Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS20525 AZOBR_RS20525 FAD-binding molybdopterin dehydrogenase
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__azobra:AZOBR_RS20525 Length = 332 Score = 119 bits (298), Expect = 1e-31 Identities = 89/276 (32%), Positives = 136/276 (49%), Gaps = 16/276 (5%) Query: 4 LTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATIS 63 + F R + ADA+ A T + GT+LL ++ + P LVD++ + L I Sbjct: 1 MRSFTYARADSAADAIGRAGASGTAFVAGGTNLLDLMKADVLRPEGLVDISRLP-LDRIE 59 Query: 64 TLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCT 123 A+G LR+GA A A + ++T +P L++A + A R AT GGNL Q TRC Sbjct: 60 ETAEGGLRLGALARNADTAYDERVQTRYPMLSKAILAGASAQLRNMATNGGNLLQRTRCY 119 Query: 124 FY-------NQSEWWRSGNGYCLKYKGDKCHVIV-KSDRCYATYHGDVAPALMVLDARAE 175 ++ N+ E G+G ++ H I+ SD+C A + D+ AL L+A + Sbjct: 120 YFYDTATPCNKRE---PGSGCGAIGGVNRIHAILGASDQCIAVHPSDLCVALAALEAVVQ 176 Query: 176 IVGPAGKRTVPVAQLFRESGAE---HLTLEKGELLAAIEVPPTG-AWSAAYSKVRIRDAV 231 + GP G+R++P + R G L G+L+ AI++P G A + Y KVR R + Sbjct: 177 VTGPEGERSIPFGEFHRLPGDRPEIDTVLRPGDLITAIDLPAKGFAEHSTYLKVRDRASY 236 Query: 232 DFPLAGVAAALQRDGDRIAGLRVAITGSNSAPLMVP 267 F L VAA L+ DG + R+A+ G P P Sbjct: 237 AFALVSVAAGLEMDGGTVREARLALGGVAHKPWRDP 272 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: 234 Number of extensions: 14 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: 324 Length of database: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 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