Align 2-keto-4-pentenoate hydratase 3; EC 4.2.1.80; 2-hydroxypentadienoic acid hydratase 3 (uncharacterized)
to candidate H281DRAFT_05455 H281DRAFT_05455 2-keto-4-pentenoate hydratase
Query= curated2:Q706S1 (269 letters) >FitnessBrowser__Burk376:H281DRAFT_05455 Length = 267 Score = 159 bits (402), Expect = 6e-44 Identities = 100/255 (39%), Positives = 145/255 (56%), Gaps = 7/255 (2%) Query: 10 AQSLYQAMQSGKPIAPLRDTFPDMNVDDAYAIQS-INTQRRISLGRRVVGRKIGLTSVVV 68 A+ LY A + + P+ ++D AYAI + R +LG R VGRK+GLT+ V Sbjct: 15 ARELYDARVGVYTVPYVSPRLPERDLDAAYAISAEFAALRERNLGVRRVGRKVGLTNPNV 74 Query: 69 QQQLGVDEPDFGALFDDMSFGDAETIPLSILHQPKVEAEIGFVLGRDLDTEQPTHQEVLQ 128 Q+++G+ EPD+G + DDM F +P S ++ +EAE+ FVL D+ T + V Sbjct: 75 QKRVGISEPDYGVIHDDMVFQSGAVLPKSRYNRLLIEAEVAFVLKSDIF--DATLERVAA 132 Query: 129 AVDYVVPALEIVGSRIADWNIKFVDTVADNASSGVYVLGSTPISPRGLDLSLVGMCLSRR 188 A+DYV PA E+V R + VDT+ADNA V+G +DL V M ++ Sbjct: 133 AIDYVTPAFEVVDFRFDGSVGQIVDTIADNAGCSGIVVGEEKHPYGSVDLKAVEMVITGG 192 Query: 189 GEPVSTGAGAACLGTPLNAVVWLARTMSRLGKPLRAGELILSGALGPMVAVKPGDVFEC- 247 G+ ++ G G+ LG P+NAV+WLA T R G+PLRAGE++LSG++G + P DV EC Sbjct: 193 GKEITRGVGSNVLGDPINAVLWLADTAIRTGQPLRAGEVLLSGSIG-YIEPWPVDV-ECV 250 Query: 248 -HINGVGSVRTEFES 261 I G+G V +S Sbjct: 251 ATITGLGRVVASVDS 265 Lambda K H 0.318 0.135 0.392 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: 214 Number of extensions: 12 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: 269 Length of database: 267 Length adjustment: 25 Effective length of query: 244 Effective length of database: 242 Effective search space: 59048 Effective search space used: 59048 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: 41 (21.7 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