Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate SMc00035 SMc00035 hypothetical protein
Query= reanno::Phaeo:GFF3567 (333 letters) >FitnessBrowser__Smeli:SMc00035 Length = 336 Score = 227 bits (578), Expect = 4e-64 Identities = 135/333 (40%), Positives = 180/333 (54%), Gaps = 5/333 (1%) Query: 2 MTNPVPMTEVWRGPLLESLHLGHAVVCNAKGEIVRSWGDPDAVIYPRSSAKMIQALPLIT 61 M+NPV + EV RG L+ES H G V + G+ + S G+ DA I+PRS+ K +QALPLI Sbjct: 1 MSNPV-LVEVTRGNLVESRHRGMIVAVDGDGKTLFSLGETDAHIFPRSACKAMQALPLIE 59 Query: 62 SGAAAKYGLTSEQLALACASHNGAEIHTSRVNAWLDQLSMTDHDFRCGPQLPDDIPARNA 121 SGAA G +LALAC+SH+G H + L CG D A Sbjct: 60 SGAADANGFGDRELALACSSHSGEPEHVALAAKMLSAAGRDVQALECGAHWSSDQKTLIA 119 Query: 122 LIKTDTSPCQVHNNCSGKHAGFLTLSQHLGAGPE-YVEIDHPVQQACRSAFEQVTEEV-- 178 ++ +P +HNNCSGKHAGF+ H G + Y+ DHP+QQ R ++T V Sbjct: 120 QARSLEAPSALHNNCSGKHAGFVCACCHSGTEVKGYIGYDHPIQQEIRGVMAELTGAVLD 179 Query: 179 SPGYGIDGCSAPNFATSVKGLARAMAWFAAASDRSDRDADAAQELVSAMMAHPELVAGET 238 G+DGCS P +A S++GLA A A+ A A++ L+ A MA P VAG Sbjct: 180 RDNCGVDGCSIPTYALSMRGLAHGFARMASGVGLGAERARASKRLIEACMAEPFFVAGTK 239 Query: 239 RACTNLMRAMGGTVAIKTGAEAVFIAILPEQKLGVALKITDGATRASECAIASILVGLGV 298 RACT LM+ G + KTGAE VF A +PE+ +G+ALK DG TRA+E +A+ L Sbjct: 240 RACTRLMKTAPGRIFAKTGAEGVFCAAIPEKGIGIALKCEDGTTRAAEAMVAATLARFFS 299 Query: 299 LDAD-HPATLKYRNAPLINRRGIDCGSIRPSAE 330 DA+ H A + N + N GI G +R E Sbjct: 300 DDAEIHEALMAQANHAMRNWNGIHVGDVRVVTE 332 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: 350 Number of extensions: 14 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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 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