Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate BPHYT_RS06110 BPHYT_RS06110 3-carboxymuconate cyclase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >FitnessBrowser__BFirm:BPHYT_RS06110 Length = 385 Score = 310 bits (793), Expect = 6e-89 Identities = 158/364 (43%), Positives = 235/364 (64%), Gaps = 7/364 (1%) Query: 26 YQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSKDQRHLFVVNENG 85 Y +LVG+YT +S+G+Y FD++TG+ A+ + ++ NPS+L +S+D+R ++ VNE Sbjct: 23 YDMLVGTYTGPKSEGLYVYRFDTKTGE--ATRVSAAQTVNPSYLVVSRDRRFVYAVNEM- 79 Query: 86 PGQTDPV---GRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNYSVAED 142 PG P G +S+F D + L+ +++V S GN+P + SLS DG +L +NYSVA D Sbjct: 80 PGDNGPATQRGGISAFRFDAASGQLTFLNKVSSDGNDPCYLSLSPDGKYLLTANYSVAAD 139 Query: 143 PGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFANDLGAD 202 PGG+ AV P+ ADG++ A V H RQ ++HVHST+ SPDG Y+FA DLGAD Sbjct: 140 PGGSFAVFPLQADGQVGASVLTVHHEGGGPVKGRQDNSHVHSTVFSPDGHYLFAQDLGAD 199 Query: 203 KVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQVAVFDY 262 K+++YR+ P + L P + Q GSGPRHL+F ADGKHA+LT EM+A V+ FDY Sbjct: 200 KLYSYRYTPDGSRGL-FGPTDWRYNQEKAGSGPRHLVFGADGKHAYLTSEMAATVSTFDY 258 Query: 263 HDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPATGHLS 322 +DG+L Q Q + L AAA+H S DG+FLY +NRG AN +++F++DP GHL Sbjct: 259 NDGKLTQVQTLPLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDANDIVIFSVDPTNGHLK 318 Query: 323 ELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPMDAPSD 382 ++ ++ G PREF++DP+G +L++ NQ S+ + V +RD ++GLL + + AP D Sbjct: 319 KVGHQSSMGKSPREFAIDPTGNWLIVGNQNSDTVYVFKRDQQSGLLEANPKHFELGAPVD 378 Query: 383 LRFL 386 + + Sbjct: 379 FKLV 382 Lambda K H 0.316 0.132 0.382 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: 582 Number of extensions: 45 Number of successful extensions: 8 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: 389 Length of database: 385 Length adjustment: 30 Effective length of query: 359 Effective length of database: 355 Effective search space: 127445 Effective search space used: 127445 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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