Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_085639493.1 MGEO_RS14935 D-glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_002115805.1:WP_085639493.1 Length = 328 Score = 259 bits (662), Expect = 6e-74 Identities = 138/320 (43%), Positives = 207/320 (64%), Gaps = 7/320 (2%) Query: 5 VFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLEN 64 V +TR++P+ +++ +++ L + L + V+E D LV +TD++D L+ Sbjct: 8 VVVTRRLPDAVETRLKELFDVRLRDSDTPMTQAELTDAVKEADVLVPTLTDRIDAGLIGQ 67 Query: 65 A-PKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123 A +L++IA Y G D+ID++ A RGI V+NTPGV+T+ TAD+ AL+L+V RRI E Sbjct: 68 AGERLRLIANYGAGVDHIDVDTARSRGILVSNTPGVVTEDTADMVMALMLSVTRRIPEGL 127 Query: 124 AFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTR 183 + +++G+W GW P FLG L G+ LGI+G GRIGQA+A+RAK FGM+I Y++R R Sbjct: 128 SVMQTGDWD----GWAPTAFLGGRLGGRRLGILGMGRIGQAVARRAKAFGMQIHYHNRRR 183 Query: 184 -KPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 + E E+ + A Y + + ++ D +S++ P T T+H++ + LKL+KP+A+++NTSR Sbjct: 184 LRSEIEDALEATYWESLDQMVARMDILSVNCPHTPSTFHLLNARRLKLLKPSAVIVNTSR 243 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMA 301 G V+D NAL + LK G +AGAGLDV+E N EL + NVV+ PH+GSAT E R M Sbjct: 244 GEVIDENALTRMLKAGELAGAGLDVYEHGHRGNPELRNMPNVVMLPHMGSATQEGRLEMG 303 Query: 302 ELVAKNLIAFAKGEIPPNLV 321 E V N+ FA G PP+ V Sbjct: 304 EKVIINVKTFADGHRPPDQV 323 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: 277 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: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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: 49 (23.5 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