Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 7024660 Shewana3_1837 alcohol dehydrogenase (RefSeq)
Query= BRENDA::O58389 (348 letters) >FitnessBrowser__ANA3:7024660 Length = 379 Score = 122 bits (306), Expect = 2e-32 Identities = 110/372 (29%), Positives = 176/372 (47%), Gaps = 46/372 (12%) Query: 4 KMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQ 63 K A + PG ++ EVDV P GEVL++++AT +C TD ++ P Sbjct: 10 KSKAAVAWGPGQPLKIEEVDVMLPKAGEVLVRIVATGVCHTDAFTLSGDD---PEGVFPA 66 Query: 64 IMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQN---TKIFGVD 120 I+GHE G V ++G GV ++VGD+V CG+C C G+ ++CQ T+ G+ Sbjct: 67 ILGHEGGGIVEQVGEGVTSVQVGDHVIPLYTPECGECKFCLSGKTNLCQKIRATQGKGLM 126 Query: 121 TDG------------------VFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDTVL 162 DG F+EY V+P ++ K K+ P E L LG V T + Sbjct: 127 PDGTTRFYKDGQPIFHYMGCSTFSEYTVLPEISLAKVNKTAPLEEICL---LGCGVTTGM 183 Query: 163 AGPIS------GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYV 216 ++ G +V I G G +GL I A + A +I + ++ + ELA+K+GA Sbjct: 184 GAVMNTAKVEEGATVAIFGLGGIGLSAIIGATMAKASRIIAIDINESKFELARKLGATDC 243 Query: 217 INP--FEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPGKV 273 INP F++ + + ++++TDG GVD E G + L+ G ++G+ Sbjct: 244 INPKHFDKPIQEVIVEMTDG-GVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQ 302 Query: 274 TIDFN--NLI---IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKY 328 I L+ +++ G+ GR + V + L +G+ LD ITH G ++ Sbjct: 303 EISTRPFQLVTGRVWRGSAFGGVKGRS--QLPKIVEQYL-AGEFKLDDFITHT-MGLEQV 358 Query: 329 EEAFELMRAGKT 340 EAF+LM GK+ Sbjct: 359 NEAFDLMHEGKS 370 Lambda K H 0.318 0.139 0.418 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: 322 Number of extensions: 19 Number of successful extensions: 6 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: 348 Length of database: 379 Length adjustment: 29 Effective length of query: 319 Effective length of database: 350 Effective search space: 111650 Effective search space used: 111650 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 (21.7 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