Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate WP_010442059.1 G7G_RS0114000 adenylosuccinate lyase
Query= curated2:O31385 (451 letters) >NCBI__GCF_000192475.1:WP_010442059.1 Length = 434 Score = 157 bits (396), Expect = 8e-43 Identities = 124/423 (29%), Positives = 187/423 (44%), Gaps = 9/423 (2%) Query: 9 LAPMLSSAAMRAACDDRSTLQNMLDFEAALARAEAATGVIPAAAVGPIETACKAATFDIA 68 + P S M A S + + EA A A GVIP + A K FD+A Sbjct: 1 MIPRYSRPEMVAIWSPESKFRIWYEIEAHACDAMADLGVIPRENAEAVWKA-KDVEFDVA 59 Query: 69 ALAEAATRSGNLAIPLVKALTANVAKADAEAARYVHWGATSQDVIDTATMLTLRAAIDAL 128 + E + + I + L +V +E AR+VH G TS DV+DT + L A D L Sbjct: 60 RIDEIEAVTKHDVIAFLTHLAEHVG---SEEARFVHQGMTSSDVLDTCLNVQLTRAADIL 116 Query: 129 DADLSRAIKGFAALARNHRNTAMVARTWLQHALPMPFGLKAAEYAASLARARCRLRRLSR 188 +DL + A H+NT + R+ HA P GL A + A + R R+R Sbjct: 117 ISDLEGLLAALKRRAIEHKNTIRIGRSHGIHAEPTTMGLTFARFYAEMDRNLSRMRDARA 176 Query: 189 DGLALQFGGAAGTLAALGDKGLVVAERLAQELNL-PLPEAPWHTHRDRIAEAASALAILA 247 + GA GT A + + V E + +L L P P + RDR A + L ++A Sbjct: 177 EIATGAISGAVGTFANVDPQ---VEEHVCDKLGLVPEPISTQVIPRDRHAAFFATLGVIA 233 Query: 248 GSCGKIARDVSLMMQTDVAEAFEPAGEGRGGSSTMPHKRNPVAAASALGCATMAPQLAAT 307 S IA ++ M +T+V E E G+ GSS MPHK+NPV + G A M Sbjct: 234 SSIENIAIEIRHMQRTEVLEGAEFFSMGQKGSSAMPHKKNPVLTENLTGLARMVRAAVIP 293 Query: 308 IFAAQVQDHERSAGPWHAEWPTLPQLMLVTSGALAAIVDIAEGLDVDAARMRSNLDATHG 367 HER E P + A A + + + + + M N++ G Sbjct: 294 AMENVALWHERDISHSSVERMIGPDATITLDFAFARLTGVIDKMLIFPENMLENMNKFPG 353 Query: 368 LIMAEAVTFALAER-IGKSDAHHLIEAASKRAVAEKKHLREVLAADSQVTAHLSPEKIAA 426 L+M++ V AL + + + DA+ +++ + + + +E L AD+ VTA LSPE+I Sbjct: 354 LVMSQRVLLALTQAGVSREDAYSMVQRNALKVWEHRTDFKEELLADADVTAALSPEEIEE 413 Query: 427 LFE 429 F+ Sbjct: 414 KFD 416 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: 301 Number of extensions: 8 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: 434 Length adjustment: 32 Effective length of query: 419 Effective length of database: 402 Effective search space: 168438 Effective search space used: 168438 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