Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate WP_012401474.1 BPHY_RS10650 lactonase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >NCBI__GCF_000020045.1:WP_012401474.1 Length = 385 Score = 315 bits (806), Expect = 2e-90 Identities = 164/376 (43%), Positives = 243/376 (64%), Gaps = 8/376 (2%) Query: 15 AMGVQVASAED-YQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSK 73 A G+ A+ Y L+VG+YT +S+GIY FD+++G DA P+ K+ NPS++ S+ Sbjct: 11 AQGLAAPPADGVYDLIVGTYTGPKSEGIYVYRFDTKSG--DAIPMSSAKTDNPSYVIASR 68 Query: 74 DQRHLFVVNENGPGQTDPV---GRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGS 130 D RH++ VNE PG P G +S+F+ D + L+ +++V S GN+P + S+S DG Sbjct: 69 DGRHVYAVNEQ-PGDNGPAEQRGGISAFSFDARNGQLTFLNRVSSDGNDPCYLSISPDGK 127 Query: 131 HLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPD 190 +L +NYSVA +PGG+ AV P+ ADG++ A V H S RQ +AHVHST+ SPD Sbjct: 128 YLTTANYSVAANPGGSFAVFPLQADGQVGASVLTVHHDGSGPVKGRQDNAHVHSTVFSPD 187 Query: 191 GRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLT 250 G+++FA DLG DK+++YR+ P + L P + + GSGPRHL F ADGK+A+LT Sbjct: 188 GKFLFAQDLGTDKLYSYRYTPDGSRGL-FGPTEKRYTDVKAGSGPRHLAFGADGKYAYLT 246 Query: 251 MEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLL 310 E+SA V VF Y DG L Q Q+V + AAA+H S DG+FLY SNRG AN+++ Sbjct: 247 SELSATVTVFRYDDGTLTQLQVVPMTKPGFKGQVGAAAIHLSPDGRFLYASNRGDANEIV 306 Query: 311 VFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGK 370 ++A+DPA GHL E+ R++ G PREFS+DP+G++L++ NQ S+ V RD ++GLL Sbjct: 307 IYAVDPANGHLREVGRQSSLGKAPREFSIDPTGQWLIVGNQLSDTAYVFRRDPQSGLLEP 366 Query: 371 TVQKLPMDAPSDLRFL 386 +++ + +P D +++ Sbjct: 367 NPKRIDIGSPVDFQWV 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: 613 Number of extensions: 51 Number of successful extensions: 12 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 24 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