Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate HSERO_RS01270 HSERO_RS01270 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS01270 Length = 256 Score = 144 bits (362), Expect = 2e-39 Identities = 91/260 (35%), Positives = 138/260 (53%), Gaps = 12/260 (4%) Query: 2 MEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFC 61 M+ LS + GV+T+ +R ++ N+ M+ QLA+ LK+ E D +R +L TG + F Sbjct: 3 MDIQLSKAD-GVLTIHFDREDKKNAITAAMYQQLADALKEAESDSAVRAILFTGKPKAFS 61 Query: 62 AGQDLND--RNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLAL 119 AG DL D +N T AP V +F + +++ KP++ AV+GVA G G TL L Sbjct: 62 AGNDLEDFLKNPPKTQDAP-----VFQF----LWQISHASKPIVAAVSGVAVGIGTTLLL 112 Query: 120 GGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWG 179 D+V AA +AKF M F++LGL P+ + LLP +AG RA LLG A++A + G Sbjct: 113 HCDLVYAADNAKFSMPFTQLGLCPEAASSLLLPHIAGYQRAAEKLLLGEAFGADEACQMG 172 Query: 180 MIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAG 239 + +V+ E L AQQ A LA P + + KQ + + Q+ E ++ Sbjct: 173 FVNRVMAQEELLPYAQQQAAKLAALPAASIRVTKQLMKKNRVTATEQQMVAEIEHFSRML 232 Query: 240 RSADYREGVSAFLAKRSPQF 259 + + +E +AF KR P F Sbjct: 233 TAPEAKEAFTAFFEKRKPDF 252 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: 111 Number of extensions: 2 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: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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