Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_012275539.1 SHAL_RS02065 mandelate racemase/muconate lactonizing enzyme family protein
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_000019185.1:WP_012275539.1 Length = 373 Score = 202 bits (515), Expect = 9e-57 Identities = 116/359 (32%), Positives = 196/359 (54%), Gaps = 29/359 (8%) Query: 32 VLVEIECDDGTVGWGECLGPARPNAAVVQA---------YSGWLIGQDPRQTEKIWAVLY 82 V+V++ D G VG GE A ++A LIG++ + E++W +Y Sbjct: 28 VIVKVHTDKGIVGIGEADSSPLVVQACIEAPQTNFYCNGLKRLLIGENALEIERLWNKMY 87 Query: 83 NALRDQGQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNV 142 G+RG + A+S IDIALWDI G+ YG + LLGG++RE +R Y T Sbjct: 88 WGSNYMGRRGAGIHAISAIDIALWDIAGQFYGVPVHTLLGGKYREKIRCYGTFI----PA 143 Query: 143 DRVSDNASEMAERRAEGFHACKIKIGFGV-----EEDLRVIAAVREAIGPDMRLMID-AN 196 D+ DN + + + +GF + IK G GV + D ++ AVREA GP+M + ID A+ Sbjct: 144 DKPEDNVAIVQGLKDQGFTS--IKFGGGVMGDDPDTDYAIVKAVREAAGPEMEVQIDLAS 201 Query: 197 HGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQ 256 +T + + R F ++W EEPV+ + L +Y ++ +AGGE+ RY + Sbjct: 202 KWHTCGHSAMMAKRLEEFNLNWIEEPVLADSLISYEKLSRQVSQKIAGGESLTTRYEFQE 261 Query: 257 ALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTP 316 ++ DI+QPD+ CGG +E++KI +A ++G +++PH + TG+ + A++ F+AA Sbjct: 262 FITKSNADIVQPDITRCGGITEMKKIYDIAQMNGTQLIPHGFSTGILLHASVHFLAACEQ 321 Query: 317 DPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTEFRM 375 +MEF ++ +P ++++ L+ NG V + D PGLGIE++ + + ++R+ Sbjct: 322 G--------TLMEFSQSSSPLFTSLVKNQLQFDNGFVAVSDAPGLGIELDEELIAKYRV 372 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: 378 Number of extensions: 20 Number of successful extensions: 5 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: 373 Length adjustment: 30 Effective length of query: 348 Effective length of database: 343 Effective search space: 119364 Effective search space used: 119364 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 Sep 24 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