Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF1785 PS417_09080 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__WCS417:GFF1785 Length = 270 Score = 89.0 bits (219), Expect = 1e-22 Identities = 80/250 (32%), Positives = 115/250 (46%), Gaps = 24/250 (9%) Query: 20 PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPA-PDGPYSVRDLSEDVLAL 78 PVV+L S + MW PQI ALS + RV+ + GHGES + P S+ DL+ L L Sbjct: 20 PVVLLGSSYLWDADMWSPQIEALSQQYRVIVPELWGHGESASLPAQTRSLDDLARQALTL 79 Query: 79 LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQA----------W 128 +D L + + VGLS+GG L AP R+ SL L+ T EP+A Sbjct: 80 IDQLDIAQINLVGLSVGGMWGARLALRAPERINSLVLMDTYLG-AEPEATRQYYFSLFKM 138 Query: 129 IERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALAD 188 IE A A PE L D V +F G+ R+ + +R+ + S E L Sbjct: 139 IEDAGAI----PEPLLDVVAPIFFRPGI-DRESALYQDFRKQLQGYSKERLLQSIVPLGR 193 Query: 189 WDFTAD-----LSRISA-PTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANL 242 F+ + L R+ A TLV+ GE+D PP+ + +A G+ ++ A H++ Sbjct: 194 LIFSREDILEQLPRLDADTTLVMCGEQDKPRPPAESEEMA-GLIGCSLILIPEAGHISAR 252 Query: 243 EQAGAVTALL 252 E V L Sbjct: 253 ENPDFVNEAL 262 Lambda K H 0.318 0.132 0.392 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: 241 Number of extensions: 14 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: 400 Length of database: 270 Length adjustment: 28 Effective length of query: 372 Effective length of database: 242 Effective search space: 90024 Effective search space used: 90024 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: 41 (21.7 bits) S2: 49 (23.5 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