Align 4-hydroxybenzoyl-CoA reductase subunit beta; 4-HBCR subunit beta; EC 1.3.7.9 (characterized)
to candidate WP_057507660.1 ABB28_RS05440 xanthine dehydrogenase family protein subunit M
Query= SwissProt::O33820 (324 letters) >NCBI__GCF_001431535.1:WP_057507660.1 Length = 316 Score = 107 bits (266), Expect = 5e-28 Identities = 100/305 (32%), Positives = 144/305 (47%), Gaps = 22/305 (7%) Query: 7 FRTHRPATLADAVNALA-AEATLPLGAGTDLLPNLRRGLGHPAALVDLTGIDGLATISTL 65 F R T A+A A A + + GT+LL ++ + P+ L+D+ G+ L TI Sbjct: 4 FTYERARTPAEAAAAAARTQGARFIAGGTNLLDLMKLEIEIPSHLIDVNGLK-LDTIEAT 62 Query: 66 ADGSLRIGAGATLEAIAEHDAIRTTWPALAQAAESVAGPTHRAAATLGGNLCQDTRCT-F 124 DG +RIGA +A IR + L +A + A R AT GNL Q TRC F Sbjct: 63 DDGGVRIGALVRNTDLAADSRIRRDYALLTRALVAGASGQLRNKATTAGNLLQRTRCPYF 122 Query: 125 YNQSEWWRS---GNGYCLKYKG--DKCHVIVKSDRCYATYHGDVAPALMVLDARAEIVGP 179 Y+ ++ G+G C G + VI S C AT+ D+A A+M+LDA E V P Sbjct: 123 YDTAQPCNKRLPGSG-CAAIGGVSRQLAVIGTSPACIATHPSDMAVAMMLLDATVETVRP 181 Query: 180 AGK-RTVPVAQLFRESG-AEHL--TLEKGELLAAIEVPPTGAWSAAYSKVRIRDAVDFPL 235 G R + + +R G H+ L+KGEL+AA+ +P + Y KVR R + F L Sbjct: 182 DGSTRRIALDDFYRAPGKTPHIDSVLDKGELIAAVTLPAPLGGTHIYRKVRDRASYAFAL 241 Query: 236 AGVAAALQRDGD---RIAGLRVAITGSNSAPLMVP------VDALLGGNWDDAAAETLAQ 286 VAA LQ DG + G+ S++A ++P V +LL G + Q Sbjct: 242 VSVAAVLQADGSGRVALGGVAYKPWRSDAADALLPQGARAVVGSLLQGATPSPENQFKVQ 301 Query: 287 LVRKT 291 L +T Sbjct: 302 LAERT 306 Lambda K H 0.319 0.133 0.399 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: 235 Number of extensions: 19 Number of successful extensions: 4 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: 324 Length of database: 316 Length adjustment: 28 Effective length of query: 296 Effective length of database: 288 Effective search space: 85248 Effective search space used: 85248 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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