Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Synpcc7942_1347 Synpcc7942_1347 2-hydroxyacid dehydrogenase-like
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__SynE:Synpcc7942_1347 Length = 331 Score = 153 bits (386), Expect = 7e-42 Identities = 97/288 (33%), Positives = 146/288 (50%), Gaps = 24/288 (8%) Query: 48 ALVTLVTDKVDKELLENAPKLKI--IAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATA 105 A+ + V D++D LE +L + +A G++ +D+ A + G+ V P A A Sbjct: 47 AVCSFVNDRLDAITLEALAELGVEHVALRCAGFNQVDLSAAERLGLRVVRVPAYSPHAVA 106 Query: 106 DLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQAL 165 + A AL+L + R+I A A R G + + +G+ L G T+GI+G GRIG L Sbjct: 107 EHAIALILTLNRKIHRAYARTREGNFALDGL-------VGFDLNGCTVGIIGTGRIGAVL 159 Query: 166 AKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEK 225 + +GFG ++ + P+ GA Y D + L +E+ ISLH PLT +TYH++ + Sbjct: 160 TQILRGFGCHVLAHDLVENPDCLAA-GAVYTDLDQLWQEAQIISLHCPLTPQTYHLVNRE 218 Query: 226 ELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFE-EEPYYNEE-------- 276 + M+P +LINTSRG +VDT A+I+ LK I GLDV+E EEP + ++ Sbjct: 219 AIAKMQPGTMLINTSRGGLVDTQAVIEGLKLKRIGALGLDVYEQEEPLFFQDHSTEIIHD 278 Query: 277 -----LFKLKNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPN 319 L NVV+ H T A +AE NL +G PN Sbjct: 279 DVFQRLLTFPNVVITGHQAFLTDTALHNIAETTLSNLTDLEQGRACPN 326 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: 219 Number of extensions: 12 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: 331 Length adjustment: 28 Effective length of query: 303 Effective length of database: 303 Effective search space: 91809 Effective search space used: 91809 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