Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate SM_b20396 SM_b20396 dehydrogenase
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__Smeli:SM_b20396 Length = 327 Score = 134 bits (336), Expect = 4e-36 Identities = 99/270 (36%), Positives = 138/270 (51%), Gaps = 11/270 (4%) Query: 4 LTDFRTHRPATLADAVNALAAEATLPL-GAGTDLLPNLRRGLGHPAALVDLTGIDGLATI 62 + F R A L AV L+ L G GT+L+ +R + P ALVD+TG+ L I Sbjct: 1 MKSFAYARAADLEAAVKLLSKTPNAKLLGGGTNLVDLMRENIEQPDALVDVTGLP-LDRI 59 Query: 63 STLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRC 122 DG L IGA A+A H +R +P LAQA A R AT+ GNL Q TRC Sbjct: 60 EERPDGGLVIGATVRNTAVAGHPVVRDRYPLLAQAIVFGASGQIRNMATVAGNLMQRTRC 119 Query: 123 T-FYNQSEWW--RSGNGYCLKYKG-DKCHVIV-KSDRCYATYHGDVAPALMVLDARAEIV 177 FY+ + R+ C G ++ H I+ SD C AT+ D+ AL LDA+ ++ Sbjct: 120 LYFYDHAARCNKRAPGAGCDAIGGFNRMHAILGASDSCIATHPSDMCVALAALDAKVNVI 179 Query: 178 GPAGKRTVPVAQLFR---ESGAEHLTLEKGELLAAIEVPPTG-AWSAAYSKVRIRDAVDF 233 GP+G RT+ + R ++ L+ GEL+ IE+PP G A + Y KVR R + F Sbjct: 180 GPSGARTIAFEEFHRLPEDTPDIETDLQPGELITGIEIPPLGFARRSLYRKVRDRASYAF 239 Query: 234 PLAGVAAALQRDGDRIAGLRVAITGSNSAP 263 L VAAAL+ D ++ +R+A+ G P Sbjct: 240 ALVSVAAALEVDSGKVRNVRLALGGVAHKP 269 Lambda K H 0.319 0.133 0.399 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: 262 Number of extensions: 14 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: 324 Length of database: 327 Length adjustment: 28 Effective length of query: 296 Effective length of database: 299 Effective search space: 88504 Effective search space used: 88504 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: 48 (23.1 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