Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS12745 HSERO_RS12745 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS12745 Length = 260 Score = 165 bits (417), Expect = 1e-45 Identities = 103/259 (39%), Positives = 147/259 (56%), Gaps = 8/259 (3%) Query: 2 SELIVSRQQRVLLLTLNRPAARNALNNAL--LMQLVNELEAAATDTSISVCVITGNA-RF 58 + L + + +LTL+ P A AL L +LV EL A D I V+TG +F Sbjct: 5 TNLKLEKTGHTAVLTLSNPPANTWTRAALADLTRLVKELNA---DRDIYTLVVTGEGEKF 61 Query: 59 FAAGADLNEMAEKDLAATLNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELALLCDV 116 F+AGADL A+ D A R + + L AF IAA+NGYA+G G E AL CD+ Sbjct: 62 FSAGADLKLFADGDKAMAREMARRFGEAFETLSAFRGVSIAAINGYAMGGGLECALACDI 121 Query: 117 VVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSD 176 +A E A+ LPE +G++P AGGTQ L VG+ A +M+L GE + A+ A + GLV + Sbjct: 122 RIAEEQAQMALPEAAVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVNAETALRIGLVEE 181 Query: 177 VFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATED 236 V P E AL LA + + SP ++ A+KQ ++ ++ L L ER+LF L T+D Sbjct: 182 VVPRGQARERALALAQQAEKQSPSSVAASKQLIQGARHNPLGTILQTERELFVDLFDTQD 241 Query: 237 RHEGISAFLQKRTPDFKGR 255 + EG+ AFL+KR+P +K + Sbjct: 242 QREGVQAFLEKRSPQWKNQ 260 Lambda K H 0.318 0.130 0.356 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: 137 Number of extensions: 3 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: 255 Length of database: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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 (21.8 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