Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 3609936 Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Dino:3609936 Length = 531 Score = 215 bits (547), Expect = 2e-60 Identities = 126/333 (37%), Positives = 189/333 (56%), Gaps = 17/333 (5%) Query: 1 MKPKVFITRQIPENGIKM-----IEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTD 55 M PKV ++ ++ E +++ IE +E L KD + L E + + D L Sbjct: 1 MAPKVLVSDKLSETAVQIFRDRGIEVDFEPSLGKD-----KDKLAEVIGKYDGLAIRSAT 55 Query: 56 KVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAV 115 KV ++LL +A LK++ + +G DN+D A+K+G+ V NTP TA+ A A++ AV Sbjct: 56 KVTEKLLAHADNLKVVGRAGIGTDNVDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAV 115 Query: 116 ARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMK 175 AR+I EA A +G+W+KS+ F+G L KTLG++G G IG + +RA G MK Sbjct: 116 ARQIPEASASTHAGKWEKSK-------FMGVELTAKTLGVIGAGNIGGIVCERALGLKMK 168 Query: 176 IIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAI 235 +I Y E +++G E VD +TLL +DFI+LHVPLT +T +++ + L+ K Sbjct: 169 VIAYDPFLSEERADKLGVEKVDLDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVR 228 Query: 236 LINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHE 295 +IN +RG +VD AL LK G +AGA DVF EEP LF L NVV PH+G++T E Sbjct: 229 IINCARGGLVDEQALADLLKSGHVAGAAFDVFAEEPATENPLFGLPNVVCTPHLGASTTE 288 Query: 296 AREGMAELVAKNLIAFAKGEIPPNLVNKDVLTS 328 A+E +A VA+ + + N +N +T+ Sbjct: 289 AQENVALQVAEQMSNYLLSGAVENALNMPSVTA 321 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: 370 Number of extensions: 15 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: 531 Length adjustment: 32 Effective length of query: 299 Effective length of database: 499 Effective search space: 149201 Effective search space used: 149201 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