Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 120 bits (302), Expect = 2e-32 Identities = 91/260 (35%), Positives = 140/260 (53%), Gaps = 12/260 (4%) Query: 3 LKERQDG-VLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAG 60 ++ R+DG VL + ++RP K NAI A+ ++ +D E+R +++GAG + F AG Sbjct: 5 VRTRRDGAVLEVVIDRP-KANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAG 63 Query: 61 QDL--TEFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLA 118 DL GD D + + + + E L L KP++ AVNG+ G G+ +AL DL +A Sbjct: 64 WDLKAAASGDAV-DGDYGVGGFGGLQE-LRDLNKPVICAVNGLCCGGGLEIALSTDLIIA 121 Query: 119 AVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVP 178 A A+F +R G V D+ S LP+ + A ++LL L EA G V+ VVP Sbjct: 122 AEHATFALPEIRSGTVADAA-SIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVP 180 Query: 179 AEKLMEEALSLAKELAQGPTRAYALTKKLLLE----TYRLSLTEALALEAVLQGQAGQTQ 234 AE+LME A LA+ L GP YA K+++ E T++ ++ + + + ++ Sbjct: 181 AERLMERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSE 240 Query: 235 DHEEGVRAFREKRPPRFQGR 254 D EG RAF EKR P ++GR Sbjct: 241 DQLEGARAFAEKRSPIWKGR 260 Lambda K H 0.318 0.135 0.371 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: 142 Number of extensions: 9 Number of successful extensions: 4 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: 254 Length of database: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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 Apr 09 2024. 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