Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate H281DRAFT_01075 H281DRAFT_01075 benzoate 1,2-dioxygenase, alpha subunit
Query= SwissProt::O85673 (471 letters) >FitnessBrowser__Burk376:H281DRAFT_01075 Length = 452 Score = 403 bits (1036), Expect = e-117 Identities = 204/448 (45%), Positives = 295/448 (65%), Gaps = 17/448 (3%) Query: 10 QNFVQGCIDFRPNDGVYRIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTV 69 ++ + + +GV+R RD+FT +L+ELEM+ IFE W+Y HES+IP+NND+ T Sbjct: 12 EDLLSNAVQDDKENGVFRCRRDIFTNADLYELEMKHIFESNWVYLAHESQIPDNNDYYTT 71 Query: 70 QIGRQPMIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKV 129 IGRQP++++RD GELHA++NAC H+GA L R GN+S FTCPFH W + + G+L+KV Sbjct: 72 SIGRQPIVITRDKTGELHAVINACAHKGAMLCRRKHGNKSSFTCPFHGWTFSNAGKLLKV 131 Query: 130 K--APGEYCEDFDKS-SRGLKQ-GRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMV 185 K EY F+K S LK+ R SYRGF+F SL+ LED+LG+ KV +D +V Sbjct: 132 KDEKTTEYPVQFNKQGSHDLKKVARFESYRGFLFGSLNADVMP-LEDYLGETKVIIDQIV 190 Query: 186 DQSPTGELEVLQGKSAYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDE 245 Q+P G LEVL+G S+Y + GNWK+Q ENG DGYHVSTVH+NY +T+ R++ Sbjct: 191 AQAPDG-LEVLRGNSSYIYDGNWKMQMENGCDGYHVSTVHWNYAATMGRRKEEGTKA--- 246 Query: 246 LDTLDYSKLGAGDSETDDGWFSFKNGHSVLFSDMPNPTVRPGYNTVMPYLVEKFGEKRAE 305 +D +SK AG + F++GH +L+++ NP VRP Y + + GE + + Sbjct: 247 VDANSWSKSIAGV-------YGFEHGHILLWTNTMNPEVRPVYRH-RDEITARVGEDKGK 298 Query: 306 WAMHRLRNLNLYPSLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQF 365 + +++ RNL LYP++F MDQ S+Q+R++RP++ ++TEV C KGES+E R RIRQ+ Sbjct: 299 FVINQTRNLCLYPNVFLMDQFSTQIRVVRPISVDRTEVSIFCFAPKGESAEDRATRIRQY 358 Query: 366 EDFFNVSGLGTPDDLVEFREQQKGFQGRIERWSDISRGYHQWTYGPTQNSQDLGIEPVIT 425 EDFFNVSG+GT DDL EFR Q G+ G W+D+SRG W +GP +N++ +G+ P+I+ Sbjct: 359 EDFFNVSGMGTSDDLEEFRACQSGYAGSTTMWNDLSRGAPLWIHGPDENAKSMGLNPLIS 418 Query: 426 GREFTHEGLYVNQHGQWQRLILDGLNKK 453 G EGL+V QH W +++ + L K+ Sbjct: 419 GERSEDEGLFVVQHEYWLQVMREALRKE 446 Lambda K H 0.319 0.136 0.420 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: 564 Number of extensions: 22 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: 471 Length of database: 452 Length adjustment: 33 Effective length of query: 438 Effective length of database: 419 Effective search space: 183522 Effective search space used: 183522 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