 126 +CGMAGARQGW EAGYI+ PA LA I A ++P RDIRILPGLAQRD PDVMRGE Sbjct: 66 VCGMAGARQGWVEAGYIDVPAPLASILTGAVSVPGESRDIRILPGLAQRDIARPDVMRGE 125 Query: 127 ETQLLGAAAHLGAGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGELFDTIARHTILSHAV 186 ETQLLGA +G+ VCMPGTHSKWV + D +V GFSTFMTGELFD I++HTILSHAV Sbjct: 126 ETQLLGALGRASSGAQAVCMPGTHSKWVHVTDSKVTGFSTFMTGELFDVISKHTILSHAV 185 Query: 187 AEADTFAAGSAAFTDAVSRTRENPALATNLLFSVRAGQLLHGTAAADARAQLSGTLIGLE 246 A+ A +AAF AVS PALA+NLLF+ R+GQLLHG +AA A+A+LSGTLIGLE Sbjct: 186 TGAEEQPADAAAFEAAVSAVFARPALASNLLFAARSGQLLHGISAAAAQARLSGTLIGLE 245 Query: 247 IAGALAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAVRAGLSAAARAIWP 305 IAGAL + + + LV SG L LY A + L A+DAD AVR GLSAAA AIWP Sbjct: 246 IAGALQDAANGTTITLVASGRLQALYEQAFRTLSLAFTAIDADAAVRRGLSAAAEAIWP 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: 326 Number of extensions: 7 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