Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate BPHYT_RS29710 BPHYT_RS29710 FAD-binding molybdopterin dehydrogenase
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS29710 Length = 333 Score = 145 bits (366), Expect = 1e-39 Identities = 99/275 (36%), Positives = 142/275 (51%), Gaps = 11/275 (4%) Query: 11 RPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATISTLADGSL 70 R +A AV A + +G GT+LL ++ G+ P L+D+T I GL ++TL DG + Sbjct: 8 RAGDVAGAVRAAQQPGAVFIGGGTNLLDLMKGGVARPMRLIDITHISGLDMVTTLPDGGI 67 Query: 71 RIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRC-----TFY 125 R+GA A H +R +P L+QA + A R AT+GGNL Q TRC T + Sbjct: 68 RLGALVRNSDAANHALVREQYPLLSQAFLAGASSQLRNMATVGGNLLQRTRCGYFYDTAF 127 Query: 126 NQSEWWRSGNGYCLKYKGDKCHVIV-KSDRCYATYHGDVAPALMVLDARAEIVGPAGKRT 184 Q G+G ++ H I+ S +C A D++ AL LDA + GPAG+RT Sbjct: 128 TQCNKRMPGSGCAALDGHNRTHAILGASPQCIAVNPSDMSVALAALDAVVRVSGPAGERT 187 Query: 185 VPVAQLFRESGAE---HLTLEKGELLAAIEV-PPTGAWSAAYSKVRIRDAVDFPLAGVAA 240 + A R G TL+ GEL+ A+++ PP + ++ Y KVR R + F L VAA Sbjct: 188 IAFADFHRLPGDRPDVDTTLQPGELITAVDLPPPLFSANSHYLKVRDRASYAFALVSVAA 247 Query: 241 ALQRDGDRIAGLRVAITGSNSAPLMVPV-DALLGG 274 ALQ DG R+ R+A+ G P V + +L G Sbjct: 248 ALQMDGGRVKTARIALGGVAHKPWRASVAEQMLNG 282 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: 264 Number of extensions: 18 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