Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate Ac3H11_3192 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3192 Length = 292 Score = 90.5 bits (223), Expect = 4e-23 Identities = 72/248 (29%), Positives = 113/248 (45%), Gaps = 11/248 (4%) Query: 14 VATITLNVP-NSNWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVADHV- 71 V T+TLN P N L M+ + AL D +D +++++V AG KAFC G ++ D Sbjct: 48 VVTLTLNDPARFNALGSEMLAALQRALDDAGRDESVRVVVLAAAG-KAFCAGHNLKDMAA 106 Query: 72 -PEKV--DEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVIASEKAKIGQ 128 PE ++ M + + V + V G + GC+L+A CD+ +A++ A Sbjct: 107 HPELAYYQQLFAQCSRMMLTIHKLSVPVIARVQGMATAAGCQLVAQCDLAVAADTASFAT 166 Query: 129 PEINLAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVEGFREAAQ 188 I+ +F + + + K+AME++LTG I A A A GLVN V+ + + Sbjct: 167 SGIHYGLFCATPSVPLVRNVPAKRAMEMLLTGDFIDAPTALAQGLVNRVVLADALDAEVE 226 Query: 189 KFMADFTSKSRPVAMWARRAI--MAGLNLDFLQALKASEIIYMQGCMATEDANEGLASFL 246 K + K R + + L +D L M M E A EG +F Sbjct: 227 KLVLSILQKPRVAVAMGKALVYQQRELGMDAAYQLAGQA---MATNMMDEAAQEGARAFA 283 Query: 247 EKRKPVFK 254 EKR+P +K Sbjct: 284 EKRQPGWK 291 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: 153 Number of extensions: 7 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: 256 Length of database: 292 Length adjustment: 25 Effective length of query: 231 Effective length of database: 267 Effective search space: 61677 Effective search space used: 61677 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