Align 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011383118.1 AMB_RS03470 enoyl-CoA hydratase
Query= metacyc::MONOMER-16071 (271 letters) >NCBI__GCF_000009985.1:WP_011383118.1 Length = 260 Score = 229 bits (585), Expect = 3e-65 Identities = 116/247 (46%), Positives = 160/247 (64%) Query: 15 GFATLWLSREDKNNAFNAQMIRELIVAIDQLAEDASLRFVLLRGRGRHFSAGADLAWMQQ 74 G T+ L+R +++NAF+ +I EL A A +R V+L G+ FSAGADL WM++ Sbjct: 11 GVRTITLNRAERHNAFDDALIAELAAAFRDAATAPGIRAVVLDSTGKSFSAGADLEWMKR 70 Query: 75 SAQLDFNTNLDDAHELGELMYALHRLKAPTLAVVQGAAFGGALGLISCCDMAIGAEDAQL 134 A NL DA L +++ A+ P + VVQGAA+GG +GL++CCD+A+ AE A Sbjct: 71 MAGYSHEENLADAQALSDMLEAIDACPRPVIGVVQGAAYGGGVGLVACCDLAVAAEGATF 130 Query: 135 CLSEVRIGLAPAVISPFVVKAIGERAARRYALTAERFTGVRARELGLLAEVYPASELDDH 194 CLSEV++G+ PAVISP+VV+A+G RAARRYA+TAE F A+ GL+ EV PA L + Sbjct: 131 CLSEVKLGIIPAVISPYVVRAMGGRAARRYAVTAELFDAAEAKATGLVHEVVPAEHLAEV 190 Query: 195 VEAWVSNLLQNSPQALRATKDLLREVDDGELSPALRRYCENTIARIRVSAEGQEGLRAFL 254 + W++ + N PQA+ A K L+R D L +LR + IA R S EG+EG+RAFL Sbjct: 191 RDKWLARVKGNGPQAMSAAKGLIRRAADQPLDESLRAWTAGQIAERRASDEGKEGIRAFL 250 Query: 255 EKRRPAW 261 EKR+PAW Sbjct: 251 EKRKPAW 257 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: 210 Number of extensions: 6 Number of successful extensions: 1 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: 260 Length adjustment: 25 Effective length of query: 246 Effective length of database: 235 Effective search space: 57810 Effective search space used: 57810 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