Align asparaginase (EC 3.5.1.1) (characterized)
to candidate WP_015944362.1 DHAF_RS15300 asparaginase
Query= BRENDA::J9H7D1 (324 letters) >NCBI__GCF_000021925.1:WP_015944362.1 Length = 327 Score = 213 bits (541), Expect = 7e-60 Identities = 120/324 (37%), Positives = 183/324 (56%), Gaps = 11/324 (3%) Query: 1 MKKLLLIHTGGTISMSQDETNKVVTNSDNPISNHQDIIKQYADVTE-----ITPF-NVPS 54 M+K+ LI TGGTI+M +D K V P D+++ ++ E + F NV S Sbjct: 1 MQKIKLIATGGTIAMRKDSFGKTV-----PAVTGHDLLESIPELQESAFWNVEEFSNVAS 55 Query: 55 PHMNIKYVETLKHIIEDANRDENYDGFVITHGTDTLEETAYLLDLTINVSKPITITGAMR 114 + N + + L +E+A D + G +ITHGTDTLEETAY L+LT+ S+P+ +T + R Sbjct: 56 CNFNPERMLQLARRVEEAFADPDCMGIIITHGTDTLEETAYFLELTVKDSRPVILTASQR 115 Query: 115 SSNEIGSDGLYNFISAIRVASSDNAADMGVMVVFNDEIHTARNVTKTHTSNTNTFQSPNH 174 ++E SDG N +++R+A +A + GV++ N+EIH AR+V K HTS+ + F S Sbjct: 116 DASERDSDGPRNLHNSMRIAMDPHAKERGVLIALNEEIHAARDVRKLHTSHVDAFSSGEV 175 Query: 175 GPLGVVTKNSVQFHHKPYEHLVLNDINHDLNIPLVKAYMGMNNDVLNFYSEHQVDGIIIE 234 G LG + + V +H KP + + + + K Y GM+ +L + QV+GI+IE Sbjct: 176 GSLGSIDHDEVLWHRKPEPSIKFDLPEKLAKVMICKGYTGMDGRMLECMVDAQVEGIVIE 235 Query: 235 GLGQGNLPPTCLEGLEKCLDKEIPVVLVSRSFNGIVGPIYAYEGGGATLAEKGVVFSNGL 294 G+GNLPP + + K + IPVV+ SR G PIY Y GGGA L +G +F+ L Sbjct: 236 AFGRGNLPPEVVPSIGKITAENIPVVITSRCLFGRTAPIYGYPGGGAELQRRGALFAGDL 295 Query: 295 NGPKARLKLLVGLSNQLNAKQLKK 318 + K RL L + L ++ +LK+ Sbjct: 296 STEKVRLLLSIALGQNVSHTRLKE 319 Lambda K H 0.315 0.134 0.383 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: 243 Number of extensions: 5 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: 324 Length of database: 327 Length adjustment: 28 Effective length of query: 296 Effective length of database: 299 Effective search space: 88504 Effective search space used: 88504 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: 42 (22.0 bits) S2: 48 (23.1 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