Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_075617952.1 GY23_RS04320 glutathione-dependent formaldehyde dehydrogenase
Query= BRENDA::B2ZRE3 (347 letters) >NCBI__GCF_001939075.1:WP_075617952.1 Length = 378 Score = 217 bits (552), Expect = 4e-61 Identities = 132/376 (35%), Positives = 194/376 (51%), Gaps = 33/376 (8%) Query: 1 MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGS-VLGH 59 M+AV F+ + V VK V P +Q D +V++ ICGSDLHL HG IP L V+GH Sbjct: 1 MKAVTFQGVKNVQVKNVKDPSIQKADDIIVKLTTTAICGSDLHLIHGMIPNLGEDYVIGH 60 Query: 60 EFVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLC-------ERGGVYGYG 112 E +G VE VG+ + ++ GD V+ PF+IACG C YC + C E G +GY Sbjct: 61 EPMGIVEEVGKDVTKVKKGDRVIIPFNIACGQCWYCNHELESQCDNANENGEMGAYFGYS 120 Query: 113 PMFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPGD 170 G G QAE +RVP++N K+P N ++ E + D STA+ + ++ GD Sbjct: 121 DTTGGFPGGQAEFMRVPYANFTPFKIPENSEVADESLVLLADAASTAFWSVDNAGVKAGD 180 Query: 171 SVAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPI-NAEQENPVRRVR 229 +V ++G GPVGL+A + A + GA +++A+D + RL+ A + I N E Sbjct: 181 TVVILGCGPVGLLAQKFAWLKGAKRVIAVDYVGYRLKHAKRTNKVEIVNFEDHENCGEYL 240 Query: 230 SETNDEGPDLVLEAVG--------------------GAATLSLALEMVRPGGRVSAVGVD 269 E G D+V++ VG L +A + VR GG + GV Sbjct: 241 REITQGGADVVIDCVGMSGKMTPLEFLASGLKLQGGAMGALVIASQAVRKGGTIQITGVY 300 Query: 270 NAPSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPRG 329 A FPL +++ R G A V Y+ + L+A G++ P IV+H LPL++A G Sbjct: 301 GARYNAFPLGDIFQRNVNIRTGQAPVIHYMQHLYNLIAEGKVDPSDIVTHVLPLDQAKHG 360 Query: 330 YELFDRK--EALKVLL 343 YE+FD K + +KV+L Sbjct: 361 YEVFDTKMEDCIKVVL 376 Lambda K H 0.321 0.141 0.420 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: 373 Number of extensions: 19 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: 347 Length of database: 378 Length adjustment: 29 Effective length of query: 318 Effective length of database: 349 Effective search space: 110982 Effective search space used: 110982 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: 49 (23.5 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