Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate AZOBR_RS02000 AZOBR_RS02000 5-carboxymethyl-2-hydroxymuconate isomerase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__azobra:AZOBR_RS02000 Length = 227 Score = 115 bits (287), Expect = 1e-30 Identities = 76/224 (33%), Positives = 110/224 (49%), Gaps = 18/224 (8%) Query: 53 TLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEP-IIFMKATSAIVGPNDD 111 T+P G+P + C+G NY+ HA E GA EP FMK AIV Sbjct: 12 TVPVAGGDP------FPVRRIYCVGRNYAAHAREMGADPDREPPFFFMKPADAIVADGTA 65 Query: 112 LVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQT--ERHGQ- 168 ++ P + E+EL + IG + + ALD+V GY D++ R Q ++ G+ Sbjct: 66 ILYPPRTANLHHEIELVVAIGTGGRDIPVERALDHVYGYGVGLDMTRRDLQNAAKKEGKP 125 Query: 169 WTKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLS 228 W GK D P G L ++ P ++ L VNGE Q G +++ + +SYLS Sbjct: 126 WDMGKGFDQSAPCGT-LRRAADIGHPDKGSVTLSVNGELRQKGDLADLIWSVSETISYLS 184 Query: 229 QFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGS 272 + L+PGD+I TGTP GVG + AGD +E +EG+GS Sbjct: 185 GLVELQPGDLIYTGTPEGVGP-------VVAGDRLEGAVEGVGS 221 Lambda K H 0.315 0.136 0.408 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: 235 Number of extensions: 22 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: 281 Length of database: 227 Length adjustment: 24 Effective length of query: 257 Effective length of database: 203 Effective search space: 52171 Effective search space used: 52171 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: 42 (22.0 bits) S2: 46 (22.3 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