Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 188 bits (478), Expect = 8e-53 Identities = 108/253 (42%), Positives = 156/253 (61%), Gaps = 8/253 (3%) Query: 10 VLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDL------ 63 V+V LNRPEK NA++ +LD+L AL +E+ ++ ++TGAG AF +G DL Sbjct: 12 VMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGGDLGRRAAE 71 Query: 64 TEFGDRKP-DYEAHLRRY-NRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121 + GD P + + L++ ++V A+ EKPL+ AVNG A GAGM L+L D+R A+ Sbjct: 72 SAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRFASES 131 Query: 122 ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEK 181 A F A++R+GL+P +G +LLPR+VG AKA ELL +SAEEALALG+V+RV ++ Sbjct: 132 ARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVFSDDE 191 Query: 182 LMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVR 241 LM++ L A LA GP KKLL ++ R L +L A T D++E ++ Sbjct: 192 LMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQSTDDYKEAIK 251 Query: 242 AFREKRPPRFQGR 254 A++EKR PRF G+ Sbjct: 252 AYKEKRKPRFIGK 264 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: 152 Number of extensions: 5 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: 264 Length adjustment: 24 Effective length of query: 230 Effective length of database: 240 Effective search space: 55200 Effective search space used: 55200 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