Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate PP_3283 PP_3283 1,2-epoxyphenylacetyl-CoA isomerase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Putida:PP_3283 Length = 263 Score = 328 bits (841), Expect = 7e-95 Identities = 161/260 (61%), Positives = 198/260 (76%) Query: 3 EFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCA 62 + IL +E GV L+LNRPE+LNSFN MH ++ E L+QV + R LLLT GRGFCA Sbjct: 4 QHILFSIEDGVAFLSLNRPEQLNSFNTAMHLEVREALRQVRQSSDARVLLLTAEGRGFCA 63 Query: 63 GQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGD 122 GQDL+DRNV P PDLG S+++FYNPLVR L LP PVICAVNGVAAGAGA + L D Sbjct: 64 GQDLSDRNVAPGAEMPDLGQSIDKFYNPLVRTLRDLPLPVICAVNGVAAGAGANIPLACD 123 Query: 123 IVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIW 182 +V+AARSA F+ AF K+GL+PD GGTWLLPR+ G ARA LA+LG +L AEQA +WG+I+ Sbjct: 124 LVLAARSASFIQAFCKIGLVPDSGGTWLLPRLVGMARAKALAMLGERLGAEQAEQWGLIY 183 Query: 183 QVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSA 242 +VVDD L D A LARHLA QPT+GL LIK+++N++ N + QL+LERD QRLAGRS Sbjct: 184 RVVDDAALRDEALTLARHLAAQPTYGLTLIKRSLNASFDNGFEAQLELERDLQRLAGRSE 243 Query: 243 DYREGVSAFLAKRSPQFTGK 262 DYREGV+AF+ KR+P F G+ Sbjct: 244 DYREGVNAFMNKRTPAFKGR 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: 200 Number of extensions: 3 Number of successful extensions: 1 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: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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