Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate BPHYT_RS07330 BPHYT_RS07330 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS07330 Length = 306 Score = 190 bits (483), Expect = 3e-53 Identities = 96/203 (47%), Positives = 135/203 (66%), Gaps = 12/203 (5%) Query: 79 NYSDHAAETGATVPPE----PIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKT 134 NY +HA E G + P P +FMKA +++V ++V+P +E+ DWEVEL +VIGKT Sbjct: 99 NYYEHAREMGTELAPREESTPYMFMKAETSVVPTLAEVVIPPHAERVDWEVELAVVIGKT 158 Query: 135 AKYVSEAEALDYVAGYCTVHDVSERAFQTE-----RHGQWTKGKSCDTFGPTGPWLVTKD 189 +++++ +A DY+AGY ++DVS R +H W +GKS DTFGP GPW V + Sbjct: 159 GRHIAQQDAYDYIAGYTILNDVSARDLNRRTDYPFKH-DWFRGKSFDTFGPLGPWFVPRA 217 Query: 190 EVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGM 249 +A+PQ+L M L VNGE MQDG+T M++ A + YLS ++L+PGD+I+TGTP GVGM Sbjct: 218 CIAEPQNLRMRLSVNGEMMQDGNTSGMIFNIAEQIEYLSTILTLQPGDLIATGTPTGVGM 277 Query: 250 GMKPPRYLKAGDVVELGIEGLGS 272 G YLKAGDV+ I+G+GS Sbjct: 278 GRGV--YLKAGDVMVASIDGIGS 298 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: 272 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: 306 Length adjustment: 26 Effective length of query: 255 Effective length of database: 280 Effective search space: 71400 Effective search space used: 71400 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