Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate WP_086508611.1 BZY95_RS03565 carboxymuconolactone decarboxylase
Query= BRENDA::Q0SH24 (400 letters) >NCBI__GCF_002151265.1:WP_086508611.1 Length = 399 Score = 213 bits (543), Expect = 6e-60 Identities = 130/387 (33%), Positives = 198/387 (51%), Gaps = 14/387 (3%) Query: 4 ALAHEISGPRSGAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGES---P 60 ++A+ + GP + P+VVL LG ++++WD + AL RV+ D GHG S P Sbjct: 10 SVAYRLLGPEA----LPLVVLAHPLGMSQAVWDELLPALLPRYRVLTWDLPGHGASQAWP 65 Query: 61 APDGPYSVRDLSEDVLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAA 120 A G + L+ + LAL++ GV HFVG S+GG + Q L + R+ S++L T A Sbjct: 66 AEGGEITPAALAREALALVEHAGVSRFHFVGTSIGGVVGQQLISEHAERLYSITLTNTGA 125 Query: 121 KFGEPQAWIERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYA 180 G + W RA R +G ++A+ +V RWF+ + +P + + E YA Sbjct: 126 VIGNAELWSTRAERIRQEGLAAMAEEIVPRWFAPACFEAEPALKAGWCTQMGRGDDESYA 185 Query: 181 ACCDALADWDFTADLSRISA--PTL---VIAGEEDPSTPPSVMQILADGITEARFEVLSP 235 C+ L DF L A P + ++ G D +TPP +Q LA A E+L Sbjct: 186 RLCEMLGRTDFRGKLKGPLAEHPDIGVHLLGGSADVATPPETLQALAAECGGAPLEILEG 245 Query: 236 AAHVANLEQAGAVTALLREHIVGAGYARGRR-AAHAQGMTVRRSILGDAHVDRSVAGTTD 294 AHV ++E A+ L + G ++A G+ R+ +LG+ HV R+ Sbjct: 246 IAHVPSVEAPAAMAKRLLLWMASEREDVGEHGVSYADGLETRKQVLGEEHVARASRNANS 305 Query: 295 FTAPFQDFITRTAWGDIWSRPGLDHELRRLLTIAVLTAVGNEHELDMHIRAALRAGVDAD 354 APFQ ITR AWG++WS L R L+T +L A+G E EL +H++ A R G+ Sbjct: 306 LDAPFQQMITRLAWGELWSNDDLTRRERSLITTGILAALGRE-ELVLHLKTAKRIGLSEA 364 Query: 355 TIGEVLLHTSVYAGVPNSNLGFALGKQ 381 + +VL+H ++YAGVP +N FAL K+ Sbjct: 365 ELRQVLMHVAIYAGVPAANHAFALAKE 391 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: 422 Number of extensions: 21 Number of successful extensions: 5 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: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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