Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_084936660.1 HA51_RS21730 fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_002095475.1:WP_084936660.1 Length = 278 Score = 152 bits (385), Expect = 6e-42 Identities = 94/267 (35%), Positives = 137/267 (51%), Gaps = 12/267 (4%) Query: 19 SDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNP--------RLGPCVAGT 70 S GI+R+ GA P L V L A S P R P V Sbjct: 15 SYGIVREEGVIDVGSRLGAECPDLKSLLQRGAVSDLEAFSSLPADHPYSAIRFLPVVENP 74 Query: 71 GKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIV 130 GK C+G+NY+D E T+ P +F++ ++ G L+ P +++ D+E EL ++ Sbjct: 75 GKVFCVGMNYADKRKEFAETLDA-PTLFVRFADSLAGHEQPLLKPATTQEFDYEGELAVI 133 Query: 131 IGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDE 190 IGK A V A+AL +VAGY D + R Q +T GK+ G GPW+ T DE Sbjct: 134 IGKAAYQVKAADALQHVAGYSCFMDATVRDMQFT---WFTAGKNWQQTGGFGPWMTTADE 190 Query: 191 VADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMG 250 + DPQ LA+ +N +Q+ +T +MV+ A ++ Y+S F L PGD+I TG+P GVG Sbjct: 191 IPDPQQLAIKTWLNEREVQNDTTASMVHPVAKIIEYISAFSPLSPGDVIITGSPGGVGKK 250 Query: 251 MKPPRYLKAGDVVELGIEGLGSQKQRV 277 PP ++ GDV+E+ IE +G + V Sbjct: 251 RTPPLFMFPGDVIEVEIEKIGRLRHTV 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: 234 Number of extensions: 15 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: 278 Length adjustment: 26 Effective length of query: 255 Effective length of database: 252 Effective search space: 64260 Effective search space used: 64260 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