Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate GFF4077 HP15_4017 formaldehyde dehydrogenase (glutathione-dependent)
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__Marino:GFF4077 Length = 370 Score = 112 bits (281), Expect = 1e-29 Identities = 112/372 (30%), Positives = 171/372 (45%), Gaps = 47/372 (12%) Query: 6 MVKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLP 65 M+KS+AA+ + ++PL I +V++ PQ EVL+RI GVC TD G + + F P Sbjct: 1 MIKSRAAVAFEANKPLEIVEVDVAPPQEGEVLVRIVATGVCHTDAYTLSGADPEGLF--P 58 Query: 66 IILGHENAGTIVEVGELAK-VKKGDNVVVYATWGDLTCRYCREGKFNIC-------KNQI 117 ILGHE G + VG K ++ GD+V+ T C++C GK N+C + Sbjct: 59 TILGHEGGGIVEAVGPGVKNLEVGDHVIPLYTAECGECKFCTSGKTNLCGAVRATQGKGV 118 Query: 118 IPGQTT----NG----------GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTSMG 162 +P T+ NG FSEY ++ L K+ +P++ L G TT +G Sbjct: 119 MPDGTSRFSYNGQPLYHYMGCSTFSEYTVLPEIS-LAKIPKDAPLDKVCLLGCGVTTGIG 177 Query: 163 AIRQALPFISKFAE-PVVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALELG 221 A+ +K E V + G+GG+ + I I + K I+G+ + D A +LG Sbjct: 178 AVLNT----AKVEEGATVAIFGLGGIGLAAI-IGAKMAKAGRIIGVDINPGKFDIAKQLG 232 Query: 222 ADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIILVG 274 A V D + +I +TDG GA + VG + + + E II V Sbjct: 233 ATDVVNPNDYDKPIQEVIVDMTDG-GADYTFECVGNVKLMRAALEACHKGWGESTIIGVA 291 Query: 275 MEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVRLSESGKIKPYII---KVPLDD 328 G+ +S F VW G G +L V +E G+I + ++PL+D Sbjct: 292 GAGEEISTRPFQLVTGRVWRGSAFGGVKGR-TELPGYVEKAEKGEIPLDVFITHEMPLED 350 Query: 329 INKAFTNLDEGR 340 INKAF + EG+ Sbjct: 351 INKAFDLMHEGK 362 Lambda K H 0.317 0.136 0.389 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: 363 Number of extensions: 29 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: 349 Length of database: 370 Length adjustment: 29 Effective length of query: 320 Effective length of database: 341 Effective search space: 109120 Effective search space used: 109120 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 (21.6 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