Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate Pf1N1B4_5706 Fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5706 Length = 373 Score = 125 bits (314), Expect = 1e-33 Identities = 92/276 (33%), Positives = 134/276 (48%), Gaps = 42/276 (15%) Query: 41 SKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEP--IIF 98 + +D+LA L L G +L V +F+C G NY H E+G + +IF Sbjct: 97 NSIDDLAQLKGTEL--AEGEVKLLSPVTRNQQFVCQGANYRQHMIESGMDPDAKKFNMIF 154 Query: 99 MKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKT---AKYVSEAEALDYVAGYCTVHD 155 KATS +V + DL+ PR D+E+ELG+V+ + A V++A +++AG V+D Sbjct: 155 TKATSCLVAADSDLIKPRTVRFLDYEIELGLVMKRAINGAVAVTDANLHEFIAGVVIVND 214 Query: 156 VSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKD--EVADPQDLAMWLKVNGETMQDGST 213 S R Q + Q+ KGKS TFGP GP+L D + ++L + L VN + Q+ ST Sbjct: 215 YSARDIQIPQM-QFYKGKSFRTFGPVGPYLCLLDATNIHYLKELQLRLTVNDQVRQNDST 273 Query: 214 KTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPP------------------- 254 +VYG A ++ LS GD+I+TGTP G + + P Sbjct: 274 ANLVYGPAETLTELSALQDFAAGDLIATGTPAGCALTVPSPAKQRIAALMPEATKWKLFL 333 Query: 255 -------RYLKAGDVVEL------GIEGLGSQKQRV 277 +YLK GDVVE G+ LG Q+ RV Sbjct: 334 KAQEGRTQYLKPGDVVEARIRSADGVIDLGVQRNRV 369 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: 295 Number of extensions: 26 Number of successful extensions: 6 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: 373 Length adjustment: 28 Effective length of query: 253 Effective length of database: 345 Effective search space: 87285 Effective search space used: 87285 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: 48 (23.1 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