Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_086509088.1 BZY95_RS06130 galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_002151265.1:WP_086509088.1 Length = 384 Score = 163 bits (412), Expect = 8e-45 Identities = 120/355 (33%), Positives = 177/355 (49%), Gaps = 23/355 (6%) Query: 32 VLVEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQG 89 + ++IE D+G GWGE + G A A V + +LIGQDP + E +W LY A +G Sbjct: 16 LFLKIETDEGCYGWGEPVIEGRAATVEAAVHELADYLIGQDPHRIEHLWNTLYRAGFYRG 75 Query: 90 QRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRA--YA-TGSFKRDNVDRVS 146 L ++A++GID ALWD+KG+ G + LLGG RE +R YA TG DR S Sbjct: 76 GPIL-MSAIAGIDQALWDLKGRDLGVPVHQLLGGAVRERMRMRMYAWTGG------DRPS 128 Query: 147 DNASEMAERRAEGFHACK---------IKIGFGVEEDLRVIAAVREAIGPDMRLMIDANH 197 + + E A GF A K + ++E + +A REA+GP++ + ID + Sbjct: 129 EVGAGARELVARGFTAFKMNGTAEMQIVDSHRKIDEAVARVAEAREAVGPEVGISIDFHG 188 Query: 198 GYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQA 257 A L + + EEP+ PE L A + G P+A GE H R+ Sbjct: 189 RVHRPMAKALLRELEPYHPMFVEEPLAPEHLPALKHIADGLAYPLATGERLHTRFEFRDL 248 Query: 258 LSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPD 317 L+ G +DI+QPDL C G SE KIA LA+ H V + PH + +AA+LQ A Sbjct: 249 LAEGMIDIVQPDLSHCDGISEGLKIAALASAHDVALAPHCPLGPLTLAASLQLDAVSHNA 308 Query: 318 PVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372 ++ + + +++ ++ V + L G IP GPGLG+EI+ + E Sbjct: 309 FIQEQSMG--IHYNQGNDVLDYLVDKSALAIEEGFCAIPQGPGLGVEIDEAFVEE 361 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: 408 Number of extensions: 18 Number of successful extensions: 6 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: 384 Length adjustment: 30 Effective length of query: 348 Effective length of database: 354 Effective search space: 123192 Effective search space used: 123192 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