Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Ac3H11_2719 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2719 Length = 271 Score = 169 bits (427), Expect = 7e-47 Identities = 101/262 (38%), Positives = 151/262 (57%), Gaps = 9/262 (3%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGEL-LDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 +L ER VL LNRPE NA+T +D L A ++ D ++AL+LTG G AF AG Sbjct: 10 LLIERDGPVLTARLNRPETRNALTDPAHMDELVALCRQIRADHSIKALVLTGEGSAFCAG 69 Query: 61 QDLTEFGDRKPDY--------EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALW 112 ++ + R + +++ R+ AL L+ P++ AVNG A GAG+ LA Sbjct: 70 GNVKDMQQRGGIFAGSPYEVRDSYRDTIQRIPLALYELDVPVIAAVNGPAIGAGLDLACM 129 Query: 113 GDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGL 172 D+R+A+ A F +FV++G+VP G ++LLPR++G+ KA L + A +AL+ GL Sbjct: 130 CDIRIASDKALFAESFVKVGIVPGDGGAWLLPRVIGMPKASLLAFTGDTIDAAKALSWGL 189 Query: 173 VHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ 232 V V PA++L+ +A +LA+ +A P+ A LTK+LL E + L L L + Q + Sbjct: 190 VADVFPADQLLGQAQALAQRIALNPSHALRLTKRLLREGQHVRLDTLLELSSAYQALSHH 249 Query: 233 TQDHEEGVRAFREKRPPRFQGR 254 T+DH E V AF +KRP +F GR Sbjct: 250 TEDHLEAVNAFLDKRPAQFTGR 271 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: 162 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: 254 Length of database: 271 Length adjustment: 25 Effective length of query: 229 Effective length of database: 246 Effective search space: 56334 Effective search space used: 56334 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