Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate GFF2389 Psest_2437 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__psRCH2:GFF2389 Length = 257 Score = 139 bits (349), Expect = 8e-38 Identities = 86/259 (33%), Positives = 133/259 (51%), Gaps = 5/259 (1%) Query: 1 MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59 M F T+L + +++VA ITLN P + N L ++ E+N+AL ++ DP I +V + K Sbjct: 1 MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSA-K 59 Query: 60 AFCDGVDVADHVPEKVDEM-IDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIV 118 AF G D+ + ++ +D F +A + V G +LGGGCEL CD++ Sbjct: 60 AFAAGADIKEMAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMI 119 Query: 119 IASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVV 177 A++ A+ GQPE+NL V P + + +G KAM++ LTG+ + A EAE GLV V Sbjct: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179 Query: 178 LPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATED 237 P E E K KS P M + ++ + ++ ++ AT D Sbjct: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVF-HAVFATAD 238 Query: 238 ANEGLASFLEKRKPVFKDK 256 EG+A+F EKRKP F ++ Sbjct: 239 QKEGMAAFSEKRKPEFTNR 257 Lambda K H 0.322 0.136 0.401 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: 156 Number of extensions: 12 Number of successful extensions: 5 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: 256 Length of database: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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