Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate HSERO_RS08110 HSERO_RS08110 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS08110 Length = 326 Score = 277 bits (708), Expect = 3e-79 Identities = 149/328 (45%), Positives = 206/328 (62%), Gaps = 6/328 (1%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 MKPK+F+ R + + +E+ +E+E +D + L K + D L T ++ V Sbjct: 1 MKPKIFVARAVFPEVLARLEQHFEVESNQDDRIYSAAELQAKAQGKDGLFTTPSEPVTAA 60 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 L P+LK + AVGY+NID+ AT+ G+ TNTP VL + TAD +AL++A ARRI Sbjct: 61 LFAANPQLKAVCNMAVGYNNIDVAAATQAGVMATNTPDVLNETTADFGWALMMAAARRIT 120 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180 E++ F+R+G+WKK W F+G + G TLGI+G GRIGQA+A+R+ GF M+++Y++ Sbjct: 121 ESEHFLRAGKWKK----WSYDSFVGPDIHGATLGIIGMGRIGQAIARRSLGFDMQVLYHN 176 Query: 181 RTR-KPEAEEEIG-AEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILIN 238 R+R PE E A YV E LL+++D + L +P +K+T+H I EL LMKP A L N Sbjct: 177 RSRLAPELEARANHARYVSKEELLRQADHVILVLPYSKDTHHTIAAAELALMKPTATLTN 236 Query: 239 TSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEARE 298 +RG +VD ALI AL+EG IA AG+DVFE EP + E L NVVL PHI SA+ R Sbjct: 237 IARGGIVDDAALIAALREGRIAAAGVDVFENEPAFKPEFLDLSNVVLTPHIASASTPTRL 296 Query: 299 GMAELVAKNLIAFAKGEIPPNLVNKDVL 326 MA A NLIA G+ PPNL+N DV+ Sbjct: 297 AMANCAADNLIAALSGQRPPNLLNPDVV 324 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: 250 Number of extensions: 9 Number of successful extensions: 3 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: 326 Length adjustment: 28 Effective length of query: 303 Effective length of database: 298 Effective search space: 90294 Effective search space used: 90294 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