Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_012042026.1 BBTA_RS08325 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000015165.1:WP_012042026.1 Length = 261 Score = 164 bits (416), Expect = 1e-45 Identities = 90/241 (37%), Positives = 144/241 (59%), Gaps = 5/241 (2%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQFNQLT- 74 +TLNRP++LNAL+ +L++ L + + E+D +R II+TG G +AF AGADI +F Sbjct: 16 LTLNRPERLNALSYRLIDALMAMLDRIETDAGVRAIILTGAGDRAFSAGADIHEFAASVG 75 Query: 75 ---PAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGL 131 F ++G+ + ++EA KP IA +NG A GGG E+ A + +A+ A Sbjct: 76 DGRSVALRDFVRRGQAMTSRLEAFPKPIIAAVNGLAFGGGCEITEAVHLAVASTRASFAK 135 Query: 132 PEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQET 191 EI LG+ P +GGTQRL R++G+ R LE+++TGD IP + A + GLVN VVP + Sbjct: 136 SEIRLGMPPTFGGTQRLPRLVGRKRGLELLLTGDAIPAQRAAEIGLVNAVVPHDQMLPAA 195 Query: 192 RKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEK 251 R+LA++I + P ++ + RGL+ + GL +E +G + + + G++A+ E+ Sbjct: 196 RELAKRIIRHGPEAVTSVITAATRGLNMAIGEGLQVEGEQFGRLVGGRELEHGLAAWRER 255 Query: 252 R 252 R Sbjct: 256 R 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: 132 Number of extensions: 5 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: 259 Length of database: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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