Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate AZOBR_RS04805 AZOBR_RS04805 dihydrolipoyllysine acetyltransferase
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__azobra:AZOBR_RS04805 Length = 377 Score = 91.3 bits (225), Expect = 4e-23 Identities = 85/255 (33%), Positives = 122/255 (47%), Gaps = 34/255 (13%) Query: 19 APVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSEDVLAL 78 A V+L+ G + W I AL+ V A+D GHG+S ++ LS+ V Sbjct: 136 ATTVLLVHGFGGDLDNWLFTIDALAEGATVYALDLPGHGQSAKTLPDPTLTGLSKAVRDF 195 Query: 79 LDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE-PQAWIER--AAAS 135 +D++G++AAH VG SMGGA++ AP RV+SLSL+C+A E Q +I A S Sbjct: 196 MDAVGIEAAHLVGHSMGGAVSMRTALDAPERVVSLSLICSAGLGREINQDYIAGFIDATS 255 Query: 136 RTDGPESL----ADA-VVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWD 190 R D L ADA +V+R ++ L K Y+ + +G A+A Sbjct: 256 RRDLKPVLETLFADAGLVSRQMTDDLLK--------YKRL------DGVDGALRAIASSM 301 Query: 191 F-----TADLSR----ISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVAN 241 F TA L PTLV+ G ED P + L + AR EV+ A H+ Sbjct: 302 FENGEQTALLGEAVGAAKVPTLVVWGAEDRVIPAAHATALG---SAARVEVVPKAGHMVQ 358 Query: 242 LEQAGAVTALLREHI 256 +E AG V LL++H+ Sbjct: 359 MEAAGTVNTLLKDHV 373 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: 377 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 377 Length adjustment: 30 Effective length of query: 370 Effective length of database: 347 Effective search space: 128390 Effective search space used: 128390 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 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