Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_092348920.1 BLU87_RS12270 hypothetical protein
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_900107645.1:WP_092348920.1 Length = 261 Score = 129 bits (324), Expect = 6e-35 Identities = 79/252 (31%), Positives = 142/252 (56%), Gaps = 3/252 (1%) Query: 5 ERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDL 63 E + + ++TLN P K N + G++L + + E +++ ++R + TG G RAF AG D+ Sbjct: 11 EVNNKIALVTLNLP-KYNILNGQMLRDIRDVMNELKQEADLRCAIFTGEGDRAFCAGADV 69 Query: 64 TEFGDRKPDYEAHLRRYNR-VVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGA 122 EF D D + + R ++ L+ P + A+NG A G G+ LAL D+R+A+ A Sbjct: 70 GEFTDPTIDDLEEVDVWARGILTKLANFPIPTIAAINGYALGGGLELALACDIRVASETA 129 Query: 123 SFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKL 182 +G++ G S + R +G +A++++ + ++SAE+AL +GLV V AE+L Sbjct: 130 KMGLVETSLGMIAGWGGSQRMVRTIGAGQAKKMMFTADKISAEKALQIGLVQEVYKAEEL 189 Query: 183 MEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRA 242 ++ + +A+++A A LTK+ + + + L LE +L A +++D +EG++A Sbjct: 190 IDRTMEMAQKIAANSPVANRLTKQGVNCYLNQGINDGLDLERMLDRAAYESEDSKEGMKA 249 Query: 243 FREKRPPRFQGR 254 F EKR P F+ + Sbjct: 250 FEEKRTPDFKNK 261 Lambda K H 0.318 0.135 0.371 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: 254 Length of database: 261 Length adjustment: 24 Effective length of query: 230 Effective length of database: 237 Effective search space: 54510 Effective search space used: 54510 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 24 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