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 GFF721 PGA1_c07360 2-dehydro-3-deoxygalactonokinase DgoK
Query= SwissProt::Q92RN7 (306 letters) >FitnessBrowser__Phaeo:GFF721 Length = 325 Score = 186 bits (473), Expect = 5e-52 Identities = 118/307 (38%), Positives = 158/307 (51%), Gaps = 15/307 (4%) Query: 2 TTAGYYAAVDWGTSSFRLWIIGEDGAVLAERRSAEGMTTAAKTGFHTILDGHLAAVSAPA 61 T+A + A DWGT+ RLW++ V+ S GM+ + L G L P Sbjct: 15 TSAPVWIAADWGTTQLRLWVMDAQNQVIDRITSDRGMSRLRPQDYEPTLLGLLGGHLTPG 74 Query: 62 H------LPIIICGMAGARQGWKEAGYIETPAALAEIA-GRATAIPDVDRDIRILPGLAQ 114 +P+I CGMAG+RQGW EA Y P IA I D + +LPG+ Sbjct: 75 DYSDTDPIPVICCGMAGSRQGWAEAPYATAPCPPPGIAEATRPVIQDKRLTVYLLPGIKT 134 Query: 115 RDRRHPDVMRGEETQLLGAAAHLG--AGSHLVCMPGTHSKWVRLADDRVEGFSTFMTGEL 172 D DVMRGEETQ+ G A G ++C+PGTHSKW +L RV FSTFMTGE+ Sbjct: 135 TDPA--DVMRGEETQIAGYLAQDSNQTGPQVICLPGTHSKWAKLDQGRVISFSTFMTGEM 192 Query: 173 FDTIARHTILSHAVAEADTFAAGSAAFTDAVSRTRENPALATNLLFSVRAGQLLHGTAAA 232 F + ++L H ++E AF AV++ +PA + LF +RA LL G +A Sbjct: 193 FALLQGQSVLRHCISED---GWDEKAFKHAVAKALSSPAAISAQLFRIRANALLSGQSAQ 249 Query: 233 DARAQLSGTLIGLEIAGALAGSGSVDGVCLVGSGGLGTLYRTALESQGLNVRAVDADEAV 292 RA+LSG LIG E+A A G S V ++G+ L Y TAL + G + VDA+ Sbjct: 250 TGRARLSGLLIGAELA-ATRGYWSHKSVTILGTDTLARCYETALSALGCTPQRVDAETLT 308 Query: 293 RAGLSAA 299 +GL AA Sbjct: 309 LSGLCAA 315 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: 262 Number of extensions: 12 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: 325 Length adjustment: 27 Effective length of query: 279 Effective length of database: 298 Effective search space: 83142 Effective search space used: 83142 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