Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF47 HP15_47 fumarylacetoacetate (FAA) hydrolase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Marino:GFF47 Length = 288 Score = 130 bits (326), Expect = 4e-35 Identities = 83/221 (37%), Positives = 120/221 (54%), Gaps = 14/221 (6%) Query: 65 PCVAGTGKFICIGLNYSDHAAETGATVPP-EPIIFMKATSAIVGPNDDLVLPRGSEKTDW 123 P + + + G NY H + + PP +PI F+KA A++G +D + P +E+ D+ Sbjct: 64 PPIEPVNRVVVAGANYLKHLKDDFSLEPPKQPIAFLKAYGALIGADDPIRFPPLTEELDY 123 Query: 124 EVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKG------KSCDT 177 EVEL +VIG +K V + D V GY +DVS R Q R G G KS D Sbjct: 124 EVELVVVIG--SKEVDTTKPYDSVLGYTVGNDVSARDLQ--RSGPKGIGMDLFAAKSQDK 179 Query: 178 FGPTGPWLVTKDEVADPQD-LAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPG 236 GPW+VT+DE + L + L VNGE QDG+T M + A L++++ + S G Sbjct: 180 TTGLGPWIVTRDEFPEGMPALRLTLSVNGEVRQDGNTSEMTWTVAELITFVHERSSFACG 239 Query: 237 DIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRV 277 D++ TG+P GVGM R+L GDVVE +EG+G+ + V Sbjct: 240 DVLFTGSPAGVGMA--TGRFLNPGDVVEASVEGVGTLRNVV 278 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: 271 Number of extensions: 16 Number of successful extensions: 5 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: 288 Length adjustment: 26 Effective length of query: 255 Effective length of database: 262 Effective search space: 66810 Effective search space used: 66810 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 Apr 09 2024. 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