Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39 (characterized)
to candidate 3609762 Dshi_3145 HpcH/HpaI aldolase (RefSeq)
Query= SwissProt::O05151 (258 letters) >FitnessBrowser__Dino:3609762 Length = 253 Score = 143 bits (360), Expect = 4e-39 Identities = 93/247 (37%), Positives = 125/247 (50%), Gaps = 4/247 (1%) Query: 6 NSFKKALAEGRTQIGFWLALGDAYSAEVCAGAGFDWLLIDGEHAPQDLRSVLAQLQVIGA 65 N + LA+ + WL++ Y AE GFD + +D +H + ++ LQ I A Sbjct: 4 NKLRTLLAQDTPIVNAWLSIPSGYVAEGAGHQGFDSVTVDLQHGLIGFETAVSMLQAISA 63 Query: 66 YRDCHAAVRVPSADTTVIKQYLDLGAQSLLVPMVDTADEAAAVVRACRYPPGGIRGVGGA 125 + VR PS VI LD GA ++ PM+ T +EAAA V ACRYPP G R G A Sbjct: 64 -TEAVPLVRSPSKAPEVIMHLLDAGAYGVICPMISTPEEAAAFVAACRYPPQGSRSFGPA 122 Query: 126 RASRWGRYPRYLHEADEQVCVVVQAETALALSNLEAIAEVDGIDGVFIGTADLAASLG-F 184 R +G P Y A+ ++ + ETA A+ +EAI V G+D +++G DLA LG Sbjct: 123 RGKLYGG-PDYFEAANAEILAIPMIETAEAVDRIEAILAVPGVDMIYVGPNDLALDLGEG 181 Query: 185 PGNPAHPE-VQDAILDALQRVRAAGKAPGVLTPVEDLAQKYLAHGAVFVAVGIDTHLLAK 243 PG HP DAI L R RAAG A G+ L+++ LA G V G D +LL Sbjct: 182 PGAEWHPRATTDAIAHVLDRARAAGVATGIFCGDGALSRQRLAEGFDLVTPGNDFNLLMG 241 Query: 244 QTSALAA 250 SA A Sbjct: 242 AMSAAIA 248 Lambda K H 0.320 0.135 0.400 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: 186 Number of extensions: 12 Number of successful extensions: 4 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: 258 Length of database: 253 Length adjustment: 24 Effective length of query: 234 Effective length of database: 229 Effective search space: 53586 Effective search space used: 53586 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