Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_011385558.1 AMB_RS16130 phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000009985.1:WP_011385558.1 Length = 526 Score = 190 bits (482), Expect = 8e-53 Identities = 117/321 (36%), Positives = 176/321 (54%), Gaps = 11/321 (3%) Query: 3 PKVFITRQIPENGIKMI-EKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 PKV I+ ++ +++ ++ E ++ K AP L + + D L KV E+ Sbjct: 2 PKVLISDKLSPAAVQIFKDRGIETDV-KTGLAPDE--LKAIIGQYDGLAIRSNTKVTTEI 58 Query: 62 LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 L A LK++ + +G DN+D+ AT RGI V NTP + TA+ A A++ A+AR I E Sbjct: 59 LAAATNLKVVGRAGIGVDNVDVPAATARGIVVMNTPFGNSITTAEHAIAMMFALAREIPE 118 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSR 181 A+A +G+W+K+ F+G L GK LGIVG G IG +A RA+G M++I Y Sbjct: 119 ANASTHAGKWEKNR-------FMGVELTGKVLGIVGCGNIGAIVADRAQGLRMRVIAYDP 171 Query: 182 TRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 E +E+ E V+ + L +DFI+LH PLT T ++I K + MK +IN +R Sbjct: 172 FLSVERAKELNVEKVELDELFPRADFITLHTPLTDATRNIIDAKAMAKMKKGVRIINCAR 231 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMA 301 G +V L+ AL+ G +AGA LDVF+ EP LF VV PH+G++T EA+E +A Sbjct: 232 GGLVVEEDLLAALESGQVAGAALDVFKTEPAKENALFGNPKVVCTPHLGASTSEAQENVA 291 Query: 302 ELVAKNLIAFAKGEIPPNLVN 322 VA+ + + N +N Sbjct: 292 LQVAEQMADYLLTGAVTNALN 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: 386 Number of extensions: 16 Number of successful extensions: 2 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: 526 Length adjustment: 31 Effective length of query: 300 Effective length of database: 495 Effective search space: 148500 Effective search space used: 148500 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: 50 (23.9 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