Align L-asparaginase 1; L-asparaginase I; L-ASNase I; L-asparagine amidohydrolase I; EC 3.5.1.1 (characterized)
to candidate WP_086509657.1 BZY95_RS09260 asparaginase
Query= SwissProt::P0A962 (338 letters) >NCBI__GCF_002151265.1:WP_086509657.1 Length = 350 Score = 200 bits (508), Expect = 5e-56 Identities = 125/341 (36%), Positives = 184/341 (53%), Gaps = 11/341 (3%) Query: 4 KSIYVAYTGGTIGMQRSEQGYIP---VSGHLQRQLALMPEFHRPEMPDFTIHEYTPLMDS 60 + + V YTGGT+GM S +G +P + L+ L +P + ++P+F +H +DS Sbjct: 9 RPVLVLYTGGTLGMMPSAEGLVPAGDIETRLRNALDGLPPSRQSQLPEFVVHTVASPIDS 68 Query: 61 SDMTPEDWQHIAEDIKAHYDDYDGFVILHGTDTMAYTASALSFMLENLGKPVIVTGSQIP 120 S TP DWQ +A I + G V+LHGTDT+A++AS+L+F L+ L +PV+VTG+ P Sbjct: 69 SAATPHDWQRLAATIADRIGQHAGIVVLHGTDTLAWSASSLAFQLQGLDRPVVVTGAMHP 128 Query: 121 LAELRSDGQINLLNALYVAANYPINEVTLFFNNRLYRGNRTTKAHADGFDAFASPNLPPL 180 L SD N+ AL AA + E+ + F RL RG R++K H++ DAFASPN P L Sbjct: 129 LEAEGSDALANIELALRFAARPELQEIAVAFAGRLLRGARSSKTHSENDDAFASPNYPLL 188 Query: 181 LE-AGIHI-----RRLNTPPAPHGEGELIVH-PITPQPIGVVTIYPGISADVVRNFLRQP 233 E G + R L T EL + P+ + + ++PGI A + +L Sbjct: 189 GEQVGDDVVLYPARCLETQQRGAPRFELPDYSPLAKGGVVRLALWPGIQAWQLEAWLGDD 248 Query: 234 -VKALILRSYGVGNAPQNKAFLQELQEASDRGIVVVNLTQCMSGKVNMGGYATGNALAHA 292 V+ +L +G GN P + + L +AS G ++ ++QC G + G YA G L A Sbjct: 249 RVQGALLEVWGGGNIPPDPEVIGVLAKASGEGKLIAAISQCRWGGIAPGRYAAGQGLIEA 308 Query: 293 GVIGGADMTVEATLTKLHYLLSQELDTETIRKAMSQNLRGE 333 GV+ G DMT EA +TKL +LL+ LD R+ L GE Sbjct: 309 GVLSGDDMTPEAAITKLVHLLALPLDATERRRLFLTPLVGE 349 Lambda K H 0.318 0.136 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: 366 Number of extensions: 21 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: 338 Length of database: 350 Length adjustment: 29 Effective length of query: 309 Effective length of database: 321 Effective search space: 99189 Effective search space used: 99189 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 (21.7 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