Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate RR42_RS25850 RR42_RS25850 3-carboxy-cis,cis-muconate cycloisomerase
Query= uniprot:A0A0C4YE08 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS25850 Length = 456 Score = 367 bits (942), Expect = e-106 Identities = 213/454 (46%), Positives = 264/454 (58%), Gaps = 13/454 (2%) Query: 1 MPTSSRLTDPM-----FGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAI 55 +P +S + D + FG+A FSD A +QR +D E ALA+AEA GVIPA+AAE I Sbjct: 6 VPMASTVVDSILFRDAFGTARMREIFSDRALIQRYIDAEIALAKAEARVGVIPAEAAEVI 65 Query: 56 AATCRAGEIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTG 115 A R IDFD + G +PLV QL A RYVHWGAT+QD +DT Sbjct: 66 ARESRIERIDFDHMREETDIVGYPILPLVHQLVGMCG----DAGRYVHWGATTQDIMDTA 121 Query: 116 MVLQLREALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDAL 175 + LQ+R+AL ++D D++ L A LA +HRDTPM RT LQ ALP TFG K A WL Sbjct: 122 VALQVRDALDSIDTDIRELRAILADLAVKHRDTPMAGRTHLQQALPVTFGYKVAIWLAMF 181 Query: 176 RRDLRRLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRM 235 R +RL R + A ++F GAAGTLASLG AV A+ L L V T WH RD Sbjct: 182 DRHQQRLAELRPRVAVVEFAGAAGTLASLGDKGFAVQQAMAGELGLGVPATTWHVARDGF 241 Query: 236 VEVATTLGMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLT 295 E L ++TGSLGKIA D+ +M TE AEV EP GRG SSTMP KRNP+ +L Sbjct: 242 AEAVNLLALITGSLGKIALDIMIMASTEFAEVYEPFVKGRGASSTMPQKRNPISSELMLA 301 Query: 296 AAVRVPPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAA 355 A+ V M+ MVQ+ ERA G W AEW +P+ ++GAL Q +GGL VD Sbjct: 302 ASKAVRQHAGLMVDAMVQDFERATGPWHAEWIAIPESFIFSSGALHQAKFALGGLVVDTE 361 Query: 356 RMRANLGVTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAED 415 RM+ NLG+T GLI+AEA M+ + GR AH +V ACR +G TL +AL A L E Sbjct: 362 RMKHNLGITRGLIVAEAVMMGMAPFTGRQQAHDIVYDACRTVNEKGGTLAEALMA-LPEV 420 Query: 416 AAHAGLMDAAALDRVCDPANYAGQAAGFVDAVLA 449 H D AA+DR+ DPANY G A VD +A Sbjct: 421 TQH---FDRAAIDRLTDPANYLGLAPQMVDRAVA 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: 431 Number of extensions: 24 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