Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39 (uncharacterized)
to candidate 8501164 DvMF_1898 HpcH/HpaI aldolase (RefSeq)
Query= curated2:O86013 (262 letters) >FitnessBrowser__Miya:8501164 Length = 259 Score = 115 bits (287), Expect = 1e-30 Identities = 83/238 (34%), Positives = 120/238 (50%), Gaps = 16/238 (6%) Query: 12 LREGPVQLGFWLALAHPDIAEICAGQGYDWLLIDGEHGPQTLPGIVAQLRAVEATPPCSA 71 +R G +G W+ + D+AEI GYDW+ +D EH T + RA+E + Sbjct: 11 MRRGEATIGTWMQIPSTDVAEILGRSGYDWVAVDLEHAAFTRSQLPDAFRAIE-LGGAAP 69 Query: 72 IVRVPGHDSVTIKQVLDLGAQTLMVPMVETAEQAKAIVTASRYP----PAGERGLGGARA 127 RV IK LD GA+ L+ PM+ET EQ A + + YP P+G RG+G RA Sbjct: 70 FARVAEATLTDIKASLDSGARGLIFPMIETREQLDAAIGWALYPRTDGPSGVRGVGYCRA 129 Query: 128 SRWG-GYPAYVAEANAQVCIIAQIETATAVDNIEAIAAVDGIDALFLGPADLAATEGLLG 186 + +G + YV E +AQIE AVDN++AI + +DA+ +GP DL+ + GL Sbjct: 130 NLFGREFTPYVNETARDTLFVAQIEHIRAVDNLDAILSHPRLDAIMVGPYDLSGSMGL-- 187 Query: 187 ASSFD------ALFKLTGEALARIVATGKPAGILSRDERLVQQFLDGGARFIANGIDS 238 + FD AL ++ A A V G I+ D + + + G RFIA ID+ Sbjct: 188 TAQFDHPDFLAALDRIAAAARAHDVPMG--LHIVQPDTADLARRIGEGYRFIAWCIDA 243 Lambda K H 0.320 0.136 0.406 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: 216 Number of extensions: 14 Number of successful extensions: 5 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: 262 Length of database: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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 (21.8 bits) S2: 47 (22.7 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