Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_106711064.1 CU102_RS10005 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_003010955.1:WP_106711064.1 Length = 307 Score = 184 bits (468), Expect = 2e-51 Identities = 108/293 (36%), Positives = 164/293 (55%), Gaps = 9/293 (3%) Query: 16 IKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYA 75 ++ +E+ Y +E + K G L + A VT + ++++ P ++I++ + Sbjct: 17 LEELERRYAVERLYEEK-DALGFLQQNAARFRAAVTSTFTGLKADMIDLLPAVEIVSSFG 75 Query: 76 VGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSE 135 VG D++D+ A K+GI V NTP VL + TA++A ALLLA R IV D FVR G W + E Sbjct: 76 VGTDSLDVAYANKKGIKVANTPDVLNEDTANMAIALLLATTRDIVANDRFVREGRWARGE 135 Query: 136 VGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEY 195 L G++GK +G+VG GRIG +A++ FG + Y++R +KP+ A+ Sbjct: 136 TPP-----LAQGIEGKKVGLVGLGRIGSVIAEKLLAFGCDVTYHTRNKKPDVSYNHCADL 190 Query: 196 VDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALK 255 V + ++ + +P T +I + L+ + IN +RG+VVD AL++ L+ Sbjct: 191 V---AMARDCAVLIAILPGGDATQGIISREVLQALGSKGTFINIARGSVVDEVALVELLQ 247 Query: 256 EGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMAELVAKNL 308 G + AGLDVF +EP E LF L NVVL PH+GSAT E RE MA+ V NL Sbjct: 248 SGGLGRAGLDVFADEPRAPEALFALDNVVLQPHMGSATVETREAMADRVVSNL 300 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: 243 Number of extensions: 9 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: 307 Length adjustment: 28 Effective length of query: 303 Effective length of database: 279 Effective search space: 84537 Effective search space used: 84537 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 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