Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_011339098.1 RSPH17029_RS19735 fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000015985.1:WP_011339098.1 Length = 232 Score = 103 bits (258), Expect = 3e-27 Identities = 68/206 (33%), Positives = 100/206 (48%), Gaps = 11/206 (5%) Query: 75 CIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKT 134 CIG NY H E A P+IFMK A+V ++ P +E +E EL +V+ Sbjct: 30 CIGKNYVAHIREMNADERDPPVIFMKPADAVVRNGGEIPYPVFTENFHYECELVVVLKSG 89 Query: 135 AKYVSEAEALDYVAGYCTVHDVSERAFQ---TERHGQWTKGKSCDTFGPTGPWLVTKDEV 191 +S A+A ++ GY D++ R Q E+ W K+ D P GP + +E Sbjct: 90 GYNISVADAASHIYGYAVGLDMTRRDHQKGVLEKGLPWEVTKAFDLSAPIGP-VTRAEEC 148 Query: 192 ADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGM 251 + LKVNGE QD M++ +++ LS+ L+PGDII TGTP GVG Sbjct: 149 GVLTSGQLTLKVNGEVKQDADIGLMIWKVDEIIAKLSEQHRLQPGDIIMTGTPAGVGA-- 206 Query: 252 KPPRYLKAGDVVELGIEGLGSQKQRV 277 + GDV++ +EGL + R+ Sbjct: 207 -----VVTGDVLDCTMEGLEPMQVRI 227 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: 195 Number of extensions: 10 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: 281 Length of database: 232 Length adjustment: 24 Effective length of query: 257 Effective length of database: 208 Effective search space: 53456 Effective search space used: 53456 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: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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