Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate Echvi_0343 Echvi_0343 Enoyl-CoA hydratase/carnithine racemase
Query= CharProtDB::CH_091794 (261 letters) >FitnessBrowser__Cola:Echvi_0343 Length = 258 Score = 125 bits (314), Expect = 9e-34 Identities = 85/256 (33%), Positives = 133/256 (51%), Gaps = 6/256 (2%) Query: 5 NVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVA 64 +V E++G++ V ++RP+ NALN+ + + + E V VI+ G K F + Sbjct: 4 HVKFEQKGRIGYVILSRPEKRNALNAAMVSGLQAALDRCEAIETVKVVIIKAEG-KVFCS 62 Query: 65 GADISEMKEM--NTIEGRKFGILG-NKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDI 121 GAD+ +++ M NT + G K+F RL K VIA V G AL GGC + CD Sbjct: 63 GADLQDIERMQDNTFDENLADSEGLKKLFLRLYTFPKVVIAQVQGHALAGGCGLVSVCDF 122 Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181 A A+ G EV +G P L R +G G AK+L+ T + + A A IGL+ + Sbjct: 123 AYAVPTAKLGYTEVRIGFVPAM-VLVFLVRKLGEGKAKELLLTGELLVAPAAKEIGLIQE 181 Query: 182 VVEPSELMNTAKEIANKIVS-NAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTE 240 V EP+ L +EIA +++S N+ ++ L+K+ I ++ AL + + + TE Sbjct: 182 VFEPAALDGAVQEIAERLISQNSGESMALTKKMIAAVQDLPLEEALEYAARMNAKARETE 241 Query: 241 DQKDAMTAFIEKRKIE 256 D K + AF+ K+KIE Sbjct: 242 DCKRGIAAFLGKKKIE 257 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: 163 Number of extensions: 8 Number of successful extensions: 4 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: 258 Length adjustment: 24 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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 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