Align Isoaspartyl peptidase/L-asparaginase; Asparaginase-like protein 1; Asparaginase-like sperm autoantigen; Beta-aspartyl-peptidase; Glial asparaginase; Isoaspartyl dipeptidase; L-asparagine amidohydrolase; EC 3.4.19.5; EC 3.5.1.1 (characterized)
to candidate YP_004134273.1 Mesci_6097 peptidase t2 asparaginase 2
Query= SwissProt::Q8VI04 (333 letters) >NCBI__GCF_000185905.1:YP_004134273.1 Length = 300 Score = 167 bits (422), Expect = 4e-46 Identities = 94/227 (41%), Positives = 133/227 (58%), Gaps = 14/227 (6%) Query: 28 VVVHGGGASNISPGRKELVSEGIAKAATEGYNILKAGGSAVDAVEGAVTMLENDPEFNAG 87 +++HGG A I P +E G KA G +L GG+AVDAVE A +LE DP FNAG Sbjct: 4 LILHGG-AKEIDPEEEEAHRNGCIKALEAGRAVLAGGGTAVDAVEAAGRVLETDPTFNAG 62 Query: 88 YGSVLNADGDIEMDASIMDGKDLSAGAVSAVRCIANPVKLARLVMEKTPHCFLTGRGAEK 147 YGS LN+DG++EM A +M+G++ + GAV+ ++ + +P+ +A+ ++ + P L GA + Sbjct: 63 YGSALNSDGEVEMCAGVMEGRNFNVGAVAVIKGVRHPISVAKAMLHEEP-ILLASDGARR 121 Query: 148 FAADMGIPQTPAEKLITERTKKHLEKEKLEKGAQKADCPKNSGTVGAVALDCKGNLAYAT 207 FAAD + L+T + + K + + T+G VALD G+LA T Sbjct: 122 FAADKQLELCDPADLVTPQQRDLASKSEAK------------DTIGVVALDQYGDLAVGT 169 Query: 208 STGGIVNKMVGRVGDSPCIGAGGYADNNLGAVSTTGHGESILKVNLA 254 STGG+ GRVGDSP G G YADN LGAV+ +G GE I + LA Sbjct: 170 STGGLDGSAPGRVGDSPQPGCGYYADNQLGAVAFSGDGEHIARKALA 216 Lambda K H 0.313 0.131 0.379 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: 277 Number of extensions: 15 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: 333 Length of database: 300 Length adjustment: 27 Effective length of query: 306 Effective length of database: 273 Effective search space: 83538 Effective search space used: 83538 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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