Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate RR42_RS14190 RR42_RS14190 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Cup4G11:RR42_RS14190 Length = 332 Score = 255 bits (651), Expect = 1e-72 Identities = 138/330 (41%), Positives = 204/330 (61%), Gaps = 9/330 (2%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 KP V +TR + I + ++++++ + A L ++ ++ D++D L Sbjct: 3 KPSVLVTRAVFPEVIDRLAQYFDVDDNQPDVALDGAALKARLAGKAGVLANAADRIDAGL 62 Query: 62 LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 + P L+ + AVGY+N+D+ T GI TNTP VLT+ TAD +ALL+A ARR+ E Sbjct: 63 VAGLPALRAVCNMAVGYNNLDVPALTAAGIVATNTPDVLTETTADFGWALLMATARRVTE 122 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSR 181 ++ ++R+G+W++ W MFLG L TLGI+G GRIGQALA+RA GFGM ++Y++R Sbjct: 123 SEHWLRAGKWER----WSYDMFLGMDLYRSTLGILGMGRIGQALARRAAGFGMSVLYHNR 178 Query: 182 TRKPEAEEEI-GAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTS 240 +R PE E + A YV LL +SD + L +P + +++H IG EL MKP+A L+N + Sbjct: 179 SRLPEDTERVLNARYVSKAELLAQSDHLLLVLPYSAQSHHSIGAAELAQMKPSATLVNLA 238 Query: 241 RGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGM 300 RG VVD AL +AL+EG I AGLDVFE EP + +L + NVVL PHI SA+ + R M Sbjct: 239 RGGVVDDAALARALREGRIFAAGLDVFEAEPQVHPDLLTVPNVVLTPHIASASEKTRRAM 298 Query: 301 AELVAKNLIAF----AKGEIPPNLVNKDVL 326 A+L A NLIA + PP+++N +V+ Sbjct: 299 ADLAADNLIAALGVGPQAGQPPSVINPEVM 328 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: 264 Number of extensions: 12 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: 332 Length adjustment: 28 Effective length of query: 303 Effective length of database: 304 Effective search space: 92112 Effective search space used: 92112 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