Align L-asparaginase 1; L-asparaginase I; L-ASNase I; L-asparagine amidohydrolase I; EC 3.5.1.1 (characterized)
to candidate 5209470 Shew_1940 cytoplasmic asparaginase I (RefSeq)
Query= SwissProt::P0A962 (338 letters) >FitnessBrowser__PV4:5209470 Length = 337 Score = 466 bits (1199), Expect = e-136 Identities = 235/337 (69%), Positives = 271/337 (80%) Query: 1 MQKKSIYVAYTGGTIGMQRSEQGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYTPLMDS 60 M+K SIYVAYTGGTIGMQ+++ G+ PV G L + MPEF EMPDF I EY PL+DS Sbjct: 1 MKKPSIYVAYTGGTIGMQKTDNGFAPVPGFLTDCVKAMPEFFHQEMPDFVISEYCPLIDS 60 Query: 61 SDMTPEDWQHIAEDIKAHYDDYDGFVILHGTDTMAYTASALSFMLENLGKPVIVTGSQIP 120 S+M P DWQ IA+DIKA+YD YDGFVILHGTDTMA+TASALSFML+ L KPVIVTGSQIP Sbjct: 61 SNMAPTDWQMIADDIKANYDKYDGFVILHGTDTMAFTASALSFMLQGLTKPVIVTGSQIP 120 Query: 121 LAELRSDGQINLLNALYVAANYPINEVTLFFNNRLYRGNRTTKAHADGFDAFASPNLPPL 180 LA+LRSDGQ NLLNALY+AANYP+ EV LFFNN+L+RGNRTTKAHADGFDAFASPN P L Sbjct: 121 LAQLRSDGQTNLLNALYIAANYPVAEVCLFFNNKLFRGNRTTKAHADGFDAFASPNFPIL 180 Query: 181 LEAGIHIRRLNTPPAPHGEGELIVHPITPQPIGVVTIYPGISADVVRNFLRQPVKALILR 240 LEAGI IR + L V+ I+PQPIGVVT+YPGI+ +++ N L+QPVKALIL Sbjct: 181 LEAGIKIRLKAGRISESKANTLTVNKISPQPIGVVTLYPGITTEIIDNILQQPVKALILL 240 Query: 241 SYGVGNAPQNKAFLQELQEASDRGIVVVNLTQCMSGKVNMGGYATGNALAHAGVIGGADM 300 +YGVGNAPQN L+ L++A++RGI++VNLTQC+ GKVNMGGYATGNALA AGVI G DM Sbjct: 241 TYGVGNAPQNPELLECLRKANERGIILVNLTQCLQGKVNMGGYATGNALAKAGVISGFDM 300 Query: 301 TVEATLTKLHYLLSQELDTETIRKAMSQNLRGELTPD 337 T EA LTKLHYLLS EL IR M Q+L GELT D Sbjct: 301 TTEAALTKLHYLLSTELSPSDIRVQMQQDLCGELTED 337 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: 440 Number of extensions: 13 Number of successful extensions: 2 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: 337 Length adjustment: 28 Effective length of query: 310 Effective length of database: 309 Effective search space: 95790 Effective search space used: 95790 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 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