Align asparaginase (EC 3.5.1.1) (characterized)
to candidate H281DRAFT_04915 H281DRAFT_04915 asparaginase
Query= BRENDA::Q9RFN5 (371 letters) >FitnessBrowser__Burk376:H281DRAFT_04915 Length = 368 Score = 439 bits (1130), Expect = e-128 Identities = 224/354 (63%), Positives = 266/354 (75%), Gaps = 11/354 (3%) Query: 16 RGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAKPAQALAILETEGVAGYGFDD 75 RG VEN+HR H AVVD+ GRLLY+ G+P+R+TLARSAAKPAQALA+LET + +GFDD Sbjct: 15 RGDSVENTHRAHVAVVDSNGRLLYSFGDPSRVTLARSAAKPAQALAVLETGALERFGFDD 74 Query: 76 ADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAV 135 AD+ALMCASHSSE RHI R R ML+K +A E DLRCGGHP LS+ V WIK+DF P AV Sbjct: 75 ADLALMCASHSSEPRHIERARQMLAKAQASETDLRCGGHPPLSDAVYVDWIKRDFKPGAV 134 Query: 136 CSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNL 195 CSNCSGKH GMLAGAR+IGA GY P+HP+Q RVK TVA++CDL V+W TDGCNL Sbjct: 135 CSNCSGKHAGMLAGARSIGAALSGYEQPEHPLQIRVKHTVADVCDLPDDGVQWATDGCNL 194 Query: 196 PTPAFPLDRLGRIYAKLASAADG-SDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCT 254 PTPAFPLDRL R++AKLA+A D S +G +TR AALA I+RAM +PE+V GEGR+CT Sbjct: 195 PTPAFPLDRLARLFAKLAAAQDEVSSSGAAPNTRTAALARIYRAMTAYPELVGGEGRFCT 254 Query: 255 MLMRAFDGALVGKLGADASYAIGVRASDATR----------QLGTDGALGISVKIEDGNL 304 +LM AF GALVGKLGAD SY IGVRAS+ T GT GALGI+VKIEDGN+ Sbjct: 255 ILMNAFGGALVGKLGADGSYGIGVRASNRTAAHTSKAGAQDAQGTQGALGIAVKIEDGNV 314 Query: 305 EMLYAVVTELLERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKLRGSK 358 +LYAVV E+L +L IG+ R++L SFH P+ +NTMGV TG F L S+ Sbjct: 315 GVLYAVVAEVLAQLDIGTAGQRAKLDSFHTPRMLNTMGVATGRRVFSVALEASR 368 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: 468 Number of extensions: 22 Number of successful extensions: 4 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: 368 Length adjustment: 30 Effective length of query: 341 Effective length of database: 338 Effective search space: 115258 Effective search space used: 115258 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