Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate WP_090443572.1 BLS63_RS09975 naphthalene 1,2-dioxygenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >NCBI__GCF_900100495.1:WP_090443572.1 Length = 449 Score = 144 bits (362), Expect = 8e-39 Identities = 103/351 (29%), Positives = 164/351 (46%), Gaps = 17/351 (4%) Query: 36 EPELFDLEMELIFEKNWIYACHESEIANPNDFLTMRAGRQPMIITRDGNNQLHALINACQ 95 + ELF E+E IF +NW++ H+S I +P D++T + G +I++R + + A +N C+ Sbjct: 23 DEELFQRELETIFARNWLFLTHDSLIPSPGDYVTAKMGVDEVIVSRQNDGSIRAFLNVCR 82 Query: 96 HRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVKAPGE-YPEGFDKATRGLKK-ARIE 153 HRG TL GN F C +H W + ++G L V E Y E DK GLK+ AR+E Sbjct: 83 HRGKTLVHAEAGNAKGFVCSYHGWGFGANGELQSVPFEKELYGEALDKKCMGLKEVARVE 142 Query: 154 SYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVAQSPTGELEILPGKSTYSYDGNWKLQH 213 S+ GF++ D + SL+DY+GDA + + M S G LE++ NWK Sbjct: 143 SFHGFIYGCFD-EEAPSLKDYMGDAGWYLEPMFKHS--GGLELIGPPGKVIIKANWKAPA 199 Query: 214 EN-GLDGYHVSTVHYNYVSTVQHRQQVNAANGGVSDTLDYSKLGAG---DAETDDGWFSF 269 EN D YHV H + + + Q A N + GAG ++ G Sbjct: 200 ENFAGDAYHVGWTHASSLRSGQSVFSSLAGNAALPPE------GAGLQMTSKYGSGMGVL 253 Query: 270 KNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQQQAEWMMHRLRNLNIYPSLFFMDQISS 329 +G+S + S P + A RL +E G+ +A L N ++P+ F+ S Sbjct: 254 WDGYSGVHSADLVPELMAFGGAKQERLNKEIGEVRARIYRSHL-NGTVFPNNSFL-TCSG 311 Query: 330 QLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQFEDFFNVSGMGTPDD 380 ++ P+ N TE+ + + K + + + + F +G DD Sbjct: 312 VFKVWHPIDANTTEVWTYAMVEKDMPEDLKRRLVDAVQRTFGPAGFWESDD 362 Lambda K H 0.318 0.135 0.415 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: 568 Number of extensions: 26 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: 461 Length of database: 449 Length adjustment: 33 Effective length of query: 428 Effective length of database: 416 Effective search space: 178048 Effective search space used: 178048 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: 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