Align 3-Carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) (characterized)
to candidate 3610093 Dshi_3474 fumarate lyase (RefSeq)
Query= BRENDA::Q2HNZ1 (353 letters) >FitnessBrowser__Dino:3610093 Length = 348 Score = 260 bits (664), Expect = 4e-74 Identities = 159/345 (46%), Positives = 203/345 (58%), Gaps = 8/345 (2%) Query: 7 EHPFLSGLFGDSEIIELFSAKADIDAMIRFETALAQAEAEASIFADDEAEAIVSGLSEFA 66 ++ GLF D EI LFSA+ +E AL EA+ ++ +A I + +++F Sbjct: 6 QNRLFDGLFADPEIAALFSAETMFAHFRHYEMALT--EAQGAVGRVKDAARIAARIAKFE 63 Query: 67 ADMSALRHGVAKDGVVVPELIRQMRAAVAGQGADKVHFGATSQDVIDTSLMLRLKMAAEI 126 A+ V +DGV VP + + AA+ G A VH ATSQD++DTSL L L+ +E+ Sbjct: 64 IAPDAISDRVTQDGVPVPAYVAALEAAL-GVDAAAVHLDATSQDLMDTSLALSLRRLSEV 122 Query: 127 IATRLGHLIDTLGDLASRDGHKPLTGYTRMQAAIGITVADRAAGWIAPLERHLLRLETFA 186 +A RL +I L L + G + L G TRMQAA+ I VA R W PL R R Sbjct: 123 LAARLDRVIVALDGLQAAQGARTLMGRTRMQAALPIPVATRLEAWQTPLLRARDRFPEAR 182 Query: 187 QNGFALQFGGAAGTLEKLGDNAGAVRADLAKRLGLADR-PQWHNQRDGIPEFANLLSLVT 245 LQFGG G + A+ LAK L L P WH+ RDG+ + L+LVT Sbjct: 183 AGVEQLQFGGPVG---QRSPQMAAIAERLAKALDLPPPGPVWHSTRDGVVGYGTWLALVT 239 Query: 246 GTLGKFGQDIALMAEIG-SEIRLSGGGGSSAMPHKQNPVNAETLVTLARFNAVQISALHQ 304 G+LGK GQDIALM++ G + RLSGGG SSAMPHKQNP+ AETLVTLARFNAVQI LHQ Sbjct: 240 GSLGKMGQDIALMSQQGLDDARLSGGGTSSAMPHKQNPIAAETLVTLARFNAVQIGGLHQ 299 Query: 305 SLVQEQERSGAGWMLEWLTLPQMVTATGTSLLVAERLAAQIDRLG 349 ++V EQERSGA W LEW+ LPQ+ ATG +L A L I+ LG Sbjct: 300 AMVHEQERSGAAWALEWMILPQICEATGAALRHAAALLDSIETLG 344 Lambda K H 0.318 0.133 0.376 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: 347 Number of extensions: 17 Number of successful extensions: 5 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: 353 Length of database: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 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 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