Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate PP_0495 PP_0495 type 1 L-asparaginase
Query= reanno::pseudo5_N2C3_1:AO356_11100 (334 letters) >FitnessBrowser__Putida:PP_0495 Length = 329 Score = 354 bits (909), Expect = e-102 Identities = 181/325 (55%), Positives = 224/325 (68%) Query: 8 AAQHVMVLYTGGTIGMQASAHGLAPASGFEARMRDYLHSQPELVVPQWRFREMSPLIDSA 67 A ++++VLYTGGTIGM + GLAPA GFEARMR++ QW E++PL+DSA Sbjct: 3 AVKNLLVLYTGGTIGMLETPEGLAPAGGFEARMREHFAQMANAPQVQWTLHELNPLLDSA 62 Query: 68 NMTPAYWQQLREAVVDAVDVQGCDSVLILHGTDTLAYSAAAMSFQLLGLHARVCFTGSML 127 NM W +R+A+V AVDV G D VL+LHGTD++AYSAAA+SF LL L A V TGSML Sbjct: 63 NMQQHNWLAMRDAIVAAVDVAGHDGVLVLHGTDSMAYSAAALSFLLLDLPAPVVLTGSML 122 Query: 128 PAGVTDSDAWENLSGALVALGQGLAPGVHLYFHGELLAPTRCAKVRSFGRHPFKRLERQG 187 PAGV DSDAW+NL GAL GL GV LYFHG+LL R +K+RS F L R Sbjct: 123 PAGVPDSDAWDNLCGALRQFEHGLEDGVQLYFHGQLLHGCRASKLRSEAFDAFAALPRHR 182 Query: 188 GGTPAPTLPTQLNYNQPKQLTNIAALPLFPGISAQILDGLLGSGIQGLVLECYGSGTGPS 247 A T+P +L Y QP++ N+A +P+FPG+ A L L+ SG+QGL+LECYGSGTGPS Sbjct: 183 DAERADTIPAELGYKQPRKPVNLAVVPVFPGLQAGHLQALIDSGVQGLLLECYGSGTGPS 242 Query: 248 DNPAFLASLERARDSGVVVVAVTQCHEGGVELDVYEAGSRLRGVGVLSGGGMTREAALGK 307 D+ A L L AR GV++ A++QC EG V D Y AG+RLRG G++SGGGMTREAALGK Sbjct: 243 DDQALLNVLSTARQRGVMLAAISQCPEGSVVFDTYAAGNRLRGAGLVSGGGMTREAALGK 302 Query: 308 LQALIGAGLPVEEVRRLVELDLCGE 332 + AL+GAGL + R LDLCGE Sbjct: 303 MVALLGAGLDADAADRWFVLDLCGE 327 Lambda K H 0.319 0.137 0.412 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: 382 Number of extensions: 18 Number of successful extensions: 1 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: 334 Length of database: 329 Length adjustment: 28 Effective length of query: 306 Effective length of database: 301 Effective search space: 92106 Effective search space used: 92106 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