Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate Pf6N2E2_1863 putative dioxygenase hydroxylase component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2740 (461 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1863 Length = 419 Score = 195 bits (496), Expect = 2e-54 Identities = 132/396 (33%), Positives = 193/396 (48%), Gaps = 49/396 (12%) Query: 28 RVARDMFTEPELFDLEMELIFEKNWIYACHESEIANPNDFLTMRAGRQPMIITRDGNNQL 87 RV ++T+ ELF LE+E I+ + W+Y H SE+ NDF+ G QP+I+TRDG Q+ Sbjct: 18 RVHGSVYTDEELFQLELERIWYRTWVYVGHVSEVPKLNDFVVKSIGPQPVIMTRDGEGQI 77 Query: 88 HALINACQHRGATLTRVSKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPEGFDKATRGL 147 H L+N C HRG + GN+ +FTCP+H W + + G L Y EG D++T GL Sbjct: 78 HLLLNRCPHRGNQVCLEHAGNRRSFTCPYHGWTFSNTGTLRGYPFAAGY-EGTDRSTLGL 136 Query: 148 -KKARIESYKGFVFISLDVNGSDSLEDYLGDAKVFFDMMVAQSPTGELEILPGKSTYSYD 206 K ARI Y+GFVF S+ V G +LE++LG A+ D +V SP GE+EI G + Sbjct: 137 GKVARIGIYQGFVFGSMAVEG-PTLEEHLGAARGALDALVVTSPEGEVEITAGFLQHKAK 195 Query: 207 GNWKLQHENGLDGYHVSTVHYNYVSTVQHRQQVNAANGGVSD------TLDYSKLGAGDA 260 NWK EN DGYH VH + + A+ G+ D T +G G Sbjct: 196 SNWKFIVENETDGYHPQFVHASI---------FDVASSGIGDLYSADSTAVARDMGGGHT 246 Query: 261 ETD-----------DGWFSFKNGHSLLFSDMPNPTVRAGYATVMPRLIEEYGQQQA-EWM 308 E D GWF T A + ++ E YG ++A E M Sbjct: 247 EIDLRPEFRRIGQPMGWFG---------------TTEARLPEYVSKMREAYGTERANEIM 291 Query: 309 MHRLRNLNIYPSLFFMDQISSQLRIVRPVAWNKTEITSQCIGVKGESDADRENRIRQFED 368 + ++ I+P+LF + Q+ +++P+A ++T + KG D +R R +Q Sbjct: 292 IDGTPHIMIFPNLFIAE---IQIFVIQPLAVDETVQHVTALQFKGAPDLNRRLR-QQTMG 347 Query: 369 FFNVSGMGTPDDLVEFREAQRGFQARLERWNEVSRG 404 +G DD + QRG ++R WN + RG Sbjct: 348 SVGPAGFLLADDSEMYERTQRGVRSRNPEWNYLGRG 383 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: 526 Number of extensions: 20 Number of successful extensions: 4 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: 419 Length adjustment: 32 Effective length of query: 429 Effective length of database: 387 Effective search space: 166023 Effective search space used: 166023 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