Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate Ac3H11_600 Galactonate dehydratase (EC 4.2.1.6)
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_600 Length = 382 Score = 166 bits (421), Expect = 8e-46 Identities = 117/350 (33%), Positives = 180/350 (51%), Gaps = 19/350 (5%) Query: 34 VEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQR 91 ++IE D+G GWGE + G A AA V + +LIG+DPR E W VLY +G Sbjct: 18 LKIETDEGITGWGEPVLEGRAHTVAAAVDELADYLIGKDPRHIEDHWTVLYRGGFYRGG- 76 Query: 92 GLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASE 151 G+ ++AL+GID ALWDIKGK G +S LLGG R ++ Y+ DR S+ A+ Sbjct: 77 GVHMSALAGIDQALWDIKGKALGVPVSELLGGNVRSHIKVYSW-----IGGDRPSETAAA 131 Query: 152 MAERRAEGFHACKI----KIGF-----GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVT 202 A GF A K+ ++ + VE L+ +AAVREA+GP++ + +D + Sbjct: 132 AQAAVARGFTAVKMNGTEEVQYVDSYDKVERCLQNVAAVREAVGPNVGIGVDFHGRVHRP 191 Query: 203 EAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQALSAGA 262 A L + + + EEPV+ E +A + P+A GE + R+ + L G Sbjct: 192 MAKVLVKELEPYKLMFIEEPVLSEHEEALKEIARISSTPIALGERLYSRWDFKRVLQGGY 251 Query: 263 VDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVN 322 DI+QPD GG +E +KIA++A + V + H + +AA LQ A ++ Sbjct: 252 ADIIQPDPSHAGGITETRKIASMAEAYDVALALHCPLGPIALAANLQLDAVCYNAFIQEQ 311 Query: 323 PIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372 + + +++ ++ E +G+V IP+GPGLGIE+N D + E Sbjct: 312 SLG--IHYNQANDLMDYVSNPEVFAYEDGMVAIPNGPGLGIEVNEDYVRE 359 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: 404 Number of extensions: 17 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: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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