Align asparaginase (EC 3.5.1.1) (characterized)
to candidate Synpcc7942_0166 Synpcc7942_0166 hypothetical protein
Query= BRENDA::Q9RFN5 (371 letters) >FitnessBrowser__SynE:Synpcc7942_0166 Length = 317 Score = 164 bits (414), Expect = 4e-45 Identities = 106/315 (33%), Positives = 159/315 (50%), Gaps = 36/315 (11%) Query: 16 RGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAKPAQALAILETEGVAGYGFDD 75 R GI+E+SH V A V D +GR L+ GNP + RSA KP QAL +L+T + +G D Sbjct: 18 REGILESSHLVEAVVCDRRGRTLFIAGNPEHSSFIRSALKPLQALVVLKTGTMERFGLSD 77 Query: 76 ADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAV 135 D+A++C+SH + +L K ++ L+C + + RS ++ Sbjct: 78 RDLAIICSSHKGSVEQARQAFNILWKADIDQTALQCP-----TPVGRRSPLEY------- 125 Query: 136 CSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNL 195 NCSGKH GMLA ++ +GY HP+Q + V +L + A + D C + Sbjct: 126 --NCSGKHAGMLAASKQQNWPLEGYMRRSHPVQQAILSIVGDLLGIPAAEFIVARDDCGV 183 Query: 196 PTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTM 255 PT + L ++ +YA L+S D+ E L I RAM HP+++AGEG + T Sbjct: 184 PTVSMELQQMATLYAHLSS----GDSPE--------LERIQRAMTYHPDLIAGEGEFDTE 231 Query: 256 LMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELL 315 LMR +G LV K GA+ IG Q+G LG+++K++DG AV + L Sbjct: 232 LMRLTEGRLVSKTGAEGVQCIG--------QVGE--GLGLAIKVQDGAKRAKIAVAIQAL 281 Query: 316 ERLGIGSPDVRSQLA 330 ++G SP + LA Sbjct: 282 RQIGWISPAIADLLA 296 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: 297 Number of extensions: 10 Number of successful extensions: 5 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: 317 Length adjustment: 29 Effective length of query: 342 Effective length of database: 288 Effective search space: 98496 Effective search space used: 98496 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