Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate YP_004144073.1 Mesci_4918 L-asparaginase II
Query= reanno::Phaeo:GFF3567 (333 letters) >NCBI__GCF_000185905.1:YP_004144073.1 Length = 334 Score = 221 bits (564), Expect = 2e-62 Identities = 138/336 (41%), Positives = 178/336 (52%), Gaps = 9/336 (2%) Query: 2 MTNPVPMTEVWRGPLLESLHLGHAVVCNAKGEIVRSWGDPDAVIYPRSSAKMIQALPLIT 61 MTNPV + EV RG ++ES H G V + G+ V GD ++PRS+ K IQALPL+ Sbjct: 1 MTNPV-LIEVLRGAIVESAHRGSVAVFDGDGKPVWEIGDTAKPVFPRSAVKAIQALPLVE 59 Query: 62 SGAAAKYGLTSEQLALACASHNGAEIHTSRVNAWLDQLSMTDHDFRCGPQLPDDIPARNA 121 SGAA YG + +LALACASH+G H + L + + CG P + A A Sbjct: 60 SGAADAYGFGNRELALACASHSGEPAHVDLARSMLAKAGLDGSALECGTHWPSNHDAEIA 119 Query: 122 LIKTDTSPCQVHNNCSGKHAGFLTLSQHLG-AGPEYVEIDHPVQQACRSAFEQVTEEV-- 178 L + SP +HNNCSGKH+GFL H G A YV+ H +Q R A + VT V Sbjct: 120 LARAGGSPNALHNNCSGKHSGFLCTCVHAGIAHRGYVKPGHGLQDMVRDAMQSVTGAVHG 179 Query: 179 SPGYGIDGCSAPNFATSVKGLARAMAWFAAASDRSDRDADAAQELVSAMMAHPELVAGET 238 IDGCS P +A ++ A A A S A AA+ L+SA MA P V+G Sbjct: 180 EDQRAIDGCSIPTYAVPLRSFALGFARMATTSGFGPERAKAAKRLLSACMAEPFFVSGSG 239 Query: 239 RACTNLMRAMGGTVAIKTGAEAVFIAILPEQKLGVALKITDGATRASECAIASILVGLGV 298 R LM A G + K GAE V A +PE LG+ALK DGA RA E +A++L L Sbjct: 240 REDVALMEAAPGRIFTKGGAEGVHCAAIPELGLGIALKCDDGAGRAGEAMVAAVLAKL-- 297 Query: 299 LDADHPAT---LKYRNAPLINRRGIDCGSIRPSAEM 331 L AD L+ N P+ NR G G++RP+A + Sbjct: 298 LRADEALAAKLLELANTPIENRNGAKVGALRPTATL 333 Lambda K H 0.318 0.131 0.398 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: 314 Number of extensions: 18 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: 333 Length of database: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 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 (21.8 bits) S2: 49 (23.5 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