Align Muconate cycloisomerase 1; EC 5.5.1.1; Cis,cis-muconate lactonizing enzyme I; MLE; Muconate cycloisomerase I (uncharacterized)
to candidate WP_015448791.1 R2APBS1_RS16550 dipeptide epimerase
Query= curated2:P95608 (373 letters) >NCBI__GCF_000230695.2:WP_015448791.1 Length = 365 Score = 163 bits (412), Expect = 8e-45 Identities = 113/361 (31%), Positives = 185/361 (51%), Gaps = 11/361 (3%) Query: 4 LSIVSVETTILDVPLVRPHKFATTSMTAQPLLLVAVTTAGGVTGYGEGVVPGGPWWGGES 63 + I ++ +L VPL P K A ++ ++V V T G GYGE P G++ Sbjct: 1 MKITDIQFGMLRVPLKTPFKTALRTVNTVEDIVVMVHTDTGQVGYGEA--PATAVITGDT 58 Query: 64 VETMQAIVERYIVPVLLGRGVDEITGIMPDIERVVANARFAKAAVDVALHDAWARSLGVP 123 ++ + YI P L+G+ + E+ + I+ + AKAAV++A++D W + G P Sbjct: 59 HGSIIDAIRHYISPRLIGQDIAELNHLTQLIQSSMEKNTSAKAAVEIAVYDLWGQLYGAP 118 Query: 124 VHTLLGGAFRK-SVDVTWALGAAPAEEIIEEALDLVESKRHF-SFKLKMGALDPAVDTAR 181 ++ LLGG + D+T + ++++ +++ VE R F S K+K+G D VD R Sbjct: 119 LYKLLGGGDPVITTDIT--ISVDYIDKMVADSVSAVE--RGFESLKIKVGK-DIGVDIER 173 Query: 182 VVQIAQALQGKAGVRIDVNARWDRLTALKYVPRLVEGGV--ELIEQPTPGEQLEVLAELN 239 V I A++G+A +R+D N W A+ + L E G+ ELIEQP L + + Sbjct: 174 VKAIYAAVEGRALLRLDANQGWTAKQAVYALQTLEEAGIKLELIEQPVKARDLAGMRYVT 233 Query: 240 RLVPVPVMADESVQTPHDALEVARRGAADVIALKTTKCGGLQKSREVVAIAKAAGIACHG 299 V PVMADESV P + +E+ R AAD+I +K K GG+ + + IA GI C Sbjct: 234 ERVHTPVMADESVFGPMEVIELIRLRAADIINIKLMKTGGISNAVRIADIAAMHGIECMI 293 Query: 300 ATSIEGPIGTAASIHFACAEPGIDFGTELFGPLLFSEELLQEPIRYADGQVFLPEGPGLG 359 +E I AA++H A A+ + +L GP L + + + + ++ + + PGLG Sbjct: 294 GCMLETSISVAAAVHVAVAKSNVITKVDLDGPSLCQFNPVDGGVIFNESEISVTDAPGLG 353 Query: 360 V 360 + Sbjct: 354 I 354 Lambda K H 0.318 0.136 0.400 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: 278 Number of extensions: 21 Number of successful extensions: 4 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: 373 Length of database: 365 Length adjustment: 30 Effective length of query: 343 Effective length of database: 335 Effective search space: 114905 Effective search space used: 114905 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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