Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate GFF2647 Psest_2699 benzoate 1,2-dioxygenase, large subunit
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >FitnessBrowser__psRCH2:GFF2647 Length = 453 Score = 435 bits (1119), Expect = e-126 Identities = 222/455 (48%), Positives = 309/455 (67%), Gaps = 15/455 (3%) Query: 12 EYIQGCLDFRPAEGIYRVARDMFTEPELFDLEMELIFEKNWIYACHESEIANPNDFLTMR 71 +Y+ L+ +GI+R R++FT PELF+LEM+ IFE NWIY HES+I ND+ T Sbjct: 6 DYLDSLLEEDKEKGIFRCKREIFTAPELFELEMKHIFEGNWIYLAHESQIPEKNDYYTTT 65 Query: 72 AGRQPMIITRDGNNQLHALINACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVK 131 GRQP+ I R+ + L+A INAC HRGATL R +GN++T+TCPFH W + + G+L+KVK Sbjct: 66 MGRQPIFIARNKDGVLNAFINACSHRGATLCRYKRGNKATYTCPFHGWTFNNSGKLLKVK 125 Query: 132 APGE--YPEGFD-KATRGLKK-ARIESYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVA 187 P E YPE FD + LKK AR ESY+GF+F SL+ + S SLED+LG+++ DM+V Sbjct: 126 DPKEAGYPESFDCDGSHDLKKVARFESYRGFLFGSLNPDVS-SLEDFLGESRKIIDMIVD 184 Query: 188 QSPTGELEILPGKSTYSYDGNWKLQHENGLDGYHVSTVHYNYVSTVQHRQQVNAANGGVS 247 QSP G LE+L G STY +DGNWKLQ ENG DGYHV+ VH+NY +T Q R+ +A + Sbjct: 185 QSPEG-LEVLRGSSTYVFDGNWKLQAENGADGYHVTAVHWNYAATQQQRKLKDAGD---- 239 Query: 248 DTLDYSKLGAGD-AETDDGWFSFKNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQQQAE 306 D + AG + G++SF+NGH LL++ NP R ++ RL+EE+G+ +A+ Sbjct: 240 ---DIRAMSAGGWGKKGGGFYSFENGHMLLWTRWDNPEDRPLFSQ-RDRLVEEFGEARAD 295 Query: 307 WMMHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQF 366 WM+ RNL +YP+L+ MDQ SQLRI RP++ +KTE+T CI KGES R RIRQ+ Sbjct: 296 WMIGHSRNLCLYPNLYLMDQFGSQLRIARPISVDKTEVTIYCIAPKGESAEARARRIRQY 355 Query: 367 EDFFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRGSEKWVEGPTPNSEVLGINPVLT 426 EDFFNVSGM TPDDL EFR Q GFQ R +WN++SRG+ W+EG +++ + ++P+L+ Sbjct: 356 EDFFNVSGMATPDDLEEFRACQEGFQGRSLQWNDMSRGAAHWIEGADESAQQIDLHPLLS 415 Query: 427 GTEFTHEGLYINQHGSWQRFLLQGLEQKALKLKEV 461 G EGLY+ QHG W+ +++ ++++ +L V Sbjct: 416 GVRTEDEGLYVVQHGYWRDQMVKAVKKEQDQLIHV 450 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: 660 Number of extensions: 27 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: 453 Length adjustment: 33 Effective length of query: 428 Effective length of database: 420 Effective search space: 179760 Effective search space used: 179760 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 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