Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate SM_b21558 SM_b21558 aldehyde or xanthine dehydrogenase, iron-sulfur subunit protein
Query= SwissProt::O33818 (161 letters) >FitnessBrowser__Smeli:SM_b21558 Length = 207 Score = 119 bits (298), Expect = 3e-32 Identities = 62/147 (42%), Positives = 86/147 (58%) Query: 5 LRLTLNGRAREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPRLACSTL 64 L +T+NGR + +V + +LD LRE + LTGTK+GC+ G CGACTVL+D + AC L Sbjct: 56 LEVTVNGRVHQLVVDPRLSVLDMLRERLSLTGTKKGCNQGACGACTVLIDGQRVNACLAL 115 Query: 65 AHQVAGKKVETVESLATQGTLSKLQAAFHEKLGTQCGFCTPGMIMASEALLRKNPSPSRD 124 A G K+ T+E +A L LQ AF E QCG+CT G IM+ + + + S + Sbjct: 116 AVMYDGAKITTIEGVAEGEALHPLQVAFIEHDAFQCGYCTSGQIMSGLGCISEGHASSAE 175 Query: 125 EIKAALAGNLCRCTGYVRSSKSVETAA 151 EI ++GN+CRC Y +V AA Sbjct: 176 EISYWMSGNICRCGAYPGIVAAVAQAA 202 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: 122 Number of extensions: 4 Number of successful extensions: 1 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: 207 Length adjustment: 19 Effective length of query: 142 Effective length of database: 188 Effective search space: 26696 Effective search space used: 26696 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: 44 (21.6 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