Align 4-hydroxybenzoyl-CoA reductase, γ subunit (EC 1.3.7.9) (characterized)
to candidate PP_4278 PP_4278 xanthine dehydrogenase subunit XdhA
Query= metacyc::MONOMER-14378 (158 letters) >FitnessBrowser__Putida:PP_4278 Length = 484 Score = 122 bits (307), Expect = 6e-33 Identities = 63/147 (42%), Positives = 88/147 (59%), Gaps = 13/147 (8%) Query: 15 EDAVAGNALLIDYLRDTLGLTGTKQGCDGGECGACTVLV-------DGQPRL------AC 61 E A+ N ++ YLR+ LG TGTK+GC G+CGACTV+V G L +C Sbjct: 13 EHALDPNMTVLQYLREHLGKTGTKEGCASGDCGACTVVVGELIQDDQGNDSLRYRSLNSC 72 Query: 62 CTLAHSVAGHSIETIEGLSHEGNLSRLQRAFHEHLGSQCGFCTPGMIMAAEALLRRNPQP 121 T S+ G + ++EGL +G L +Q+A + GSQCGFCTPG +M+ AL + + P Sbjct: 73 LTFVSSLHGKQLISVEGLKQQGQLHSVQQAMADCHGSQCGFCTPGFVMSLFALQKNSSGP 132 Query: 122 SRDEIRAALAGNLCRCTGYVKIIESVE 148 + + ALAGNLCRCTGY I+++ E Sbjct: 133 DLHQAQEALAGNLCRCTGYRPILDAAE 159 Lambda K H 0.320 0.135 0.412 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: 225 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: 158 Length of database: 484 Length adjustment: 25 Effective length of query: 133 Effective length of database: 459 Effective search space: 61047 Effective search space used: 61047 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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