Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate PfGW456L13_2984 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2984 Length = 257 Score = 137 bits (344), Expect = 3e-37 Identities = 86/260 (33%), Positives = 135/260 (51%), Gaps = 7/260 (2%) Query: 1 MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59 + + TIL E +V ITLN P + N L ++ E+N+AL + D I +V K Sbjct: 1 VSYETILLETHGRVGLITLNRPQALNALNAQIVSELNQALDGFEADSNIGCIVLT-GSKK 59 Query: 60 AFCDGVDVADHVPEKVDEMI--DLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDI 117 AF G D+ + ++ DLF R +A + VNG +LGGGCEL CD Sbjct: 60 AFAAGADIKEMAELTYPQIYIDDLFSDSDR-VANRRKPIIAAVNGFALGGGCELALMCDF 118 Query: 118 VIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNV 176 ++A + A+ GQPEINL V P + + +G KAME+ L+G++I A EAE G+V Sbjct: 119 ILAGDNARFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIVAR 178 Query: 177 VLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATE 236 ++P + + A K A KS P+AM + ++ + + ++ ++ AT+ Sbjct: 179 IVPSDELLDEALKVAALIAKKSLPIAMMVKESVNRAFEVSLAEGVRFERRVF-HAAFATQ 237 Query: 237 DANEGLASFLEKRKPVFKDK 256 D EG+A+F+ KR+ F+ K Sbjct: 238 DQKEGMAAFIAKREAEFQGK 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: 169 Number of extensions: 12 Number of successful extensions: 4 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