Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__PV4:5210229 Length = 261 Score = 131 bits (329), Expect = 2e-35 Identities = 96/257 (37%), Positives = 136/257 (52%), Gaps = 12/257 (4%) Query: 6 RQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDLT 64 R +L + L+RP K NAI + + +D E+R ++TGAG R FSAG DL Sbjct: 9 RNGSILEIVLDRP-KANAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGARFFSAGWDLK 67 Query: 65 EFGDRK-PDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGAS 123 + + PD + + + E L L+KP++ AVNG A G G LAL DL + A AS Sbjct: 68 AAAEGEAPDADFGPGGFAGLTE-LFDLDKPVIAAVNGYAFGGGFELALAADLIVCADNAS 126 Query: 124 FTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLM 183 F ++G+VPDSG LP+L+ EL++ + A+EAL G+V+RVV E LM Sbjct: 127 FALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEALRWGVVNRVVEQEALM 186 Query: 184 EEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAG------QTQDHE 237 E A LA E++Q A A K++ ET LS+ + A + GQ ++D Sbjct: 187 ETARELANEISQSAPLALAAIKEIYRETGELSVEQGYA--HIRGGQLKHYPSVLHSEDAL 244 Query: 238 EGVRAFREKRPPRFQGR 254 EG AF EKR P +QG+ Sbjct: 245 EGPAAFAEKRDPVWQGK 261 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: 172 Number of extensions: 11 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: 254 Length of database: 261 Length adjustment: 24 Effective length of query: 230 Effective length of database: 237 Effective search space: 54510 Effective search space used: 54510 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