Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate AZOBR_RS16515 AZOBR_RS16515 S-(hydroxymethyl)glutathione dehydrogenase
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__azobra:AZOBR_RS16515 Length = 372 Score = 121 bits (304), Expect = 3e-32 Identities = 113/373 (30%), Positives = 174/373 (46%), Gaps = 49/373 (13%) Query: 6 MVKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLP 65 MVKS+AA+ + PL IE+V + P+ EVL+RI GVC TD G++++ F P Sbjct: 1 MVKSRAAVAWEAKRPLEIEEVEVAAPRQGEVLVRIVATGVCHTDAYTLSGMDSEGVF--P 58 Query: 66 IILGHENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICK-------NQI 117 ILGHE AG + EVG + V+ GD+V+ T C++C GK N+C+ + Sbjct: 59 AILGHEGAGIVEEVGPGVTSVQVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKGL 118 Query: 118 IPGQTT--------------NGGFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTSMG 162 +P T+ FSEY ++ + K+N +P+E L G TT MG Sbjct: 119 MPDGTSRFTAKGQPVFHYMGTSTFSEYTVLPEIA-VAKINKAAPLEKVCLLGCGVTTGMG 177 Query: 163 AIRQALPFISKFAEP--VVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALEL 220 A+R EP V + G+GG+ + I I + K I+GI + + A +L Sbjct: 178 AVRNTAK-----VEPGSTVAIFGLGGIGLSAI-IGAVMAKASRIIGIDINPDKFEIAKQL 231 Query: 221 GADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIILV 273 GA V KD + ++ ++TDG G + + +G + + + E II V Sbjct: 232 GATDVVNPKDYDRPIQEVLVEMTDG-GVDYSFECIGNVKVMRAALECCHKGWGESVIIGV 290 Query: 274 GMEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVR--LSESGKIKPYII-KVPLD 327 G+ +S F VW G G ++L D V L ++ +I + L+ Sbjct: 291 AGAGEEISTRPFQLVTGRVWRGSAFGGVRGR-SELPDYVERYLKGEFELDTFITHTMGLE 349 Query: 328 DINKAFTNLDEGR 340 DINKAF + EG+ Sbjct: 350 DINKAFDLMHEGK 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: 344 Number of extensions: 23 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: 372 Length adjustment: 29 Effective length of query: 320 Effective length of database: 343 Effective search space: 109760 Effective search space used: 109760 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