Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate WP_011426360.1 RHE_RS15975 xanthine dehydrogenase small subunit
Query= SwissProt::O33818 (161 letters) >NCBI__GCF_000092045.1:WP_011426360.1 Length = 488 Score = 109 bits (272), Expect = 7e-29 Identities = 73/168 (43%), Positives = 91/168 (54%), Gaps = 18/168 (10%) Query: 1 MKNILRLTLNGR--AREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPR 58 M + +R LNG A D+ P LL D+LR LTGTK+GC G+CGACTVLV R Sbjct: 1 MNDSIRFILNGEDIALTDVGPTETLL-DFLRLKRRLTGTKEGCAEGDCGACTVLVG---R 56 Query: 59 LACSTLAHQ-----------VAGKKVETVESLATQ-GTLSKLQAAFHEKLGTQCGFCTPG 106 LA LA++ + V TVE LA + G L +Q A + G+QCGFCTPG Sbjct: 57 LADGKLAYESVNACIRFLGSLHATHVVTVEHLAGRDGALHPVQQALVDCHGSQCGFCTPG 116 Query: 107 MIMASEALLRKNPSPSRDEIKAALAGNLCRCTGYVRSSKSVETAAAAR 154 +M+ L P R EI+ AL GNLCRCTGY K+ E + R Sbjct: 117 FVMSLYGLWLTKEKPGRREIEKALQGNLCRCTGYEPIVKAAEQVSLMR 164 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: 190 Number of extensions: 13 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: 488 Length adjustment: 25 Effective length of query: 136 Effective length of database: 463 Effective search space: 62968 Effective search space used: 62968 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 Apr 09 2024. 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