Align muconate cycloisomerase (EC 5.5.1.1) (characterized)
to candidate HSERO_RS18290 HSERO_RS18290 muconate cycloisomerase
Query= metacyc::MONOMER-14643 (382 letters) >FitnessBrowser__HerbieS:HSERO_RS18290 Length = 386 Score = 436 bits (1121), Expect = e-127 Identities = 219/377 (58%), Positives = 279/377 (74%) Query: 3 ATAIESIETIIVDLPTIRPHKLAMHTMQNQTLVIIRVRCADGIEGIGESTTIGGLAYGNE 62 AT+IE++E +++D+PTIRPH+L+M TM QTLV++R+ DG+ G GE+TTIGGLAYG E Sbjct: 7 ATSIETVEVLLLDVPTIRPHRLSMTTMHRQTLVLVRITGNDGVAGWGEATTIGGLAYGEE 66 Query: 63 SPDSIKTNIDKHFAPLLIGQDSGNVNAAMLRLERSIRGNTFAKSGIETALLDAHGKRLGL 122 SP+SIK NID + PLL+G D+ V A M ++ ++GN FAK IETAL DA +RLG+ Sbjct: 67 SPESIKVNIDTYITPLLLGADANQVAARMHHIDEHVQGNRFAKCAIETALSDALARRLGV 126 Query: 123 PVSELLGGRVRDALPVAWTLASGDTEKDIAEAEKMLDLRRHRIFKLKIGAGEVNRDLAHV 182 P+S L GGRVRD+LP+AWTLASGDT +DI EAEKML RRH +FKLKIGA V +D AHV Sbjct: 127 PLSTLFGGRVRDSLPIAWTLASGDTARDIDEAEKMLAQRRHNLFKLKIGARTVQQDCAHV 186 Query: 183 IAIKKALGDRASVRVDVNQAWDEAVALRACRILGTNGIDLVEQPISRNNRGGMARLNAMS 242 AIK+ALG+R SVRVDVNQAW E A+ + L G+DLVEQPI+ +N G+ RL + Sbjct: 187 AAIKRALGERGSVRVDVNQAWTETEAMLGMQWLADAGVDLVEQPIAASNHDGLRRLRQKN 246 Query: 243 PAPIMADESIECVEDAFNLAREGAASVFALKIAKNGGPRAVLRTASIAEAAGIALYGGTM 302 IMADES+ +DA+ LAR GAA VFA+KI ++GG + A+IA AA + LYGGTM Sbjct: 247 RIAIMADESLHGPQDAYQLARAGAADVFAVKINQSGGLAGAQQVAAIASAAQVELYGGTM 306 Query: 303 LEGGLGTMASAHAFVTLNKLAWDTELFGPLLLTEDILSEPLVYRDFELHVPNTPGLGLSL 362 LEG +GTMASA F T LAW +ELFGPLLLTE+IL+ PL YRDF L +P PGLG++L Sbjct: 307 LEGAIGTMASAQLFATFGTLAWGSELFGPLLLTEEILATPLRYRDFALELPTGPGLGITL 366 Query: 363 DEERLAFFRRDKTSTAI 379 DE+R+ RRD+ + + Sbjct: 367 DEDRVNALRRDRKTPLV 383 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: 427 Number of extensions: 15 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: 386 Length adjustment: 30 Effective length of query: 352 Effective length of database: 356 Effective search space: 125312 Effective search space used: 125312 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