Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF1326 PS417_06740 4-carboxymuconolactone decarboxylase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__WCS417:GFF1326 Length = 132 Score = 119 bits (298), Expect = 5e-32 Identities = 56/118 (47%), Positives = 78/118 (66%) Query: 269 HAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWGDIWSRPGLDHELRRLLTIA 328 +A+G+ VRR +LGDAHVDRS+ T+F + FQ+ ITR AWGDIW+RPGL R L+TIA Sbjct: 7 YAEGLQVRREVLGDAHVDRSLNALTEFNSEFQEMITRHAWGDIWTRPGLPRHTRSLITIA 66 Query: 329 VLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGVPNSNLGFALGKQALADL 386 +L + EL +H+RAA GV I EVL+ +++Y G+P +N F L + +L Sbjct: 67 MLIGMNRSEELKLHLRAAASNGVTRAEIKEVLMQSAIYCGIPAANATFHLAESVWDEL 124 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: 121 Number of extensions: 5 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: 132 Length adjustment: 22 Effective length of query: 378 Effective length of database: 110 Effective search space: 41580 Effective search space used: 41580 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: 46 (22.3 bits)
Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate GFF4008 PS417_20530 3-oxoadipate enol-lactonase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__WCS417:GFF4008 Length = 267 Score = 113 bits (283), Expect = 6e-30 Identities = 77/240 (32%), Positives = 118/240 (49%), Gaps = 9/240 (3%) Query: 22 VVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSEDVLALLDS 81 ++L+ LGS+ W+ QI L+ R++ VD RGHG S P YS++ + D+LAL++ Sbjct: 22 LILIHGLGSSSQDWELQIPVLARHYRLIVVDVRGHGRSDKPRERYSIQGFTLDLLALIEH 81 Query: 82 LGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQA-----WIERAAASR 136 L + AAH VGLSMGG IA L P +V SL ++ +A + A W +R + +R Sbjct: 82 LDLPAAHVVGLSMGGMIAFQLAVDEPAQVKSLCIVNSAPEVKVRSADDYWQWAKRWSLAR 141 Query: 137 TDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTADLS 196 ++ A+ R F + + + R E A Y A DA+ W LS Sbjct: 142 VLSLATIGKALGDRLFPK---PQQADLRRKMAERWAKNDKRAYLASFDAIVGWGVQERLS 198 Query: 197 RISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLREHI 256 RI+ PTLVI+ + D TP + + + AR V+ + H L+Q A L + + Sbjct: 199 RITCPTLVISADHD-YTPVAQKENYVKLLPNARLVVIEDSRHATPLDQPEVFNATLLDFL 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: 233 Number of extensions: 11 Number of successful extensions: 2 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