Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)
Query= CharProtDB::CH_091794 (261 letters) >FitnessBrowser__Burk376:H281DRAFT_03491 Length = 266 Score = 161 bits (408), Expect = 1e-44 Identities = 100/258 (38%), Positives = 150/258 (58%), Gaps = 13/258 (5%) Query: 6 VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIEN---DSEVLAVILTGAGEKSF 62 V+ E +G VA +T+NRP+ NAL ++ +D ++ +E D V A++LTGAG +F Sbjct: 5 VLYELDGGVATITLNRPETRNALTE--MEVVDALVESLERAQADLNVRAIVLTGAGP-AF 61 Query: 63 VAGADISEMK-EMNTIEGRKFGILGN------KVFRRLELLEKPVIAAVNGFALGGGCEI 115 +G +I M+ E+ T G I N ++ R L+ P IAAVNG A G GC++ Sbjct: 62 SSGGNIKHMRDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDL 121 Query: 116 AMSCDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALR 175 A+ CDIRIA+ +A F + +GI PG GG L R VG+ A ++IFT I A AL Sbjct: 122 ALMCDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALD 181 Query: 176 IGLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGE 235 GLV++VV +EL++TA+E+A +I SN P +++SK+ I G + D+ + L + G Sbjct: 182 WGLVSRVVPDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAAFQGI 241 Query: 236 CFSTEDQKDAMTAFIEKR 253 T D ++A+ A EKR Sbjct: 242 VHRTADHREALAATFEKR 259 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: 169 Number of extensions: 8 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: 261 Length of database: 266 Length adjustment: 25 Effective length of query: 236 Effective length of database: 241 Effective search space: 56876 Effective search space used: 56876 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