Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate H281DRAFT_00974 H281DRAFT_00974 L-alanine-DL-glutamate epimerase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Burk376:H281DRAFT_00974 Length = 405 Score = 150 bits (380), Expect = 5e-41 Identities = 112/365 (30%), Positives = 175/365 (47%), Gaps = 35/365 (9%) Query: 32 VLVEIECDDGTVGWGECLG----PARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRD 87 + V+++ D G G GE P V +S +L+ DP E++W Y++ Sbjct: 24 IFVKLKTDCGIEGVGEIYSATFHPKAMTHIVDDVFSRYLLDHDPHHVERLWREAYSSGFT 83 Query: 88 QGQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYA-------TGSFKRD 140 Q + +SG+++A WDI GK G + LLGG +R+Y G + D Sbjct: 84 QRPDLTMMGVVSGLEMACWDIIGKAAGKPVYELLGGMVNPRLRSYTYLYPKNNRGEYDYD 143 Query: 141 NVDRVSDNASEMAERRAEGFHACKIKIG------FGVEEDLRVI-------AAVREAIGP 187 + D ++ A+E +R GF A K G + + V+ VREA+G Sbjct: 144 DPDLAAECAAENVKR---GFTAVKFDPAGPYTAYSGHQLSMEVLDRCETFCRRVREAVGS 200 Query: 188 DMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGET 247 L+ + + AI L R + WFEEPV P Q DA A+V IPVA GE Sbjct: 201 KADLLFGTHGQMVPSSAIRLAKRLEKYDPLWFEEPVPPGQEDAMAQVARHTSIPVAAGER 260 Query: 248 WHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAA 307 +Y ++ L AGA ILQ ++ GG E +K+A LA ++ +I PH++ + AA+ Sbjct: 261 LTTKYEFFKLLQAGAASILQLNVARVGGLLEAKKVAALAEVYYAQIAPHLYNGPIGAAAS 320 Query: 308 LQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINR 367 +Q +AA TP+ + I E T + F AVL++PL+ +G + PGLG+E+N Sbjct: 321 IQ-LAACTPNFL-------IQESIGTWDGFHAAVLKKPLQWEDGYIIPSREPGLGVELNM 372 Query: 368 DALTE 372 + + + Sbjct: 373 EVVAQ 377 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: 432 Number of extensions: 27 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: 378 Length of database: 405 Length adjustment: 31 Effective length of query: 347 Effective length of database: 374 Effective search space: 129778 Effective search space used: 129778 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