Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_025272518.1 HALAL_RS0102655 amidase
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_000527155.1:WP_025272518.1 Length = 468 Score = 218 bits (554), Expect = 5e-61 Identities = 161/483 (33%), Positives = 232/483 (48%), Gaps = 43/483 (8%) Query: 7 TLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADRRIAAGE 66 T EL A ++E+S EAT A LDRI EL+ + NA+ V PE AL A ++ R G Sbjct: 10 TASELAAAYATREISPVEATKAALDRINELDGKYNAYCLVDPEAALKSARDSEARWFEGN 69 Query: 67 -ADVLTGIPLAVKDIFLTEGTLTTCGSRILN-----NFIPPYSATSFEKLKQRGMVLLGK 120 L G+P ++KD+FLT+G T GSR ++ N P +A +L++ G+VLLGK Sbjct: 70 PTGWLDGVPTSIKDMFLTQGWPTLRGSRCIDPEQSWNTDSPVTA----RLRKHGLVLLGK 125 Query: 121 LNQDEFAMGSSNESSASGPCRNPWNTDCIPGGSSGGSAAAIAARQATVTLGTDTGGSIRQ 180 E + +S G RNPWN + PGGSSGGSAAA+AA +++GTD GGS+R Sbjct: 126 TTTAELGWKAVTDSPLEGITRNPWNPELTPGGSSGGSAAAVAAGMGELSVGTDAGGSVRI 185 Query: 181 PASHCGCVGLKPTYGRVSRYGVIAYASSLDQVGPLTRDVTDCAIMLGALAGHDPKDSTSV 240 PAS CG VG KPT R+ Y + L GP+ R V D A++L LA D +D T++ Sbjct: 186 PASFCGIVGFKPTGSRIPLYPASPF-GPLAHAGPMARSVDDIALLLDVLAVPDYRDPTAL 244 Query: 241 DRPVPDYQAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEISLPH 300 Y+ A+ D+RGLR +DP+V + A+ G E S P Sbjct: 245 PPLPAAYREAVRRDVRGLRAAYSPNLGYLDVDPEVDHIVGSAVAALNDEGL-LVEQSDPG 303 Query: 301 TDYAVASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRRIML 360 V ++ L+ + A+ + + EG +E R Q + Sbjct: 304 FSDPVEAFELLWSTGAAKWIDSF-----------PEGSVEKLDRGLQQVWEK-------- 344 Query: 361 GTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIGEKVNDPLQM 420 G +S Y DA L + M +F D+++TP P F G V P Sbjct: 345 GLTHSASEYLDA--LAVSAALGIRMGEFHAQH---DVLITPTVAIPPFEAGYDV--PPGS 397 Query: 421 YLSDI-----FTIPVNLAGTCAMSLPAGISGQGLPIGVQLIGKPFGEETILRAAHAFEQA 475 LS F+ P N+ A+S+P G++ GLP+G+Q+IG ++ +L A E+ Sbjct: 398 GLSSWQRWAGFSYPFNMTRQPAISVPVGLTSNGLPVGMQIIGPRHSDDLVLAVAKLAEEV 457 Query: 476 TEW 478 W Sbjct: 458 QPW 460 Lambda K H 0.318 0.134 0.389 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: 549 Number of extensions: 30 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: 485 Length of database: 468 Length adjustment: 33 Effective length of query: 452 Effective length of database: 435 Effective search space: 196620 Effective search space used: 196620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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