Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Koxy:BWI76_RS13115 Length = 255 Score = 177 bits (449), Expect = 2e-49 Identities = 101/252 (40%), Positives = 148/252 (58%), Gaps = 6/252 (2%) Query: 10 KEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQ 69 + + +TLNRP NALN LL ++ + A DP + V +I+G + F AGAD+ + Sbjct: 8 RHARVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGADLNE 67 Query: 70 F--NQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEA 127 N L PA + + +I+A SKP IA +NGYALG G ELAL CD+ +A + A Sbjct: 68 MAENDL-PATLDDIRPR---LWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNA 123 Query: 128 QLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANL 187 + GLPEI LG+ PG GGTQRL R +GK A M+++G+ I A + GLV+ V P A Sbjct: 124 RFGLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALT 183 Query: 188 EQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSA 247 ++ LA +A+ SP++L K+ + + L +GL E + ++ +TED++EG+ A Sbjct: 184 DEYALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGIDA 243 Query: 248 FLEKREPTFKGK 259 FL KR FKG+ Sbjct: 244 FLHKRTAEFKGR 255 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: 114 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: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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