Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Ac3H11_2341 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2341 Length = 322 Score = 213 bits (542), Expect = 5e-60 Identities = 125/281 (44%), Positives = 166/281 (59%), Gaps = 11/281 (3%) Query: 32 KAPPRGVLLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGI 91 +A P+G L + E +VT + + E++ P L++I+ + VG+D +DI AT RG+ Sbjct: 36 QADPQGFLAAQGAEFSGVVTTASIGLQGEVIAALPHLQVISSFGVGFDALDIGTATARGV 95 Query: 92 YVTNTPGVLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGK 151 V TPGVL D AD+AFAL+L V+R I +D FVR G+W K+ LG + GK Sbjct: 96 QVGYTPGVLNDCVADMAFALMLDVSRGIAASDRFVRQGQWPKARFA------LGTRVSGK 149 Query: 152 TLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKE-SDFISL 210 LGIVG GRIGQA+A+RA GF M++ Y++R E Y + T L + +D++ L Sbjct: 150 RLGIVGMGRIGQAVAERAAGFRMEVSYHNR----RPAEGCALSYFESLTALAQWADYLVL 205 Query: 211 HVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEE 270 V T H++ L + P LIN +RG+VVD ALI AL E IAGAGLDVF+ E Sbjct: 206 TVAGGAGTRHLVNRDVLDALGPQGYLINVARGSVVDEAALIDALAERRIAGAGLDVFDNE 265 Query: 271 PYYNEELFKLKNVVLAPHIGSATHEAREGMAELVAKNLIAF 311 P L L NVVL PH SATHE R MA+LV +NL AF Sbjct: 266 PQVPAALMALDNVVLTPHTASATHETRRAMADLVLENLHAF 306 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: 235 Number of extensions: 12 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: 322 Length adjustment: 28 Effective length of query: 303 Effective length of database: 294 Effective search space: 89082 Effective search space used: 89082 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