Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF2987 HP15_2931 glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Marino:GFF2987 Length = 320 Score = 174 bits (441), Expect = 3e-48 Identities = 109/278 (39%), Positives = 162/278 (58%), Gaps = 16/278 (5%) Query: 39 LLEKVREVDALVTLVTDKV--DKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNT 96 +LE++R D T++ +KV +E + P+LK IA A G +NID A GI V N Sbjct: 47 ILERIRGFD---TVLVNKVVLTREHFDACPELKTIAVVATGLNNIDQAAAKDHGIKVMNV 103 Query: 97 PGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGW---HPLMFLGYGLKGKTL 153 A AL+LA+A R+++ V++G W KS++ HP+M L+G+TL Sbjct: 104 TNYGRSTVAQHTMALMLALATRLLDYTRDVQAGHWGKSDMFCLMDHPIM----ELEGRTL 159 Query: 154 GIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVP 213 GIVG+G +GQ +A+RA FGMK++ +R + + G + + LL ++D +SLH Sbjct: 160 GIVGYGDLGQGVAERAAAFGMKVLLGARPGQEPGVVD-GYSRIPLDELLPQADVVSLHCL 218 Query: 214 LTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYY 273 LT ET +IG +ELK+MKP+++LINTSRG +V+ AL AL+ G I GAG DV EEP Sbjct: 219 LTDETRDLIGARELKMMKPDSLLINTSRGGLVNEQALADALRAGEIGGAGFDVLTEEPPR 278 Query: 274 NEELF---KLKNVVLAPHIGSATHEAREGMAELVAKNL 308 N + N+++ PH A+ EAR+ + + A NL Sbjct: 279 NGNPLLADDIPNLIVTPHSAWASREARQRIVGITAVNL 316 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: 238 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: 320 Length adjustment: 28 Effective length of query: 303 Effective length of database: 292 Effective search space: 88476 Effective search space used: 88476 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