Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate BPHYT_RS03835 BPHYT_RS03835 D-lactate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS03835 Length = 332 Score = 163 bits (413), Expect = 5e-45 Identities = 106/291 (36%), Positives = 156/291 (53%), Gaps = 24/291 (8%) Query: 47 DALVTLVTDKVDKELLE--NAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDAT 104 D + V D VD +L +A ++IA + G++++D+ A + GI V P A Sbjct: 46 DVVCPFVNDNVDAAVLARLHAGGTRMIALRSAGFNHVDLAAAERLGITVARVPAYSPHAV 105 Query: 105 ADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQA 164 A+ A L+LA+ RR+ A A R G++ H L LG+ L GKT+G++G G IG+ Sbjct: 106 AEHAVGLILALNRRLPRAVARTREGDFSL-----HGL--LGFDLHGKTVGVIGTGMIGRV 158 Query: 165 LAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGE 224 + GFGM+++ Y + +GA YV + LL ESD +SLH PL +TYH+I Sbjct: 159 FGRIMAGFGMQVLAYDPGKPAADLLALGARYVPLDALLAESDVVSLHCPLVPDTYHLING 218 Query: 225 KELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEE-----------PYY 273 L MK A+LINT RG +V++NALI ALK+G + GLDV+EEE P Sbjct: 219 PALAKMKRGAMLINTGRGGLVESNALIGALKDGQLGHLGLDVYEEESGLFFEDHSNLPLQ 278 Query: 274 NEELFKL---KNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPNLV 321 ++ L +L NV++ H T EA +A+ N+ A+ G P N+V Sbjct: 279 DDVLARLLMFPNVIVTAHQAFFTREAMNEIAQTTLDNVAAWQAG-TPRNVV 328 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: 249 Number of extensions: 9 Number of successful extensions: 2 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: 332 Length adjustment: 28 Effective length of query: 303 Effective length of database: 304 Effective search space: 92112 Effective search space used: 92112 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