Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate WP_039103773.1 FPB0191_RS02510 fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >NCBI__GCF_000807275.1:WP_039103773.1 Length = 280 Score = 153 bits (386), Expect = 5e-42 Identities = 95/290 (32%), Positives = 152/290 (52%), Gaps = 21/290 (7%) Query: 1 MKLLRYGEPGQEKPGLLGSDGII----------RDLSGHVSDLAAGALDPSKLDELANLD 50 MKL+ Y G+ GLL GI+ DL ++D A+ + L++ +++D Sbjct: 1 MKLVSYLVSGRASFGLLTQHGIVDLGKKLGDKYTDLKSLLADEKGLAIAKTYLNDPSDID 60 Query: 51 VETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPND 110 + + + P + K +C+G+NY++ AE T P +F++ + G Sbjct: 61 EKDITYL-------PVIPNPNKILCVGMNYAEKRAEFNET-SSAPTLFVRFPDSQTGHKT 112 Query: 111 DLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWT 170 +++ P + + D+E EL IVIGK+ + + +AL YVAGY D S R +Q + +T Sbjct: 113 NIIKPAITNELDYEGELAIVIGKSGFRIKQEDALSYVAGYSCYMDGSIRDWQ---YTWFT 169 Query: 171 KGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQF 230 GK+ + G GP L T DE+ DP+ L + +NG+ MQ S +V+ L+SY+S F Sbjct: 170 AGKNWPSTGAFGPCLTTTDEIPDPKALTLVTYLNGQEMQRDSVNNLVHTVPELISYISTF 229 Query: 231 MSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRAD 280 L PGD+I TG+P GVG PP ++K GD +E+ I G+G V A+ Sbjct: 230 THLSPGDVILTGSPGGVGKKRNPPIFMKDGDKIEVEITGIGRLTNYVVAE 279 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: 251 Number of extensions: 18 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: 280 Length adjustment: 26 Effective length of query: 255 Effective length of database: 254 Effective search space: 64770 Effective search space used: 64770 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