Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS27480 AZOBR_RS27480 hypothetical protein
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__azobra:AZOBR_RS27480 Length = 333 Score = 135 bits (339), Expect = 2e-36 Identities = 99/282 (35%), Positives = 140/282 (49%), Gaps = 22/282 (7%) Query: 11 RPATLADAVNALAA--EATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATISTLADG 68 R T +A+ A A E+ + GT+L ++ G+ PA L+D+ +DG I T D Sbjct: 8 RARTAREAIEAFVAAGESARYIAGGTNLYDLMKLGIEKPAHLIDIADLDGANRIDTDGD- 66 Query: 69 SLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCTFYNQS 128 L G A + +AEH +R +P LA++ A R AT+GGNL Q TRC ++ Sbjct: 67 RLFFGGAALMADVAEHPVVRDDYPVLAESLSKAASQQLRNMATVGGNLLQRTRCPYFRNG 126 Query: 129 EWWRSGNGYCLKYK-GDKCHVIVKSDR----------CYATYHGDVAPALMVLDARAEIV 177 +G C K + G C I DR C A GD ALM +DA E+ Sbjct: 127 ---ANGAYPCNKREPGSGCAAIGGLDRSQAVLGASAACNAVSPGDWPVALMAMDAAIELQ 183 Query: 178 GPAGKRTVPVAQLFR-ESGAEHL--TLEKGELLAAIEVPPTGAW-SAAYSKVRIRDAVDF 233 G G R +P+A+L+R S HL T+ + E++ I VP T A ++ Y KVR R++ F Sbjct: 184 GLDGTRVIPIAELYRPPSRTPHLEFTIGREEIVTGISVPKTTAGRTSTYLKVRDRESYAF 243 Query: 234 PLAGVAAALQRDGDRIAGLRVAITGSNSAPLMV-PVDALLGG 274 L A AL+ DGDR+ VA+ G + P P +ALL G Sbjct: 244 ALVSAAVALEMDGDRVRQAHVALGGVATVPWRARPAEALLRG 285 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: 252 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: 324 Length of database: 333 Length adjustment: 28 Effective length of query: 296 Effective length of database: 305 Effective search space: 90280 Effective search space used: 90280 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