Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_103235037.1 C1634_RS07230 D-2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_002899945.2:WP_103235037.1 Length = 319 Score = 166 bits (420), Expect = 7e-46 Identities = 113/331 (34%), Positives = 178/331 (53%), Gaps = 46/331 (13%) Query: 4 KVFITRQIPENGIKMI-EKFYEIELWKDPKAPPRGVLLEKVRE--VDALVTLVTDKVDKE 60 KV + ++GI + EK +E+ K P+ L++ + E + L+ +V K+ Sbjct: 2 KVLANDGLDQSGIDALTEKGFEVITTKVPQE----FLVDYINEHKIRTLLVRSATQVRKD 57 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 +++N P + II + VG DNID++ A ++GI+V NTP +++ A+L FA L + AR + Sbjct: 58 IIDNCPSIDIIGRGGVGMDNIDVDYAREKGIHVINTPSASSESVAELVFAHLFSGARFLQ 117 Query: 121 EADAFV------RSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGM 174 +++ + G KK+ G L+GKT+GI+G GRIGQ +A+ A G GM Sbjct: 118 DSNRKMPLVGDTEFGGLKKAYAA-------GIELRGKTIGIIGMGRIGQEVARIALGLGM 170 Query: 175 KIIYYSRTRKPEAEEEIGAEY------------VDFET-----LLKESDFISLHVPLTKE 217 +++ A+ IG VD ET +LK SDFI+LHVP K+ Sbjct: 171 RVV--------AADNNIGKASIKVKFYNNQFINVDIETEPLQEVLKHSDFITLHVPAQKD 222 Query: 218 TYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEEL 277 Y MIG+ E +MK ++N SRG V+D ALI AL G + AGLDVF EP ++E+ Sbjct: 223 GY-MIGKNEFDMMKDGVAIVNCSRGGVIDETALIHALDSGKVRFAGLDVFINEPTPSKEI 281 Query: 278 FKLKNVVLAPHIGSATHEAREGMAELVAKNL 308 + L PH G++T EA++ + +A+ + Sbjct: 282 LNHSKISLTPHTGASTLEAQDRIGLSLAEQI 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: 240 Number of extensions: 11 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: 319 Length adjustment: 28 Effective length of query: 303 Effective length of database: 291 Effective search space: 88173 Effective search space used: 88173 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 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