Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_020564182.1 A3OW_RS0114555 homogentisate 1,2-dioxygenase
Query= reanno::psRCH2:GFF3448 (379 letters) >NCBI__GCF_000372865.1:WP_020564182.1 Length = 371 Score = 502 bits (1292), Expect = e-147 Identities = 224/369 (60%), Positives = 281/369 (76%) Query: 5 WISFPIREGESSRQAHCDFPQGTYEREMGREGFFGPASHLHHKHPPTGWIDWEGPLRPHA 64 WI P EG +SRQAH D P TYERE+G+EGF+GPA+ +HH+HPPTGW EGPL+PHA Sbjct: 3 WIQIPKVEGTASRQAHADLPANTYERELGKEGFYGPATQMHHRHPPTGWSAIEGPLKPHA 62 Query: 65 FNFNQIPSEGDCPLQAPLALHNADVKLRLWKTNGAMRHLVRNGDGDELLFIHEGAGHLYC 124 F+ ++ + G+ P Q+PL N +++R K M HL RN DGDELLFIH GAG LYC Sbjct: 63 FDTQKLDAAGEGPWQSPLLFSNPAIRIRFLKLANNMDHLARNADGDELLFIHRGAGDLYC 122 Query: 125 DFGHLEFRDGDYLMIPRGTAWRIEATQPVFMLLIENTDGAYQLPDKGLVGPHAIFDAAVL 184 D+G L FR+GDYLM+PRGT WRI+ + V L+IE T+ +Y+LP+KGLV AIFD A+L Sbjct: 123 DYGRLTFREGDYLMLPRGTMWRIDVKEAVGALMIEATEDSYRLPEKGLVSHQAIFDPAIL 182 Query: 185 DHPRLDDAFRAQQDENPWQIRIKRRDQITTVTYPYNPLDVVGWHGDNTVVRLNWRDIRPL 244 D P++D+AF AQQDE+ W++ +K+++ ++T+TYP+NPLD VGWHG VRLNWRDIRPL Sbjct: 183 DTPKIDEAFLAQQDESAWRVVVKKKNDLSTLTYPFNPLDAVGWHGTLMPVRLNWRDIRPL 242 Query: 245 MSHRYHLPPSAHTTFVANGFVVCTFTPRPVESDPGALKVPFFHNNDDYDEVLFYHRGNFF 304 MSHRYH+PPSAHTTF A FVVCTF PRP ESDP L VPFFH+NDDYDE++FYH G FF Sbjct: 243 MSHRYHVPPSAHTTFAAGRFVVCTFVPRPFESDPHVLNVPFFHSNDDYDELIFYHAGQFF 302 Query: 305 SRDNIEQGMVTFHPCGFPHGPHPKALKKAQDDPATFADEVAVMIDTRRALEVGEAAAAVD 364 SRD+I GM+T HP G PHGPHPKAL+ A+ T DEVAVM+DTR AL+V + A A++ Sbjct: 303 SRDHIYPGMMTLHPGGIPHGPHPKALQNAEKKRGTMTDEVAVMVDTRDALDVTDEARAIE 362 Query: 365 VPEYVNSWR 373 YV+SW+ Sbjct: 363 WAGYVDSWK 371 Lambda K H 0.322 0.140 0.464 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: 640 Number of extensions: 28 Number of successful extensions: 3 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: 379 Length of database: 371 Length adjustment: 30 Effective length of query: 349 Effective length of database: 341 Effective search space: 119009 Effective search space used: 119009 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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