Align 2-dehydro-3-deoxy-D-arabinonate dehydratase (EC 4.2.1.141) (characterized)
to candidate 3609154 Dshi_2542 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (RefSeq)
Query= BRENDA::Q97UA0 (298 letters) >FitnessBrowser__Dino:3609154 Length = 308 Score = 69.7 bits (169), Expect = 8e-17 Identities = 61/188 (32%), Positives = 88/188 (46%), Gaps = 19/188 (10%) Query: 120 IFFKATPNRCVGHG-EAIAVRSDSEWTLPEPELAVVLDSNGK----------ILGYTIMD 168 ++F VGHG + + S SE E ELAVV+ + G+ + GYTI++ Sbjct: 123 VYFTKPATAVVGHGGDVLIFPSVSEKIDYEVELAVVIGTTGRDIPKDRAFAHVFGYTILN 182 Query: 169 DVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEGS 228 D++ARD++ + + K G C GP IVT+DEI +P L I+L + E R + Sbjct: 183 DITARDVQRRHGGQYFKGKSLDGSCPIGPWIVTADEITDPQDLSISLSVNGELR----QN 238 Query: 229 VNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPG----RDKGLKDEDIVEITISNI 284 T+ M I I L + G I+ TGT G + LK D V I+NI Sbjct: 239 GWTHDMIFDIPTLIASLSEGLTLEPGDIIATGTPSGVGYAMDPPQYLKPGDTVICDIANI 298 Query: 285 GTLITPVK 292 G L V+ Sbjct: 299 GQLKNTVR 306 Lambda K H 0.319 0.139 0.400 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: 11 Number of successful extensions: 1 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: 298 Length of database: 308 Length adjustment: 27 Effective length of query: 271 Effective length of database: 281 Effective search space: 76151 Effective search space used: 76151 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: 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