Align subunit of 4-oxalomesaconate hydratase (EC 4.2.1.83) (characterized)
to candidate H281DRAFT_06355 H281DRAFT_06355 4-oxalomesaconate hydratase
Query= metacyc::MONOMER-3243 (342 letters) >FitnessBrowser__Burk376:H281DRAFT_06355 Length = 346 Score = 467 bits (1201), Expect = e-136 Identities = 218/345 (63%), Positives = 268/345 (77%), Gaps = 6/345 (1%) Query: 1 MIIDVHGHYTTAPAALGAWRDLQIAGLKDPSKTPSVADLKISDDEIRETIETNQLRLMKE 60 MIID HGHYTT+P AWR QIA LKD P A ISDDEIRE+IET QLR+ +E Sbjct: 1 MIIDCHGHYTTSPPQHEAWRTQQIAALKDGHTPP--ARPNISDDEIRESIETGQLRIQRE 58 Query: 61 RGSDLTIFSPRASFMAHHIGDFQTSSTWAAICNELCFRVSELFPDHFIPAAMLPQSPGVD 120 RG+DLTIFSPRA+ M HH+ Q ++ W+ CN+L RV LFP +F+ LPQ+PGV Sbjct: 59 RGTDLTIFSPRAAGMGHHLATAQANAQWSRECNDLVHRVCSLFPRNFVGVCQLPQAPGVP 118 Query: 121 PATCIPELVKCVEQYGNVGLNLNPDPSGGHWTSPPLSDKSWYPIYEKMVEYDIPAMIHVS 180 PA CI EL +CVE+ G +G NLNPDPSGGHW+ PL+D+SWYP+YE MVE D+PAMIHVS Sbjct: 119 PANCIDELRRCVEELGFIGCNLNPDPSGGHWSGLPLTDRSWYPLYEAMVELDVPAMIHVS 178 Query: 181 TSCNSCFHTTGSHYLNADTTAFMQCLTSDLFKDFPTLKFLIPHGGGAVPYHWGRFRGLAQ 240 +SCN FH TG+HY+N DT+AFMQ LT DLF DFPTL+F+IPHGGGAVPYHWGR+RGLAQ Sbjct: 179 SSCNPNFHATGAHYINGDTSAFMQLLTGDLFADFPTLRFIIPHGGGAVPYHWGRYRGLAQ 238 Query: 241 EMKKPLLEEHLLNNIYFDTCVYHQPGINLLTEVIPTKNILFASEMIGAVRGIDPQTGHYY 300 +MK+PLL ++LL N++FDTCVYHQPG LL +VIP +NILFASE IGAV+G+DP+TGH+Y Sbjct: 239 DMKRPLLRDYLLKNVFFDTCVYHQPGAELLAKVIPVENILFASETIGAVQGVDPETGHHY 298 Query: 301 DDTKRYIEATQNLTADEKHAVYEGNARRVFTR----LDKALKAKG 341 DDT+RYI+A + L+ E+ +YE NAR V+ R LD+ L A+G Sbjct: 299 DDTRRYIDAIEWLSDAERQRIYEDNARAVYPRLSRQLDRQLAAQG 343 Lambda K H 0.320 0.137 0.429 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: 476 Number of extensions: 23 Number of successful extensions: 2 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: 342 Length of database: 346 Length adjustment: 29 Effective length of query: 313 Effective length of database: 317 Effective search space: 99221 Effective search space used: 99221 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: 49 (23.5 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