Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 3609257 Dshi_2643 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Dino:3609257 Length = 316 Score = 224 bits (570), Expect = 3e-63 Identities = 124/321 (38%), Positives = 186/321 (57%), Gaps = 9/321 (2%) Query: 4 KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63 K+ I+R +PE + ++ L + + L +R+ D ++ + D E+ Sbjct: 2 KLLISRPLPEAVLARARARFDCTLRETTQPMRAEELRGALRDYDLVLPTLGDAFSAEVFA 61 Query: 64 NAP--KLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 + P + +++A + VGY++ID A G+ VTNTPG +TDATAD A L+L ARR E Sbjct: 62 DVPEPRARLLANFGVGYNHIDAVAARAAGVAVTNTPGAVTDATADTALTLILMAARRAGE 121 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKIIYYS 180 + VR+G W GWHP LG + GKTLG++G GRIGQA+A R GFGM++++Y+ Sbjct: 122 GERLVRAGTW----TGWHPTQMLGLHVTGKTLGVIGMGRIGQAIAARCHHGFGMEVVFYN 177 Query: 181 RTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTS 240 R+ P+ + + ++ +D + + VP ET+H+IG + M+P+A+ +N + Sbjct: 178 RS--PKTPDLPARQLASVAEVMAAADIVVVAVPGGAETHHLIGAEAFAAMQPHAVFVNIA 235 Query: 241 RGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGM 300 RG VVD ALI AL+ G + AGLDV+E EP E L ++NVVL PH+G+A E RE M Sbjct: 236 RGDVVDEAALIAALQAGQLGAAGLDVYEFEPAVPEALIGMENVVLLPHLGTAALEVREAM 295 Query: 301 AELVAKNLIAFAKGEIPPNLV 321 + NLIA A+G PN V Sbjct: 296 GHMALDNLIACAEGAPLPNPV 316 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: 244 Number of extensions: 12 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: 316 Length adjustment: 28 Effective length of query: 303 Effective length of database: 288 Effective search space: 87264 Effective search space used: 87264 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