Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate WP_086511961.1 BZY95_RS21650 benzoate 1,2-dioxygenase large subunit
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >NCBI__GCF_002151265.1:WP_086511961.1 Length = 455 Score = 413 bits (1061), Expect = e-120 Identities = 203/452 (44%), Positives = 306/452 (67%), Gaps = 15/452 (3%) Query: 7 ITQWQEYIQGCLDFRPAEGIYRVARDMFTEPELFDLEMELIFEKNWIYACHESEIANPND 66 + Q + ++G + +GI+R R MFT+P F+LEM+ +FE NW++ HES+I+ P D Sbjct: 5 LDQLEARVRGAVVDDAEKGIFRCHRSMFTDPAFFELEMKHVFEGNWLFLAHESQISEPGD 64 Query: 67 FLTMRAGRQPMIITRDGNNQLHALINACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGR 126 ++T+ GRQP++ITRD + +LHALINAC HRGATL R +GN+ TFTCPFH W +K+DG+ Sbjct: 65 YMTVTMGRQPVVITRDKSGELHALINACAHRGATLCRRKRGNKGTFTCPFHGWTFKNDGK 124 Query: 127 LVKVKAP--GEYPEGFDK-ATRGLKKA-RIESYKGFVFISLDVNGSDSLEDYLGDAKVFF 182 L+K K+ G YP+ F + + LK+ R ESYKGF+F SL+ + L++YLG+ Sbjct: 125 LLKAKSEKVGAYPDSFKQDGSHDLKRVPRFESYKGFLFGSLNEDVKP-LQEYLGETTKVI 183 Query: 183 DMMVAQSPTGELEILPGKSTYSYDGNWKLQHENGLDGYHVSTVHYNYVSTVQHRQQVNAA 242 D +V Q+P G LE+L G S+Y++ GNWKLQ ENG DGYHVSTVH+NY ST+ R Sbjct: 184 DNIVDQAPEG-LEVLRGTSSYTFKGNWKLQAENGADGYHVSTVHWNYASTMDRRNY---- 238 Query: 243 NGGVSDTLDYSKLGAGDAETDDGWFSFKNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQ 302 G + +D G +++ G++S++NGH LL++ + NP VR Y + ++G+ Sbjct: 239 EAGGTKAVDAD----GWSKSQGGFYSYENGHMLLWTRLLNPEVRPVYQN-REWIQAQFGE 293 Query: 303 QQAEWMMHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENR 362 +A+ ++++ RNL +YP+++ MDQ S+Q+R++RP++ ++TE+T C KGES +R R Sbjct: 294 ARADSIVNQTRNLCLYPNVYLMDQFSTQIRVLRPISVDETEVTIYCFAPKGESAENRRVR 353 Query: 363 IRQFEDFFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRGSEKWVEGPTPNSEVLGIN 422 IRQ+EDFFNVSGMGTPDDL EFR Q G+ L WN++SRG+++W+EG N++ +G+ Sbjct: 354 IRQYEDFFNVSGMGTPDDLEEFRGCQDGYHGALAEWNDLSRGAKQWIEGADDNAKAIGMQ 413 Query: 423 PVLTGTEFTHEGLYINQHGSWQRFLLQGLEQK 454 P+L+G EGLY+ H W +L+ +E++ Sbjct: 414 PLLSGASPEDEGLYVLHHKHWVEEMLRAIEKE 445 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: 650 Number of extensions: 28 Number of successful extensions: 6 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: 455 Length adjustment: 33 Effective length of query: 428 Effective length of database: 422 Effective search space: 180616 Effective search space used: 180616 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