Align Muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate RR42_RS21835 RR42_RS21835 muconate cycloisomerase
Query= reanno::WCS417:GFF4626 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS21835 Length = 373 Score = 447 bits (1151), Expect = e-130 Identities = 231/367 (62%), Positives = 276/367 (75%) Query: 6 IESIDTIIVDLPTLRPHKLAMHTMQNQTLVIIRLRCADGIEGIGEATTIGGLSYGNESPD 65 + S++ I+VDLPT+R H+LAM TMQ QTLVI+RLRC+DGIEGIGEATTIGGLSYG+ESP+ Sbjct: 5 VTSVEAILVDLPTIRAHQLAMTTMQRQTLVIVRLRCSDGIEGIGEATTIGGLSYGDESPE 64 Query: 66 SIKVNIDRHFAPLLIGQDASNINAAMLRLERSIRGNTFAKSGIESALLDALGKRLNLPVS 125 IK+ ID + AP L G DA NI+AAM RL RGN FAKS +ESALLDA GKRL LP+S Sbjct: 65 GIKLTIDTYLAPALAGIDACNIHAAMQRLASVARGNRFAKSALESALLDAQGKRLGLPLS 124 Query: 126 ELLGGRVRDALPVAWTLASGNTEKDIAEAEKMLDLRRHRLFKLKIGAGEVSHDLAHVIAI 185 ELLGG VR L WTLASG+T +DI EAE +L RRH FKLKIG V D+AHV AI Sbjct: 125 ELLGGAVRPNLACLWTLASGDTGRDIEEAETLLAERRHNTFKLKIGRRSVRDDVAHVSAI 184 Query: 186 KKALGDRASVRVDVNQAWDEAVALRACKVLGDNGIDLIEQPISRNNRGGMARLNLSSPAP 245 K+ALGDRA V VDVNQAW+EA A +L GIDL+EQP+ R RG +ARL P Sbjct: 185 KRALGDRARVTVDVNQAWNEADAATGIAMLEAAGIDLVEQPVPREQRGALARLAARFVVP 244 Query: 246 IMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTAAIAEAAGIGLYGGTMLEG 305 +MADE++ EDA LAR A VFALKI+K+GG +LRTAA+ +AAGI LYGGTMLEG Sbjct: 245 VMADEAVCGPEDAMELARIAGADVFALKISKSGGIFEMLRTAAVGDAAGIALYGGTMLEG 304 Query: 306 GIGTLASAHAFLTLNKLAWDTELFGPLLLTEDILTEPPVYRDFQLHVSTAPGLGLAIDEE 365 +GT+A+AH F TL +LAW TELFGPLLL +D++T P YRDF LH+ PGLGL +DE+ Sbjct: 305 SVGTIAAAHGFATLPRLAWGTELFGPLLLKDDVVTARPEYRDFALHLPVGPGLGLTLDED 364 Query: 366 RLAFFRR 372 +LA +RR Sbjct: 365 KLAHYRR 371 Lambda K H 0.320 0.137 0.394 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: 433 Number of extensions: 11 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: 375 Length of database: 373 Length adjustment: 30 Effective length of query: 345 Effective length of database: 343 Effective search space: 118335 Effective search space used: 118335 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 (21.8 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