Align L-asparaginase (EC 3.5.1.1) (characterized)
to candidate GFF4005 Psest_4078 L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D
Query= reanno::pseudo1_N1B4:Pf1N1B4_2023 (334 letters) >FitnessBrowser__psRCH2:GFF4005 Length = 327 Score = 316 bits (809), Expect = 6e-91 Identities = 172/327 (52%), Positives = 217/327 (66%), Gaps = 8/327 (2%) Query: 10 QHVMVLYTGGTIGMQASAHGLAPASGFEARMR--EYLHSQPELVVPQWRFREMAPLIDSA 67 + ++VLYTGGTIGMQ SA GL PASGFEAR+R + L + P +P W FRE+ PL+DSA Sbjct: 6 ERLLVLYTGGTIGMQQSAAGLMPASGFEARLRAQQALETGP---LPSWTFRELQPLLDSA 62 Query: 68 NMTPAYWQQLREAVVDAVDVQGCDSVLILHGTDTLAYSAAAMSFQLLGLHARVVFTGSML 127 NM P++W Q+ AV +AV CD+VL+LHGTDTLAYSAAA+SF LL L V+ TG+ML Sbjct: 63 NMQPSHWLQMATAVREAVAQSDCDAVLLLHGTDTLAYSAAALSFLLLDLEIPVLLTGAML 122 Query: 128 PAGVTDSDAWENLSGALVALGQGLAPGVHLYFHSELLDPTRCAKVRSFGRHPFKRLERQG 187 PAG SDAW NL GA+ AL G GV L+F+ LL R +K+RS F R+ Sbjct: 123 PAGSPGSDAWPNLFGAMRALQAGRVEGVRLFFNGVLLHGARVSKLRSDAFDAFAEAPRKR 182 Query: 188 GGVKATSVPAQLNYNQPKQLAKVAALPLFPGIGAEQLDGLLNSGIQGLVLECYGSGTGPS 247 P L P+Q A+V LPL+PG+GA Q+ L+ SG Q L+LECYGSGTGP+ Sbjct: 183 SATVVGERPPML---LPQQPAQVVVLPLYPGVGAAQVQALVASGAQALLLECYGSGTGPA 239 Query: 248 DNPAFLASLERARDKGVVVVAVTQCHEGGVQLDVYEAGSRLRDAGVLSGGGMTREAAFGK 307 + F+ +L +A +GVV+ A++QC G V VY GS LRDAG++SGGGMTREAA GK Sbjct: 240 GDAPFIEALRQAHRQGVVLAAISQCPGGHVDFGVYATGSGLRDAGLVSGGGMTREAALGK 299 Query: 308 LHALLGAGLETTEVRRLVELDLCGELS 334 L ALL AGL +V DLCGE++ Sbjct: 300 LFALLTAGLNQAQVEHWFCRDLCGEMA 326 Lambda K H 0.319 0.135 0.401 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: 366 Number of extensions: 14 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: 334 Length of database: 327 Length adjustment: 28 Effective length of query: 306 Effective length of database: 299 Effective search space: 91494 Effective search space used: 91494 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