Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Ac3H11_2599 Glyoxylate reductase (EC 1.1.1.79) / Glyoxylate reductase (EC 1.1.1.26) / Hydroxypyruvate reductase (EC 1.1.1.81); 2-ketoaldonate reductase, broad specificity (EC 1.1.1.215) (EC 1.1.1.-)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2599 Length = 329 Score = 268 bits (685), Expect = 1e-76 Identities = 150/326 (46%), Positives = 202/326 (61%), Gaps = 6/326 (1%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 KP++ + R I + + + + +++E D L ++ + D ++T + ++D L Sbjct: 3 KPRILVARAIFPDIVDRLREHFDVEANPDDVIWTPQELAARLADKDGVLTTGSQRIDAAL 62 Query: 62 LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 L AP+LKI A AVGY+N D++ T G+ TNTP VLT+ TAD FALL+A ARR+ E Sbjct: 63 LAAAPRLKICANMAVGYNNFDVDAMTAAGVQGTNTPDVLTETTADFGFALLMATARRMTE 122 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKR-AKGFGMKIIYYS 180 ++ ++R+G+W K W MF G + G TLGI+G GRIGQ +AKR A GFGMK+IY++ Sbjct: 123 SEHYLRAGQWTK----WSYDMFAGSDIHGSTLGIIGMGRIGQGIAKRGAHGFGMKVIYHN 178 Query: 181 RTR-KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 R+R E E E A YV + LL+ +D + L VP T ++H IG EL LMKP A LIN Sbjct: 179 RSRLSAELEAECKASYVGKDELLRTADHVMLVVPYTAASHHTIGAAELALMKPTATLINI 238 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299 +RG +VD AL AL+EG IA AGLDVFE EP + +L + NVVL PHI SAT R Sbjct: 239 ARGGIVDDAALAVALREGRIAAAGLDVFEGEPSVHPDLLTVPNVVLTPHIASATVPTRRA 298 Query: 300 MAELVAKNLIAFAKGEIPPNLVNKDV 325 MA L A NLIAF G P VN+ V Sbjct: 299 MANLAADNLIAFLGGRGPLTPVNQPV 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: 257 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: 329 Length adjustment: 28 Effective length of query: 303 Effective length of database: 301 Effective search space: 91203 Effective search space used: 91203 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