Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate BWI76_RS13120 BWI76_RS13120 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Koxy:BWI76_RS13120 Length = 262 Score = 151 bits (382), Expect = 1e-41 Identities = 91/258 (35%), Positives = 137/258 (53%), Gaps = 4/258 (1%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGA 65 I ++ E + ITLNRPD+LN+ N + ++L + QAE D ++R +++TG G+ FCAG Sbjct: 5 ILSEVEQGVMTITLNRPDRLNSFNDLMHQQLAACLKQAERDDDVRCLLLTGAGRGFCAGQ 64 Query: 66 DITQFNQ----LTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121 D+ N P + ++ ++ AL KP I +NG A G G LAL CDI Sbjct: 65 DLNDRNVDPSGPAPDLGLSVERFYNPLVRRLAALPKPVICAVNGVAAGAGATLALGCDIV 124 Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181 +AA A+ + LG+ P GG+ L RV G+ RA+ + + GD + + A ++G++ +V Sbjct: 125 LAARSAKFVMAFSKLGLVPDCGGSWFLPRVAGRARAMGLALLGDSLSAEQAAQWGMIWQV 184 Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDK 241 V A L+ LA +A + L LIK+ + L L LE + + D Sbjct: 185 VDDAELKDTGLALARHLAAQPTYGLGLIKKALQLAETQTLDQQLDLERDYQRLAGRSADY 244 Query: 242 KEGVSAFLEKREPTFKGK 259 +EGVSAFL KR P F GK Sbjct: 245 REGVSAFLAKRPPQFSGK 262 Lambda K H 0.315 0.135 0.382 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: 149 Number of extensions: 4 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: 259 Length of database: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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