Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate AZOBR_RS26635 AZOBR_RS26635 mandelate racemase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__azobra:AZOBR_RS26635 Length = 393 Score = 288 bits (738), Expect = 1e-82 Identities = 162/386 (41%), Positives = 223/386 (57%), Gaps = 13/386 (3%) Query: 1 MKITAVRTHLLEHRLDTP-FESASMRFDRRAHVLVEIECDDGTVGWGEC--LGPARP-NA 56 M I + T +L+ L+ F S+ F R +LV I DDG VGWGE GPA P + Sbjct: 1 MLIKKIDTFVLKTPLNAKTFYSSQAAFPERNSLLVRITTDDGLVGWGEGGQYGPAEPPES 60 Query: 57 AVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGAS 116 ++ + LIG+ Q +++ LY+ RD GQ+G + ALS IDIALWD+ GK Sbjct: 61 CIIDVLAPRLIGRRADQPVRVFEDLYSFCRDFGQKGTYIEALSAIDIALWDLWGKSLNRP 120 Query: 117 ISMLLGGRWRESVRAYATGSFKRD---NVDRVSDNASEMAER-RAEGFHACKIKIGF-GV 171 + L+GG +R+ V AY TG + D + R+ +E A+R R G A KIKIG + Sbjct: 121 VHALMGGAFRDKVAAYGTGCYYPDYFRDTPRMMAALAEEAQRYREAGLPAIKIKIGLLPI 180 Query: 172 EEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAY 231 +D+ +A VR+ +GPD +M+DANH Y AI +G F + WFEEPV PE Y Sbjct: 181 AQDIERVALVRDVLGPDTLIMVDANHAYNTAGAIRIGRALERFDVRWFEEPVPPEDRQGY 240 Query: 232 ARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGV 291 RVR +P+AGGE + RYG + L+ G +DI QPDLC GGF+E QKI L T HGV Sbjct: 241 RRVRDSIDVPIAGGECEYTRYGFRELLAGGCIDIAQPDLCCAGGFTEWQKILALTTAHGV 300 Query: 292 RIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPI----EPIMEFDRTHNPFRQAVLREPLE 347 VPH+WG+G+ +AAALQ +A P + EP++EFDRTHNP R +L + Sbjct: 301 MTVPHIWGSGIALAAALQALATAPLVPYTALGVPLQNEPMVEFDRTHNPLRDDLLIDNFT 360 Query: 348 AVNGVVTIPDGPGLGIEINRDALTEF 373 V+G + +P G GLG+E++ D L + Sbjct: 361 LVDGCLALPGGAGLGVEVDPDQLARY 386 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: 496 Number of extensions: 24 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: 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 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