Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39 (characterized)
to candidate GFF1907 PGA1_c19370 4-hydroxy-2-oxovalerate aldolase BphF
Query= SwissProt::O05151 (258 letters) >FitnessBrowser__Phaeo:GFF1907 Length = 254 Score = 224 bits (571), Expect = 1e-63 Identities = 118/253 (46%), Positives = 160/253 (63%), Gaps = 1/253 (0%) Query: 1 MQSPINSFKKALAEGRTQIGFWLALGDAYSAEVCAGAGFDWLLIDGEHAPQDLRSVLAQL 60 MQ+P N FK A+A G Q+G W +G E+ GAGF+W+L+D EHA + VL L Sbjct: 1 MQNPKNRFKSAIANGTRQLGVWNTIGGNTVPELLGGAGFEWVLVDCEHAAIETIEVLPAL 60 Query: 61 QVIGAYRDCHAAVRVPSADTTVIKQYLDLGAQSLLVPMVDTADEAAAVVRACRYPPGGIR 120 Q IG D A VRV + D T+ K+ LD+GAQ+++VP V TA EAAA V A RY P G+R Sbjct: 61 QAIGQNPDTSAVVRVAANDATLFKRVLDMGAQNVMVPYVQTAREAAAAVHAMRYGPHGMR 120 Query: 121 GVGG-ARASRWGRYPRYLHEADEQVCVVVQAETALALSNLEAIAEVDGIDGVFIGTADLA 179 G+ G RA+R+G+ Y A++++C++VQ ET L NL+AIA DG+D VFIG ADL+ Sbjct: 121 GMAGMTRATRYGKVDDYFDVAEDELCLIVQVETQTGLENLDAIAGTDGVDAVFIGPADLS 180 Query: 180 ASLGFPGNPAHPEVQDAILDALQRVRAAGKAPGVLTPVEDLAQKYLAHGAVFVAVGIDTH 239 AS+G G HP+V A+ +A+ R+ G GV+ D+A +YLA GA FVAV +D Sbjct: 181 ASMGLRGQMTHPDVDKAVSNAINRLGEMGVPAGVMALDPDIADRYLALGATFVAVAVDLV 240 Query: 240 LLAKQTSALAARF 252 +LA S + RF Sbjct: 241 VLADAVSNIRNRF 253 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: 176 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: 258 Length of database: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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