Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate SMc01943 SMc01943 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Smeli:SMc01943 Length = 325 Score = 255 bits (651), Expect = 1e-72 Identities = 147/324 (45%), Positives = 201/324 (62%), Gaps = 8/324 (2%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 KP++ ITR+ P+ +++ + ++ L ++ + R L + +R DA++ V+D++ ++ Sbjct: 5 KPRILITRRWPQAVERVLAERFDTVLNEEDRPLDRSALADALRNFDAVLPTVSDRLPADV 64 Query: 62 LENAP-KLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 + +I+ + VGY++ID A + GI VTNTPGVLTD TADLA +LLLA ARR Sbjct: 65 FTGGGLRTRILGNFGVGYNHIDAGAAKEAGIVVTNTPGVLTDCTADLAVSLLLAAARRTG 124 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKIIYY 179 E + VR+G W GW P +G + GKTLGI+GFGRIG+A+AKR GF M I++Y Sbjct: 125 EGERQVRAGAWD----GWRPTHMIGTKVTGKTLGIIGFGRIGKAMAKRCHFGFDMDIVFY 180 Query: 180 SRTR-KPEAEEEIGAEYVD-FETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237 +R+R PE GA +D E +L+ +DF+SLH P E H+I L MKP A LI Sbjct: 181 NRSRVAPEEAARFGARQLDTVEDVLRAADFVSLHCPGGGENRHLINAARLAAMKPAAYLI 240 Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAR 297 NTSRG VVD ALI AL++G I GAGLDV+E EP L L+NVVL PH+GSAT E R Sbjct: 241 NTSRGDVVDEAALIAALEKGVIRGAGLDVYEAEPDVPTRLRALENVVLLPHLGSATEETR 300 Query: 298 EGMAELVAKNLIAFAKGEIPPNLV 321 M V N+ AF G PP+ V Sbjct: 301 TAMGMKVVDNITAFFAGLQPPDRV 324 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: 269 Number of extensions: 13 Number of successful extensions: 5 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: 325 Length adjustment: 28 Effective length of query: 303 Effective length of database: 297 Effective search space: 89991 Effective search space used: 89991 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 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