Align 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF1427 PGA1_c14440 enoyl-CoA hydratase-like protein
Query= metacyc::MONOMER-16071 (271 letters) >FitnessBrowser__Phaeo:GFF1427 Length = 262 Score = 101 bits (251), Expect = 2e-26 Identities = 75/256 (29%), Positives = 111/256 (43%), Gaps = 8/256 (3%) Query: 12 DPRGFATLWLSREDKNNAFNAQMIRELIVAIDQLAEDASLRFVLLRGRGRHFSAGADLAW 71 D G ATL L+ D+ NA + M+ +D L +D R V+L GRG+ F AG DL Sbjct: 8 DSNGIATLHLNAPDRLNALSDAMLAAFQAELDSLRDDRETRVVILAGRGKAFCAGHDLRE 67 Query: 72 MQQSAQLDFNTNL---DDAHELGELMYALHRLKAPTLAVVQGAAFGGALGLISCCDMAIG 128 M Q + D E+M L ++ P +A V G A L++ CDMA+ Sbjct: 68 MTAGRQAEDGGQTYFADLFARCTEVMLGLQQIPQPVIAQVHGIATAAGCQLVASCDMAVA 127 Query: 129 AEDAQLCLSEVRIGLAPAVISPFVVKAIGERAARRYALTAERFTGVRARELGLLAEVYPA 188 AE + ++ V IGL + + + I + A T E RA ELGL+ + A Sbjct: 128 AEGTRFGVNGVNIGLFCSTPMVALTRNISRKHAFEMLTTGEFINAARAEELGLINRIAAA 187 Query: 189 SELDDHVEAWVSNLLQNSPQALRATKDLLREVDDGELSPALRRYCENTIARIR--VSAEG 246 +L+ +A + A++ K R D P Y + + + Sbjct: 188 EDLEQTTKALAQTVAGKLDAAVKIGK---RAFYDQLQLPTADAYAHTGAVMVENLMLRDT 244 Query: 247 QEGLRAFLEKRRPAWQ 262 EG+ AFLEKR P W+ Sbjct: 245 IEGIDAFLEKRDPDWK 260 Lambda K H 0.321 0.135 0.394 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: 131 Number of extensions: 2 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: 271 Length of database: 262 Length adjustment: 25 Effective length of query: 246 Effective length of database: 237 Effective search space: 58302 Effective search space used: 58302 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 Apr 09 2024. 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