Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate RR42_RS03015 RR42_RS03015 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS03015 Length = 265 Score = 184 bits (467), Expect = 2e-51 Identities = 105/266 (39%), Positives = 150/266 (56%), Gaps = 7/266 (2%) Query: 1 MMEFILSHVEKGVMTLTLNRPERLNSFNDEMH-AQLAECLKQVERDDTIRCLLLTGAGRG 59 M F+ + ++TLT+N P+R N A E + ++ RD ++R +++TGAG Sbjct: 1 MTSFLRYEQQGHIVTLTMNEPQRRNPLTGNTAVADFLEAIDRIHRDASVRAVIITGAGTA 60 Query: 60 FCAGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLA----KLPKPVICAVNGVAAGAGA 115 F +G ++ D +G P GM + + Y ++RL L PVI AVNG A GAG Sbjct: 61 FSSGGNIRDMERQASGQVP--GMEIRQDYRLGIQRLPLALFNLEVPVIAAVNGAAMGAGL 118 Query: 116 TLALGGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQA 175 LA D+ IA+ A+F +F KLG+IP GG WLLPRV G ARA L G + A QA Sbjct: 119 DLACMCDMRIASEQAQFAESFVKLGIIPGDGGAWLLPRVIGLARAAELTFTGQVIDARQA 178 Query: 176 HEWGMIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQ 235 EW ++ +VV + L TA +LA +A P + L K+ + A LDT L+L +Q Sbjct: 179 LEWNLVSRVVPPDQLLPTANELAERIAANPPHAVRLAKRLLREALHTRLDTLLELSAGFQ 238 Query: 236 RLAGRSADYREGVSAFLAKRSPQFTG 261 L+ +++D+RE VSAFL KR P+FTG Sbjct: 239 ALSHQTSDHREAVSAFLDKRKPEFTG 264 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: 144 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: 265 Length adjustment: 25 Effective length of query: 237 Effective length of database: 240 Effective search space: 56880 Effective search space used: 56880 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