Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate BPHYT_RS16405 BPHYT_RS16405 galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS16405 Length = 382 Score = 167 bits (422), Expect = 6e-46 Identities = 118/356 (33%), Positives = 185/356 (51%), Gaps = 31/356 (8%) Query: 34 VEIECDDGTVGWGECL--GPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQR 91 ++IE D+G VGWGE + G A AA V+ S +LIG+DP E W V+Y R R Sbjct: 18 LKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLIEDHWQVMY---RSGFYR 74 Query: 92 G--LSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNA 149 G ++++A++G+D ALWDIKGKH+G I LLGG+ R+ ++ Y+ D V++NA Sbjct: 75 GGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSW--IGGDRPSDVANNA 132 Query: 150 SEMAERRAEGFHACKIKIGFGVEEDLRVI-------------AAVREAIGPDMRLMIDAN 196 + ER GF A K+ E+L++I AAVREA+GP++ + +D + Sbjct: 133 RAVVER---GFKAVKMN----GSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIGVDFH 185 Query: 197 HGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQ 256 A L + + + EEPV+ E +A + P+A GE + R+ Sbjct: 186 GRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKH 245 Query: 257 ALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTP 316 LS G VDI+QPD GG +E +KIA++A + V + H + +A LQ A Sbjct: 246 ILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQIDAVSYN 305 Query: 317 DPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTE 372 ++ + + +++ ++ E + +G V+IP GPGLGIE+N + + E Sbjct: 306 AFIQEQSLG--IHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVRE 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: 447 Number of extensions: 25 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: 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 Apr 09 2024. 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