Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= BRENDA::Q4J9F2 (255 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 157 bits (397), Expect = 2e-43 Identities = 94/251 (37%), Positives = 142/251 (56%), Gaps = 8/251 (3%) Query: 6 LKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVEL-LEDRLNQIVQELRGMGKEVLGVKA 64 L K IVTGA GIG+AIA KFA + + +L +++ + EL MG + G + Sbjct: 4 LDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYAS 63 Query: 65 DVSKKKDVEEFVRRTFETYSRIDVLCNNAGIM-DGVTPVAEVSDELWERVLAVNLYSAFY 123 + + +D + V + + RID+L NNAGI DG+ + +S++ W+ V+ VNL SAF Sbjct: 64 NAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGL--MMRMSEQQWDMVINVNLKSAFN 121 Query: 124 SSRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRA 183 A P+M++Q G I+N AS+ G+ G A Y +K G+I L +SIA G +GIRA Sbjct: 122 FIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIRA 181 Query: 184 VAVLPGTVKTNIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNG 243 A+ PG + T++ S E+ K+ R PED+AN+ FLASD +S+V+G Sbjct: 182 NAIAPGFILTDMTAALS--DEVRAEWAKKIP--LRRGGTPEDVANIATFLASDMSSYVSG 237 Query: 244 DAVVVDGGLTV 254 + VDGG+ + Sbjct: 238 QVIQVDGGMNM 248 Lambda K H 0.318 0.135 0.369 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: 156 Number of extensions: 7 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: 255 Length of database: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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: 46 (22.3 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