Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_003463377.1 J416_RS01495 glutathione-dependent formaldehyde dehydrogenase
Query= BRENDA::B2ZRE3 (347 letters) >NCBI__GCF_000359605.1:WP_003463377.1 Length = 377 Score = 215 bits (547), Expect = 2e-60 Identities = 126/375 (33%), Positives = 196/375 (52%), Gaps = 32/375 (8%) Query: 1 MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGSVLGHE 60 M++V ++ K VAV +V P ++ D +V++ ICGSDLHLY G P+ G +GHE Sbjct: 1 MKSVTYQGKYEVAVTQVPFPTIEDDEDVIVKITSTAICGSDLHLYQGNFPLPIGYQIGHE 60 Query: 61 FVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCER-------GGVYGYGP 113 +G VE VG + ++ GD VV PF IACG CPYC+ H + C++ GG GY Sbjct: 61 PMGIVEEVGPKVTKVKKGDRVVIPFTIACGQCPYCKTHHESQCDQANPHYDSGGYLGYSE 120 Query: 114 MFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPGDS 171 FGN G QAE LRVPF N +P + L +F D+L TA + ++ GD+ Sbjct: 121 KFGNYPGGQAEYLRVPFGNYTPFLIPEDCELDDASLLFLSDVLPTALWSVEHAGVKAGDT 180 Query: 172 VAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPI-NAEQENPVRRVRS 230 V V+G GP+GLM + A A++++A+D IP RLE A + + N Q + + Sbjct: 181 VIVLGCGPIGLMVQKFAWQKRANRVIAVDYIPYRLEHARKENRVEVFNFTQYDDMGETLK 240 Query: 231 ETNDEGPDLVLEAV--------------------GGAATLSLALEMVRPGGRVSAVGVDN 270 E + G D+V++ V G + +A + V+ G V GV Sbjct: 241 EITNGGADVVIDCVGMDGKKSPLEFVEQKTKLQGGTIGPIQIATKAVKKCGVVQMTGVYG 300 Query: 271 APSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPRGY 330 FPL + +++ ++G A+ Y+ ++ + +G + P I++H LPLE+A GY Sbjct: 301 GNYNLFPLGAFFSRNVQLKMGQAHARSYMASIYRQIVNGDIDPTTIITHQLPLEDASHGY 360 Query: 331 ELFDRKE--ALKVLL 343 ++F+ K+ +KV+L Sbjct: 361 DIFNGKKENCMKVVL 375 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: 350 Number of extensions: 9 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: 347 Length of database: 377 Length adjustment: 29 Effective length of query: 318 Effective length of database: 348 Effective search space: 110664 Effective search space used: 110664 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