Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate Ac3H11_559 Hypothetical protein of L-Asparaginase type 2-like superfamily
Query= reanno::Phaeo:GFF3567 (333 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_559 Length = 336 Score = 170 bits (431), Expect = 4e-47 Identities = 116/326 (35%), Positives = 161/326 (49%), Gaps = 7/326 (2%) Query: 6 VPMTEVWRGPLLESLHLGHAVVCNAKGEIVRSWGDPDAVIYPRSSAKMIQALPLITSGAA 65 VP+ EV RG L E H G V N +G+++ GDP V + RS+ K QALP + +G A Sbjct: 4 VPLIEVSRGGLPECQHWGAVAVANRQGQVLAQVGDPYVVTFTRSTIKAFQALPFMQAGGA 63 Query: 66 AKYGLTSEQLALACASHNGAEIHTSRVNAWLDQLSMTDHDFRCGPQLPDDIPARNALIKT 125 G +LAL CASHNG +H + + L + H RCG P + Sbjct: 64 RAQGWGQGELALLCASHNGEPMHVEQASRMLASVGQDYHALRCGCHRPLFAELGLGTLPP 123 Query: 126 DTSPCQVHNNCSGKHAGFLTLSQHLGAGPE-YVEIDHPVQQACRSAFEQVTEEVSP---G 181 P + HNNCSGKHAGF+ G E +++ HP+Q A R+ Q ++P Sbjct: 124 GFVPDERHNNCSGKHAGFVAHCVREGLPLEDHLDPTHPLQVAIRNHVAQAV-GLAPDQLA 182 Query: 182 YGIDGCSAPNFATSVKGLARAMAWFAAASDRSDRDADAAQELVSAMMAHPELVAGETRAC 241 GIDGCSAPN+A + LAR A A + +D ++ L AM+A PEL +G R Sbjct: 183 MGIDGCSAPNYAMPLAHLARGYARLAGGAPDTDLH-ESLTTLADAMVARPELGSGTGRHD 241 Query: 242 TNLMRAMGGTVAIKTGAEAVFIAILPEQKLGVALKITDGATRASECAIASILVGLGVLDA 301 + M+ G KTGA+ V + + ALKI DG A A ++ LG LDA Sbjct: 242 LDFMQVGQGDWVSKTGADGVQVVGSRSRGEAFALKIMDGNMVAQVAAAVEVMDQLGWLDA 301 Query: 302 -DHPATLKYRNAPLINRRGIDCGSIR 326 A + R+A ++N +G+ G R Sbjct: 302 GQREALARRRSAHIVNAKGLTVGGRR 327 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: 309 Number of extensions: 13 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: 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