Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_059150767.1 V474_RS04200 crotonase/enoyl-CoA hydratase family protein
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_001046635.1:WP_059150767.1 Length = 267 Score = 151 bits (382), Expect = 1e-41 Identities = 95/260 (36%), Positives = 145/260 (55%), Gaps = 10/260 (3%) Query: 6 VILEKEGK-VAVVTINRPKALNALNS-DTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63 V+ E + K + ++T+NRP N ++ + ++ + + +E D ILTGAG K F Sbjct: 5 VLYEIDDKGIVLLTLNRPALRNPISDPEVIEALLAALAYLEADPAARVAILTGAG-KGFS 63 Query: 64 AGADISEMKEMNTIEGRKFGILG---NKVFRRLEL----LEKPVIAAVNGFALGGGCEIA 116 +G DI++MK + + + +RL L LE PVIAAVNG A+G GC++ Sbjct: 64 SGGDINQMKPGGNLNSGSPAVTRLNYKRGIQRLPLAFAALEVPVIAAVNGAAMGAGCDLT 123 Query: 117 MSCDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRI 176 CD+RIA +A+F + V LG+ G GG+ L R+VG A ++ T I A EAL Sbjct: 124 CMCDLRIAGESAKFAESFVKLGLIAGDGGSWLLPRVVGWSKAAEMALTGDPIDAAEALAC 183 Query: 177 GLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGEC 236 GLV++VV ELMN A+ +A +I N P AV+++K+ + G + D+ + L S Sbjct: 184 GLVSRVVPDGELMNAARALALRIAVNPPHAVRMTKRLLWEGRRADLASLLEMASAMQAAA 243 Query: 237 FSTEDQKDAMTAFIEKRKIE 256 +T D +A+TAF+EKR E Sbjct: 244 HATADHAEAVTAFLEKRPPE 263 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: 186 Number of extensions: 10 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: 267 Length adjustment: 25 Effective length of query: 236 Effective length of database: 242 Effective search space: 57112 Effective search space used: 57112 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