Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Dsui_2041 Dsui_2041 enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::Q9LKJ1 (378 letters) >FitnessBrowser__PS:Dsui_2041 Length = 261 Score = 82.0 bits (201), Expect = 2e-20 Identities = 73/232 (31%), Positives = 107/232 (46%), Gaps = 9/232 (3%) Query: 5 MASQSQVLVEEKSSVRILTLNRPKQLNALSFHMISRLLQLFLAFEEDPSVKLVILKGHGR 64 M+ ++ VL ++K + LTLNRP NALS MI+ L F DPS+ +VIL G+G Sbjct: 1 MSEEALVLRQDKDGIARLTLNRPAARNALSRPMIAALQAEFDRIAADPSIGVVILAGNGP 60 Query: 65 AFCAGGDVAAVVRDINQGNWRLGANYFSSEYMLNYVMATYSKAQVSILNGIVMGGGAGVS 124 AFCAG D+ +R + G R + F + L + + + ++ ++GI GA + Sbjct: 61 AFCAGHDLKE-MRGADYGE-RYAEDLFEACARLMQRIVSLPQPVIARVHGIATAAGAQLV 118 Query: 125 VHGRFRIATENTVFAMPETALGLF---PDVGASYFLSRLPGFFGEYVGLTGARLDGAEML 181 IAT++ FA P +GLF P V S +S + LTG +D L Sbjct: 119 ASADLAIATDDARFATPGVNIGLFCSTPMVALSRNISHKHAL---QMLLTGDLIDAPTAL 175 Query: 182 ACGLATHFVPSTRL-TALEADLCRINSNDPTFASTILDAYTQHPRLKQQSAY 232 GL V +L A+EA +I S + AY + L AY Sbjct: 176 RFGLINEHVSGEQLDVAVEALAVKIASKSRHTLAVGKAAYYRQAELPLDEAY 227 Lambda K H 0.321 0.136 0.396 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: 192 Number of extensions: 7 Number of successful extensions: 2 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: 378 Length of database: 261 Length adjustment: 27 Effective length of query: 351 Effective length of database: 234 Effective search space: 82134 Effective search space used: 82134 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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