Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate CA265_RS17230 CA265_RS17230 D-glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Pedo557:CA265_RS17230 Length = 319 Score = 243 bits (619), Expect = 6e-69 Identities = 143/318 (44%), Positives = 196/318 (61%), Gaps = 7/318 (2%) Query: 4 KVFITRQIPENGIKMIEKF-YEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELL 62 KVFI+ I GIK +E+ I WK+ + L+ ++ DAL+++ +K++ L Sbjct: 2 KVFISGNIASVGIKELEENNITITQWKENRQITAEELIAACQDQDALISVGPNKINAAFL 61 Query: 63 ENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEA 122 + LK+IA ++VGYD +D+ A K I + NTPGVL+ ATAD AF L+LAV+R+ A Sbjct: 62 KACSHLKVIALHSVGYDQVDVAAAKKLNIPIGNTPGVLSKATADTAFLLMLAVSRKAFFA 121 Query: 123 DAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKG-FGMKIIYYSR 181 + GEWK E P LG + GKTLGI G G+IG +AK+ G + M +IY++R Sbjct: 122 HKKIIKGEWKNYE----PTPELGIEVNGKTLGIFGLGKIGLEMAKKCIGAYQMPVIYHNR 177 Query: 182 TRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 +R EAE+EIGA+YV FETLL +SD +S+H LT ET K MK N+I INT+R Sbjct: 178 SRNEEAEKEIGAKYVSFETLLAQSDVLSVHTALTPETKDKFTLDVFKQMKANSIFINTAR 237 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSATHEAREGM 300 GA+ + LIKAL++ I GAGLDV EP N L ++NV + PHIGSAT E R M Sbjct: 238 GAIHNEKDLIKALEKKIIWGAGLDVTNPEPMDKNNPLLSMENVAVLPHIGSATEETRAAM 297 Query: 301 AELVAKNLIAFAKGEIPP 318 A+++ KN+IA GE P Sbjct: 298 AQIIVKNIIAGLNGEKLP 315 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: 262 Number of extensions: 9 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: 319 Length adjustment: 28 Effective length of query: 303 Effective length of database: 291 Effective search space: 88173 Effective search space used: 88173 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