Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate H281DRAFT_03491 H281DRAFT_03491 short chain enoyl-CoA hydratase (EC 4.2.1.17)/Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__Burk376:H281DRAFT_03491 Length = 266 Score = 90.5 bits (223), Expect = 3e-23 Identities = 81/261 (31%), Positives = 124/261 (47%), Gaps = 19/261 (7%) Query: 6 ILFEKKDKVATITLNVPNS-NWLT-IPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCD 63 +L+E VATITLN P + N LT + ++ + E+L + D ++ +V AG AF Sbjct: 5 VLYELDGGVATITLNRPETRNALTEMEVVDALVESLERAQADLNVRAIVLTGAGP-AFSS 63 Query: 64 GVDVADHVPEKVDEM--------IDLFHGMFRNMAA---MDVTSVCLVNGRSLGGGCELM 112 G ++ H+ ++V + G+ R A +D+ + VNG + G GC+L Sbjct: 64 GGNIK-HMRDEVGTFGGNSAQIRENYRRGIQRIPRAFHELDLPCIAAVNGPAHGAGCDLA 122 Query: 113 AFCDIVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAI 171 CDI IA+ A + + + P AW P+ +GL +A E+I TG I A+ A Sbjct: 123 LMCDIRIAAHSALFAESFAKIGIIPGDGGAWLLPRAVGLSRAAEMIFTGTPIDAQCALDW 182 Query: 172 GLVNVVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQG 231 GLV+ V+P A++ A S V ++R I G +D L+ S QG Sbjct: 183 GLVSRVVPDAELLSTARELAARIASNPPNVLRMSKRLIREGQRMDLPSLLELSAA--FQG 240 Query: 232 CM-ATEDANEGLASFLEKRKP 251 + T D E LA+ EKR P Sbjct: 241 IVHRTADHREALAATFEKRTP 261 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: 145 Number of extensions: 6 Number of successful extensions: 3 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: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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