Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate CCNA_00006 CCNA_00006 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Caulo:CCNA_00006 Length = 262 Score = 220 bits (561), Expect = 2e-62 Identities = 117/245 (47%), Positives = 169/245 (68%), Gaps = 7/245 (2%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPA 76 I LNRP+ LNALN LL EL +A++ A++D + I++TG KAF AGADI + + T A Sbjct: 21 IRLNRPEALNALNTALLGELAQALAAAQADDSVGCIVLTGSAKAFAAGADIKEMSDKTYA 80 Query: 77 EAWK---FSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPE 133 + +K F+ R I E KP IA + GYALGGG ELA+ CD +AA+ A+ G PE Sbjct: 81 QMFKADFFTAGARAI----EQCRKPIIAAVAGYALGGGCELAMMCDFILAADTAKFGQPE 136 Query: 134 INLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRK 193 INLG+ PG GGTQRLTR +GK +A++M++TG + ++AE+ GLV+R+ P +L ET Sbjct: 137 INLGVAPGIGGTQRLTRFVGKSKAMDMILTGRMMGAEEAERSGLVSRIFPADSLVDETLA 196 Query: 194 LAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKRE 253 +A KIA +SP+++A+ KE+V ++ L +G+ALE + +F+ ED+KEG++AF+EKR+ Sbjct: 197 IAAKIAGQSPLAVAMNKELVEAAYETTLTTGVALERRLFHSLFAFEDQKEGMTAFVEKRK 256 Query: 254 PTFKG 258 P FKG Sbjct: 257 PLFKG 261 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: 154 Number of extensions: 6 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