Align Isoaspartyl peptidase/L-asparaginase; Asparaginase-like protein 1; Beta-aspartyl-peptidase; Isoaspartyl dipeptidase; L-asparagine amidohydrolase; EC 3.4.19.5; EC 3.5.1.1 (characterized)
to candidate 8500076 DvMF_0839 Asparaginase (RefSeq)
Query= SwissProt::Q5BKW9 (310 letters) >FitnessBrowser__Miya:8500076 Length = 329 Score = 196 bits (497), Expect = 8e-55 Identities = 121/326 (37%), Positives = 178/326 (54%), Gaps = 33/326 (10%) Query: 3 PVVVVHGGAGHIPKERTEESTIGVKEAARTGYAILQRGGSAVDAVVEAVALMETNPRFNA 62 P ++VHGGA IP +R + G + A + L+RG A++AV AV ++E +P ++A Sbjct: 4 PRIIVHGGAWTIPADRRKAHVDGCRAAVDAVWGELRRGMPALEAVRLAVNVLEADPTYDA 63 Query: 63 GRGSVLNIKGEVEMDALVMDGRTLDSGAVSAVRRIANPVQLARLVMEKTKHLCLTAEGAS 122 GRG+VLN G +E+DA +MDG TL+ GAV+AVR +PV +AR VM+ T+ L EGA Sbjct: 64 GRGAVLNADGRIELDAAIMDGATLNFGAVAAVRNFLHPVDIARKVMD-TEFCFLVGEGAE 122 Query: 123 KFARSMGVPEVPEESLITD-----YAKMRWKKNLE------------------PDANPVE 159 +FAR +G+ + L+ + Y ++R + P N Sbjct: 123 RFAREVGIEAIDPAELVVEREVRLYNELRARAGFSTHDSFRPRAGANGAAVEAPAVNGTA 182 Query: 160 CQMGK----MGTVGAVAVDMDGNIACATSTGGMINKMEGRVGDTPCVGCGGYADNKIGAV 215 C+ + GTVGAVA+D GNIA ATSTGG K GRVGD+P G G YADN+ G Sbjct: 183 CRCPEPDMPKGTVGAVALDAAGNIAAATSTGGTPMKRPGRVGDSPLCGAGTYADNETGGA 242 Query: 216 SPTGHGEAIMKVTLSRLVL-FHMEQGKTPEEASDLALAYMKERVDGLGGVVVVDHNGTWA 274 S TG GE I++V ++R F + G +P +A+ A+ + RV G G++++D G + Sbjct: 243 SATGFGEGIIRVLMTRSACDFLRDGGASPADAARRAIELLHRRVAGHAGLIMLDRQGRYG 302 Query: 275 ARFSSLQMSWAAAQQGKLHFGLFHGD 300 ++ ++ A A G G H D Sbjct: 303 VHCNTEHIAHAYALPG----GGIHAD 324 Lambda K H 0.316 0.132 0.389 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: 318 Number of extensions: 17 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: 310 Length of database: 329 Length adjustment: 28 Effective length of query: 282 Effective length of database: 301 Effective search space: 84882 Effective search space used: 84882 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 (21.6 bits) S2: 48 (23.1 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