Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate BPHYT_RS14520 BPHYT_RS14520 2-hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS14520 Length = 329 Score = 260 bits (664), Expect = 4e-74 Identities = 143/328 (43%), Positives = 204/328 (62%), Gaps = 11/328 (3%) Query: 4 KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63 K+ + R I + I+ ++++++++ W L ++ + D +T D V L Sbjct: 3 KILVARPIFPDVIERLKQYFDVD-WNQGDVLAADELKRRLADKDGALT-AGDPVGAAELA 60 Query: 64 NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEAD 123 AP+L++++ AVGY+N D+ + TNTP VL ++TAD +AL++A ARRI E++ Sbjct: 61 AAPRLRVVSNMAVGYNNFDVAAFNAANVLGTNTPDVLNESTADFGWALMMAAARRITESE 120 Query: 124 AFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTR 183 ++R G+W+K W FLG L G TLG++G GRIGQALA+RAKGF M++IY++R+R Sbjct: 121 HWLRGGQWQK----WAYDAFLGSDLHGSTLGVIGMGRIGQALARRAKGFDMQVIYHNRSR 176 Query: 184 -KPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRG 242 PE E E+ AEYV + LL+ +D + L +P TKE +H IG EL LMKP A L N +RG Sbjct: 177 VAPEIEAELNAEYVSKQDLLRRADHVVLVLPYTKENHHTIGAAELALMKPTATLTNIARG 236 Query: 243 AVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMAE 302 +VD AL++AL+ IA AGLDVFE EP N++L + NVVL PHI SAT R MA Sbjct: 237 GIVDDAALVEALRSKQIAAAGLDVFEGEPNLNQDLLSVPNVVLTPHIASATEATRRAMAN 296 Query: 303 LVAKNLIA----FAKGEIPPNLVNKDVL 326 L A NLIA + PPN VN +V+ Sbjct: 297 LAADNLIAGLGEGPRAGRPPNPVNPEVI 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: 278 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: 329 Length adjustment: 28 Effective length of query: 303 Effective length of database: 301 Effective search space: 91203 Effective search space used: 91203 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