Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_029133990.1 A3GO_RS0114405 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000428045.1:WP_029133990.1 Length = 261 Score = 263 bits (673), Expect = 2e-75 Identities = 141/263 (53%), Positives = 184/263 (69%), Gaps = 4/263 (1%) Query: 1 MELNNVILEK-EGKVAVVTINRPKALNALNSDTLKEMDYVIGE-IENDSEVLAVILTGAG 58 ME N++LE+ E + +T+NRP++ NALNS TL E+ Y GE + N + +++TGAG Sbjct: 1 MEFENILLEQVETGIYKLTVNRPRSFNALNSATLDEI-YAAGEQLANTPDARVLLVTGAG 59 Query: 59 EKSFVAGADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMS 118 +K+FVAGADI+EM++ + IEG+ F G + FRRLE L+ PVIA VNG+ LGGG E+AMS Sbjct: 60 DKAFVAGADIAEMRDKSAIEGQVFSQKGMRAFRRLETLDIPVIAVVNGYCLGGGNELAMS 119 Query: 119 CDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGL 178 CD IAS A+FGQPEV LG++PGFGG+QRL+RL+G A +L+ T + IKADEAL GL Sbjct: 120 CDWIIASEKAQFGQPEVNLGVSPGFGGSQRLTRLIGRAKAMELLVTGRQIKADEALAWGL 179 Query: 179 VNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFS 238 N V ELM A E A I PV+V+L+KQA+ RG D+D A ES+ FG CFS Sbjct: 180 ANHVYAADELMEKALETARLINQKGPVSVRLTKQAVQRGQDLDLDNACLLESQVFGLCFS 239 Query: 239 TEDQKDAMTAFIEKRKIEGFKNR 261 TEDQK+ M AF+EKR + FK R Sbjct: 240 TEDQKEGMGAFLEKRAAQ-FKAR 261 Lambda K H 0.317 0.134 0.365 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: 214 Number of extensions: 3 Number of successful extensions: 1 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: 261 Length of database: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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: 41 (21.6 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