Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate BWI76_RS19325 BWI76_RS19325 mandelate racemase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Koxy:BWI76_RS19325 Length = 384 Score = 130 bits (326), Expect = 8e-35 Identities = 108/346 (31%), Positives = 168/346 (48%), Gaps = 22/346 (6%) Query: 33 LVEIECDDGTVGWGECLGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRG 92 ++ I DDGT G+ V + ++GQDP E+IW L + R + Sbjct: 37 MLTITADDGTRGFSFAPPEVVRPFVVNTFFRKVMVGQDPFNRERIWQDLNHWQRGSAHQ- 95 Query: 93 LSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVS--DNAS 150 L+ ALS ++ ALWD+ G+ + LLGG +R++V AY + D +S + + Sbjct: 96 LTERALSFVEQALWDLIGRKLNMPVYKLLGG-YRDTVPAYGSTMCGDDLPGGLSTPEEYA 154 Query: 151 EMAERR-AEGFHACKIK-----IGFGVEE--DLRVIAAVREAIGPDMRLMIDANHGYTVT 202 AE+ A G+ A K+ I F D++ AAVREA+GPD+ LMID H Y+ Sbjct: 155 AFAEKLVARGYKAIKLHTWMPPIAFAPNPKMDIKACAAVREAVGPDIDLMIDGYHWYSRA 214 Query: 203 EAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGM-WQALSAG 261 EA+ +G WFEEP+ + + +YA + IP+ G E++ G++ M + + AG Sbjct: 215 EALWIGKELEKLNFAWFEEPMEEDSMSSYAWLAENLSIPIVGPESFGGKHHMRAEWVKAG 274 Query: 262 AVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDP-VR 320 A DIL+ G GG + K+A LA G+ H G G AA+L + A+ Sbjct: 275 ACDILRAGANGVGGITPTMKVAALAESFGMDCEVH--GNG---AASLAVVGAIRNCRWYE 329 Query: 321 VNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEIN 366 + P +++D V +P++ G V + PGLG +IN Sbjct: 330 RGLLHPFLDYDEPAAYLNSIV--DPMDD-QGFVHLSQRPGLGEDIN 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: 416 Number of extensions: 24 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: 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 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