Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011842447.1 RSPH17029_RS17990 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::F4JML5 (301 letters) >NCBI__GCF_000015985.1:WP_011842447.1 Length = 257 Score = 140 bits (354), Expect = 2e-38 Identities = 82/247 (33%), Positives = 134/247 (54%), Gaps = 5/247 (2%) Query: 52 DSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKE 111 D G+ V LDRP NA++ E+ ++ F + +D + RV ++ VFC G D+ + Sbjct: 13 DRGLAVVTLDRPPA-NAVSLEVYDEIRRTFHRLGEDPAMRVAVLTG-AGKVFCGGNDVND 70 Query: 112 RRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVF 171 + Y+ +R F+ + IP + AI GAA+G G+ +A CD+RI E AVF Sbjct: 71 FVDLEFDRATEYLAHVRLTFNALYDCPIPVVGAINGAAVGTGIVLASLCDIRIASERAVF 130 Query: 172 GLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHE 231 LPE + ++ GG++ + RL G+ +++ +++TGR++ A EA +V+ V E Sbjct: 131 ALPEIDVGVL---GGSRHVMRLAGQGMTRWMMYTGRRVRADEALRARIVDEVVPPEEVMP 187 Query: 232 KAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFA 291 +A+ +A++I K P AI++AK ++ E NM G E E + T + EG AF Sbjct: 188 RAMAIAEEIASKSPPAIRLAKLGLNRTEEMNMKEGYEFECTLTAAVRRTPEAREGAMAFL 247 Query: 292 EKRKPLY 298 EKR+P Y Sbjct: 248 EKRQPSY 254 Lambda K H 0.318 0.134 0.373 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: 134 Number of extensions: 6 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: 301 Length of database: 257 Length adjustment: 25 Effective length of query: 276 Effective length of database: 232 Effective search space: 64032 Effective search space used: 64032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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