Align asparaginase (EC 3.5.1.1) (characterized)
to candidate AO353_25970 AO353_25970 asparaginase
Query= BRENDA::Q9RFN5 (371 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25970 Length = 346 Score = 406 bits (1043), Expect = e-118 Identities = 200/339 (58%), Positives = 255/339 (75%), Gaps = 8/339 (2%) Query: 16 RGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAKPAQALAILETEGVAGYGFDD 75 RG +EN+H H AVVDA+GRLL G+P+RMTLARSAAKPAQALA++ET + +G DD Sbjct: 13 RGNSIENTHIAHVAVVDAQGRLLSGFGDPSRMTLARSAAKPAQALAVMETGALEQFGLDD 72 Query: 76 ADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAV 135 AD+ALMC SHSSE RHI R ML+K A EAD+RCGGHP +S+ V R+WIK DF+P V Sbjct: 73 ADLALMCGSHSSETRHIQRALGMLAKAGASEADMRCGGHPPISDEVYRAWIKSDFVPGPV 132 Query: 136 CSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNL 195 CSNCSGKH GMLA A+A+GA +GYHLP HP+Q RV +TVAE+C++ ++W TDGCNL Sbjct: 133 CSNCSGKHAGMLAAAQALGATLEGYHLPAHPLQQRVMQTVAEVCEVSGDAIQWATDGCNL 192 Query: 196 PTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTM 255 PTPAF LDRL ++AK+ASAAD ++ +S R A LA I+RAMA +PE+VAG+GR+CT Sbjct: 193 PTPAFALDRLALLFAKIASAADTGES--ARSPREAELARIYRAMATYPELVAGKGRFCTA 250 Query: 256 LMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELL 315 LM+AF+G LVGK+GADASYAIG+R + A GI+VK+EDGN +LYAVV E+L Sbjct: 251 LMKAFNGQLVGKVGADASYAIGIRG------VTDQQARGIAVKVEDGNQTVLYAVVCEVL 304 Query: 316 ERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKL 354 +L IG+ R+QL+++HHP +NT+ V TG + F L Sbjct: 305 TQLNIGTAAQRAQLSAWHHPPMLNTVKVQTGRIELTFSL 343 Lambda K H 0.319 0.134 0.397 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: 433 Number of extensions: 13 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: 371 Length of database: 346 Length adjustment: 29 Effective length of query: 342 Effective length of database: 317 Effective search space: 108414 Effective search space used: 108414 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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