Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate GFF3380 Psest_3445 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs
Query= SwissProt::O33820 (324 letters) >FitnessBrowser__psRCH2:GFF3380 Length = 328 Score = 129 bits (325), Expect = 8e-35 Identities = 95/272 (34%), Positives = 138/272 (50%), Gaps = 17/272 (6%) Query: 4 LTDFRTHRPATLADAVNALAAEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATIS 63 +T F RP + A+ AL + + GT+LL ++ + P L+D+ G+ L I Sbjct: 1 MTPFSYQRPERIDQAI-ALHGPQSRYIAGGTNLLDLMKENVLQPGQLIDINGLP-LRDIE 58 Query: 64 TLADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCT 123 A+G LRIGA + +A H I +P L++A + A P R A+ GGNL Q TRC Sbjct: 59 QTAEGGLRIGALVSNADLAWHPQIEQRYPLLSKAILAGASPQLRNMASTGGNLLQRTRCY 118 Query: 124 FY-------NQSEWWRSGNGYCLKYKGDKCHVIV-KSDRCYATYHGDVAPALMVLDARAE 175 ++ N+ E G+G + ++ H I+ S+ C A + D+ AL LDAR Sbjct: 119 YFYDTATPCNKRE---PGSGCSARDGRNRIHAILGASEHCVAVHPSDMCVALAALDARVH 175 Query: 176 IVGPAGKRTVPVAQLFRESG---AEHLTLEKGELLAAIEVPPTG-AWSAAYSKVRIRDAV 231 + GP G+R + + R G + L +GEL+ AIE+P G A AY KVR R + Sbjct: 176 VEGPHGQRRLELVDFHRLPGDQPQQDNVLVEGELITAIELPVEGFASHCAYLKVRDRASY 235 Query: 232 DFPLAGVAAALQRDGDRIAGLRVAITGSNSAP 263 F L VAAAL+ DGD I R+A+ G P Sbjct: 236 AFALVSVAAALEMDGDIIRRARIALGGVAHKP 267 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: 246 Number of extensions: 17 Number of successful extensions: 5 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: 328 Length adjustment: 28 Effective length of query: 296 Effective length of database: 300 Effective search space: 88800 Effective search space used: 88800 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