Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate H281DRAFT_01072 H281DRAFT_01072 muconate cycloisomerase (EC 5.5.1.1)
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_01072 Length = 403 Score = 452 bits (1162), Expect = e-131 Identities = 229/369 (62%), Positives = 280/369 (75%) Query: 6 IESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYGNESPD 65 I S+E I+VDLPTIR H+L+M TMQ QT+VIIR+R +D IEGIGE+TTIGGL+YG ESP+ Sbjct: 33 ITSVEAILVDLPTIRAHQLSMATMQQQTMVIIRLRASDDIEGIGEATTIGGLSYGEESPE 92 Query: 66 SIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRLGLPVS 125 IK ID + AP+L+GQD+ ++N ML+L ++ RGN FAKSGIETALLDA GKRLG+P+S Sbjct: 93 GIKLTIDTYLAPVLVGQDATDINDVMLKLNKAARGNRFAKSGIETALLDAQGKRLGVPLS 152 Query: 126 ELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAHVIAI 185 LLGG VR LPV WTLASGDT +DI EAE +L RRH FKLKIG V D+AHV I Sbjct: 153 ALLGGSVRKTLPVLWTLASGDTNRDIEEAEMLLAERRHDTFKLKIGRRSVRDDVAHVSKI 212 Query: 186 KKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNAMSPAP 245 K ALGDRA + VDVNQAW+E A L GIDL+EQP R RG +ARL A P Sbjct: 213 KAALGDRARITVDVNQAWNEIDAALGIAALEAAGIDLIEQPTPREQRGALARLAARFIVP 272 Query: 246 IMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGTMLEG 305 IMADE + EDA +L R A VFALKIAK+GG A++RTA++A+AAG+ALYGGTMLEG Sbjct: 273 IMADEGVTGPEDALDLVRGSCADVFALKIAKSGGIYAMMRTAAVADAAGVALYGGTMLEG 332 Query: 306 GLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLSLDEE 365 +G++ASAH F L +L+W TELFGPLLL +D+++ YRDF+LH+P PGLGL +DEE Sbjct: 333 SIGSIASAHGFSALPQLSWGTELFGPLLLKDDVVTARPQYRDFDLHLPEGPGLGLQIDEE 392 Query: 366 RLAFFRRDK 374 +LAF+RRDK Sbjct: 393 KLAFYRRDK 401 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: 424 Number of extensions: 17 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: 403 Length adjustment: 31 Effective length of query: 351 Effective length of database: 372 Effective search space: 130572 Effective search space used: 130572 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