Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_013450471.1 CALNI_RS01690 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000183405.1:WP_013450471.1 Length = 263 Score = 189 bits (479), Expect = 6e-53 Identities = 105/248 (42%), Positives = 159/248 (64%), Gaps = 4/248 (1%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAE 70 V L ++RP A NALN+ ++ +L + E D SI V+TG + F AGAD+ EM Sbjct: 16 VFKLVIDRPNALNALNSDVIAELQSFFEKIVNDCSIKAIVLTGGGEKSFVAGADIKEMVN 75 Query: 71 KDLAATLNDTRPQLWARLQAFN--KPLIAAVNGYALGAGCELALLCDVVVAGENARFGLP 128 ++N R L +N KP+IAAVNGYALG G E++L CD++ A ENA+FG P Sbjct: 76 LTAQDSMNFARKGQQLLLTMYNCPKPIIAAVNGYALGGGFEMSLCCDMIFASENAKFGFP 135 Query: 129 EITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPS-DLTLEYA 187 E+TLGI+PG GGTQ L R VG+ A ++LSGE I+A +A + +V+ +F + + + A Sbjct: 136 EVTLGIIPGFGGTQILRRLVGEKAAKYLILSGEIISAAEAYRMNVVNRLFKTPEEVVNGA 195 Query: 188 LQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQK 247 ++ A+K+A++SP ++ AK+A+ S +++++ GL E LF L TED+ EG+ AF++K Sbjct: 196 VEFAAKIAKNSPSSVAYAKKAVNVSFDLSMERGLEYESSLFGTLFNTEDQKEGMKAFIEK 255 Query: 248 RTPDFKGR 255 R +FKG+ Sbjct: 256 RKAEFKGK 263 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: 130 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: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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 24 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