Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF1024 HP15_1003 enoyl-CoA hydratase/isomerase
Query= reanno::pseudo5_N2C3_1:AO356_01590 (273 letters) >FitnessBrowser__Marino:GFF1024 Length = 268 Score = 209 bits (531), Expect = 7e-59 Identities = 114/264 (43%), Positives = 167/264 (63%), Gaps = 1/264 (0%) Query: 2 DNFNTLELHSDPRGVATLWLSRESKNNAFNAEMIRELILALDHVSSDPNLRFLLIRGRGK 61 DN + + L G+A + L+R K NAF+ +I++LI L V++D +++ ++ + Sbjct: 3 DNESAVLLKRRDEGIAEVVLNRPDKRNAFDDVIIQQLISTLTEVNADNSVKVVICAPKAS 62 Query: 62 HFSAGADLAWMQQSAELDYHTNLDDARELAELMYNLAKLKIPTLAVVQGAAFGGALGLIS 121 GADL WM++ AE NLDD+RELA LM L L P + +VQGAAFGGA+GL + Sbjct: 63 TSPPGADLGWMRRMAENSRQENLDDSRELARLMNVLNHLSKPVIGLVQGAAFGGAVGLAA 122 Query: 122 ACDMAIGADEAQFCLSEVRIGLAPAVISPFVVQAIGERAARRYALTAERFDGQRAKEIGL 181 CD+ I +++ FCLSEV++GL PAVISP+VV+AIGER ARRY ++AE F ++A+E GL Sbjct: 123 CCDIVIATEKSSFCLSEVKLGLIPAVISPYVVRAIGERQARRYFISAEVFTAKQAQEYGL 182 Query: 182 LS-ESYPVETLDQQVEQWIDNLLLNSPAAMRASKELLREVGNGALTPALRRYTENAIARI 240 + V+ ++ + + + L +N P AM+A+K+L+ V + + + T + IA I Sbjct: 183 VHIVCDDVDAMEARCNEMLQQLAMNGPEAMKAAKDLVFAVSHKPINDDVIDDTAHRIADI 242 Query: 241 RVSPEGQEGLRAFLQKRAPNWQAE 264 RV EGQEGL AFL KR NW E Sbjct: 243 RVGEEGQEGLSAFLNKRKANWVPE 266 Lambda K H 0.318 0.133 0.382 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: 185 Number of extensions: 7 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: 273 Length of database: 268 Length adjustment: 25 Effective length of query: 248 Effective length of database: 243 Effective search space: 60264 Effective search space used: 60264 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 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