Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate WP_066330220.1 BLR17_RS12195 lactonase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >NCBI__GCF_900100165.1:WP_066330220.1 Length = 369 Score = 202 bits (515), Expect = 1e-56 Identities = 127/368 (34%), Positives = 203/368 (55%), Gaps = 23/368 (6%) Query: 21 ASAEDYQLLVGSYTAG-QSQGIYRLAFDSRTG--QIDASPLQVIKSANPSWLTLSKDQRH 77 A + + L++G+YT +S+GIY F++ TG Q +S VI NPS++++SK+ Sbjct: 19 AQEKKFNLIIGTYTKSCESKGIYVYDFNAETGDFQFKSSTENVI---NPSFVSVSKNNDF 75 Query: 78 LFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNY 137 ++ VNE+GP T VS+F D + +++ Q + N P + D ++ +NY Sbjct: 76 IYSVNEDGPKST-----VSAFKYDTSNAKIEFVNK-QEIHN-PGPCYIINDDKNVITANY 128 Query: 138 SVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFAN 197 + GG++AV +G L + Q+ H +NP RQ +HVHS SPD ++V A Sbjct: 129 T-----GGSVAVFGKNKNGSLTELKQLIKHSGKGINPARQEKSHVHSVQFSPDHQFVLAT 183 Query: 198 DLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQV 257 DLG DK++ Y+++PK L L + +++ GSGPRH FS +G+ +L E+ + Sbjct: 184 DLGTDKMYLYQYNPKVAKPLELKDS----IKVKAGSGPRHFAFSKNGQQLYLLQELDGTL 239 Query: 258 AVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPA 317 +VF+Y+ G+L Q + A AA +H S D +FLY +NR AN + F I Sbjct: 240 SVFNYNKGKLVLVQETTVLAPDFKGTSTAADIHISPDQRFLYATNRKEANTISCFKI-LK 298 Query: 318 TGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPM 377 G L+ R + GD PR F++DP+G FLL+ +Q +N +VV +R+ TG L T +++ + Sbjct: 299 DGKLALASRTSSLGDGPRNFAIDPTGNFLLVGHQYTNNVVVFKRNKETGALTDTGKRIEL 358 Query: 378 DAPSDLRF 385 AP L F Sbjct: 359 CAPVCLVF 366 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: 375 Number of extensions: 19 Number of successful extensions: 4 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: 369 Length adjustment: 30 Effective length of query: 359 Effective length of database: 339 Effective search space: 121701 Effective search space used: 121701 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