Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate WP_086511713.1 BZY95_RS20345 muconate/chloromuconate family cycloisomerase
Query= metacyc::MONOMER-14643 (382 letters) >NCBI__GCF_002151265.1:WP_086511713.1 Length = 372 Score = 440 bits (1131), Expect = e-128 Identities = 227/371 (61%), Positives = 277/371 (74%) Query: 2 LATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYGN 61 ++ I+SIET++VDLPTIRPHKL+M TM QTLVI+R+R +DGIEG+GE TTIGGLAYG Sbjct: 1 MSATIQSIETLLVDLPTIRPHKLSMTTMACQTLVIVRMRHSDGIEGLGEGTTIGGLAYGP 60 Query: 62 ESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRLG 121 ESP+SIK NID + APLLIGQ SGNVNA RLER RGN AKS +ETALLDA GKRLG Sbjct: 61 ESPESIKRNIDTYLAPLLIGQPSGNVNALRARLERHARGNMIAKSALETALLDAQGKRLG 120 Query: 122 LPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAH 181 L V+ELLGG + LPV WTLASGDT KDI EA+ L+ RRH FKLKIGA V D+ H Sbjct: 121 LSVAELLGGARQTHLPVLWTLASGDTAKDIEEAQLRLEQRRHGDFKLKIGANPVKHDVRH 180 Query: 182 VIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNAM 241 V AIK+ALGDRA VRVDVNQAWDE+ A+ + L GI+L+EQ I G+ RL Sbjct: 181 VAAIKEALGDRAGVRVDVNQAWDESTAVYGIQALQDAGIELIEQAIPAREHAGLTRLADR 240 Query: 242 SPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGT 301 P++ADE+++ D +LAR G + FALKIAK+GG VL A +A+AAGI LYGGT Sbjct: 241 FNVPMLADEAVQDARDGLDLARGGFSGAFALKIAKSGGINGVLELAHVAQAAGIGLYGGT 300 Query: 302 MLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLS 361 +LEG +GT AS HA+ TL ++AW TE+FGPLLL +DI+ EPL YR+F + +P PGLG+S Sbjct: 301 LLEGTIGTAASLHAWATLPEMAWGTEMFGPLLLKDDIVVEPLHYREFGVDLPVGPGLGIS 360 Query: 362 LDEERLAFFRR 372 LDE++LA + R Sbjct: 361 LDEDKLAHYAR 371 Lambda K H 0.319 0.136 0.386 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: 427 Number of extensions: 25 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: 382 Length of database: 372 Length adjustment: 30 Effective length of query: 352 Effective length of database: 342 Effective search space: 120384 Effective search space used: 120384 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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