Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate BPHYT_RS10675 BPHYT_RS10675 muconate cycloisomerase
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__BFirm:BPHYT_RS10675 Length = 385 Score = 429 bits (1104), Expect = e-125 Identities = 218/375 (58%), Positives = 280/375 (74%), Gaps = 2/375 (0%) Query: 1 MLATA--IESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLA 58 M+AT IES++TI+VD+PTIRPH+L++ TM QTLV++R+RCADG+ G+GE TTIGGLA Sbjct: 1 MIATPVKIESVDTILVDVPTIRPHRLSVATMNCQTLVLVRIRCADGLIGVGEGTTIGGLA 60 Query: 59 YGNESPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGK 118 YG ESP+SIK NID +FAPLL G D+ AAM +L +GN FAKS +ETAL DA + Sbjct: 61 YGEESPESIKVNIDTYFAPLLKGMDATRPGAAMAKLRELFQGNRFAKSALETALFDAQAQ 120 Query: 119 RLGLPVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRD 178 RLG+P+SEL GGRVRD++ VAWTLASGDT++DI EAE++ + +RHR+FKLKIG V D Sbjct: 121 RLGVPLSELFGGRVRDSVEVAWTLASGDTQRDIDEAEQVYEAKRHRVFKLKIGTRAVADD 180 Query: 179 LAHVIAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARL 238 +AHV+AI+KA+ R VRVDVNQAW E+ A+ A R G+ L+EQPI+ NR G+ RL Sbjct: 181 VAHVVAIQKAVQGRGEVRVDVNQAWSESDAIWAARRFADAGVTLIEQPIAAENRAGLKRL 240 Query: 239 NAMSPAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALY 298 ++ PIMADE++ DAF +A AA VFA+KIA++GG A+IA AA I LY Sbjct: 241 TDLALVPIMADEALHGPADAFVVASARAADVFAVKIAQSGGLVGAAHVAAIASAANIDLY 300 Query: 299 GGTMLEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGL 358 GGTMLEG +GT+ASA F T +L W TELFGPLLLTE+IL+EPL Y +F LH+P PGL Sbjct: 301 GGTMLEGAVGTIASAQLFSTFGELKWGTELFGPLLLTEEILTEPLRYENFALHLPEGPGL 360 Query: 359 GLSLDEERLAFFRRD 373 G++LD +++ RRD Sbjct: 361 GVTLDWDKIDRLRRD 375 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: 399 Number of extensions: 8 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: 385 Length adjustment: 30 Effective length of query: 352 Effective length of database: 355 Effective search space: 124960 Effective search space used: 124960 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