Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate HSERO_RS20640 HSERO_RS20640 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS20640 Length = 263 Score = 134 bits (338), Expect = 1e-36 Identities = 84/245 (34%), Positives = 128/245 (52%), Gaps = 1/245 (0%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRA 77 V+TL+ P N+ M+ +A+ +++ DPS+R +++TGA FCAG +L Sbjct: 16 VITLNRPDKLNSFTVAMHLELRDAIATLQADPSVRVLLLTGAGRGFCAGQDLGDRAVKPG 75 Query: 78 KDPSVQAQSID-LLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136 D +SID + +LR PVI AV+G AAGAG +L LACD+++AA A FV Sbjct: 76 DDGVDLGESIDKYYGPLVKSLRALPFPVICAVNGVAAGAGANLPLACDIVLAARSASFVE 135 Query: 137 SYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAA 196 + ++GL PD GG++FL + + A + + G+ I A + G++ K + A Sbjct: 136 VFCKLGLIPDTGGTYFLPRLVGTARAMGMALLGEKISAEQAERWGLIWKCVDDDQLMEEA 195 Query: 197 VAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEK 256 A A + +A K + A+ L E L ERD A R+ EG++AFLEK Sbjct: 196 HAMAAHFARAPTKGLAATKATLYASPAHTLPEQLDLERDTMRALGRSRDYREGVTAFLEK 255 Query: 257 RAPVY 261 RAP + Sbjct: 256 RAPQF 260 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: 169 Number of extensions: 5 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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