Align 2-dehydro-3-deoxygalactonokinase; EC 2.7.1.58; 2-keto-3-deoxy-galactonokinase; 2-oxo-3-deoxygalactonate kinase (uncharacterized)
to candidate Ga0059261_1624 Ga0059261_1624 2-keto-3-deoxy-galactonokinase
Query= curated2:P31459 (292 letters) >FitnessBrowser__Korea:Ga0059261_1624 Length = 292 Score = 166 bits (420), Expect = 6e-46 Identities = 102/286 (35%), Positives = 156/286 (54%), Gaps = 9/286 (3%) Query: 6 IAIDWGSTNLRAWLYQGDHCLESRQSEAGVTRLNGKSPAAVLAEVTTDWREEKTPVVMAG 65 +A+DWG+TN R +L + + + + GVT + + A+ A++ + + P+++AG Sbjct: 10 LAVDWGTTNRRVYLLEDGAVARTERDDRGVTAV--RDFASEAADIRARFGD--LPMLIAG 65 Query: 66 MVGSNVGWKVAPYLSVPACFSSIGEQLTSVGDNIWIIPGLCVSHDDNHNVMRGEETQLIG 125 MVGSN+GW+ APY+ PA + L + + I+PG+ +VMRGEE QL+G Sbjct: 66 MVGSNIGWRTAPYVPAPAGVGELAANLLKIDERTAIVPGVSTLAHQRPDVMRGEEVQLLG 125 Query: 126 ARA--LAP-SSLYVMPGTHCKWVQADSQQINDFRTVMTGELHHLLLNHSLIGAGLPPQEN 182 A A LAP +L V PGTHCKW Q +I F T MTGEL LL +H L+ A L + + Sbjct: 126 AVAAGLAPGDALLVQPGTHCKWAQMRGGRITGFTTAMTGELFALLRSHGLLAAQLTGEVS 185 Query: 183 SADAFTAGLERGLNTPAILPQLFEVRASHVLGTLPREQVSEFLSGLLIGAEVASMRDYVA 242 + AF G+E + LF +RA+ +LGT + + SGLLIG++VA+ D A Sbjct: 186 ANTAFRQGVEEAKRRD-LAASLFGIRAAKILGTRDDADAAAYASGLLIGSDVAARIDQ-A 243 Query: 243 HQHAITLVAGTSLTARYQQAFQAMGCDVTAVAGDTAFQAGIRSIAH 288 + +++G L Y A + + + TAF AGI +I + Sbjct: 244 PDAEMFILSGPELGNLYIAAIEMHDRAASLIDSQTAFVAGILAIGN 289 Lambda K H 0.319 0.132 0.399 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: 238 Number of extensions: 11 Number of successful extensions: 4 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: 292 Length of database: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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