Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate BPHYT_RS07855 BPHYT_RS07855 benzoate 1,2-dioxygenase subunit alpha
Query= SwissProt::O85673 (471 letters) >FitnessBrowser__BFirm:BPHYT_RS07855 Length = 452 Score = 404 bits (1039), Expect = e-117 Identities = 210/435 (48%), Positives = 291/435 (66%), Gaps = 17/435 (3%) Query: 23 DGVYRIARDMFTEPELFELEMELIFEKVWIYACHESEIPNNNDFVTVQIGRQPMIVSRDG 82 +GV+R RD+FT ELFELEM+ IFE W+Y HES+IPNNND+ T IGRQP++V+RD Sbjct: 25 NGVFRCRRDIFTNAELFELEMKHIFESNWVYLAHESQIPNNNDYYTTWIGRQPVVVTRDK 84 Query: 83 KGELHAMVNACEHRGATLTRVAKGNQSVFTCPFHAWCYKSDGRLVKVK--APGEYCEDFD 140 GELHA++NAC H+GA L R GN+ FTCPFH W + + G+L+KVK EY F+ Sbjct: 85 SGELHAVINACAHKGAMLCRKKHGNKGTFTCPFHGWSFANTGKLLKVKDVKTTEYPIQFN 144 Query: 141 KS-SRGLKQ-GRIASYRGFVFVSLDTQATDSLEDFLGDAKVFLDLMVDQSPTGELEVLQG 198 + S LK+ R SYRGF+F +L+ A LED+LG+ +V +D +VDQ+P G LEVL+G Sbjct: 145 TNGSHDLKKVARFQSYRGFLFGTLNADAIP-LEDYLGETRVIIDQIVDQAPDG-LEVLRG 202 Query: 199 KSAYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNAAKGDELDTLDYSKLGAGD 258 S+Y + GNWK+Q ENG DGYHVSTVH+NY +T+ R++V K +D +SK AG Sbjct: 203 NSSYIYDGNWKVQMENGCDGYHVSTVHWNYAATMD-RRKVEGTKA--VDANSWSKSVAGV 259 Query: 259 SETDDGWFSFKNGHSVLFSDMPNPTVRPGYNTVMPYLVEKFGEKRAEWAMHRLRNLNLYP 318 + F++GH +L++ NP VRP Y + + GE +A++ +++ RNL LYP Sbjct: 260 -------YGFEHGHILLWTKTMNPEVRPVYQ-YRDEIKARVGEVKADFIVNQTRNLCLYP 311 Query: 319 SLFFMDQISSQLRIIRPVAWNKTEVISQCIGVKGESSEARRNRIRQFEDFFNVSGLGTPD 378 ++F MDQ S+Q+R++RP++ +KTEV C KGES+ R RIRQ+EDFFNVSG+GT D Sbjct: 312 NVFLMDQFSTQIRVVRPISVDKTEVSIFCFAPKGESASDRATRIRQYEDFFNVSGMGTAD 371 Query: 379 DLVEFREQQKGFQGRIERWSDISRGYHQWTYGPTQNSQDLGIEPVITGREFTHEGLYVNQ 438 DL EFR Q G+ G W+D+SRG W G N++++G++PVI+G EGL+V Q Sbjct: 372 DLEEFRACQAGYAGTTAMWNDLSRGAPLWVEGADANAKNMGLKPVISGERSEDEGLFVCQ 431 Query: 439 HGQWQRLILDGLNKK 453 H W ++ D L K+ Sbjct: 432 HEYWVHVMRDALRKE 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: 600 Number of extensions: 23 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