Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate H281DRAFT_05516 H281DRAFT_05516 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Burk376:H281DRAFT_05516 Length = 264 Score = 162 bits (409), Expect = 9e-45 Identities = 92/258 (35%), Positives = 148/258 (57%), Gaps = 7/258 (2%) Query: 9 KKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADI 67 + G++ I +NR +++N+LN + +EL A D + V ++TG G KAFCAGAD+ Sbjct: 7 ESHGHVRLIIINRAERMNSLNFEANDELVGAFESFNDDDDAYVAVVTGAGEKAFCAGADL 66 Query: 68 TQFN-QLTPAEAWKFSKK-----GREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121 + + A F +K G + + + KP +A +NG+A+ GG ELALA D+R Sbjct: 67 KTYTVNFARSPAPDFRRKYTNGPGFAGITRNMDIFKPVVAAVNGFAISGGFELALAADLR 126 Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181 + A+ L + G + GG RL +++G G A+E++++G+R+ + A + GLVNR+ Sbjct: 127 FCSPNAEFALQDAKWGFHACDGGLIRLPQIVGLGHAMEIILSGERLNAEHAYRIGLVNRI 186 Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDK 241 VP +L +ET + A+ +A +SP+S KEV+ R + P+ L LES + TED Sbjct: 187 VPAESLLEETMRYAQMLASRSPLSHRFAKEVMKRAIGMPMDEALRLESRSFYDFGMTEDL 246 Query: 242 KEGVSAFLEKREPTFKGK 259 EG ++F E+R FKGK Sbjct: 247 VEGTTSFRERRPANFKGK 264 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: 138 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: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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