Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate Ac3H11_2750 Large subunit naph/bph dioxygenase
Query= reanno::pseudo3_N2E3:AO353_05950 (462 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2750 Length = 466 Score = 147 bits (372), Expect = 6e-40 Identities = 73/195 (37%), Positives = 114/195 (58%), Gaps = 5/195 (2%) Query: 35 TEPQLFDLEMELIFEKNWIYACHESELANNHDFITMRAGRQPMIITRDGDGQLNALINAC 94 ++P+L++LEME IF K W++ HESE+ N+ DF+T G +++TRD G+++ L+N C Sbjct: 32 SDPELYELEMERIFGKIWVFLGHESEIPNSGDFVTRDMGSDSVLVTRDKSGEVHVLLNLC 91 Query: 95 QHRGTTLTRVGKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPEG--FDKATRGLKKARI 152 HRG ++ + GN TC +H W ++ +G + E G K GLKKAR+ Sbjct: 92 THRGMRVSTLDAGNTQIHTCIYHGWAFRPNGAFLGAPVEKETMHGKMMSKEELGLKKARV 151 Query: 153 QSYKGFVFISLDVHGDNSLEDFLGDAKVFFDMMVAQSPTGELEVLPGKSAYTYDGNWKLQ 212 Y G +F + ++ G S E+FLGDAK ++D++ ++ G +EVL +T NWK Sbjct: 152 TLYGGLIFATWNIDGP-SFEEFLGDAKWYYDILFKRTDKG-MEVLGPPQRFTVRANWKAA 209 Query: 213 NE-NGLDGYHVSTVH 226 E + DGYH T+H Sbjct: 210 GEQSAADGYHTLTLH 224 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: 567 Number of extensions: 32 Number of successful extensions: 5 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: 466 Length adjustment: 33 Effective length of query: 429 Effective length of database: 433 Effective search space: 185757 Effective search space used: 185757 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 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