Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate PfGW456L13_3411 Fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3411 Length = 294 Score = 129 bits (325), Expect = 6e-35 Identities = 88/239 (36%), Positives = 131/239 (54%), Gaps = 11/239 (4%) Query: 45 ELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSA 104 ++ +L E LP +S L P G+ F +GLNY H G+ P P+ +MK SA Sbjct: 44 DILDLADEWLP-LSAARLLAPLEPGSRVF-GVGLNYLSHLKRLGSDAPAHPLAYMKPESA 101 Query: 105 IVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSER--AFQ 162 +VG +D++ + + D+EVEL V+G+ + E A D + GY +D+S R Q Sbjct: 102 LVGADDEIDYSPLTTQLDYEVELVAVVGRPL--LDEPHASDCLLGYTVGNDISARDAGKQ 159 Query: 163 TERHGQWTKGKSCDTFGPTGPWLVTKDE--VADPQDLAMWLKVNGETMQDGSTKTMVYGA 220 R T+ K+ D P GPW+VT DE VA L M L VN E Q +T+ M++ Sbjct: 160 IGRLDLLTQ-KAMDRATPVGPWIVTVDELGVAGQPALEMRLSVNDELRQQDNTRQMIFSL 218 Query: 221 AHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRA 279 L++YL +SLRPGD++ TG+ GV G++ R+L++GD VE IEG+G + + A Sbjct: 219 DELLNYLDARISLRPGDLVFTGSTHGV--GLESGRFLQSGDRVEAQIEGIGRLRNTIAA 275 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: 263 Number of extensions: 17 Number of successful extensions: 4 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: 294 Length adjustment: 26 Effective length of query: 255 Effective length of database: 268 Effective search space: 68340 Effective search space used: 68340 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 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