Align 2-dehydro-3-deoxy-D-arabinonate dehydratase (EC 4.2.1.141) (characterized)
to candidate Ga0059261_2636 Ga0059261_2636 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= BRENDA::Q4J7I6 (292 letters) >FitnessBrowser__Korea:Ga0059261_2636 Length = 284 Score = 69.3 bits (168), Expect = 9e-17 Identities = 53/172 (30%), Positives = 86/172 (50%), Gaps = 23/172 (13%) Query: 126 GHGEAIVVRSDSEWTLPEPELAVVI----------DSRGKILGYTILDDVSARDLEADNP 175 G + + + DS+ T E EL +VI D+ + GY +++DVS R + + Sbjct: 107 GPNDPVTIPKDSKKTDWEVELGIVIGTAAHNVSEADALDHVAGYCVVNDVSERHWQTERG 166 Query: 176 LYLPQSKIYYGCCAFGPFIVTPDEVGNPYSLDIRLKIMREGRVLFEGSVNTNKMRRKIEE 235 + + K + GP++VT DEVG+P +L + L + G+ + +G NT M + + Sbjct: 167 MTWDKGKGFPTFGPIGPWMVTADEVGDPQNLSMWLSV--NGKKVQDG--NTRTMIFTVAQ 222 Query: 236 QIQYLLRDNPVPDGTILTTGTAIIPGKDKG-------LRHGDVVEISITKLG 280 + YL + + G ++TTGT PG G L+ GDVVE+ I KLG Sbjct: 223 IVSYLSQIMTLLPGDVITTGTP--PGVGLGQKPEPWYLKAGDVVELGIEKLG 272 Lambda K H 0.319 0.140 0.413 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: 217 Number of extensions: 9 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: 292 Length of database: 284 Length adjustment: 26 Effective length of query: 266 Effective length of database: 258 Effective search space: 68628 Effective search space used: 68628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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