Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate WP_086509129.1 BZY95_RS06270 aromatic ring-hydroxylating dioxygenase subunit alpha
Query= reanno::pseudo3_N2E3:AO353_05950 (462 letters) >NCBI__GCF_002151265.1:WP_086509129.1 Length = 425 Score = 116 bits (290), Expect = 2e-30 Identities = 68/221 (30%), Positives = 111/221 (50%), Gaps = 8/221 (3%) Query: 27 FRIARDIFTEPQLFDLEMELIFEKNWIYACHESELANNHDFITMRAGRQPMIITRDGDGQ 86 F + + + + +LF L+M+ IF K W++A E+ +++T++ G P+I+ R G Sbjct: 28 FSLPQPFYNDARLFALDMQEIFGKEWLFAGMTCEIPAKGNYMTLQVGDNPVILVRGDGGT 87 Query: 87 LNALINACQHRGTTLTRVGKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPEGFDKATRG 146 ++A N C+HRG+ L KG + CP+H W Y+ DGRL + A + E FD + G Sbjct: 88 IHAFHNVCRHRGSRLCVSDKGKVAKLVCPYHQWTYELDGRL--LFAGSDMGENFDLGSYG 145 Query: 147 LKKARIQSYKGFVFISLDVHGDNSLEDFLGDAKVFFDMMVAQSPTGELEVLPGKSAYTYD 206 LK +++ GF+FISL ++DFL + + + G L+V +S Sbjct: 146 LKPVHVRTGGGFIFISL-AEQPPVIDDFL----ITLEHYLEPYEMGNLKVAV-ESNIVEQ 199 Query: 207 GNWKLQNENGLDGYHVSTVHYNYVATVQHRQQVDSKNGTRA 247 NWKL EN + YH + H + ++Q D T A Sbjct: 200 ANWKLVIENNRECYHCNGSHPELLNSLQEFDDTDDPRATPA 240 Lambda K H 0.319 0.136 0.418 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: 485 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 462 Length of database: 425 Length adjustment: 32 Effective length of query: 430 Effective length of database: 393 Effective search space: 168990 Effective search space used: 168990 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: 51 (24.3 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