Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate BWI76_RS13690 BWI76_RS13690 muconate and chloromuconate cycloisomerase
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__Koxy:BWI76_RS13690 Length = 372 Score = 416 bits (1068), Expect = e-121 Identities = 213/371 (57%), Positives = 273/371 (73%), Gaps = 1/371 (0%) Query: 2 LATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYGN 61 + IE IE+ +VD+PTIRPHKL+M TM QTL IIRV +DGI GIGE+TTIGGL+YG Sbjct: 1 MTATIERIESWLVDIPTIRPHKLSMTTMGCQTLAIIRVTRSDGICGIGEATTIGGLSYGV 60 Query: 62 ESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRLG 121 ESP++I + I+ + PLL GQ + N+NA R++ +++GNTFAKS IETALLDA GK LG Sbjct: 61 ESPEAIVSAINHYLTPLLKGQAADNLNALTSRMDGAVKGNTFAKSAIETALLDAQGKALG 120 Query: 122 LPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAH 181 LPVS LLGG + +LPV WTLASGDTEKDIAE EK+L RRH+ FKLKIGA + DL H Sbjct: 121 LPVSALLGGALTTSLPVLWTLASGDTEKDIAEGEKLLAERRHQAFKLKIGARALETDLRH 180 Query: 182 VIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNAM 241 AI +ALGDRAS+RVDVNQAWD VA + CR L G+DL+EQP+ + + RL+ Sbjct: 181 TRAIVEALGDRASIRVDVNQAWDATVAAKGCRELAAMGVDLIEQPVGAQDNAALVRLSHH 240 Query: 242 SPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGT 301 I+ADE++ D + LA++G + +ALKIAK GGP +VL A +A+AAGI LYGGT Sbjct: 241 IDTAILADEAVATHYDGYRLAQQGFSGAYALKIAKAGGPNSVLALAKVAQAAGIGLYGGT 300 Query: 302 MLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLS 361 MLEG +GT+AS HA+ TL L W +E+FGPLLL +DI+S PL + + E+ +P TPGLG+ Sbjct: 301 MLEGTVGTLASLHAWSTL-PLQWGSEMFGPLLLKDDIVSVPLTFAEGEVTLPQTPGLGVE 359 Query: 362 LDEERLAFFRR 372 LDE++L F+ R Sbjct: 360 LDEDKLRFYSR 370 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: 343 Number of extensions: 18 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: 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 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