Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_003217355.1:WP_110804536.1 Length = 258 Score = 140 bits (354), Expect = 2e-38 Identities = 89/250 (35%), Positives = 132/250 (52%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 ++ E +DGV ++ LNRPE LNA+ +LL L ALK + D VR +LTG+ +AF+AG Sbjct: 6 LIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGSDKAFAAGA 65 Query: 62 DLTEFGDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121 D+ E D+ + +A+ KP++ AV G A G G LA+ D L A Sbjct: 66 DIKEMADKSFTDMFLQDFFGTEGDAILRTRKPIIAAVAGYALGGGCELAMMCDFILCAEN 125 Query: 122 ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEK 181 A F + +G+V G + L R VG +K+ E+ L + A EA GLV RV+P Sbjct: 126 AKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAERSGLVSRVLPLAD 185 Query: 182 LMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVR 241 L+ EAL+ A+++A A + K + Y +L E + E + T+D +EG+ Sbjct: 186 LVPEALTTARKIAAKSAIATMVAKDCVNRAYETTLREGVLYERRVFHALFATEDQKEGMA 245 Query: 242 AFREKRPPRF 251 AF EKRP +F Sbjct: 246 AFTEKRPAKF 255 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: 161 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: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 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 24 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