Align 4-hydroxybenzoyl-CoA reductase subunit gamma; 4-HBCR subunit gamma; EC 1.3.7.9 (characterized)
to candidate CCNA_02702 CCNA_02702 xanthine dehydrogenase small subunit
Query= SwissProt::O33818 (161 letters) >FitnessBrowser__Caulo:CCNA_02702 Length = 482 Score = 95.5 bits (236), Expect = 1e-24 Identities = 64/169 (37%), Positives = 91/169 (53%), Gaps = 21/169 (12%) Query: 1 MKNILRLTLNGRAREDLVPD-NMLLLDYLRETVGLTGTKQGCDGGECGACTVLVDD---- 55 M ++R L+G +E + LL++LR + TGTK+GC G+CG+CTVLV + Sbjct: 1 MGGVIRFWLDGEVQEVRGANPTTTLLEHLRGPMRRTGTKEGCAEGDCGSCTVLVGEADGD 60 Query: 56 ----RPRLACSTLAHQVAGKKVETVESLATQG----TLSKLQAAFHEKLGTQCGFCTPGM 107 R +C + GK + TVESL + L +Q A +K G+QCGFCTPG+ Sbjct: 61 GVAWRAVNSCIQFLPMLHGKALMTVESLGARAGCDQALHPVQQAMVDKHGSQCGFCTPGI 120 Query: 108 IMA--SEALLRKNPSPSRDEIKAALAGNLCRCTGY---VRSSKSVETAA 151 +M+ S A+ K E+ LAGNLCRCTGY + ++ VE A Sbjct: 121 VMSLYSRAVGAKGADAPVGEV---LAGNLCRCTGYGPIIEVAQGVEAEA 166 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: 191 Number of extensions: 11 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: 482 Length adjustment: 25 Effective length of query: 136 Effective length of database: 457 Effective search space: 62152 Effective search space used: 62152 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