Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_011841246.1 RSPH17029_RS09140 FAA hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000015985.1:WP_011841246.1 Length = 281 Score = 422 bits (1086), Expect = e-123 Identities = 203/281 (72%), Positives = 234/281 (83%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60 MKLLR+G G E+PGL+ +DG +RDLSG V D+A L L +L ++D +LP V+ Sbjct: 1 MKLLRHGPAGAERPGLVWTDGTLRDLSGVVPDIAGEVLTDEGLAKLRDIDGASLPVVAEG 60 Query: 61 PRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEK 120 RLGPCVAGT KF+CIGLNYSDHAAETGA VPPEPIIFMKA SAI GPND +++PRGS K Sbjct: 61 TRLGPCVAGTTKFVCIGLNYSDHAAETGAQVPPEPIIFMKANSAICGPNDPIIIPRGSVK 120 Query: 121 TDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGP 180 TDWEVEL I+IGK AKYVSEAEALD+VAGY +DVSERAFQ+ER GQWTKGKSCD FG Sbjct: 121 TDWEVELAIIIGKKAKYVSEAEALDHVAGYAVANDVSERAFQSERSGQWTKGKSCDNFGQ 180 Query: 181 TGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIS 240 GPWLVT+DEVADPQ+L +WL VNGE MQ+G+T TMVYG A+LVSYLSQFM+L PGD+IS Sbjct: 181 LGPWLVTRDEVADPQNLPLWLSVNGEKMQNGTTGTMVYGVAYLVSYLSQFMTLHPGDVIS 240 Query: 241 TGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRADA 281 TGTPPGVG+GMKPPR+LK GDVVELG+EGLG Q+Q V ADA Sbjct: 241 TGTPPGVGLGMKPPRFLKPGDVVELGVEGLGQQRQEVVADA 281 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: 407 Number of extensions: 8 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: 281 Length of database: 281 Length adjustment: 26 Effective length of query: 255 Effective length of database: 255 Effective search space: 65025 Effective search space used: 65025 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 Sep 24 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