Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate AZOBR_RS30035 AZOBR_RS30035 (2Fe-2S)-binding protein
Query= SwissProt::O33818 (161 letters) >FitnessBrowser__azobra:AZOBR_RS30035 Length = 152 Score = 125 bits (313), Expect = 4e-34 Identities = 67/151 (44%), Positives = 98/151 (64%), Gaps = 3/151 (1%) Query: 4 ILRLTLNGRAREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPRLACST 63 ++RL +NG+ R+ VP +M LL LR+ + LTGTK GC +CGACTV +D P AC T Sbjct: 1 MIRLNINGQDRDVDVPGDMPLLWVLRDELNLTGTKFGCGIAQCGACTVHMDGTPIRACQT 60 Query: 64 LAHQVAGKKVETVESLATQGTLSK-LQAAFHEKLGTQCGFCTPGMIMASEALLRKNPSPS 122 A AG K+ T+E ++ GT+++ +QAA+ + QCG+C G IM++ ALL N +P+ Sbjct: 61 PAESAAGTKITTIEGVS--GTVAQAVQAAWQKLDVVQCGYCQSGQIMSAVALLTDNRNPT 118 Query: 123 RDEIKAALAGNLCRCTGYVRSSKSVETAAAA 153 D+I AA+ GN+CRC Y R +++ AA A Sbjct: 119 DDDIDAAMDGNVCRCATYPRIRAAIKDAAKA 149 Lambda K H 0.318 0.132 0.389 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: 88 Number of extensions: 5 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: 161 Length of database: 152 Length adjustment: 17 Effective length of query: 144 Effective length of database: 135 Effective search space: 19440 Effective search space used: 19440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 43 (21.2 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