Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Pf1N1B4_679 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_679 Length = 249 Score = 121 bits (304), Expect = 1e-32 Identities = 80/240 (33%), Positives = 123/240 (51%), Gaps = 3/240 (1%) Query: 5 ERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLT 64 ER+ G+L L +NRPEK NA+T + L L+ + D E+ A+L+TG+ F+AG D+ Sbjct: 8 ERERGLLTLRINRPEKKNALTRAMYSQLAEGLRLADSDPEINAVLITGSAECFTAGNDIF 67 Query: 65 EFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASF 124 +F + P Y+ ++ L KP++ AV G A G G +L L DL + A Sbjct: 68 DFLQQPPSI-LDSPVYHFMLNLLE-CRKPVIAAVAGAAVGIGTTLLLHCDLVYVSTDARL 125 Query: 125 TTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVV-PAEKLM 183 FV +GL P+ G S +LPR++G AKA ELLLL S E+A A G+ + E + Sbjct: 126 RMPFVNLGLCPEFGSSLILPRMLGHAKAAELLLLGEGFSGEQAAAWGIATEALGSGEAAL 185 Query: 184 EEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRAF 243 +A +A P A ++K+L+ R L + + E L Q ++ + + AF Sbjct: 186 AKAREMALRFEALPPEAVRISKQLMKAPGREQLRKVIEEEGALFTQRLRSPEAMAALSAF 245 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: 178 Number of extensions: 9 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: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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: 46 (22.3 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