Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate WP_086509475.1 BZY95_RS08310 hypothetical protein
Query= reanno::WCS417:GFF4624 (309 letters) >NCBI__GCF_002151265.1:WP_086509475.1 Length = 313 Score = 143 bits (361), Expect = 5e-39 Identities = 91/255 (35%), Positives = 132/255 (51%), Gaps = 22/255 (8%) Query: 47 DLEVTPEEFWKAVNYLNELG-----KHQEAGLLAAGLGLEHYLDLLMDAADEKAGKSGGT 101 +++++ EEF A+N + LG +H E +++ LG + L+M E+ T Sbjct: 55 EVKLSEEEFMAAINAVTRLGHLTRDRHNETMVMSDALG---FSTLVMILNQER------T 105 Query: 102 PRTIE----GPLYVAGAPLSK--YEARLDDGKDDAVPLFMRGQVRDTEGKPLAGAIVDVW 155 P I GP Y P + D K +PLF+ G+V +G PL GA+V+VW Sbjct: 106 PEQISPALLGPFYSRKDPEYPLGFNISRDTPKASDIPLFVSGRVTSRDGTPLPGALVEVW 165 Query: 156 QANTAGTYSWFDPTQSEFNLRRRIETDAQGNYRFRSIVPSGYGCPPSGPTQQLLDQLGRH 215 A+ G Y D +Q NLR + TDA+G YRFR+I P+ Y P G ++L+ RH Sbjct: 166 HASPEGLYENQDDSQPHLNLRGKFRTDAEGRYRFRTIRPASYPIPTHGIVGEMLEAQSRH 225 Query: 216 GQRPAHIHFFISAPGHRHLTTQINLSDDPYLHDDFAY-ATRDELIAQIRFSDDPQLAREF 274 R AH+HF +SA GHR L TQI DDP+L D + T +L + DD Q A + Sbjct: 226 PFRAAHLHFTVSAEGHRTLVTQIFPKDDPFLESDCVFGVTSADLAMEFPIHDDGQ-APDP 284 Query: 275 GVEGRFAQIDFDFEL 289 V GR+ ++ DF+L Sbjct: 285 DVRGRYCTLEVDFDL 299 Lambda K H 0.318 0.137 0.408 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: 273 Number of extensions: 13 Number of successful extensions: 2 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: 309 Length of database: 313 Length adjustment: 27 Effective length of query: 282 Effective length of database: 286 Effective search space: 80652 Effective search space used: 80652 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: 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