Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_011385204.1 AMB_RS14215 FAA hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000009985.1:WP_011385204.1 Length = 340 Score = 171 bits (433), Expect = 2e-47 Identities = 97/255 (38%), Positives = 139/255 (54%), Gaps = 9/255 (3%) Query: 25 DLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHA 84 D + VS + AG ++ +L ET P VS L P + +G NY +H Sbjct: 79 DPASMVSLIRAGDFALAQARQLMQEGPETGPLVSEVRLLAPIPEPSRNVYAVGWNYLEHF 138 Query: 85 AE------TGATVPPEPIIFMKATSAIVGPNDDLVLPRG-SEKTDWEVELGIVIGKTAKY 137 E A +P P+ F KA + GP D + S DWE EL ++IGK K Sbjct: 139 KEGEAMRLKSADLPEHPVFFTKAVGTVNGPYDPIPYDAAVSTSIDWECELAVIIGKGGKN 198 Query: 138 VSEAEALDYVAGYCTVHDVSERAFQTERHG-QWTKGKSCDTFGPTGPWLVTKDEVADPQD 196 ++EA+A+ +V G+C ++D + R Q ++HG QW KGKS D GP GPW+V ++ D Sbjct: 199 IAEADAMKHVFGFCVINDTTARDVQQKKHGGQWFKGKSLDGHGPLGPWIVPASDI-DHTR 257 Query: 197 LAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRY 256 + + +VNG QD ST+ M + +++ LS ++L PGDII+TGTPPGVG KPP + Sbjct: 258 VHLITRVNGVVKQDASTEQMYFKVPRIIAELSAGLTLEPGDIIATGTPPGVGGARKPPEF 317 Query: 257 LKAGDVVELGIEGLG 271 LK GDV+E I +G Sbjct: 318 LKPGDVMETEIVEIG 332 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: 305 Number of extensions: 14 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: 281 Length of database: 340 Length adjustment: 27 Effective length of query: 254 Effective length of database: 313 Effective search space: 79502 Effective search space used: 79502 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: 48 (23.1 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