Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate BPHYT_RS20915 BPHYT_RS20915 hypothetical protein
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS20915 Length = 335 Score = 116 bits (290), Expect = 9e-31 Identities = 92/291 (31%), Positives = 137/291 (47%), Gaps = 18/291 (6%) Query: 7 FRTHRPATLADAVNALAAEATLPLGA-------GTDLLPNLRRGLGHPAALVDLTGIDGL 59 F+ R + DA+ A A AT GA GT LL ++ + P ++D++ + L Sbjct: 4 FQLSRANGVRDAITAGATSATAQQGAQVRFLAGGTTLLDLMKLNVEQPTQVIDISRLP-L 62 Query: 60 ATISTLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQD 119 I L DG ++IGA A +A H IR + L+QA + A R AT GGNL Q Sbjct: 63 DRIEALPDGGVKIGATARNADLALHPLIRAPYAVLSQALLAGASAQLRNMATTGGNLLQR 122 Query: 120 TRCTFYNQSEW---WRSGNGYCLKYKG--DKCHVIVKSDRCYATYHGDVAPALMVLDARA 174 TRC ++ + R C +G ++ SD C AT D+ AL LDA Sbjct: 123 TRCVYFRDTAMPCNKREPGSGCPAIQGFNRTLAILGASDACIATNPSDMNVALTALDATI 182 Query: 175 EIVGPAGKRTVPVAQLFRESGA---EHLTLEKGELLAAIEVPPTGAWS-AAYSKVRIRDA 230 + G G R++ + F G L+ G+L+ + +PP A + + Y K+R R + Sbjct: 183 HVEGTGGARSIAIDDFFVLPGTTPQRENVLDAGDLITHVTLPPLPAGARSVYLKLRDRAS 242 Query: 231 VDFPLAGVAAALQRDGDRIAGLRVAITGSNSAPL-MVPVDALLGGNWDDAA 280 +F LA A + DG RI +RVA+ G + P + +A+L G DAA Sbjct: 243 YEFALASAAVVVTLDGGRIGHVRVALGGVGTRPWHALEAEAVLRGAAPDAA 293 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: 229 Number of extensions: 18 Number of successful extensions: 3 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: 335 Length adjustment: 28 Effective length of query: 296 Effective length of database: 307 Effective search space: 90872 Effective search space used: 90872 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