Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate 8501583 DvMF_2302 Dimethylmenaquinone methyltransferase (RefSeq)
Query= SwissProt::A5W059 (238 letters) >FitnessBrowser__Miya:8501583 Length = 225 Score = 137 bits (345), Expect = 2e-37 Identities = 79/217 (36%), Positives = 122/217 (56%), Gaps = 3/217 (1%) Query: 15 IQRAELDSIDALGRLGVATVHEAQNRKGLLSSKMRPIQQGTSLAGSAVTVLVAPGDNWMF 74 I R + +DA + V+ + +A NR + S++RP+ + L G+A+TV V GDN +F Sbjct: 12 ITRPDAALVDAFRSIPVSNIGDAMNRMACMHSRIRPMNRAP-LLGTALTVRVRVGDNLLF 70 Query: 75 HVAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDAGVRDTQTLRDMGFA 134 + A++ RPGDVLVV+ G + T ++ RG+ L+VD +RD + + M F Sbjct: 71 NKAMDMARPGDVLVVNAHDEQFYSIVGGQMTTWMKQRGLAGLVVDGCIRDAEEIEAMDFP 130 Query: 135 VWARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVVRRDECESTLVAAAE 194 V+A I+ G +KE G VN P+ CGG ++NPGDIV D DG+VV+ + + L A Sbjct: 131 VYATGISPNGPMKEGGGEVNFPIACGGLVVNPGDIVAGDRDGIVVISPADAPAVLERA-- 188 Query: 195 RAGLEEEKRLRLAAGELGLDIYKMRERLEAKGLRYVD 231 RA E+E R+ A + D + + L+ KG +VD Sbjct: 189 RAMAEKETRVMAAIADGTWDRTWVDKMLKEKGCAFVD 225 Lambda K H 0.318 0.136 0.390 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: 144 Number of extensions: 10 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: 238 Length of database: 225 Length adjustment: 23 Effective length of query: 215 Effective length of database: 202 Effective search space: 43430 Effective search space used: 43430 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