Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate H281DRAFT_05722 H281DRAFT_05722 short chain enoyl-CoA hydratase /Enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_05722 Length = 263 Score = 286 bits (731), Expect = 4e-82 Identities = 148/250 (59%), Positives = 179/250 (71%), Gaps = 2/250 (0%) Query: 13 VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVD 72 V T+TLNRP++LNSF MH +L L +VE R L+LTGAGRGFCAGQDL D + Sbjct: 16 VATITLNRPDKLNSFTRAMHQELNAALNEVETSGA-RALVLTGAGRGFCAGQDLADLDFT 74 Query: 73 PTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKF 132 P G DLG ++ +NPL+RRL LP PVI AVNG AAGAGA LAL DIV+AARSA F Sbjct: 75 P-GAMTDLGELIDLHFNPLIRRLQALPLPVIAAVNGTAAGAGANLALACDIVLAARSASF 133 Query: 133 VMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLAD 192 + AF K+GL+PD GGTW LP+ G ARA+GLA+ G++LSAE+A WG+IWQ VDD+ LA Sbjct: 134 IQAFVKIGLVPDSGGTWFLPQRVGMARALGLAITGDKLSAEKAESWGLIWQTVDDQELAA 193 Query: 193 TAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAFL 252 TA +LA LA QPT + IKQA+ + T TLD QLDLERD QR G S DY EGV AF+ Sbjct: 194 TAAKLAAQLAQQPTRAIAAIKQAMRAGATQTLDQQLDLERDLQRELGASHDYAEGVQAFV 253 Query: 253 AKRSPQFTGK 262 KR+P+F G+ Sbjct: 254 EKRAPRFEGR 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: 196 Number of extensions: 10 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: 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