Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase
Query= SwissProt::P94549 (258 letters) >FitnessBrowser__Smeli:SMc01669 Length = 263 Score = 173 bits (439), Expect = 3e-48 Identities = 101/261 (38%), Positives = 157/261 (60%), Gaps = 6/261 (2%) Query: 2 NAISLAVDQFVAVLTIHNPPA-NALSSRILEELSSCLDQCETDAGVRSIIIHGEG-RFFS 59 + + + + +A+LT++ P NAL+ +++ L + LD+ E D V+++I+ G G R FS Sbjct: 3 DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62 Query: 60 AGADIKEFTS--LKG-NEDSSLLAERGQQLMERIESFPKPIIAAIHGAALGGGLELAMAC 116 AG DI EF+ KG N + RGQQL R+E+FPKP+IAA++G A GGG E+ A Sbjct: 63 AGGDIHEFSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAV 122 Query: 117 HIRIAAEDAKLGLPELNLGIIPGFAGTQRLPRYVGTAKALELIGSGEPISGKEALDLGLV 176 H+ IA+E A+ PE+ L + P F GTQRLPR G +ALEL+ +G+ S + ALD+GLV Sbjct: 123 HLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLV 182 Query: 177 SIGAKDEAEVIEKAKALAAKFAEKSPQTLASLLELLYSNKVYSYEGSLKLEAKRFGEAFE 236 + E ++I A+ALA + SP A+++ + + L E+++F Sbjct: 183 NAVVPHE-QLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARMVP 241 Query: 237 SEDAKEGIQAFLEKRKPQFKG 257 S D KEG+ A+ E+R+P++ G Sbjct: 242 SHDLKEGLAAWKERREPRYAG 262 Lambda K H 0.315 0.134 0.366 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: 140 Number of extensions: 6 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: 258 Length of database: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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: 42 (22.0 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