Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate HSERO_RS06540 HSERO_RS06540 muconate cycloisomerase
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__HerbieS:HSERO_RS06540 Length = 398 Score = 439 bits (1129), Expect = e-128 Identities = 229/381 (60%), Positives = 283/381 (74%), Gaps = 6/381 (1%) Query: 6 IESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYGNESPD 65 I+ +ET +VDLPTIRPH+L+M TM QTL+++R+ C+DG G+GE TTIGGLAYG ESP+ Sbjct: 16 IDRVETFLVDLPTIRPHQLSMATMNGQTLMLVRLYCSDGSIGVGEGTTIGGLAYGAESPE 75 Query: 66 SIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRLGLPVS 125 +K ID +FAPLL+G D+ + A M RL ++I N FAK IETAL DA G+R GLPVS Sbjct: 76 GMKLAIDTYFAPLLLGADASQIPAIMARLNKAICDNRFAKCAIETALFDALGQRTGLPVS 135 Query: 126 ELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAHVIAI 185 +LLGGR R++LP+AWTLASGDT KDI EAE+ML RRH IFKLKIG EV+ D+AHV AI Sbjct: 136 QLLGGRSRESLPIAWTLASGDTAKDIDEAERMLAQRRHNIFKLKIGRREVDADVAHVAAI 195 Query: 186 KKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNAMSPAP 245 KKALGDR +VRVDVN AW E A R L G +LVEQP++ + +ARL Sbjct: 196 KKALGDRGAVRVDVNMAWSELEAQRGLAGLVDAGCELVEQPVA--SPQALARLKGRHAIA 253 Query: 246 IMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGTMLEG 305 IMADES+ AF LAR G A VFA+KI ++GG RA + A+I +AAGI LYGGTMLEG Sbjct: 254 IMADESLTGPASAFALARIGGADVFAIKIEQSGGLRAAQQVAAIGDAAGIELYGGTMLEG 313 Query: 306 GLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLSLDEE 365 +GT+ASAHAF T +L W TELFGPLLLTE+IL+EPL Y+DF+L +P+ PGLG++LDEE Sbjct: 314 AIGTIASAHAFATFRELQWGTELFGPLLLTEEILAEPLQYQDFQLAIPHRPGLGITLDEE 373 Query: 366 RLAFFRRDK----TSTAIHQA 382 RL +FRRD+ T TA+ A Sbjct: 374 RLQYFRRDRKQGATVTAVRPA 394 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: 407 Number of extensions: 17 Number of successful extensions: 3 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: 398 Length adjustment: 30 Effective length of query: 352 Effective length of database: 368 Effective search space: 129536 Effective search space used: 129536 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