Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate Pf1N1B4_5805 Muconate cycloisomerase (EC 5.5.1.1)
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5805 Length = 429 Score = 705 bits (1819), Expect = 0.0 Identities = 361/386 (93%), Positives = 371/386 (96%), Gaps = 4/386 (1%) Query: 1 MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 60 M ATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG Sbjct: 44 MRATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 103 Query: 61 NESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRL 120 NESPDSIKTNIDKHF PLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIE+ALLDA GKRL Sbjct: 104 NESPDSIKTNIDKHFTPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIESALLDAQGKRL 163 Query: 121 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA 180 GLPVSELLGGRVRDALPVAWTLASGDT KDIAEAE+MLDLRRHRIFKLKIGAGEVNRDLA Sbjct: 164 GLPVSELLGGRVRDALPVAWTLASGDTAKDIAEAEQMLDLRRHRIFKLKIGAGEVNRDLA 223 Query: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNA 240 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILG+NGIDL+EQPISRNNR GM RLN Sbjct: 224 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGSNGIDLIEQPISRNNRAGMVRLNT 283 Query: 241 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG 300 +SPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTA+IAEAAGI LYGG Sbjct: 284 VSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGG 343 Query: 301 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL 360 TMLEGG+GT+ASAHAFVTLN L WDTELFGPLLLTEDILSEPLVYRDF+LHVP TPGLGL Sbjct: 344 TMLEGGIGTLASAHAFVTLNTLGWDTELFGPLLLTEDILSEPLVYRDFQLHVPQTPGLGL 403 Query: 361 SLDEERLAFFRRDK----TSTAIHQA 382 SLDEERLAFFRRDK TSTA+HQA Sbjct: 404 SLDEERLAFFRRDKVSRTTSTAVHQA 429 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: 563 Number of extensions: 13 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: 429 Length adjustment: 31 Effective length of query: 351 Effective length of database: 398 Effective search space: 139698 Effective search space used: 139698 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 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