Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate BPHYT_RS01215 BPHYT_RS01215 hypothetical protein
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS01215 Length = 330 Score = 134 bits (338), Expect = 2e-36 Identities = 72/187 (38%), Positives = 106/187 (56%), Gaps = 5/187 (2%) Query: 94 EPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTV 153 EP F + S I P+ ++ G+E+ DWE+ELGIVIG+ ++V+ +A ++VA + Sbjct: 134 EPYFFQRPNSCIAPPDGEIHAESGTEELDWELELGIVIGRRGRHVAREDAPNFVAACLIL 193 Query: 154 HDVSERAF---QTERHGQWTKGKSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQD 210 +DV++RA Q W +GK P GP+LV + + L + L VNGE MQD Sbjct: 194 NDVTDRALIYRQDFPGADWLRGKGMPASMPAGPYLVPASVIGEIDALRLRLSVNGEVMQD 253 Query: 211 GSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGL 270 M+ L+ YLS + LRPGD+I+TGTP G G + R+L+ GDV+ I+GL Sbjct: 254 ELAGDMILDVPRLIEYLSSRVELRPGDVIATGTP--AGTGAERGRFLQDGDVIRAEIDGL 311 Query: 271 GSQKQRV 277 G Q +V Sbjct: 312 GCQMNKV 318 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: 334 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: 330 Length adjustment: 27 Effective length of query: 254 Effective length of database: 303 Effective search space: 76962 Effective search space used: 76962 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