Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate Echvi_2939 Echvi_2939 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Cola:Echvi_2939 Length = 285 Score = 323 bits (828), Expect = 3e-93 Identities = 159/279 (56%), Positives = 197/279 (70%), Gaps = 3/279 (1%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANL---DVETLPAV 57 MKLLR+G PG+EKPG+ ++GI D S D L L+ L + P + Sbjct: 1 MKLLRFGNPGEEKPGIEKANGIRIDCSAFGEDWTEDFLTQDGLNRLTTWLESNEAKCPEI 60 Query: 58 SGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRG 117 S RLGP + K ICIGLNY HA ETGA VP +PIIFMK+T+++ GPNDD+++PR Sbjct: 61 SSEVRLGPPIKRPSKIICIGLNYKLHAKETGAEVPKQPIIFMKSTTSLSGPNDDIIIPRN 120 Query: 118 SEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDT 177 SEKTDWEVEL ++IGK A YV + A+DYVAGYC ++DVSER FQ GQW KGKS DT Sbjct: 121 SEKTDWEVELAVMIGKKASYVDKENAMDYVAGYCLLNDVSERDFQLSHGGQWVKGKSNDT 180 Query: 178 FGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGD 237 F P GP+LVTKDE+ DPQ L +WLK NG+ +QD +T MV+ LVS+LS +M+L PGD Sbjct: 181 FSPLGPYLVTKDEIKDPQHLRLWLKHNGKMLQDSNTSDMVFDIPTLVSHLSNYMTLLPGD 240 Query: 238 IISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQR 276 IISTGTP GVGMG+ PP YLK GDVVELGI+GLG+ +Q+ Sbjct: 241 IISTGTPSGVGMGLTPPTYLKEGDVVELGIDGLGTSRQK 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: 322 Number of extensions: 8 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: 285 Length adjustment: 26 Effective length of query: 255 Effective length of database: 259 Effective search space: 66045 Effective search space used: 66045 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