Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ac3H11_3163 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= BRENDA::P22144 (363 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3163 Length = 371 Score = 80.1 bits (196), Expect = 9e-20 Identities = 99/346 (28%), Positives = 147/346 (42%), Gaps = 36/346 (10%) Query: 30 DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKGVTSLKVGDNVA 89 +VL+++ TG+C +D F G + P+VLGHE AG VV+VG+GVTS+K GD+V Sbjct: 29 EVLIRITDTGVCHTDA-FTLSGDDPEGLF--PVVLGHEGAGIVVEVGEGVTSVKPGDHV- 84 Query: 90 IEPGIPSRFSD-----EYKSGHYNLCPH---------MAFAATPNSKEGEP----NPPGT 131 IP ++ KSG NLC M T S G+P T Sbjct: 85 ----IPLYTAECGECLFCKSGKTNLCVSVRATQGKGVMPDGTTRFSYNGQPIYHYMGCST 140 Query: 132 LCKYFKSPEDFLVKLPDHVSLELGALVE-PLSVGVHASK-LGSVAFGDYVAVFGAGPVGL 189 +Y E L K+ + E L+ ++ G+ A K V GD VAVFG G +GL Sbjct: 141 FSEYTVVAEVSLAKVNPQANPEQVCLLGCGVTTGLGAVKNTAKVQEGDTVAVFGLGGIGL 200 Query: 190 LAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGGS--EELIKAFGGNVPNV 247 AK A +I VD +K +A+ G AT N K +++I + Sbjct: 201 AVIQGAKLAKAGRIIAVDTNPSKFDLARTFG-ATDCINPKDFDKPIQQVIVEMTTWGVDH 259 Query: 248 VLECTGAEPCIKLGVDAIAPG-GRFVQVGNAAGPVSFPITVFAMKELTLFGSFRYGFNDY 306 EC G ++ ++ G G+ V +G A F + + +G Sbjct: 260 SFECIGNVNVMRAALECAHRGWGQSVIIGVAGAGQEISTRPFQLVTGRKWLGTAFGGVKG 319 Query: 307 KTAVGIFDTNYQNGRENAPIDFEQLITHRYKFKDAIEAYDLVRAGK 352 ++ + + G+ I E +TH KD EA+DL+ GK Sbjct: 320 RSELPGMVEDAMAGK----IQLEPFVTHTMGLKDINEAFDLMHEGK 361 Lambda K H 0.318 0.138 0.411 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: 354 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 363 Length of database: 371 Length adjustment: 30 Effective length of query: 333 Effective length of database: 341 Effective search space: 113553 Effective search space used: 113553 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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