Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_084937098.1 HA51_RS22635 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >NCBI__GCF_002095475.1:WP_084937098.1 Length = 374 Score = 117 bits (294), Expect = 4e-31 Identities = 113/374 (30%), Positives = 171/374 (45%), Gaps = 47/374 (12%) Query: 4 VNMVKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFR 63 +NM+K++AA+ EPL IE+V++ PQ EVL+RI GVC TD G + + F Sbjct: 1 MNMIKTRAAVAWAAGEPLKIEEVDLMPPQKGEVLVRIVATGVCHTDAYTLSGKDPEGVF- 59 Query: 64 LPIILGHENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICK-------N 115 P ILGHE G + +GE + V GD+V+ T C++C GK N+C+ Sbjct: 60 -PAILGHEGGGVVEAIGEGVTSVAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRSTQGK 118 Query: 116 QIIPGQTT--------------NGGFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTS 160 ++P TT FSEY +V L ++ +P+E L G TT Sbjct: 119 GLMPDGTTRFFKDGKPIFHYMGTSTFSEYTVVPEIS-LAVISKEAPLEEVCLLGCGVTTG 177 Query: 161 MGAIRQALPFISKFAE-PVVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALE 219 MGA+ +K E V + G+GG+ + I I + K I+GI + D A + Sbjct: 178 MGAVMNT----AKVKEGDTVAIFGLGGIGLSAI-IGAKMAKAGRIIGIDLNTSKFDLARK 232 Query: 220 LGADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIIL 272 LGA + KD + +I +LTDG G + + +G + + + E II Sbjct: 233 LGATDLINPKDYDKPIQDVIVELTDG-GVDYSFECIGNVNVMRSALECCHKGWGESVIIG 291 Query: 273 VGMEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVRLSESGK--IKPYII-KVPL 326 V G+ +S F VW G G L +V+ GK + +I +PL Sbjct: 292 VAGAGEEISTRPFQLVTGRVWRGSAFGGVKGR-TQLPGIVQDYLDGKFALNDFITHTMPL 350 Query: 327 DDINKAFTNLDEGR 340 ++IN AF + EG+ Sbjct: 351 EEINDAFDLMHEGK 364 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: 380 Number of extensions: 32 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: 349 Length of database: 374 Length adjustment: 29 Effective length of query: 320 Effective length of database: 345 Effective search space: 110400 Effective search space used: 110400 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 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