Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate Ga0059261_3173 Ga0059261_3173 adenylosuccinate lyase
Query= curated2:Q9I6Q8 (459 letters) >FitnessBrowser__Korea:Ga0059261_3173 Length = 437 Score = 166 bits (420), Expect = 1e-45 Identities = 139/430 (32%), Positives = 203/430 (47%), Gaps = 24/430 (5%) Query: 19 MRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAACRAELYDPLALAEAVATA 78 M A++S R + EA A A GVVP +A L+D A + A Sbjct: 10 MTAIWSPETRFGIWFEIEAHATEALADLGVVPKSAAKA--------LWDWWATKPQIDVA 61 Query: 79 GNSAIPLVK-----ALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRALALLEQDL 133 AI V A VA + R++H G TS D +D+ L +QL RA +L DL Sbjct: 62 AIDAIEAVTKHDVIAFLTWVAENVGDEARFMHQGMTSSDVLDTCLSVQLVRASDILLDDL 121 Query: 134 QRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRELRPRLLV 193 +L EVL +A H TP GR+ HA PVT G+K+A R++ RL+ R + Sbjct: 122 DQLLEVLKRRAYEHKLTPTIGRSHGIHAEPVTFGLKMAEAYAEFARNKARLQAARADIAT 181 Query: 194 LQFGGASGTLAALGEQALPVAAALAEELGLALPEQPWHTQ---RDRLVEFASVLGLVAGS 250 GA GT A + + V A +AE+LGLA+ +P TQ RDR F + LG++A S Sbjct: 182 CAISGAVGTFANIDPR---VEAHVAEKLGLAV--EPVSTQVIPRDRHAMFFATLGVIASS 236 Query: 251 LGKFGRDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATRAPGLVSTLF 310 + + +V L +TE E E G+ GSS MPHKRNPV + L A Sbjct: 237 IERLAVEVRHLQRTEVLEAEEYFSPGQKGSSAMPHKRNPVLTENLTGLARMVRSATIPAM 296 Query: 311 AAMPQEHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRRNLGLTHGLV 370 + HER + E P+ + AL + G+++ L V RM++NL GLV Sbjct: 297 ENVALWHERDISHSSVERYIGPDATITLDFALARLTGVIDKLLVYPARMQKNLDRMGGLV 356 Query: 371 LAEAVSIALARR-IGREAAHHLVEQCCRRAVEQRRELR--AVLGEEARVSAELSGDELDR 427 ++ V +AL + + RE ++ LV++ + E EL +L + V+A LS E++ Sbjct: 357 HSQRVLLALTQAGVSREDSYRLVQRNAMKVWESDGELSLLELLKADPEVTAALSAQEIEE 416 Query: 428 LLDPAHYLGQ 437 D ++ Q Sbjct: 417 KFDLDYHFRQ 426 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: 382 Number of extensions: 16 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: 459 Length of database: 437 Length adjustment: 33 Effective length of query: 426 Effective length of database: 404 Effective search space: 172104 Effective search space used: 172104 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