Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF2436 PGA1_c24680 glyoxylate reductase GyaR
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Phaeo:GFF2436 Length = 318 Score = 220 bits (561), Expect = 3e-62 Identities = 129/318 (40%), Positives = 181/318 (56%), Gaps = 9/318 (2%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 M K++ITR + + E+ ++ G +RE D ++ + D+ D Sbjct: 1 MSGKLWITRPMTAAVEARARSEFGAEIRQETTPLTAGERQRALREFDVVMPTLGDQFDAA 60 Query: 61 LLE--NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARR 118 +AP+ +++A + VGY++ID++ A GI V+NTPG +TDATAD A L+L ARR Sbjct: 61 SFAGVSAPRCRLLANFGVGYNHIDVDAAKTAGIAVSNTPGAVTDATADTALTLMLMTARR 120 Query: 119 IVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKII 177 E + VRSG+W+ GWHP LG L GK +GIVGFGRIG+A+A+R GFGM + Sbjct: 121 AGEGERLVRSGQWQ----GWHPTQMLGLHLTGKHVGIVGFGRIGEAIARRCHFGFGMSVS 176 Query: 178 YYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237 Y +R+ K + A+ L D + L VP ET H+I + L M+P A+LI Sbjct: 177 YLARSEKSPGFPAVRAD--SLTALAASVDVLVLAVPGGAETRHLINAEVLAAMRPEALLI 234 Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAR 297 N +RG VVD ALI AL+ G IAGAGLDV+E EP L +++ V L PH+G+AT E R Sbjct: 235 NIARGEVVDEAALISALQTGQIAGAGLDVYEFEPEVPLALQQMEQVTLLPHLGTATEEVR 294 Query: 298 EGMAELVAKNLIAFAKGE 315 M L N+ AF G+ Sbjct: 295 SDMGHLALDNVAAFLAGK 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: 213 Number of extensions: 9 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: 318 Length adjustment: 28 Effective length of query: 303 Effective length of database: 290 Effective search space: 87870 Effective search space used: 87870 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 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