Align Alcohol dehydrogenase class-3; EC 1.1.1.1; Alcohol dehydrogenase class-III; Glutathione-dependent formaldehyde dehydrogenase; FALDH; FDH; GSH-FDH; EC 1.1.1.-; S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.284 (uncharacterized)
to candidate GFF239 PGA1_c02510 S-(hydroxymethyl)glutathione dehydrogenase FrmA
Query= curated2:P72324 (376 letters) >FitnessBrowser__Phaeo:GFF239 Length = 371 Score = 622 bits (1605), Expect = 0.0 Identities = 299/376 (79%), Positives = 338/376 (89%), Gaps = 6/376 (1%) Query: 1 MRTRAAVAVEAGKPLEIMEVNLEGPKAGEVMVEIKATGICHTDEFTLSGADPEGMFPAIL 60 +RTRAAVAV GKPLEIMEVNLEGPK GEV+VEIKATG+CHTDEFT SG DPEG+FPAIL Sbjct: 2 IRTRAAVAVAPGKPLEIMEVNLEGPKKGEVLVEIKATGLCHTDEFTRSGDDPEGIFPAIL 61 Query: 61 GHEGAGVVVEVGPGVTSVKPGDHVIPLYTPECRQCPSCLSQKTNLCTAIRGTQGQGLMPD 120 GHEGAGVVVEVG GVTS++ GDHVIPLYTPECR+C CL+ KTNLC AIR TQGQGL+PD Sbjct: 62 GHEGAGVVVEVGEGVTSLEVGDHVIPLYTPECRECEYCLNPKTNLCQAIRSTQGQGLLPD 121 Query: 121 GTSRFSMLDGTPILHYMGCSTFSNYTVLPEIAVAKVRPDAPFDKICYIGCGVTTGIGAVI 180 G++RFSMLDGTPI HYMGCSTF+N+TV+PEIA+AK+R DAPFDK+CYIGCGVTTGIGAVI Sbjct: 122 GSTRFSMLDGTPIYHYMGCSTFANHTVVPEIALAKIRKDAPFDKVCYIGCGVTTGIGAVI 181 Query: 181 NTAKVEIGAKAVVFGLGGIGLNVIQGLKLAGADMIIGVDLNNAKKEWGERFGMTHFVNPS 240 NTAKVEIG++A+VFGLGGIGLNVIQGL+LAGAD I+GVDLN K E ++FGMT FVNP+ Sbjct: 182 NTAKVEIGSRAIVFGLGGIGLNVIQGLRLAGADQIVGVDLNPGKIEMAKQFGMTDFVNPA 241 Query: 241 EIDGDVVAHLVNMTKTPFDQIGGADYTFDCTGNVKVMRQALEACHRGWGQSIVIGVAPAG 300 E+DGD+VAHLV +TK GGADYTFD TGNV+VMR ALEA H+GWG+SI+IGVAPAG Sbjct: 242 EVDGDLVAHLVELTK------GGADYTFDATGNVQVMRTALEAAHKGWGESIIIGVAPAG 295 Query: 301 AEIQTRPFQLVTGRVWKGSAFGGARGRTDVPKIVDWYMEGKIQIDPMITHILSLEEINKG 360 AEI TRPFQLVTGR W+G+AFGGA GRTDVPKIVDWYM+GKI+IDPMITH LSL+EIN G Sbjct: 296 AEISTRPFQLVTGRSWRGTAFGGAAGRTDVPKIVDWYMDGKIEIDPMITHKLSLDEINHG 355 Query: 361 FDLMHAGESIRSVVVF 376 FDLMH G+SIR+VV F Sbjct: 356 FDLMHEGKSIRAVVEF 371 Lambda K H 0.320 0.139 0.427 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: 586 Number of extensions: 21 Number of successful extensions: 2 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: 376 Length of database: 371 Length adjustment: 30 Effective length of query: 346 Effective length of database: 341 Effective search space: 117986 Effective search space used: 117986 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: 50 (23.9 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