Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011840924.1 RSPH17029_RS06550 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000015985.1:WP_011840924.1 Length = 258 Score = 211 bits (536), Expect = 2e-59 Identities = 120/263 (45%), Positives = 156/263 (59%), Gaps = 7/263 (2%) Query: 2 MEFILSHVEK--GVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRG 59 M++ VE+ G+ +TL RPE +N+ + M +L + E R L+LTG GRG Sbjct: 1 MDYRTIRVEEQGGLCRVTLARPEVMNALSSRMREELLHAV--TEAGTRARALVLTGEGRG 58 Query: 60 FCAGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLAL 119 FC+GQDL D PD + Y PL+R +A P P + AVNGVAAGAGA LAL Sbjct: 59 FCSGQDLGDARALGV---PDFERILREEYEPLLRAIAHCPLPTLAAVNGVAAGAGANLAL 115 Query: 120 GGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWG 179 D+VIAA SA F+ AF+++GLIPD GGTW LPR G ARAMG L +++SA A WG Sbjct: 116 ACDVVIAAESAGFIQAFTRIGLIPDTGGTWTLPRQIGLARAMGATLFADRISAADAARWG 175 Query: 180 MIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAG 239 MI++ V DE Q A HLA PT +KQA+ ++ N+ + QL LE Q G Sbjct: 176 MIYEAVPDEAFEARWQARAAHLAEGPTEAYRGLKQALRASFDNSFEEQLALEARLQGQCG 235 Query: 240 RSADYREGVSAFLAKRSPQFTGK 262 SAD+ EGV+AFL KR F+G+ Sbjct: 236 ASADFLEGVTAFLEKRPATFSGR 258 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: 8 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: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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 Apr 10 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