Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_008540147.1 HMPREF9454_RS12055 hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000245775.1:WP_008540147.1 Length = 326 Score = 196 bits (498), Expect = 7e-55 Identities = 115/315 (36%), Positives = 180/315 (57%), Gaps = 13/315 (4%) Query: 4 KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63 KV I+ ++ ++G+ ++E+ + + P +L ++ + D L+ + +D+E + Sbjct: 3 KVVISHKLHDDGMAVLERAGANVVITNSGKPKD--MLPELLDADGLIIRI-GSIDRETML 59 Query: 64 NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123 LK+I + VG D++D+E AT+ GI V PG T + A+ A A++ A A+ +V D Sbjct: 60 KCKNLKVIGRPGVGVDDVDVEAATELGIPVVIAPGANTRSVAEHAMAMMFACAKDMVRCD 119 Query: 124 AFVRSGEWK-KSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRT 182 +R G + +SE + Y L GK LG++G G IG LA+ A G GMK++ Y Sbjct: 120 KEMRKGNFAIRSE-------YKAYELNGKVLGLIGCGHIGNILAEMATGIGMKVLVYDPF 172 Query: 183 RKPEAEEEIGAEY-VDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 K E E G Y + E +LKE+D +S+H PLT +T +MIGEKELKLMK ILIN +R Sbjct: 173 VKAEVVEAKGYGYRAEMEDILKEADVVSIHTPLTPKTKNMIGEKELKLMKSTGILINCAR 232 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPY-YNEELFKLKNVVLAPHIGSATHEAREGM 300 G +++ AL KAL E WI A DV EP ++ LF +N+++ PH+ T EA G+ Sbjct: 233 GGIINEEALCKALSENWIHSAATDVVVHEPISVDDPLFMHENIIVTPHMAGQTKEAASGV 292 Query: 301 AELVAKNLIAFAKGE 315 A + A+ ++A G+ Sbjct: 293 ATMAAEGVMAVINGQ 307 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: 265 Number of extensions: 16 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: 326 Length adjustment: 28 Effective length of query: 303 Effective length of database: 298 Effective search space: 90294 Effective search space used: 90294 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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