Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate H281DRAFT_02594 H281DRAFT_02594 3-carboxy-cis,cis-muconate cycloisomerase
Query= uniprot:A0A0C4YE08 (470 letters) >FitnessBrowser__Burk376:H281DRAFT_02594 Length = 456 Score = 358 bits (920), Expect = e-103 Identities = 208/453 (45%), Positives = 261/453 (57%), Gaps = 13/453 (2%) Query: 2 PTSSRLTDPM-----FGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIA 56 P SS + D + FG+A A FSD A VQR +D E ALA+AEA GVIP DAA+ IA Sbjct: 7 PLSSTVFDSILFRDAFGTAKMRALFSDYALVQRYIDVEVALAKAEARVGVIPTDAADVIA 66 Query: 57 ATCRAGEIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGM 116 + IDFD + G +PLV QL +A RYVHWGAT+QD +DT + Sbjct: 67 RESQIERIDFDHMREETDIVGYPILPLVHQLVGMCG----EAGRYVHWGATTQDIMDTAV 122 Query: 117 VLQLREALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALR 176 LQ+R+AL ++DAD++ L L+ +HRDTPM RT LQ ALP TFG K A WL Sbjct: 123 ALQVRDALDSIDADIRELRGILVDLSKKHRDTPMAGRTHLQQALPVTFGYKTAIWLAMFD 182 Query: 177 RDLRRLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMV 236 R +R+ R + A ++F GAAGTLASLG V AL + L L V T WH RD Sbjct: 183 RHQQRIAQLRPRVAVVEFAGAAGTLASLGDKGFDVQKALAAELQLGVPATTWHVARDGFA 242 Query: 237 EVATTLGMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTA 296 E L ++TGSLGKIA D+ +M E EV EP GRG SSTMP KRNP+ +L A Sbjct: 243 EAVNLLALVTGSLGKIATDIMIMASNEFGEVYEPFVKGRGASSTMPQKRNPISSELMLAA 302 Query: 297 AVRVPPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAAR 356 A V M+ M+Q+ ERA G W AEW +P+ LA+GAL Q +GGL VD R Sbjct: 303 AKAVRQQAGLMVDAMIQDFERATGPWHAEWIAIPESFILASGALHQAKFALGGLIVDTDR 362 Query: 357 MRANLGVTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDA 416 M+ NLG++ GLI+AEA M+++ GR AH +V ACR G TL +AL A L E Sbjct: 363 MKHNLGISKGLIVAEAVMMQMAPYTGRQQAHDIVYDACRTVNESGGTLAEAL-AALPEVT 421 Query: 417 AHAGLMDAAALDRVCDPANYAGQAAGFVDAVLA 449 H D A++ + DPANY G A VD +A Sbjct: 422 RH---FDRDAINAMTDPANYLGLAPQMVDRAIA 451 Lambda K H 0.319 0.130 0.380 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: 424 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: 470 Length of database: 456 Length adjustment: 33 Effective length of query: 437 Effective length of database: 423 Effective search space: 184851 Effective search space used: 184851 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