Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_094578795.1 CEV32_RS19735 alcohol dehydrogenase AdhP
Query= BRENDA::Q97YM2 (349 letters) >NCBI__GCF_002252475.1:WP_094578795.1 Length = 344 Score = 137 bits (346), Expect = 3e-37 Identities = 104/345 (30%), Positives = 168/345 (48%), Gaps = 17/345 (4%) Query: 10 KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69 KAA++++F +PL+I++V IP+P ++ + I +GVC TDL +G + P I G Sbjct: 6 KAAVVREFGKPLTIDEVPIPQPGDGQIQVAIQASGVCHTDLHAAEG-DWPVKPNPPFIPG 64 Query: 70 HENAGTIVEVGELAK-VKKGDNVVV---YATWGDLTCRYCREGKFNICKNQIIPGQTTNG 125 HE G + VG+ K VK+GD V + Y G C +C G +C+ Q+ G + NG Sbjct: 65 HEGVGFVSAVGKGVKHVKEGDRVGIPWLYTACGH--CVHCLGGWETLCEEQLNTGYSVNG 122 Query: 126 GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185 GF++Y++ + ++ E AP+ AG T + + L V+++GIG Sbjct: 123 GFADYVVADPNFVGHLPKNIEFNEIAPILCAGVT----VYKGLKVTDTKPGDWVVISGIG 178 Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMK---DAESLINKLTDGL 242 GL +Q KA+ N+ V I K D A LGA K D + I K TDG Sbjct: 179 GLGHMAVQYAKAMGLNVAAVDI--DDKKLDLARRLGATVTVNAKTHNDPAAYIKKETDGG 236 Query: 243 GASIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSL 302 + + V + +G + A+ G I L G+ L F+ + + GS G+ Sbjct: 237 AQGVLVTAVSPKAFEQAIG-MAARGGTIALNGLPAGDFPLSIFNMVLNGVTVRGSIVGTR 295 Query: 303 NDLEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347 DL++ + + GK+K I +D+IN F + G+++GR V+ Sbjct: 296 LDLQESIDFAADGKVKATIRTDKIDNINAIFDEMRAGQIEGRVVM 340 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: 292 Number of extensions: 17 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: 344 Length adjustment: 29 Effective length of query: 320 Effective length of database: 315 Effective search space: 100800 Effective search space used: 100800 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