Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate N515DRAFT_4010 N515DRAFT_4010 isoquinoline 1-oxidoreductase, alpha subunit
Query= SwissProt::O33818 (161 letters) >FitnessBrowser__Dyella79:N515DRAFT_4010 Length = 177 Score = 107 bits (266), Expect = 1e-28 Identities = 65/150 (43%), Positives = 87/150 (58%), Gaps = 3/150 (2%) Query: 5 LRLTLNGRAREDLVPDNMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDDRPRLACSTL 64 + + +NGR +M LL YLR+ + LTGTK D G GA VLVD +P A S Sbjct: 24 IEVEINGRPFRHTGDPDMPLLWYLRDVLRLTGTKYASDHGLGGADLVLVDKKPVSAASVP 83 Query: 65 AHQVAGKKVETVESL-ATQGTLSKLQAAFHEKLGTQCGFCTPGMIMASEALLRKNPSPSR 123 H++A KKV TVE L A G L LQ AF ++ CG+CTPG ++AS LL ++P PS Sbjct: 84 MHELADKKVTTVEGLAAADGKLHPLQQAFVDEDAIGCGYCTPGWLIASLDLLNRHPQPSD 143 Query: 124 DEIKAALAGNLCRCTGYVRSSKSVETAAAA 153 D+I NLCRC R ++++ A+AA Sbjct: 144 DQIDQ--LPNLCRCGCQTRVRRAIKRASAA 171 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: 81 Number of extensions: 5 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: 177 Length adjustment: 18 Effective length of query: 143 Effective length of database: 159 Effective search space: 22737 Effective search space used: 22737 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