Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate AO353_00730 AO353_00730 FAD-binding molybdopterin dehydrogenase
Query= SwissProt::O33818 (161 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00730 Length = 484 Score = 115 bits (288), Expect = 1e-30 Identities = 66/165 (40%), Positives = 92/165 (55%), Gaps = 14/165 (8%) Query: 4 ILRLTLNGRAREDLVPD-NMLLLDYLRETVGLTGTKQGCDGGECGACTVLV-----DDRP 57 +++ LN R + D N+ +L+YLRE +G GTK+GC G+CGACTV+V DD Sbjct: 1 VIQFLLNQELRSEHALDPNLTVLNYLREHLGKPGTKEGCASGDCGACTVVVGELQTDDNG 60 Query: 58 RL--------ACSTLAHQVAGKKVETVESLATQGTLSKLQAAFHEKLGTQCGFCTPGMIM 109 R +C T + GK++ +VE L QG L +Q A E G+QCGFCTPG +M Sbjct: 61 REHIRYRSLNSCLTFVSSLHGKQLISVEDLKHQGKLHSVQKAMVECHGSQCGFCTPGFVM 120 Query: 110 ASEALLRKNPSPSRDEIKAALAGNLCRCTGYVRSSKSVETAAAAR 154 + AL + + + ALAGNLCRCTGY + E +A+ Sbjct: 121 SLFALQKNSDHADSHKAHEALAGNLCRCTGYRPILAAAEQVCSAK 165 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: 197 Number of extensions: 9 Number of successful extensions: 3 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: 484 Length adjustment: 25 Effective length of query: 136 Effective length of database: 459 Effective search space: 62424 Effective search space used: 62424 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: 47 (22.7 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