Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate AZOBR_RS10940 AZOBR_RS10940 3-phosphoglycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__azobra:AZOBR_RS10940 Length = 415 Score = 155 bits (393), Expect = 1e-42 Identities = 104/326 (31%), Positives = 161/326 (49%), Gaps = 14/326 (4%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKEL 61 K + + + +N I + + + P A LLE++ V L + ++ Sbjct: 10 KINILLLEGVHDNAINELAHGGYATVERLPHALDESELLERIGSVHMLGIRSRTHLTAKV 69 Query: 62 LENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121 LE A +L + + +G + +D++ A + GI V N P T + A+L ++ + R I Sbjct: 70 LEAASRLFSVGCFCIGTNQVDLKAARRLGIPVFNAPYSNTRSVAELVIGEIIMLMRGIFS 129 Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSR 181 V G W KS Y ++GKTLGIVG+G IG ++ A+ GMK+ YY Sbjct: 130 KSNLVHGGGWMKSAKD-------SYEIRGKTLGIVGYGHIGTQVSIMAESMGMKVRYYDV 182 Query: 182 TRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSR 241 K E LL SD ++LHVP T +T MIGE +++ MK A LIN +R Sbjct: 183 VNKLALGNAQPCH--SLEELLAVSDVVTLHVPDTPQTRDMIGEAQIRAMKKGAHLINAAR 240 Query: 242 GAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFK-----LKNVVLAPHIGSATHEA 296 G VV AL AL++ + GA +DVF +EP ++E+F+ L N +L PHIG +T EA Sbjct: 241 GKVVVIEALAAALRDKHLLGAAIDVFPKEPGGDKEVFESALRGLDNAILTPHIGGSTMEA 300 Query: 297 REGMAELVAKNLIAFAKGEIPPNLVN 322 + + V++ LI ++ VN Sbjct: 301 QANIGTEVSQKLIEYSDNGSTMGAVN 326 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: 278 Number of extensions: 14 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: 415 Length adjustment: 30 Effective length of query: 301 Effective length of database: 385 Effective search space: 115885 Effective search space used: 115885 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