Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Ac3H11_2775 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2775 Length = 279 Score = 197 bits (501), Expect = 2e-55 Identities = 109/257 (42%), Positives = 156/257 (60%), Gaps = 4/257 (1%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64 +E ++ G + WI LNRPD++NA+N + + A+++ +SDP +RVI+I G G + FCAG Sbjct: 24 VEVERRGGVGWIVLNRPDQINAINDDIRRGVPAALAELDSDPSVRVIVIRGAGARGFCAG 83 Query: 65 ADITQFNQL-TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIA 123 ADI + T + + +K R I + ++ KP IA I+GY +GGG+ELALACD+R A Sbjct: 84 ADIKERRAAETSVQVRRRMQKSRWI-EALDRTEKPVIAAIHGYCMGGGMELALACDLRFA 142 Query: 124 AEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVP 183 A +A LPE LG+ PG GGTQRL V+G GRAL++++TGDR+ + A GL+ R+ Sbjct: 143 ASDAVFALPETGLGLIPGGGGTQRLGAVVGPGRALDLLLTGDRVDARRAFDIGLITRMAD 202 Query: 184 LA-NLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKK 242 A +L E LAE+IA+K P + K+ L SGL LE + ++ D K Sbjct: 203 SADSLLAEVTALAERIAQKPPTATLFAKQAARAACHLDLKSGLDLELDLFAMLVPMNDVK 262 Query: 243 EGVSAFLEKREPTFKGK 259 E AF EKR P F G+ Sbjct: 263 EAALAFREKRAPCFSGE 279 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: 165 Number of extensions: 5 Number of successful extensions: 4 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: 279 Length adjustment: 25 Effective length of query: 234 Effective length of database: 254 Effective search space: 59436 Effective search space used: 59436 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