Align 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized)
to candidate BPHYT_RS29705 BPHYT_RS29705 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-17403 (163 letters) >FitnessBrowser__BFirm:BPHYT_RS29705 Length = 241 Score = 139 bits (349), Expect = 4e-38 Identities = 79/166 (47%), Positives = 95/166 (57%), Gaps = 16/166 (9%) Query: 11 RLLGLNVNGRWREDAVTDDMLLVDYLRDIAGLTGVKTGCDGGECGACTVLIDGEAAPSCL 70 R + L VNGR + + L+D LR+ AGL G K GCD G+CGACTVL DG SCL Sbjct: 63 RPVTLTVNGRAYTLQLEPRVTLLDALREYAGLMGTKKGCDRGQCGACTVLADGRRINSCL 122 Query: 71 VLAVRCEGRYIETVEGLAANGRLHRLQQTFHERLGAQCGFCTPGMIMAAEGLLR------ 124 LAV EG I TVEGLAANG L +Q+ F E QCG+CTPG + +A LL Sbjct: 123 TLAVMHEGENITTVEGLAANGVLSPIQRAFIEHDAFQCGYCTPGQLCSATALLNEFRNGT 182 Query: 125 ----------RNPSPTDEEIRTALSGNLCRCTGYAKIVESVQAAAE 160 R +DEEIR +SGN+CRC YA IV +V+A E Sbjct: 183 ASTVTADVRIRPAQLSDEEIRERMSGNICRCGAYANIVAAVRAVHE 228 Lambda K H 0.322 0.138 0.425 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: 144 Number of extensions: 6 Number of successful extensions: 2 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: 163 Length of database: 241 Length adjustment: 20 Effective length of query: 143 Effective length of database: 221 Effective search space: 31603 Effective search space used: 31603 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 (21.9 bits) S2: 45 (21.9 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