Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_068463213.1 APY04_RS12630 FAA hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_001541235.1:WP_068463213.1 Length = 282 Score = 338 bits (867), Expect = 8e-98 Identities = 161/277 (58%), Positives = 200/277 (72%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60 MKL+R+G+PG EKPGL+ S G IRDLS HV D L P+ LD+L +D +LP V Sbjct: 1 MKLVRFGQPGSEKPGLIDSQGKIRDLSAHVDDFTGANLSPATLDKLRAIDPASLPEVPAG 60 Query: 61 PRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEK 120 RLG VAGT FI IGLNY DHA ETG +P EPI+F KA S I GPNDD++ P+ SE Sbjct: 61 TRLGAPVAGTRNFIAIGLNYVDHAKETGQEIPAEPILFNKAPSCICGPNDDIMYPKNSEH 120 Query: 121 TDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGP 180 DWEVE+ VIG A+YV E +AL ++AGYC +DVSER+FQ +R GQW KGKS +TFGP Sbjct: 121 MDWEVEIAFVIGSRARYVEEKDALAHIAGYCLCNDVSERSFQVKRAGQWVKGKSAETFGP 180 Query: 181 TGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIS 240 GPWLVT D++AD Q+LA+ L VNGE Q G+T TM++ A L+SY+SQFM L PGD+++ Sbjct: 181 LGPWLVTPDDIADVQNLALTLDVNGERKQTGNTSTMIFTIAQLLSYISQFMVLEPGDVVT 240 Query: 241 TGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRV 277 TGTPPGVG KP +LKAGD V L I+GLG Q+ ++ Sbjct: 241 TGTPPGVGSARKPREFLKAGDEVVLRIDGLGEQRAKI 277 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: 327 Number of extensions: 10 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: 282 Length adjustment: 26 Effective length of query: 255 Effective length of database: 256 Effective search space: 65280 Effective search space used: 65280 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