Align Muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate BPHYT_RS07840 BPHYT_RS07840 muconate cycloisomerase
Query= reanno::WCS417:GFF4626 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS07840 Length = 375 Score = 452 bits (1163), Expect = e-132 Identities = 234/370 (63%), Positives = 279/370 (75%) Query: 6 IESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYGNESPD 65 I S++ I+VDLPT+R H+LAM TMQ QTLVI+RLR +DG+EGIGEATTIGGLSYG+ESP+ Sbjct: 5 ITSVEAILVDLPTIRAHQLAMATMQQQTLVIVRLRSSDGVEGIGEATTIGGLSYGDESPE 64 Query: 66 SIKVNIDRHFAPLLIGQDASNINAAMLRLERSIRGNTFAKSGIESALLDALGKRLNLPVS 125 IK+ ID + AP ++G DA+NIN AML+L + RGN FAK IE+ALLDA GKRL +PVS Sbjct: 65 GIKLTIDTYLAPAIVGLDATNINDAMLKLNKVARGNRFAKCAIETALLDAQGKRLGVPVS 124 Query: 126 ELLGGRVRDALPVAWTLASGNTEKDIAEAEKMLDLRRHRLFKLKIGAGEVSHDLAHVIAI 185 LLGG VR LPV WTLASG+T++DI EAE +L RRH FKLKIG V D+AHV I Sbjct: 125 TLLGGAVRKTLPVLWTLASGDTQRDIDEAETLLAERRHNTFKLKIGRRSVRDDVAHVSKI 184 Query: 186 KKALGDRASVRVDVNQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNLSSPAP 245 K ALG+RA V VDVNQAW+EA A L GIDLIEQP R RG +ARL P Sbjct: 185 KAALGERAKVTVDVNQAWNEADAALGIAALEAAGIDLIEQPTPREQRGALARLASRFIVP 244 Query: 246 IMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGGTMLEG 305 IMADE++ EDA L R A VFALKIAK+GG ++RTAAIA+AAG+ LYGGTMLEG Sbjct: 245 IMADEAVTGPEDALELVRGACADVFALKIAKSGGIYGMMRTAAIADAAGVSLYGGTMLEG 304 Query: 306 GIGTLASAHAFLTLNKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGLAIDEE 365 IG++ASAH F L +LAW TELFGPLLL +DI+T P YRDF LH++ PGLGL IDE+ Sbjct: 305 SIGSIASAHGFSALPQLAWGTELFGPLLLKDDIVTARPQYRDFDLHLTEGPGLGLHIDED 364 Query: 366 RLAFFRRDKH 375 +LAF+RRDK+ Sbjct: 365 KLAFYRRDKN 374 Lambda K H 0.320 0.137 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: 438 Number of extensions: 11 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: 375 Length of database: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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 (21.8 bits) S2: 50 (23.9 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