Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_02929 CCNA_02929 sorbitol dehydrogenase
Query= BRENDA::B2ZRE3 (347 letters) >FitnessBrowser__Caulo:CCNA_02929 Length = 346 Score = 259 bits (662), Expect = 7e-74 Identities = 148/346 (42%), Positives = 206/346 (59%), Gaps = 6/346 (1%) Query: 1 MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGK-IPVLPGSVLGH 59 M+A+ + V + ++ P Q DA+V+V ICGSDLH+YHG G +GH Sbjct: 1 MKALRYHGARDVRYESMDDPTPQSDRDAIVQVTACSICGSDLHIYHGHGFSEDLGFCVGH 60 Query: 60 EFVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCERGGVYGYGPMFGNLQ 119 E VG+V VG G+Q L+ GD V+ P + CG C C CE G YG + LQ Sbjct: 61 EAVGEVVEVGRGVQRLKVGDKVMLPAAVGCGRCRSCLSGVIQTCENGQGACYG-LSARLQ 119 Query: 120 GAQAEILRVPFSNVNLRKLPPNLSPERAIFAGDILSTAYGGLIQGQLRPGDSVAVIGAGP 179 G+QAE +RVP +++N +P +S ++A+ D L+TA+ G ++RPG SVAVIG GP Sbjct: 120 GSQAEAVRVPAADMNAVPVPDGVSMDQALMMTDALATAWFGARNAEVRPGASVAVIGLGP 179 Query: 180 VGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPINAEQENPVRRVRSETNDEGPDL 239 +GLMA+E A V+GA + AID +P R A GAI ++ ++ + RVR +T G D Sbjct: 180 IGLMAVESAYVMGAHVVYAIDPLPARRALAEEAGAIALHPDEA--LARVREDTKGRGLDC 237 Query: 240 VLEAVGGAATLSLALEMVRPGGRVSAVGVDNAPSFPFPLASGLVKDLTFRIGLANVHLYI 299 V+EAVGG AT+ AL +VRP G VS +GV A F FPL LTFR+G +V + Sbjct: 238 VIEAVGGEATVDAALRLVRPRGVVSVIGVQQAKRFAFPLERAFGAGLTFRVGTCSVPEEL 297 Query: 300 DAVLALLASGRLQPERIVSHYLPLEEAPRGYELFDRKE--ALKVLL 343 A+ L+ SGRL+PE+ +SH LPL + P Y LF+ +E ALK++L Sbjct: 298 PALFPLVRSGRLRPEKYISHRLPLSDGPEAYRLFESREAGALKMVL 343 Lambda K H 0.321 0.141 0.420 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: 354 Number of extensions: 16 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: 347 Length of database: 346 Length adjustment: 29 Effective length of query: 318 Effective length of database: 317 Effective search space: 100806 Effective search space used: 100806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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