Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate BWI76_RS27925 BWI76_RS27925 D-isomer specific 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Koxy:BWI76_RS27925 Length = 314 Score = 209 bits (533), Expect = 6e-59 Identities = 126/333 (37%), Positives = 185/333 (55%), Gaps = 26/333 (7%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 MK K+ +P+ + YE+ ++ VL E + ++T V ++ Sbjct: 1 MKLKILKQASLPDQLTAELNSLYEVYEYEALTREELAVLAE---QFTIMITNGEATVTRQ 57 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 L+ + P L++IA + VGYD +D+ A + V++TPGVLTD ADLA L+LA +R+IV Sbjct: 58 LISSLPSLELIAVFGVGYDGVDVRAAADHRVAVSHTPGVLTDDVADLAMGLMLATSRQIV 117 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180 A F+ +G W++ W + G +GIVG GRIGQA+A+R +GF M+I Y Sbjct: 118 SAQKFIEAGGWRQGGFQWTRKV------SGSRVGIVGMGRIGQAIARRCEGFAMQIAYSD 171 Query: 181 RTRKPEAEEEIGAEYV---DFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237 R P G +Y D TL ++DF+ + P + E +I E+ L + + ILI Sbjct: 172 RKAIP------GLDYPWIEDISTLASQTDFLVICTPGSAENQALIDERVLSALGASGILI 225 Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAR 297 N SRG+VVD ALIKAL++G IAGAGLDVF +EP + L + NVV+ PH+ SAT R Sbjct: 226 NISRGSVVDEFALIKALEQGIIAGAGLDVFSQEPEVPQALLRRANVVVTPHMASATWSTR 285 Query: 298 EGMAELVAKNLIAFAKGEIPPNLVNKDVLTSSP 330 E M+ LV +N+ +AK NK ++T P Sbjct: 286 EAMSRLVLENVSGWAK--------NKTLVTPVP 310 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: 218 Number of extensions: 12 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: 314 Length adjustment: 28 Effective length of query: 303 Effective length of database: 286 Effective search space: 86658 Effective search space used: 86658 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