Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate AZOBR_RS04385 AZOBR_RS04385 adenylosuccinate lyase
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__azobra:AZOBR_RS04385 Length = 431 Score = 159 bits (402), Expect = 2e-43 Identities = 128/434 (29%), Positives = 199/434 (45%), Gaps = 16/434 (3%) Query: 19 MRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAACRAELYDPLALAEAVATA 78 M ++ R + + EA A+A GV+P A A + + E+ + E Sbjct: 10 MSRIWEPENRFRIWFEIEAHACDAQAELGVIPKEAAAAVWERGKWEID---RIDEIERET 66 Query: 79 GNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALALLEQDLQRLAE 138 + I + L V R+VH G TS D +D+ L +Q+ +A LL D+ +L Sbjct: 67 RHDVIAFLTNLAEHVGP----EARFVHQGMTSSDVLDTCLAVQMTQAADLLLDDMDKLLA 122 Query: 139 VLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELRPRLLVLQFGG 198 VL +A H DT GR+ HA P T G+KLAG A R R+RL + R + G Sbjct: 123 VLKRRAYEHKDTVTIGRSHGIHAEPTTFGLKLAGHYAAFARGRERLVQARADIATCAISG 182 Query: 199 ASGTLAALGEQALPVAAALAEELGLALPEQPWHTQ---RDRLVEFASVLGLVAGSLGKFG 255 A GT A + + V +A ++GL +P TQ RDR + SVLG++A S+ Sbjct: 183 AVGTFANIDPR---VEQHVAAKMGLT--PEPVSTQVIPRDRHAFYFSVLGVIASSIENLA 237 Query: 256 RDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATRAPGLVSTLFAAMPQ 315 ++ L +TE E E G+ GSS MPHKRNPV S L A V + Sbjct: 238 VEIRHLQRTEVREAEEYFHPGQKGSSAMPHKRNPVLSENLTGLARIVRAAVVPALENVAL 297 Query: 316 EHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRRNLGLTHGLVLAEAV 375 HER + E P+ + AL + G+++ L V +RM++NL GLV ++ V Sbjct: 298 WHERDISHSSVERMFGPDATVTLDFALARLTGMMDKLVVYPERMQKNLDDLGGLVFSQRV 357 Query: 376 SIALARR-IGREAAHHLVEQCCRRAVEQRRELRAVLGEEARVSAELSGDELDRLLDPAHY 434 +AL + + RE ++ V++ + E+ +L +A V+ +S + L + D ++ Sbjct: 358 LLALTQAGMSREDSYKAVQRNAMQVWEKGGNFLDLLSSDADVAKHISRETLAPMFDMTYH 417 Query: 435 LGQARAWVERALAE 448 +R E Sbjct: 418 TKNVDMVFKRVFGE 431 Lambda K H 0.320 0.133 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: 383 Number of extensions: 12 Number of successful extensions: 2 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: 459 Length of database: 431 Length adjustment: 32 Effective length of query: 427 Effective length of database: 399 Effective search space: 170373 Effective search space used: 170373 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 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