Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_075619871.1 GY23_RS14175 glutathione-dependent formaldehyde dehydrogenase
Query= BRENDA::B2ZRE3 (347 letters) >NCBI__GCF_001939075.1:WP_075619871.1 Length = 379 Score = 212 bits (539), Expect = 1e-59 Identities = 125/377 (33%), Positives = 198/377 (52%), Gaps = 34/377 (9%) Query: 1 MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGSVLGHE 60 M+AV F+ + V VKEV +L+ D +VR+ ICGSDLH+Y G +P V+GHE Sbjct: 1 MKAVTFQGAKDVKVKEVPDAKLEKKDDIIVRITSTAICGSDLHIYRGALPAKKDYVIGHE 60 Query: 61 FVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCER---------GGVYGY 111 +G VE VG + ++ GD VV PF+++CG C YC + C+ GG +G+ Sbjct: 61 PMGIVEEVGPEVTKVKKGDRVVLPFNVSCGDCYYCNHDLESQCDNSNDNPTVDTGGYFGF 120 Query: 112 GPMFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPG 169 +GN G QAE LRVP+ N +PP+ L E +F D+L TAY + ++ G Sbjct: 121 TERYGNYAGGQAEFLRVPYGNFMPFVIPPSCELEDESLLFLSDVLPTAYWSVESSGMKAG 180 Query: 170 DSVAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAI-PINAEQENPVRRV 228 D+VAV+G+GPVGLMA + A + GA +++A+D +P RL+ A + + N ++ + + Sbjct: 181 DTVAVLGSGPVGLMAQKFAWMKGAKRVIAVDHLPYRLKHAIKMNNVEAFNFDEYDDMGAH 240 Query: 229 RSETNDEGPDLVLEAVGGAATLS--------------------LALEMVRPGGRVSAVGV 268 E + G D+V++ VG LS + L VR G + GV Sbjct: 241 IKEITNGGVDVVIDCVGMDGKLSAIEKVEQKLKLQGGTLSAIDIGLNSVRKFGTIQLTGV 300 Query: 269 DNAPSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPR 328 + FPL + +++T ++G A V Y+ + + G P I++H +PL++A + Sbjct: 301 YGSLYNMFPLGNIFERNVTLKMGQAPVIHYMPLLFDKITKGEFDPTEIITHKVPLDQASK 360 Query: 329 GYELF--DRKEALKVLL 343 Y+ F E++K +L Sbjct: 361 AYQTFHDHEDESIKFIL 377 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: 356 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 347 Length of database: 379 Length adjustment: 29 Effective length of query: 318 Effective length of database: 350 Effective search space: 111300 Effective search space used: 111300 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