Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate AZOBR_RS00830 AZOBR_RS00830 L-asparaginase
Query= reanno::Phaeo:GFF3567 (333 letters) >FitnessBrowser__azobra:AZOBR_RS00830 Length = 366 Score = 252 bits (644), Expect = 9e-72 Identities = 133/325 (40%), Positives = 194/325 (59%), Gaps = 4/325 (1%) Query: 8 MTEVWRGPLLESLHLGHAVVCNAKGEIVRSWGDPDAVIYPRSSAKMIQALPLITSGAAAK 67 + EV RG ++ES+H G A + ++ G ++ WGD A +YPRS+ K IQA+PL+ +GA Sbjct: 40 LVEVTRGGMVESVHRGRACIVDSDGRVLAQWGDIQAPVYPRSAIKAIQAIPLVETGALDA 99 Query: 68 YGLTSEQLALACASHNGAEIHTSRVNAWLDQLSMTDHDFRCGPQLPDDIPARNALIKTDT 127 Y L ++LALAC+SH+G HT AW+ ++ +T D+ CG LP D + +I+ Sbjct: 100 YELGDQELALACSSHHGEIRHTRIAEAWIKRIGLTVGDYECGAHLPTDTETAHEMIRHGE 159 Query: 128 SPCQVHNNCSGKHAGFLTLSQHLGAGPE-YVEIDHPVQQACRSAFEQVT-EEVSPG-YGI 184 +P HNNCSGKHAGFLT + H G + YV DHPVQQ EQ+T +++S +G+ Sbjct: 160 TPTAFHNNCSGKHAGFLTTALHKGEPTKGYVRFDHPVQQRILGVMEQMTGQDLSQAPWGV 219 Query: 185 DGCSAPNFATSVKGLARAMAWFAAASDRSDRDADAAQELVSAMMAHPELVAGETRACTNL 244 DGC+ P + +A AMA D D A+A + A +HP L+AG+ T + Sbjct: 220 DGCAIPTIGIPLGAIAYAMARIGDPKDLPDSRAEAVARIRRAWRSHPHLIAGKDSFDTGM 279 Query: 245 MRAMGGTVAIKTGAEAVFIAILPEQKLGVALKITDGATRASECAIASILVGLGVLDADHP 304 M+A GG V +K GAE V A+LP+Q LG+ALKI DG RA E A+A+++ VL + Sbjct: 280 MQAAGGLVLVKGGAEGVGCAVLPKQGLGIALKIDDGTPRAREVALAALIRATKVLSDEQW 339 Query: 305 ATL-KYRNAPLINRRGIDCGSIRPS 328 A + + P+ NR G++ G +RP+ Sbjct: 340 ARAGQLIHQPVTNRNGLEVGVVRPA 364 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: 386 Number of extensions: 22 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: 366 Length adjustment: 29 Effective length of query: 304 Effective length of database: 337 Effective search space: 102448 Effective search space used: 102448 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