Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434 Length = 257 Score = 110 bits (274), Expect = 4e-29 Identities = 76/243 (31%), Positives = 118/243 (48%), Gaps = 5/243 (2%) Query: 14 VATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVADHVP 72 V ITL P + N LT ++ E+ L + DP + +V KAF G D+ + Sbjct: 14 VRLITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLT-GSRKAFAAGADIKEMAE 72 Query: 73 -EKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVIASEKAKIGQPEI 131 + V + D ++ + + VNG +LGGGCEL DI+IA E A+ GQPEI Sbjct: 73 RDLVGILDDPRQASWQAITRFSKPLIAAVNGFALGGGCELAMHADIIIAGEDARFGQPEI 132 Query: 132 NLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVEGFREAAQKF 190 NL + P + +G AM+++LTG+ I A++A+ +GLV+ V E E A Sbjct: 133 NLGIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGLVSEVTQPEFTVERALHI 192 Query: 191 MADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDANEGLASFLEKRK 250 +K+ A+ A++ ++ D L+ + T D +EG+A+F EKR Sbjct: 193 AHSIAAKAPLAVRLAKEALLKAMDTDLATGLRFERHAFTV-LAGTRDRDEGIAAFQEKRS 251 Query: 251 PVF 253 P F Sbjct: 252 PTF 254 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: 136 Number of extensions: 8 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: 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