Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate BWI76_RS05690 BWI76_RS05690 fumarylacetoacetate (FAA) hydrolase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Koxy:BWI76_RS05690 Length = 282 Score = 166 bits (421), Expect = 4e-46 Identities = 108/292 (36%), Positives = 158/292 (54%), Gaps = 25/292 (8%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDP---SKLDELANLDV-ETLPA 56 MKLL + + K GL +DG+I DL AL P S L+ L +L + +TLP Sbjct: 1 MKLLSFRVNDKNKYGLATADGVI-DLQ---------ALFPQYGSLLEFLPHLHLLDTLPP 50 Query: 57 VSGNPRLG-------PCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPN 109 + P + K IC G+NY D G P P++F++ + G Sbjct: 51 SAKKTHYSFNEIAFLPVITEPKKIICAGVNYRDKNV-VGNEKPANPVLFIRFADSQTGHL 109 Query: 110 DDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQW 169 L+ P S + D+E E+ +VIG+ + + E EAL YVAGY D S R +Q H + Sbjct: 110 APLLKPERSNEFDYEGEMALVIGRGGRNIPEQEALQYVAGYSCYMDGSVRDWQ---HTCF 166 Query: 170 TKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQ 229 T GK+ G GPWLVT D++ DPQ+L + ++NG+T+Q +T +M+Y A L++Y+S Sbjct: 167 TGGKNWPATGGFGPWLVTADDIPDPQNLNITTRLNGQTVQQDNTGSMLYSIAELIAYIST 226 Query: 230 FMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRADA 281 F +L PGD+I TGTP G+G PP +++ GD VE+ IE +G V +DA Sbjct: 227 FSALSPGDVILTGTPGGIGKKRTPPLFMQPGDKVEVEIEQIGCLIHTVCSDA 278 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: 244 Number of extensions: 16 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: 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 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