Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate SMc02849 SMc02849 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Smeli:SMc02849 Length = 334 Score = 269 bits (687), Expect = 8e-77 Identities = 151/328 (46%), Positives = 208/328 (63%), Gaps = 12/328 (3%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 KP V+ITR++P+ + + ++ EL D + L+ V+ D LV VTD++D L Sbjct: 6 KPTVYITRKLPDVVETRMRELFDAELNIDDTPRSQPELVAAVKRADVLVPTVTDRIDAAL 65 Query: 62 LENA-PKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 +E A P+LK+IA ++ G DNID++ A ++GI VTNTP VLT+ TAD+ AL+LAV RR+ Sbjct: 66 IEQAGPQLKLIAAFSNGVDNIDVDAAARKGITVTNTPNVLTEDTADMTMALILAVPRRLA 125 Query: 121 EADAFV--RSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIY 178 E + R GEW GW P LG + GK +GIVG GRIG A+A+RAK FG+ I Y Sbjct: 126 EGAQVLTDRKGEW----AGWSPTWMLGRRIAGKRIGIVGMGRIGTAVARRAKAFGLSIHY 181 Query: 179 YSRTR-KPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAIL 236 ++R R KPE EE + A Y D + +L D +S++ P T TYH++ + L LM+P++ + Sbjct: 182 HNRHRVKPETEEMLEATYWDSLDQMLARVDIVSVNCPSTPATYHLLSARRLALMRPDSYI 241 Query: 237 INTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLK---NVVLAPHIGSAT 293 +NT+RG ++D ALIK+L+EG IAGAGLDVFE EP N +L KL VVL PH+ SAT Sbjct: 242 VNTARGGIIDEAALIKSLREGKIAGAGLDVFENEPCVNPKLIKLAGEGKVVLLPHMSSAT 301 Query: 294 HEAREGMAELVAKNLIAFAKGEIPPNLV 321 E R M E V N+ F G PP+ V Sbjct: 302 LEGRIDMGEKVVINIRTFFDGHRPPDRV 329 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: 289 Number of extensions: 11 Number of successful extensions: 5 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: 334 Length adjustment: 28 Effective length of query: 303 Effective length of database: 306 Effective search space: 92718 Effective search space used: 92718 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 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