Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF3551 PS417_18185 5-carboxymethyl-2-hydroxymuconate isomerase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__WCS417:GFF3551 Length = 283 Score = 188 bits (477), Expect = 1e-52 Identities = 109/281 (38%), Positives = 158/281 (56%), Gaps = 6/281 (2%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAG---ALDPSKLDELANLDVETLPAV 57 MKL + G+ G++ D +I DL S A A+ ++L EL + LP V Sbjct: 1 MKLASFIVHGRTTYGVVEGDQLI-DLESVKSTFGADLKQAIAANRLGELTPAVLAPLPRV 59 Query: 58 S-GNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPR 116 + P +A GK +CIG+NY+ H ETG +P P+IF + + V ++ P+ Sbjct: 60 PLADVTFLPVIANPGKVLCIGINYATHVRETGRDMPTYPMIFTRFADSQVAHLQPIIRPK 119 Query: 117 GSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCD 176 S K D+E EL +VIGKTA++V+ A+ALDYVAGY +D S R +Q Q+ GK+ Sbjct: 120 VSHKLDFEGELAVVIGKTARHVNAADALDYVAGYACYNDGSVRDWQKHTL-QFVPGKNFP 178 Query: 177 TFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPG 236 G GPW+VT DE+ DPQ+L + ++NGE MQ T M++ L+ Y S F L PG Sbjct: 179 QTGGFGPWMVTHDEINDPQELELTTRLNGEVMQHTRTSDMIFDVRQLIEYCSTFTELAPG 238 Query: 237 DIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRV 277 D+I +GT GVG +PP ++K GD VE+ I G+G + + Sbjct: 239 DVIVSGTTGGVGAFREPPVWMKPGDTVEVEITGIGRLRNSI 279 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: 274 Number of extensions: 12 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: 281 Length of database: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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