Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate 14423 b0285 predicted oxidoreductase with FAD-binding domain (NCBI)
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__Keio:14423 Length = 318 Score = 107 bits (267), Expect = 4e-28 Identities = 102/333 (30%), Positives = 149/333 (44%), Gaps = 27/333 (8%) Query: 1 MNILTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLA 60 M T R + PA A ++A + GT+LL ++ + P L+D+ G+ GL Sbjct: 1 MKAFTYERVNTPAEAA--LSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGL-GLD 57 Query: 61 TISTLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDT 120 I G LRIGA +A H+ +R + L++A + A R AT GNL Q T Sbjct: 58 KIEVTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRT 117 Query: 121 RCTFY---NQSEWWRSGNGYCLKYKG-DKCHVIV-KSDRCYATYHGDVAPALMVLDARAE 175 RC ++ NQ R C +G + H +V S+ C AT+ D+A A+ +LDA E Sbjct: 118 RCPYFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVE 177 Query: 176 IVGPAGK-RTVPVAQLFRESG-AEHL--TLEKGELLAAIEVPPTGAWSAAYSKVRIRDAV 231 + P GK R++ +A + G H+ L GEL+ A+ +PP Y KVR R + Sbjct: 178 TITPEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASY 237 Query: 232 DFPLAGVAAALQRDGDRIAGLRVAITGSNSAPLMVPVDALLGGNWDDAAAETLAQLVRKT 291 F L VAA +Q DG RVA+ G P + +AA L+Q + Sbjct: 238 AFALVSVAAIIQPDGSG----RVALGGVAHKPWRI-----------EAADAQLSQGAQAV 282 Query: 292 SNVLRTTITGVKYRRRVLLAISRKVVDQLWEAR 324 + L + LL R + L EAR Sbjct: 283 YDTLFASAHPTAENTFKLLLAKRTLASVLAEAR 315 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: 15 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: 318 Length adjustment: 28 Effective length of query: 296 Effective length of database: 290 Effective search space: 85840 Effective search space used: 85840 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