Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate H281DRAFT_01645 H281DRAFT_01645 muconate cycloisomerase (EC 5.5.1.1)
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_01645 Length = 378 Score = 421 bits (1082), Expect = e-122 Identities = 215/373 (57%), Positives = 272/373 (72%), Gaps = 2/373 (0%) Query: 1 MLATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYG 60 M IE IET +VDLPTIRPHKL++ TM QTL++++V C+DGI GIGE TTI G+AYG Sbjct: 1 MATATIERIETSLVDLPTIRPHKLSVATMHGQTLMLVKVFCSDGIVGIGEGTTIAGMAYG 60 Query: 61 NESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRL 120 ESP+S+K +ID + AP IG+D+ V M + + ++ N+FAKS +ETALLDAHGKRL Sbjct: 61 PESPESMKLSIDTYLAPAAIGKDATRVQQLMAYIGKLVKVNSFAKSALETALLDAHGKRL 120 Query: 121 GLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLA 180 +PVSELLGGR R+ LP+AWTLASGDT +DIAEAE+MLD RRH++FKLKIGA E+ D+A Sbjct: 121 NVPVSELLGGRRRERLPIAWTLASGDTSRDIAEAERMLDARRHKVFKLKIGAKELKTDIA 180 Query: 181 HVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNA 240 HV IK+ LG+R +VRVDVN AW E A A L G +LVEQP+ + + RL Sbjct: 181 HVAQIKRELGERGAVRVDVNMAWSETQAAWAIPALADAGCELVEQPVM--SPAALGRLMR 238 Query: 241 MSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGG 300 P +MADE ++ E AF +A+ A VFA+KI ++GG A R A+IA+AAGI LYGG Sbjct: 239 RFPIALMADEILQGPESAFEIAKHHGADVFAVKIEQSGGLFAAQRVAAIADAAGIELYGG 298 Query: 301 TMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGL 360 TMLEG GT+ASAH F + L W TELFGPLL+TE+IL++PL Y DFEL VP+ PGLG+ Sbjct: 299 TMLEGAFGTVASAHLFASFANLQWGTELFGPLLITEEILTQPLDYSDFELTVPSGPGLGI 358 Query: 361 SLDEERLAFFRRD 373 +LDE R+ F RD Sbjct: 359 ALDEARVKRFTRD 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: 367 Number of extensions: 12 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: 382 Length of database: 378 Length adjustment: 30 Effective length of query: 352 Effective length of database: 348 Effective search space: 122496 Effective search space used: 122496 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