Align 4-carboxy-4-hydroxy-2-oxoadipate aldolase; CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate H281DRAFT_06498 H281DRAFT_06498 Regulator of RNase E activity RraA
Query= SwissProt::G2IQQ8 (228 letters) >FitnessBrowser__Burk376:H281DRAFT_06498 Length = 227 Score = 123 bits (309), Expect = 3e-33 Identities = 67/201 (33%), Positives = 104/201 (51%) Query: 9 VVQNIERAPLEVIDGLAACGVATVHEAQGRTGLLASYMRPIYRGARVAGSALTISAPPGD 68 +V++ ER E++ + A + + GR G L ++ +Y ++AG A T+ PGD Sbjct: 6 IVKDFERVSPELVKKASQFQPAILSDVNGRRGALHGRIKALYPRMKLAGPAFTVEVRPGD 65 Query: 69 NWMVHVAIEQLKAGDILLLAPTSPCEDGYFGDLLATSAQARGCRGLVIDAGVRDVRDLTE 128 N M+H A+ K GD+L++ + G ++ +A+ RG G+V+DA VRD DL E Sbjct: 66 NLMIHAALAVAKPGDVLVIDGKADQTCALMGTIMMHAARERGLAGVVLDAAVRDSLDLDE 125 Query: 129 MNFPVWSKAIYAQGTVKNTLGSVNVPVVCANALVNPGDVIVADDDGVCVVPLANAEKVLE 188 ++FPV+S G K G + P+ C VNPGD I+AD DGV V E +L+ Sbjct: 126 LDFPVFSVGTNPNGPTKEVGGRIGHPIACGGVTVNPGDFIIADADGVMCVEREKLESLLD 185 Query: 189 AARAREANEGDKREKMANGVL 209 A + A E + + G L Sbjct: 186 KASEKVAWEARRIADIKEGKL 206 Lambda K H 0.318 0.136 0.397 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: 154 Number of extensions: 7 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: 228 Length of database: 227 Length adjustment: 22 Effective length of query: 206 Effective length of database: 205 Effective search space: 42230 Effective search space used: 42230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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