Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Pf1N1B4_549 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_549 Length = 267 Score = 103 bits (258), Expect = 4e-27 Identities = 76/241 (31%), Positives = 117/241 (48%), Gaps = 11/241 (4%) Query: 22 VVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSEDVLALLDS 81 ++L+ LGS+ W+ QI ALS RV+ D RGHG S P YS+ S D++AL++ Sbjct: 22 LLLVHGLGSSTLDWEMQIPALSAHYRVIVPDVRGHGRSDKPRERYSIAGFSADLIALIEH 81 Query: 82 LGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCT--AAKFGEPQAW---IERAAASR 136 L + H+VGLSMGG I L P+ + SL ++ + K +P + I+R + +R Sbjct: 82 LHLGPTHYVGLSMGGIIGFQLAVDQPQLLKSLCIVNSQPQVKMQKPSDYWWLIKRWSMAR 141 Query: 137 TDGPESLADAVVARWFSEGLAKRDPEFVRH-YREMIASTSPEGYAACCDALADWDFTADL 195 E++ A+ F K D +R A Y A DAL W L Sbjct: 142 LLSMETIGKALGRMLF----PKPDQADLRQKIAVRWAKNHKHAYLASFDALIGWGVQERL 197 Query: 196 SRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLREH 255 SR++ PTL+++ + D TP SV + + +AR V++ + H L+Q L E Sbjct: 198 SRVTCPTLIVSADHD-YTPVSVKETYVKLLPDARLVVIADSRHATPLDQPERFNQTLLEF 256 Query: 256 I 256 + Sbjct: 257 L 257 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: 232 Number of extensions: 10 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: 267 Length adjustment: 28 Effective length of query: 372 Effective length of database: 239 Effective search space: 88908 Effective search space used: 88908 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: 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