Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate WP_086508615.1 BZY95_RS03585 adenylosuccinate lyase family protein
Query= curated2:O31385 (451 letters) >NCBI__GCF_002151265.1:WP_086508615.1 Length = 457 Score = 281 bits (720), Expect = 2e-80 Identities = 180/466 (38%), Positives = 239/466 (51%), Gaps = 24/466 (5%) Query: 1 MSTALSPLLAPMLSSAAMRAACDDRSTLQNMLDFEAALARAEAATGVIPAAAVGPIETAC 60 MS AL L P +S A+ + C + + ML FE ALA + A G++P + A Sbjct: 1 MSDAL--LQHPFMSQTAL-SECSAEAMVAGMLAFELALAEVQEARGLLPEGVAAQMRKAL 57 Query: 61 KAATFDIAALAEAATRSGNLAIPLVKALTANVAKADAEAARYVHWGATSQDVIDTATMLT 120 + FDI+++ GN AIP VK A + AE R+ H GATSQDVID+A ML Sbjct: 58 EGHAFDISSIGAGVASGGNAAIPFVKQARAALP---AELRRHFHLGATSQDVIDSALMLL 114 Query: 121 LRAAIDALDADLSRAIKGFAALARNHRNTAMVARTWLQHALPMPFGLKAAEYAASLARAR 180 L+ + ALD L R AL + H T MV RT +Q ALP+ FG+K A + L +AR Sbjct: 115 LKPRLAALDTLLRRCRSAALALMQAHETTVMVGRTLMQQALPITFGVKVAHWGIGLEQAR 174 Query: 181 CRLRRLSRDGLALQFGGAAGTLAAL---------------GDKGLVVAERLAQELNLPLP 225 CRL L L +QFGGA + L G GL + + LAQ L L +P Sbjct: 175 CRLATLE---LPVQFGGAVAVHSGLDGPGLDGQGSDEADPGGLGLELMDALAQRLELSVP 231 Query: 226 EAPWHTHRDRIAEAASALAILAGSCGKIARDVSLMMQTDVAEAFEPAGEGRGGSSTMPHK 285 PWHT R I A+AL +AG+ K+A DV+L+ QT+V E EP GEG G SS+MPHK Sbjct: 232 VLPWHTDRQPIHALATALDAVAGAAEKLALDVALLTQTEVGEVSEPGGEGMGESSSMPHK 291 Query: 286 RNPVAAASALGCATMAPQLAATIFAAQVQDHERSAGPWHAEWPTLPQLMLVTSGALAAIV 345 RNPV A G A + I A Q ER G WHAEW L L+ GAL Sbjct: 292 RNPVRCALIRGAARQVHGHVSVILNAHAQPLERGLGEWHAEWTPLLDSALLVEGALEQAA 351 Query: 346 DIAEGLDVDAARMRSNLDATHGLIMAEAVTFALAERIGKSDAHHLIEAASKRAVAEKKHL 405 + EGL+V MR NL AT G IMAE V+ LA +G+ A + A++ A + Sbjct: 352 VLLEGLEVHPEAMRRNLAATGGGIMAEPVSRLLAPTLGQEAAKRISAEAAEAARLQGVAY 411 Query: 406 REVLAADSQVTAHLSPEKIAALFEPMAYQGASQAMIDRLLDSLERD 451 + L A ++ + + + +P Y G+SQA + R L+R+ Sbjct: 412 SDALQAHPELQGQVEAQALRQATDPALYLGSSQAQVRRAAAWLQRE 457 Lambda K H 0.318 0.128 0.362 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: 401 Number of extensions: 18 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: 451 Length of database: 457 Length adjustment: 33 Effective length of query: 418 Effective length of database: 424 Effective search space: 177232 Effective search space used: 177232 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 (21.8 bits) S2: 51 (24.3 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