Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_025763018.1 X939_RS0109475 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000566685.1:WP_025763018.1 Length = 259 Score = 127 bits (318), Expect = 3e-34 Identities = 77/245 (31%), Positives = 126/245 (51%), Gaps = 1/245 (0%) Query: 10 KEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADIS 69 KEG V + ++NRP +ALN + +KE+ I +D EV AV+LT G+ +F +GAD+ Sbjct: 10 KEGIVRI-SLNRPHVHHALNKELIKEITLAIEVAASDEEVRAVLLTAEGDTAFCSGADLK 68 Query: 70 EMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNAR 129 + + + N + + L KPV+ +NG A+G G +A+SCD+ +A+ +A Sbjct: 69 DTLDSKIDVDQTLREYYNPMIMAIRSLPKPVVCRLNGLAVGAGASLALSCDMVVATESAY 128 Query: 130 FGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELM 189 V +G+ P G T L RLVG A L T Q + A EA IG++ V SEL Sbjct: 129 LAFMFVQIGLMPDAGATFILPRLVGSARAFALASTGQRVTAREAQHIGMIAHAVPASELD 188 Query: 190 NTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKDAMTAF 249 +T +++ A+ KQ +N+ ++ L E + T D K+ +++F Sbjct: 189 STVEKLLLYYRHAPTQAIAAMKQVLNQSQHSSLEQMLDLERIHQHQLSKTTDAKNGISSF 248 Query: 250 IEKRK 254 ++K+K Sbjct: 249 LQKKK 253 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: 136 Number of extensions: 4 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: 261 Length of database: 259 Length adjustment: 24 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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