Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate WP_011384424.1 AMB_RS10205 4-hydroxybenzoyl-CoA reductase subunit beta
Query= SwissProt::O33820 (324 letters) >NCBI__GCF_000009985.1:WP_011384424.1 Length = 324 Score = 483 bits (1244), Expect = e-141 Identities = 237/324 (73%), Positives = 268/324 (82%) Query: 1 MNILTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLA 60 MNIL DFRT RPA+L+DAV ALA PL GTDLLPNLRRGLG P LVDLTGI G A Sbjct: 1 MNILPDFRTLRPASLSDAVAALAVPGAEPLAGGTDLLPNLRRGLGKPETLVDLTGITGFA 60 Query: 61 TISTLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDT 120 IS ADG+LRIGAGATLEA+AE + +WP LAQAA VAGP+HRAAATLGGNLCQDT Sbjct: 61 AISVGADGTLRIGAGATLEAVAEDARVLASWPVLAQAASLVAGPSHRAAATLGGNLCQDT 120 Query: 121 RCTFYNQSEWWRSGNGYCLKYKGDKCHVIVKSDRCYATYHGDVAPALMVLDARAEIVGPA 180 RC FYNQSEWWRSGNG+CLKY+GDKCHV+VKSDRCYATYHGDVAPALMVL+A AE+VGP Sbjct: 121 RCVFYNQSEWWRSGNGFCLKYEGDKCHVVVKSDRCYATYHGDVAPALMVLNASAEVVGPK 180 Query: 181 GKRTVPVAQLFRESGAEHLTLEKGELLAAIEVPPTGAWSAAYSKVRIRDAVDFPLAGVAA 240 G R VPVA LF ESGA HL+L+ GE+LAA+ VPP W+AAYSKVR+RDA+DFPLAGVA Sbjct: 181 GVRLVPVADLFVESGAAHLSLDHGEVLAALLVPPATGWTAAYSKVRVRDAIDFPLAGVAV 240 Query: 241 ALQRDGDRIAGLRVAITGSNSAPLMVPVDALLGGNWDDAAAETLAQLVRKTSNVLRTTIT 300 AL+RDG+ IAGLRVA+TG+NSAPLMVP DAL G W+D AE L Q VRK SNVL+TT+ Sbjct: 241 ALKRDGNAIAGLRVAMTGTNSAPLMVPTDALWGRPWNDETAEALVQAVRKVSNVLKTTVA 300 Query: 301 GVKYRRRVLLAISRKVVDQLWEAR 324 GVKYRRRVLLA++R+ +D LW + Sbjct: 301 GVKYRRRVLLAVARRQMDYLWNGK 324 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: 422 Number of extensions: 9 Number of successful extensions: 1 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: 324 Length adjustment: 28 Effective length of query: 296 Effective length of database: 296 Effective search space: 87616 Effective search space used: 87616 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