Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Dyella79:N515DRAFT_0930 Length = 264 Score = 112 bits (281), Expect = 6e-30 Identities = 87/256 (33%), Positives = 127/256 (49%), Gaps = 9/256 (3%) Query: 12 GVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLN-DRN 70 GV T+T+NRP+ N+F+D + A+L + L RD+ +R ++LTGAG F AG DLN R Sbjct: 12 GVRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAGASFSAGADLNWMRG 71 Query: 71 VDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSA 130 + A + S+ L+R L LPKP + VNG A G G L DI I SA Sbjct: 72 MAKASEAENREDSLR--LAALMRTLQFLPKPTVARVNGAAYGGGVGLIACCDIAIGVDSA 129 Query: 131 KFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETL 190 KF + KLGL+P +++ + G ++ L L G A A G++ Q V E L Sbjct: 130 KFGLTEVKLGLVPAVISPYVIAAI-GLRQSRRLFLTGELFDASTAQRIGLLHQCVRAEEL 188 Query: 191 ADT-AQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGR---SADYRE 246 D A LA P + A+ A + + ++R+ L R SA+ +E Sbjct: 189 DDALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAE-RIDRENAELIARLRVSAEGQE 247 Query: 247 GVSAFLAKRSPQFTGK 262 G+ AFL KR+ +T + Sbjct: 248 GLGAFLDKRAAAWTAQ 263 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: 139 Number of extensions: 6 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 237 Effective length of database: 239 Effective search space: 56643 Effective search space used: 56643 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