Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_059150767.1 V474_RS04200 crotonase/enoyl-CoA hydratase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_001046635.1:WP_059150767.1 Length = 267 Score = 153 bits (386), Expect = 4e-42 Identities = 98/250 (39%), Positives = 136/250 (54%), Gaps = 8/250 (3%) Query: 17 ITLNRPDKLNALN-AKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQF----- 70 +TLNRP N ++ +++E L A++ E+DP RV I+TG GK F +G DI Q Sbjct: 17 LTLNRPALRNPISDPEVIEALLAALAYLEADPAARVAILTGAGKGFSSGGDINQMKPGGN 76 Query: 71 -NQLTPAEAWKFSKKGREIMD-KIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQ 128 N +PA K+G + + AL P IA +NG A+G G +L CD+RIA E A+ Sbjct: 77 LNSGSPAVTRLNYKRGIQRLPLAFAALEVPVIAAVNGAAMGAGCDLTCMCDLRIAGESAK 136 Query: 129 LGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLE 188 + LG+ G GG+ L RV+G +A EM +TGD I +A GLV+RVVP L Sbjct: 137 FAESFVKLGLIAGDGGSWLLPRVVGWSKAAEMALTGDPIDAAEALACGLVSRVVPDGELM 196 Query: 189 QETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAF 248 R LA +IA P ++ + K ++ G + L S L + S +T D E V+AF Sbjct: 197 NAARALALRIAVNPPHAVRMTKRLLWEGRRADLASLLEMASAMQAAAHATADHAEAVTAF 256 Query: 249 LEKREPTFKG 258 LEKR P FKG Sbjct: 257 LEKRPPEFKG 266 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: 156 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: 267 Length adjustment: 25 Effective length of query: 234 Effective length of database: 242 Effective search space: 56628 Effective search space used: 56628 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