Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Ac3H11_1055 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1055 Length = 259 Score = 292 bits (747), Expect = 5e-84 Identities = 156/262 (59%), Positives = 190/262 (72%), Gaps = 3/262 (1%) Query: 1 MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60 M AEL R T TL+LTLSNP RNA+ P MYAAG+EAL E IR+VVITG+D Sbjct: 1 MPAEL---RSTSQGQTLILTLSNPERRNAIDPSMYAAGVEALSVAESSADIRSVVITGSD 57 Query: 61 NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLA 120 FC+GGNL RLL NR P VQAQSI+ L WI +R KPVIAAV+GAAAGAGFSLA Sbjct: 58 GMFCSGGNLQRLLANRQLPPDVQAQSIEGLHNWIETIRTYPKPVIAAVEGAAAGAGFSLA 117 Query: 121 LACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHEL 180 LACD IVAA +A FVM+Y+ V L+PDGG SW L+QALPRQ+ATE+L+ G IGA RLH L Sbjct: 118 LACDFIVAARNAVFVMAYSNVALSPDGGASWSLSQALPRQIATEILMCGDRIGAERLHAL 177 Query: 181 GVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVAS 240 G+VN++ + G+A DAA+A A++L +PN++A IK L+ A L++HL ERD+FV + Sbjct: 178 GLVNRVAEAGSALDAALALAEQLNAKAPNALASIKELLNEAPHASLTQHLGHERDHFVKN 237 Query: 241 LHHREGLEGISAFLEKRAPVYK 262 LHH G GISAFLEKR P Y+ Sbjct: 238 LHHANGGAGISAFLEKRVPRYE 259 Lambda K H 0.317 0.132 0.377 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: 205 Number of extensions: 4 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: 262 Length of database: 259 Length adjustment: 25 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 (21.7 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