Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_101588181.1 BJEO58_RS03580 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_900169175.1:WP_101588181.1 Length = 251 Score = 191 bits (485), Expect = 1e-53 Identities = 106/248 (42%), Positives = 148/248 (59%), Gaps = 3/248 (1%) Query: 12 GNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFN 71 G + +TL+RP LNAL+ L+ +L A++ AES +R I++TG KAFCAGADITQ Sbjct: 5 GGVRVLTLDRPKALNALSVDLVAQLTAALTDAESTDSVRAIVLTGSDKAFCAGADITQIP 64 Query: 72 QLTPAEAW-KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLG 130 Q+ A K + G + I L+KPTIA + G A GGG E+ALACD+ IA E AQ G Sbjct: 65 QMQKAAPLDKLAFDG--LFSTIARLNKPTIAAVRGMAFGGGCEIALACDMAIAGESAQFG 122 Query: 131 LPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQE 190 +PE+ LG+ PG GGTQRL +GK +A+ M++TG+ + AE GLV VV ++ Sbjct: 123 VPEVKLGVLPGAGGTQRLVHALGKAKAMRMLLTGEPVTATWAESAGLVAEVVADVDVLDT 182 Query: 191 TRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLE 250 + E IA +P+++ L + + L GL LE + ++ TED EG+SAF E Sbjct: 183 AVGIGETIAGNAPLAVRLTADAARHAEELGLSRGLDLERRNFLLLLGTEDAAEGISAFAE 242 Query: 251 KREPTFKG 258 +R FKG Sbjct: 243 RRTADFKG 250 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: 150 Number of extensions: 7 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: 251 Length adjustment: 24 Effective length of query: 235 Effective length of database: 227 Effective search space: 53345 Effective search space used: 53345 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