Align 4-hydroxybenzoyl-CoA reductase HbaD subunit (EC 1.3.7.9) (characterized)
to candidate H281DRAFT_02815 H281DRAFT_02815 xanthine dehydrogenase YagS FAD-binding subunit
Query= metacyc::MONOMER-17405 (327 letters) >FitnessBrowser__Burk376:H281DRAFT_02815 Length = 334 Score = 116 bits (290), Expect = 9e-31 Identities = 91/287 (31%), Positives = 130/287 (45%), Gaps = 24/287 (8%) Query: 4 LNALNLLRPGSVDEAIAALLAHPGGWLLGGGTDLLVNMRRGVTQPETLIDTTGIAEIKQL 63 +N + R V +AI A + GGT+L+ R V P+ +ID + +KQ+ Sbjct: 1 MNRFSYTRANEVSQAIEQHRAKGAAAFIAGGTNLVDLWRVNVAHPQVVIDINRLP-LKQI 59 Query: 64 VADGSG-LTIGAGVTLASLAADGLVAARYPALSEAARAVAGPGHRKLGTVGGNLCLDTRC 122 +G L IGA VT ++ A D +AARYP LS+A A A P R + +VGGNL TRC Sbjct: 60 EPTAAGGLKIGALVTNSAAAYDPQIAARYPLLSKAILAGASPQIRNVASVGGNLLQRTRC 119 Query: 123 IYYNQSEWWRRANSYCLKNR-GEICHVAPKGNRCHAAFS----------GDLAPALLVLG 171 +Y+ A + C K G C NR HA D+ AL L Sbjct: 120 VYFYD------AGTRCNKREPGTGCPALEGVNRMHAILGASEHCIAVHPSDMCVALAALD 173 Query: 172 AEVEIAGPDGRRRIPLGELYVEDG---RAHLALRPGEVVVTVRLPADPLASR--YVKVRQ 226 A V ++GPDG R + + + G +R E++ V LP A Y+KVR Sbjct: 174 ATVHLSGPDGARVLLFADFHRLPGDTPHIDTNIRDDELITAVELPKQGFAQHHAYIKVRD 233 Query: 227 RGAIDYPLAGVAVALARSGSRLAQLRIALTGTNSRPFLLAETAAFAQ 273 R + + L VA+ L G + +R AL G +P+ + A Q Sbjct: 234 RASYAFALVSVALGLELDGDVIVNVRCALGGVAHKPWRNTDAEASLQ 280 Lambda K H 0.321 0.136 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: 245 Number of extensions: 10 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: 327 Length of database: 334 Length adjustment: 28 Effective length of query: 299 Effective length of database: 306 Effective search space: 91494 Effective search space used: 91494 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 (21.9 bits) S2: 49 (23.5 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