Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_011840078.1 RSPH17029_RS20915 mandelate racemase/muconate lactonizing enzyme family protein
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_000015985.1:WP_011840078.1 Length = 393 Score = 168 bits (425), Expect = 3e-46 Identities = 135/392 (34%), Positives = 191/392 (48%), Gaps = 34/392 (8%) Query: 2 KITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECLGPARPNAAVVQA 61 +ITAVR L S ++ D H L+ + D G G+G N A+VQA Sbjct: 15 RITAVRVAPLLGESPQGGWSHEIKADDSVHALIALHTDAGISGYGSVF----TNGALVQA 70 Query: 62 YSG----WLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASI 117 + L+G++ + ++I L+ G+ G +SGIDIA+WDI G+ G S+ Sbjct: 71 AADVLTPLLLGENALEPDRIAEKLHQNTFWMGRGGSITHTISGIDIAMWDILGQATGLSV 130 Query: 118 SMLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHACKIKIG-FGVEEDL- 175 LLGGR R+ V+ Y S D +R+ + +A RA GF A KI G FG D Sbjct: 131 GRLLGGRHRDRVQPYC--SLLMDMPERME---AVIAPHRAAGFRAFKIGWGPFGRRGDAG 185 Query: 176 ---RVIAAVREAIGPDMRLMIDANHGYT-----VTEAITLGDRAAGFGIDWFEEPVVPEQ 227 +I A R A+G D +L++DA + A+ A + + WFEE + P+ Sbjct: 186 LDRAIIDAARTAVGADAQLLVDAGASDAYWPNGLKWAMNTAAMLADYDVGWFEEALPPDA 245 Query: 228 LDAYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLAT 287 ++ + +R P+P+AGGE R L GA DI+QPD+ GG SE ++IA +A Sbjct: 246 IEDFIALRRMSPVPIAGGEVLTRRQSFAPWLVRGAFDIVQPDVTKVGGISEQRRIAWMAR 305 Query: 288 LHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDR-THNPFRQAVLREPL 346 G+R V H W T +AA LQ AAM PD V I DR T PF L Sbjct: 306 DFGIRYVGHGWNTAFGLAADLQLAAAM-PDCTLVEYIGGSAYVDRLTTRPF-------VL 357 Query: 347 EAVNGVVTIPDGPGLGIEINRDALTEFRMPDP 378 +A G++ IPD PGLG+ + L + PDP Sbjct: 358 DA-EGMLAIPDLPGLGVSPDPALLARY-TPDP 387 Lambda K H 0.321 0.138 0.431 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: 436 Number of extensions: 32 Number of successful extensions: 4 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: 378 Length of database: 393 Length adjustment: 30 Effective length of query: 348 Effective length of database: 363 Effective search space: 126324 Effective search space used: 126324 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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