Align subunit of 4-oxalomesaconate hydratase (EC 4.2.1.83) (characterized)
to candidate H281DRAFT_03420 H281DRAFT_03420 4-oxalomesaconate hydratase (EC 4.2.1.83)
Query= metacyc::MONOMER-3243 (342 letters) >FitnessBrowser__Burk376:H281DRAFT_03420 Length = 341 Score = 604 bits (1558), Expect = e-178 Identities = 278/341 (81%), Positives = 313/341 (91%), Gaps = 1/341 (0%) Query: 1 MIIDVHGHYTTAPAALGAWRDLQIAGLKDPSKTPSVADLKISDDEIRETIETNQLRLMKE 60 MIID+HGHYTTAP AL AWR+ QIA L +P+ P ++L+ISDDE+RE+IETNQLRLM+E Sbjct: 1 MIIDIHGHYTTAPKALEAWRNRQIAALGNPTDAPKPSELQISDDELRESIETNQLRLMRE 60 Query: 61 RGSDLTIFSPRASFMAHHIGDFQTSSTWAAICNELCFRVSELFPDHFIPAAMLPQSPGVD 120 R DLT+FSPRASFMAHHIG+F SSTWAAICNELC+RVS+LFP+HFIPAAMLPQSPGVD Sbjct: 61 RRLDLTVFSPRASFMAHHIGNFDVSSTWAAICNELCYRVSQLFPEHFIPAAMLPQSPGVD 120 Query: 121 PATCIPELVKCVEQYGNVGLNLNPDPSGGHWTSPPLSDKSWYPIYEKMVEYDIPAMIHVS 180 ATCIPELVKCVEQYGNV +NLNPDPSGGHWTSPPLSD+ WYPIYEKMVEYDIPAM+HVS Sbjct: 121 VATCIPELVKCVEQYGNVAINLNPDPSGGHWTSPPLSDRYWYPIYEKMVEYDIPAMVHVS 180 Query: 181 TSCNSCFHTTGSHYLNADTTAFMQCLTSDLFKDFPTLKFLIPHGGGAVPYHWGRFRGLAQ 240 TSCN+CFHTTG+HYLNADTTAFMQCLTSDLF+DFPTL+F+IPHGGGAVPYHWGRFRGLAQ Sbjct: 181 TSCNACFHTTGAHYLNADTTAFMQCLTSDLFRDFPTLRFVIPHGGGAVPYHWGRFRGLAQ 240 Query: 241 EMKKPLLEEHLLNNIYFDTCVYHQPGINLLTEVIPTKNILFASEMIGAVRGIDPQTGHYY 300 EMKKPLLE+HLL NI+FDTCVYHQPGI+LLT VIP NILFASEMIGAVRGIDPQTGHY+ Sbjct: 241 EMKKPLLEKHLLKNIFFDTCVYHQPGIDLLTNVIPVDNILFASEMIGAVRGIDPQTGHYF 300 Query: 301 DDTKRYIEATQNLTADEKHAVYEGNARRVFTRLDKALKAKG 341 DDTKRY+EA + +++H +YEGNARRV+ RLD ALKA+G Sbjct: 301 DDTKRYVEAAA-MNPEQRHQIYEGNARRVYPRLDAALKAQG 340 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: 530 Number of extensions: 13 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: 341 Length adjustment: 29 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 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