Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate H281DRAFT_05383 H281DRAFT_05383 D-3-phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_05383 Length = 310 Score = 167 bits (424), Expect = 2e-46 Identities = 107/316 (33%), Positives = 161/316 (50%), Gaps = 13/316 (4%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 MKP + I + + IE ++ DP A V+ + A++T T + Sbjct: 1 MKPSLLILIHLDDASRASIEAEFDSVYAPDP-AQHAAVIATHGAMIRAVLTNGTRGISAA 59 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 ++ PKL+ ++ GY+N+ ++ A RGI + N G AD AFALLL++ R + Sbjct: 60 EIDRMPKLEFVSALGAGYENVAVDHARSRGIVLVNGAGTNDHCVADHAFALLLSIVRDVP 119 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180 D R G W+ + + + + GK LGIVG G IG+ +A+R GF M+I Y++ Sbjct: 120 RLDEATREGVWRDA-------LPMRPDVSGKRLGIVGLGNIGEKIARRGAGFDMEIGYHN 172 Query: 181 RTRKPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 R KP E Y D E L + DF+ + P T+H+IG + + + P+ ++N Sbjct: 173 R--KPR--EGTSLSYFDGVEALARWCDFLVIATPGGAGTHHLIGARVFEALGPDGFVVNV 228 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299 SRG+V+DT AL +AL G IAGA LDV+E EP L KL+NVVL PH+G + +A Sbjct: 229 SRGSVLDTAALAQALVAGTIAGAALDVYEGEPQPPAALLKLRNVVLTPHVGGRSPDAIAA 288 Query: 300 MAELVAKNLIAFAKGE 315 +N GE Sbjct: 289 AVNNFLRNAARHFAGE 304 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: 248 Number of extensions: 10 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: 310 Length adjustment: 28 Effective length of query: 303 Effective length of database: 282 Effective search space: 85446 Effective search space used: 85446 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