Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate Pf6N2E2_4087 L-asparaginase (EC 3.5.1.1)
Query= curated2:Q9Y9T8 (427 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4087 Length = 334 Score = 126 bits (316), Expect = 1e-33 Identities = 102/349 (29%), Positives = 165/349 (47%), Gaps = 27/349 (7%) Query: 71 PAEERVYIIGAGGTIASRVDYETGAVKPYLDAS--ELATTIPELQRYASIEAEQLFSILS 128 PA + V ++ GGTI + A +A + + PEL E I S Sbjct: 7 PAAQHVMVLYTGGTIGMQASAHGLAPASGFEARMRDYLHSQPELVVPQWRFREMSPLIDS 66 Query: 129 EDMKPSMWEAIVDRAARVLEA-GYDGVVVAHGTDTMAFTASALSFAFHKGLPSPVILTGS 187 +M P+ W+ + + ++ G D V++ HGTDT+A++A+A+SF GL + V TGS Sbjct: 67 ANMTPAYWQQLREAVVDAVDVQGCDSVLILHGTDTLAYSAAAMSFQL-LGLHARVCFTGS 125 Query: 188 QRSSDRPSSDAAFNLTASVLAASRAPFAEVAVVMHGETGDTYALAHRGVRVKKMHSSRRD 247 + SDA NL+ +++A + V + HGE + +R Sbjct: 126 MLPAGVIDSDAWENLSGALVALGQGLAPGVHLYFHGEL---------------LAPTRCA 170 Query: 248 AFQSVNDKPLARIYPFEGRVEMLRDDYRRRGESGLEVDNGFEERVALVKHFPGLISEVID 307 +S P R+ G ++ + ++ N +A + FPG+ +E++D Sbjct: 171 KVRSFGRHPFKRLERQGGGLKASSLPAQLNYNQPKQLAN-----IAALPLFPGISAEILD 225 Query: 308 ALLDRGFKGIVVEGTGFGHVSSDA---IKSIERARDQGVPIVITTQTVFGRVNLNVYSTG 364 LL G +G+V+E G G SD + S+ERARD GV IV TQ G V L+VY G Sbjct: 226 GLLGSGIQGLVLECYGSGTGPSDNPAFLASLERARDSGVVIVAVTQCHEGGVELDVYEAG 285 Query: 365 RKMLAAGAIPAGDMTSEAAYAKLSWILARTRELEVVRKMFQRNLAGEVS 413 ++ G + G MT EAA+ KL ++ +E VR++ + +L GE++ Sbjct: 286 SRLRGVGVLSGGGMTREAAFGKLQALIGAGLPVEEVRRLVELDLCGELA 334 Lambda K H 0.318 0.136 0.385 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: 375 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 427 Length of database: 334 Length adjustment: 30 Effective length of query: 397 Effective length of database: 304 Effective search space: 120688 Effective search space used: 120688 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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