Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 15515 b1393 enoyl-CoA hydratase-isomerase (NCBI)
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Keio:15515 Length = 255 Score = 146 bits (368), Expect = 5e-40 Identities = 94/262 (35%), Positives = 135/262 (51%), Gaps = 7/262 (2%) Query: 1 MMEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGF 60 M E I+S ++ V+ LTLNRP N+ N+ + QL L+ D +I ++TG R F Sbjct: 1 MSELIVSRQQR-VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFF 59 Query: 61 CAGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALG 120 AG DLN+ DL ++ L RL KP+I AVNG A GAG LAL Sbjct: 60 AAGADLNEM------AEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALL 113 Query: 121 GDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGM 180 D+V+A +A+F + LG++P GGT L R G++ A + L G ++A+QA + G+ Sbjct: 114 CDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGL 173 Query: 181 IWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGR 240 + V + + A QLA +A L KQA+ ++ L L ER L Sbjct: 174 VSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAA 233 Query: 241 SADYREGVSAFLAKRSPQFTGK 262 + D EG+SAFL KR+P F G+ Sbjct: 234 TEDRHEGISAFLQKRTPDFKGR 255 Lambda K H 0.321 0.136 0.403 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: 146 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: 262 Length of database: 255 Length adjustment: 24 Effective length of query: 238 Effective length of database: 231 Effective search space: 54978 Effective search space used: 54978 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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