Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_036834013.1 N784_RS08155 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000775615.1:WP_036834013.1 Length = 257 Score = 158 bits (400), Expect = 9e-44 Identities = 89/256 (34%), Positives = 142/256 (55%), Gaps = 1/256 (0%) Query: 3 FETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFC 62 +ETI+ + ITL+RP KLNA+ +L EL +A+ QA ++RVII+TG+G+AFC Sbjct: 2 YETIQYDVIQQVATITLHRPAKLNAITLQLNAELSKALKQASHSDDVRVIILTGEGRAFC 61 Query: 63 AGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRI 122 +G D+T + + G ++ +E KP IA +NG A G G LALACD R+ Sbjct: 62 SGQDLTLASDDVDYGDVLRTSYG-PVVRAMEECEKPIIAAVNGVAAGAGFSLALACDFRL 120 Query: 123 AAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV 182 +E+A + +G+ P G L++++G +ALE+ + G ++ ++A+ L +V+ Sbjct: 121 MSEKASFVQAFVQIGLIPDAGNLYYLSKLVGHAKALELSLLGGKVTAEEAKALHLATKVI 180 Query: 183 PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKK 242 P E++ A ++A ++ LIK + +S L L E+ G + T D K Sbjct: 181 PEEQWEEQVNAFAHQLANMPTKTMGLIKRNLKASWNSTLPEFLEAEANGQKIAGLTNDHK 240 Query: 243 EGVSAFLEKREPTFKG 258 EGV AFL+KR P F+G Sbjct: 241 EGVQAFLDKRPPLFQG 256 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: 143 Number of extensions: 5 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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 24 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