Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate 206303 DVU0875 fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >MicrobesOnline__882:206303 Length = 259 Score = 151 bits (381), Expect = 2e-41 Identities = 80/205 (39%), Positives = 121/205 (59%), Gaps = 10/205 (4%) Query: 67 VAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVE 126 V K +C+GLNY HA E G VP EP+ F+KA +AI+G + +VLP + D+E E Sbjct: 45 VVAPSKVVCVGLNYRGHAGELGMDVPDEPVFFLKAPTAIIGTGEPIVLPPAVGRVDYEGE 104 Query: 127 LGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLV 186 L +V+GK + ++ +A +++ G+ +DV+ R Q +R G + + K DTF P GPW+ Sbjct: 105 LALVVGKQCRNITPEQAREHIFGFTCANDVTARDIQ-KRDGLFGRCKGYDTFCPVGPWIE 163 Query: 187 TKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPG 246 T E DP +L + VNGE Q G+T M+ L+S +S+ M+L PGD++ TGTP G Sbjct: 164 TALE--DPGNLTLRTVVNGEVRQQGNTADMLVHPFELLSSISRVMTLLPGDLVLTGTPEG 221 Query: 247 VGMGMKPPRYLKAGDVVELGIEGLG 271 +G + AGD V + I+ +G Sbjct: 222 IGP-------IHAGDEVRVEIDEVG 239 Lambda K H 0.315 0.136 0.408 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: 245 Number of extensions: 16 Number of successful extensions: 3 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: 281 Length of database: 259 Length adjustment: 25 Effective length of query: 256 Effective length of database: 234 Effective search space: 59904 Effective search space used: 59904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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