Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 5210291 Shew_2734 4-carboxymuconolactone decarboxylase (RefSeq)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__PV4:5210291 Length = 127 Score = 115 bits (287), Expect = 9e-31 Identities = 51/120 (42%), Positives = 78/120 (65%) Query: 266 RAAHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWGDIWSRPGLDHELRRLL 325 +A + QG+ +RR ++GD+ VDR+++ +DFT P Q+ +TR AWG++W+R GLD R L+ Sbjct: 3 KAKYDQGLAIRREVMGDSFVDRALSSASDFTQPLQELVTRNAWGEVWAREGLDRRTRSLI 62 Query: 326 TIAVLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGVPNSNLGFALGKQALAD 385 TIA L A+ EL H+R ALR G + I EVLLH++VY G+P F + +++ Sbjct: 63 TIATLAALKASTELKGHVRGALRNGCTVEEIQEVLLHSTVYCGMPAGVEAFRAANEVISE 122 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: 127 Number of extensions: 2 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: 400 Length of database: 127 Length adjustment: 22 Effective length of query: 378 Effective length of database: 105 Effective search space: 39690 Effective search space used: 39690 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: 45 (21.9 bits)
Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate 5209389 Shew_1860 alpha/beta hydrolase fold (RefSeq)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__PV4:5209389 Length = 277 Score = 104 bits (260), Expect = 3e-27 Identities = 75/241 (31%), Positives = 121/241 (50%), Gaps = 20/241 (8%) Query: 20 PVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPA-PDGPYSVRDLSEDVLAL 78 PV++L S + +MW PQ+A LS R + D HG S P G S++ L+E LAL Sbjct: 26 PVLLLGHSYLWDSAMWAPQLAHLSQHYRCIVPDLWAHGHSDVLPSGCRSLKHLAEHYLAL 85 Query: 79 LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERA------ 132 +DSL +D +GLS+GG L APRRV +L ++ F EP+ + RA Sbjct: 86 MDSLEIDEFSILGLSVGGMWGTELTLMAPRRVKTLVMMGCFLGF-EPE--VSRAKYYAML 142 Query: 133 ----AASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCD---- 184 AA R PE L + + +FS+ + ++ PE + ++ +AS +PE + Sbjct: 143 DAMTAAGRL--PEPLIEQIAPLFFSDNVEQKQPELIASFKASLASIAPERLESISRLGRI 200 Query: 185 ALADWDFTADLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQ 244 D D+ +++ PTL++ G +D +P ++ D I + F + A H++ LEQ Sbjct: 201 IFGRRDIMEDIEQLTLPTLIMTGTQDKPSPVLEAYLMHDAIDGSEFLHIPEAGHISTLEQ 260 Query: 245 A 245 + Sbjct: 261 S 261 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: 269 Number of extensions: 14 Number of successful extensions: 4 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: 277 Length adjustment: 28 Effective length of query: 372 Effective length of database: 249 Effective search space: 92628 Effective search space used: 92628 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