Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate SMa2137 SMa2137 dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Smeli:SMa2137 Length = 324 Score = 244 bits (623), Expect = 2e-69 Identities = 139/322 (43%), Positives = 194/322 (60%), Gaps = 6/322 (1%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 +KPKV +TR+ P + ++ L + + R L + E DA++ VTDK+ + Sbjct: 7 VKPKVIVTRRWPTEVEDRLTAEFDTRLNETDQPYDRRELRAALEEADAVLPTVTDKISAD 66 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 +LE + KI+ + VG+++ID ATK G+ VTNTPGVLTDATADLA LLL ARR Sbjct: 67 MLEGGIRAKILGNFGVGFNHIDTAAATKVGLVVTNTPGVLTDATADLAMTLLLMCARRAG 126 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKIIYY 179 E + +R+G+W GW P G + GKT+GI+G GRIGQA+A+R GFGM ++++ Sbjct: 127 EGERELRAGKW----TGWRPTHLCGSHVTGKTVGIIGMGRIGQAVARRCHFGFGMDVVFF 182 Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 + + + + +L +DF+SLH P E YH+I + L MK +A LINT Sbjct: 183 D-SHSIAGLDVPARQLPSVDDVLATADFVSLHCPGGGENYHLIDDDRLACMKWSAFLINT 241 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299 +RG VVD +AL++AL+ IAGAGLDVFE EP L + ++VVL PH+GSAT E R Sbjct: 242 ARGDVVDEHALVRALETRRIAGAGLDVFEGEPRVPGRLAERQDVVLLPHLGSATKETRVA 301 Query: 300 MAELVAKNLIAFAKGEIPPNLV 321 M V +NL AF G PP+ V Sbjct: 302 MGMRVIENLKAFFSGRSPPDAV 323 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: 268 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: 324 Length adjustment: 28 Effective length of query: 303 Effective length of database: 296 Effective search space: 89688 Effective search space used: 89688 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