Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011382625.1 AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000009985.1:WP_011382625.1 Length = 261 Score = 152 bits (384), Expect = 7e-42 Identities = 102/262 (38%), Positives = 145/262 (55%), Gaps = 8/262 (3%) Query: 1 MSE-LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFF 59 MSE ++V+R V +TLNRP NA N + L + + AA D + + VITG + F Sbjct: 1 MSETILVARTGDVTTITLNRPGRINAFNVEMHGALRSAVAHAAEDGTRCL-VITGAGKGF 59 Query: 60 AAGADLNEMAEK------DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALL 113 AG DL++ K DL A+L+ L L+A P+IAAVNG A GAG LAL Sbjct: 60 CAGQDLSDRVSKPGDPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALA 119 Query: 114 CDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGL 173 CD+VVA +A F +G++P +GGT L R VG + A+ +++ GE +TA+QA Q G+ Sbjct: 120 CDIVVAARSAAFVQSFCKVGLIPDSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGM 179 Query: 174 VSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAA 233 + + L L +A+++A L K+AL +S L A L ER L T Sbjct: 180 IWRCVDDEQLLPTVLAMAAQLAAQPTRGLALMKKALARSGANTLDAQLDLERDLQTEAGC 239 Query: 234 TEDRHEGISAFLQKRTPDFKGR 255 T+D EG+ AF++KR P F+GR Sbjct: 240 TQDYQEGVRAFMEKRPPRFEGR 261 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: 124 Number of extensions: 6 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: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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