Align Muconate cycloisomerase 1; Cis,cis-muconate lactonizing enzyme I; MLE; Muconate cycloisomerase I; EC 5.5.1.1 (characterized)
to candidate PP_3715 PP_3715 Muconate cycloisomerase 1
Query= SwissProt::P08310 (375 letters) >FitnessBrowser__Putida:PP_3715 Length = 373 Score = 697 bits (1799), Expect = 0.0 Identities = 361/375 (96%), Positives = 370/375 (98%), Gaps = 2/375 (0%) Query: 1 MTSVLIERIEAIIVHDLPTIRPPHKLAMHTMQTQTLVLIRVRCSDGVEGIGEATTIGGLA 60 MTSVLIE I+AIIV DLPTIRP HKLAMHTMQ QTLV++R+RCSDGVEGIGEATTIGGLA Sbjct: 1 MTSVLIEHIDAIIV-DLPTIRP-HKLAMHTMQQQTLVVLRLRCSDGVEGIGEATTIGGLA 58 Query: 61 YGYESPEGIKANIDAHLAPALVGLPADNINAAMLKLDKLAKGNTFAKSGIESALLDAQGK 120 YGYESPEGIKANIDA+LAPAL+GLPADNINAAMLKLDKLAKGNTFAKSGIESALLDAQGK Sbjct: 59 YGYESPEGIKANIDAYLAPALIGLPADNINAAMLKLDKLAKGNTFAKSGIESALLDAQGK 118 Query: 121 RLGLPVSELLGGRVRDSLEVAWTLASGDTARDIAEAQHMLEIRRHRVFKLKIGANPLAQD 180 RLGLPVSELLGGRVRDSLEVAWTLASGDTARDIAEAQHML+IRRHRVFKLKIGANP+AQD Sbjct: 119 RLGLPVSELLGGRVRDSLEVAWTLASGDTARDIAEAQHMLDIRRHRVFKLKIGANPVAQD 178 Query: 181 LKHVVAIKRELGDSASVRVDVNQYWDESQAIRACQVLGDNGIDLIEQPISRINRSGQVRL 240 LKHVVAIKRELGDSASVRVDVNQYWDESQAIRACQVLGDNGIDLIEQPISRINR+GQVRL Sbjct: 179 LKHVVAIKRELGDSASVRVDVNQYWDESQAIRACQVLGDNGIDLIEQPISRINRAGQVRL 238 Query: 241 NQRSPAPIMADESIESVEDAFSLAADGAASIFALKIAKNGGPRAVLRTAQIAEAAGIALY 300 NQRSPAPIMADESIESVEDAFSLAADGAASIFALKIAKNGGPRAVLRTAQIAEAAGIALY Sbjct: 239 NQRSPAPIMADESIESVEDAFSLAADGAASIFALKIAKNGGPRAVLRTAQIAEAAGIALY 298 Query: 301 GGTMLEGSIGTLASAHAFLTLRQLTWGTELFGPLLLTEEIVNEPPQYRDFQLHIPRTPGL 360 GGTMLEGSIGTLASAHAFLTLRQLTWGTELFGPLLLTEEIVNEPPQYRDFQLHIP TPGL Sbjct: 299 GGTMLEGSIGTLASAHAFLTLRQLTWGTELFGPLLLTEEIVNEPPQYRDFQLHIPHTPGL 358 Query: 361 GLTLDEQRLARFARR 375 GLTLDEQRLARFARR Sbjct: 359 GLTLDEQRLARFARR 373 Lambda K H 0.319 0.136 0.385 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: 591 Number of extensions: 9 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: 375 Length of database: 373 Length adjustment: 30 Effective length of query: 345 Effective length of database: 343 Effective search space: 118335 Effective search space used: 118335 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 (21.7 bits) S2: 50 (23.9 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