Align Probable L-asparaginase periplasmic; L-ASNase; EC 3.5.1.1; L-asparagine amidohydrolase (uncharacterized)
to candidate PP_1160 PP_1160 Asparaginase family protein
Query= curated2:P43843 (349 letters) >FitnessBrowser__Putida:PP_1160 Length = 329 Score = 153 bits (386), Expect = 7e-42 Identities = 108/322 (33%), Positives = 166/322 (51%), Gaps = 21/322 (6%) Query: 22 ADLPNITILATGGTI---AGSGQSSVNSAYKAGQLSIDTLIEAVPEMKNIANIKGEQIVK 78 + LP ++I GGT+ AG+ V + L + + VP+++ +A + + Sbjct: 5 SSLPRLSIATLGGTVSMRAGAVGDGVTPS-----LDCERQLLQVPQLREMAQLNVASLCL 59 Query: 79 IGSQDMNDEVWLK-LAKAINAQCKSTDGFVITHGTDTMEETAYFLDLTVKCEKPVVLVGA 137 + S + L+ LA A + V++ GTD++EETAYFLDL + P+V+ GA Sbjct: 60 LPSASLGFATLLEVLAWARGEVERGAQALVLSQGTDSLEETAYFLDLLWPFDVPLVMTGA 119 Query: 138 MRPATEKSADGPLNLYNAVVVAADKKSSGRGVLVAMNNEVLGARDVTKTSTTAVQTFHSP 197 MR A++ DGP NL A VA + S GRGVLV MN++V A V KT++ A+ F SP Sbjct: 120 MRSASQPGNDGPANLLAAAQVALAQDSRGRGVLVVMNDQVHCAARVRKTASLAMAAFESP 179 Query: 198 NYGSLGYIHNSKVDYERSPESKHTINTPFNVEKLDSLPKVGIIYAYSNAPVEPLNALLNA 257 G LG + V Y P + + P+ ++ +V ++ A +A L A+ Sbjct: 180 GCGPLGDVVEGVVLYRHPPGRRKVLPLPYRTDQ-----RVALLEACLDADTALLQAVATL 234 Query: 258 GYQGIVSAGVGNGNVNAAHLDRLEKAAKDSVVVVRSSRVPTGYTTR------DAEVDDSK 311 GY+G+V AG G G+V+A+ + LE A V+V ++R G T R AE+D K Sbjct: 235 GYEGLVIAGFGAGHVSASWSEVLEHLAPTLPVMV-ATRTGRGLTARATYGFAGAEIDLQK 293 Query: 312 YGFVASGTLNPQKARVLLQLAL 333 G +G L P+K R+LL L + Sbjct: 294 KGVYMAGQLCPRKCRILLWLLI 315 Lambda K H 0.313 0.130 0.361 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: 223 Number of extensions: 12 Number of successful extensions: 3 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: 349 Length of database: 329 Length adjustment: 28 Effective length of query: 321 Effective length of database: 301 Effective search space: 96621 Effective search space used: 96621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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