Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_078430036.1 BK574_RS21465 D-glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_002019605.1:WP_078430036.1 Length = 320 Score = 318 bits (816), Expect = 9e-92 Identities = 163/316 (51%), Positives = 223/316 (70%), Gaps = 5/316 (1%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 MKPKV +TR +P GI+ + + ++E+ + + L++ + + DA+++L+ +++D E Sbjct: 1 MKPKVLVTRDLPGEGIERLREVADVEVHTGKEELTKEQLIQAIADKDAIISLLVNEIDAE 60 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 +++ AP LK+I+ YAVG++NID++ A +RGI VTNTP VLT++TADL +ALLLAVARRI Sbjct: 61 VMDAAPHLKVISNYAVGFNNIDVDAAQERGIIVTNTPDVLTESTADLTWALLLAVARRIP 120 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180 E+D + R G++ VGW P + LG + GKTLGI+G GRIG+A+ +RAKGFGM I+YY+ Sbjct: 121 ESDTYTREGKF----VGWAPELLLGRTVYGKTLGIIGMGRIGEAVVRRAKGFGMNIVYYN 176 Query: 181 RTR-KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 R E E E+ A Y E ++ ++DF+SLH PLT ET ++I E ELK MK A LINT Sbjct: 177 RRPLSTEKELELDASYASLEEVISQADFLSLHTPLTPETRYLIDENELKAMKDTAYLINT 236 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299 SRG +V+ AL+ ALKE IAGAGLDVFE EP EEL +NVVLAPHIGSAT E R Sbjct: 237 SRGPLVNEKALVNALKEKAIAGAGLDVFENEPAIEEELLNFQNVVLAPHIGSATIETRVE 296 Query: 300 MAELVAKNLIAFAKGE 315 MA+L N I+ KGE Sbjct: 297 MADLAINNTISILKGE 312 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: 295 Number of extensions: 8 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: 320 Length adjustment: 28 Effective length of query: 303 Effective length of database: 292 Effective search space: 88476 Effective search space used: 88476 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 Apr 09 2024. 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