Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate AZOBR_RS25270 AZOBR_RS25270 mandelate racemase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__azobra:AZOBR_RS25270 Length = 397 Score = 157 bits (398), Expect = 4e-43 Identities = 112/356 (31%), Positives = 168/356 (47%), Gaps = 30/356 (8%) Query: 32 VLVEIECDDGTVGWGE---CLGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQ 88 + V IE + G GWGE G + AA V A + LIG++ ++ L + + Sbjct: 20 LFVRIETESGIYGWGEGYVTAGKEKVVAAYVDAIAPLLIGREIWNIRQLAQTLLDDFSIR 79 Query: 89 GQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDN 148 L ALS ++IA WDI GK G + LLGG RE +R YA G + + D Sbjct: 80 RTSVDFLCALSAVEIASWDIVGKRAGLPVHKLLGGAVREKIRVYANGWWF--GASSIDDT 137 Query: 149 ASEMAERRAEGFHACKIKIGFG----------VEEDLRVIAAVREAIGPDMRLMIDANHG 198 A+ A A+G+ A K G ++ + + AVREA+GP++ L+ID + Sbjct: 138 ANRAAAVVAQGYDALKWDPIPGPWRNYVDPKDLDHAVENVRAVREAVGPNVELLIDGHRR 197 Query: 199 YTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQAL 258 + AI L +R FGI W+EEP PE LD A VR +P+ GE + + Sbjct: 198 LSPNHAIRLIERLREFGIAWYEEPCPPENLDLTAEVRRTTNVPIVSGEALYTKEQYLPLF 257 Query: 259 SAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAM---- 314 A DI+ PD+ GG + IA LA H + + PH + + + AA ++A+ Sbjct: 258 EKRAADIINPDISAVGGILAMLDIAALAQPHSIAVSPHNFNSPIVGLAATVHLSALVTNF 317 Query: 315 TPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDAL 370 T + VN +EP E + + L +G V IPD PGLG++++ + L Sbjct: 318 TIAELFVNLVEPTRE-----------LALQGLTIADGYVDIPDTPGLGVDLDVEVL 362 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: 425 Number of extensions: 21 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: 397 Length adjustment: 30 Effective length of query: 348 Effective length of database: 367 Effective search space: 127716 Effective search space used: 127716 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