Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate Pf6N2E2_1863 putative dioxygenase hydroxylase component
Query= SwissProt::Q84BZ3 (423 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1863 Length = 419 Score = 132 bits (333), Expect = 2e-35 Identities = 116/376 (30%), Positives = 171/376 (45%), Gaps = 47/376 (12%) Query: 28 RVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGA 87 RV V++ ++ E ERI+ TW +V +E+P DF +G PV++TR +G Sbjct: 18 RVHGSVYTDEELFQLELERIWYR-TWVYVGHVSEVPKLNDFVVKSIGPQPVIMTRDGEGQ 76 Query: 88 LSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADF 147 + +NRC HRG QVC + GN S TC YH W+F N G L G PF G +G Sbjct: 77 IHLLLNRCPHRGNQVCLEHAGNRRSFTCPYHGWTFSNTGTLRGYPFAAGYEGT------- 129 Query: 148 DPKQHGLRKL-RVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHKPIE-----YLG 201 D GL K+ R+ Y+G VF + + + L ++LGA R +D + E G Sbjct: 130 DRSTLGLGKVARIGIYQGFVFGSMAVEGPTLEEHLGA-ARGALDALVVTSPEGEVEITAG 188 Query: 202 CTRQYSKSNWKLYMENVKDPYHASMLHLFHTTFNIFRVGM------KARSIPDANHGLHS 255 + +KSNWK +EN D YH +H + F++ G+ + ++ G H+ Sbjct: 189 FLQHKAKSNWKFIVENETDGYHPQFVHA--SIFDVASSGIGDLYSADSTAVARDMGGGHT 246 Query: 256 IITV----TKTGD-----DTSAAYKQQNIRSFDEGFHLEDESILDLVSEYDEDCTNHIQP 306 I + + G T+ A + + E + E +E D T HI Sbjct: 247 EIDLRPEFRRIGQPMGWFGTTEARLPEYVSKMREAYGTE------RANEIMIDGTPHIM- 299 Query: 307 IFPQLVIQQIHNTLVARQILPKGPDNFELIFHFFGYA-DDTPEL-RALRIKQANLVGPAG 364 IFP L I +I + I P D E + H P+L R LR + VGPAG Sbjct: 300 IFPNLFIAEIQIFV----IQPLAVD--ETVQHVTALQFKGAPDLNRRLRQQTMGSVGPAG 353 Query: 365 YISMEDTEATELVQRG 380 ++ +D+E E QRG Sbjct: 354 FLLADDSEMYERTQRG 369 Lambda K H 0.321 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: 493 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 423 Length of database: 419 Length adjustment: 32 Effective length of query: 391 Effective length of database: 387 Effective search space: 151317 Effective search space used: 151317 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: 50 (23.9 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