Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Ga0059261_2669 Ga0059261_2669 Lactate dehydrogenase and related dehydrogenases
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Korea:Ga0059261_2669 Length = 318 Score = 244 bits (624), Expect = 2e-69 Identities = 137/317 (43%), Positives = 187/317 (58%), Gaps = 7/317 (2%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE- 60 +P++ +TR+ PE + Y++ + + L + +RE DAL VTD++ ++ Sbjct: 3 RPRILLTRRWPEAVEARLAARYDVTRNETDMSMDAAALAQAMREHDALCPTVTDRITRDV 62 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 +L + +II Y G+++ID++ A + GI VTNTP VLTDATAD+A L+L RR Sbjct: 63 ILTEGRRARIIGNYGAGFEHIDLDAAREAGIAVTNTPDVLTDATADIAMTLILMATRRAG 122 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180 E + +R+GEW GW P LG L+GK LG+VG+GRI +A+A RAK FGMKI +S Sbjct: 123 EGERELRAGEW----TGWRPTHLLGRSLRGKVLGLVGYGRIARAVADRAKAFGMKIAVHS 178 Query: 181 RTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTS 240 R+R + E + ++LL +D +SLH P T HMI L MK +A+L+NT Sbjct: 179 RSRAEDVPET--DYHASLQSLLSIADVVSLHAPGGAATRHMIDAAALSAMKRDAVLVNTG 236 Query: 241 RGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGM 300 RG ++D AL +ALK G IA AGLDV+E EP L L N VL PH GSAT E RE M Sbjct: 237 RGTLIDEAALAEALKVGTIAAAGLDVYEREPAVEAALIDLPNAVLLPHFGSATLETREAM 296 Query: 301 AELVAKNLIAFAKGEIP 317 VA NL AF G P Sbjct: 297 GMKVADNLDAFFAGHEP 313 Lambda K H 0.317 0.137 0.392 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: 249 Number of extensions: 10 Number of successful extensions: 4 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: 331 Length of database: 318 Length adjustment: 28 Effective length of query: 303 Effective length of database: 290 Effective search space: 87870 Effective search space used: 87870 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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