Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012171147.1 AZC_RS13560 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_000010525.1:WP_012171147.1 Length = 477 Score = 330 bits (847), Expect = 5e-95 Identities = 202/481 (41%), Positives = 272/481 (56%), Gaps = 31/481 (6%) Query: 2 DLFDLTLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADRR 61 DL + EL +++ E S E T A L RI ++ ++N+FITVT E ALA+A A + Sbjct: 18 DLVTAGVLELGRMIRTGETSPVEITKACLSRIERIDSKLNSFITVTAEAALAQAAAVEAE 77 Query: 62 IAAG-EADVLTGIPLAVKDIFLTEGTLTTCGSRILNNFIPPYSATSFEKLKQRGMVLLGK 120 +AAG + GIP A+KD T G L++ SRI + +P SAT KL+ G +L+GK Sbjct: 78 LAAGLDRGPFHGIPYALKDNVDTAGVLSSSHSRIFIDRVPQESATVARKLEAAGGILIGK 137 Query: 121 LNQDEFAMGSSNESSASGPCRNPWNTDCIPGGSSGGSAAAIAARQATVTLGTDTGGSIRQ 180 EFA+G + P RNPWN D +PGGSS GS AA+ R +GTDTGGSIR Sbjct: 138 TATFEFAIGGPSFDLPWPPARNPWNPDYLPGGSSSGSGAAVGGRLVPAAIGTDTGGSIRW 197 Query: 181 PASHCGCVGLKPTYGRVSRYGVIAYASSLDQVGPLTRDVTDCAIMLGALAGHDPKDSTSV 240 PA+ CG GLKPTYGR+SR GV SLD GP+ R DCA MLGA AG+DP D S+ Sbjct: 198 PAAMCGITGLKPTYGRISRRGVHPNTFSLDHCGPMARSAADCAAMLGACAGYDPLDPGSI 257 Query: 241 DRPVPDYQAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEISL-P 299 D PVPDY AALT I+GLRIGL R ++ E +V A++D A+E R+LGA ++L P Sbjct: 258 DAPVPDYTAALTGSIKGLRIGLVRHWYEEEATDEVIAAVDDAVEVLRQLGAVVEPLTLDP 317 Query: 300 HTDYAVASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRRIM 359 DY A + T + H A+ R R Q FG ++ R+M Sbjct: 318 LRDYVDAKTTISITELFAV-----------HEAD---------IRFRPQDFGRLLRSRVM 357 Query: 360 LGTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIGEKVNDPLQ 419 +G + Y A +A+ + T +MA AF DL++T PA V D + Sbjct: 358 VGGLVRAEDYVQAMRWRAE-LSTRMMA----AFSRYDLLVTAGWMAPA---DPAVPDGVD 409 Query: 420 MYLS-DIFTIPVNLAGTCAMSLPAGISGQGLPIGVQLIGKPFGEETILRAAHAFEQATEW 478 + + T+P +LAG A++LP G S +GLP+ +Q+ G+PF E T+LRA A++QATEW Sbjct: 410 FFKKRQLVTMPFSLAGLPALALPCGFSSKGLPLSLQIAGRPFDEATVLRAGDAYQQATEW 469 Query: 479 H 479 H Sbjct: 470 H 470 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: 547 Number of extensions: 33 Number of successful extensions: 4 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: 477 Length adjustment: 34 Effective length of query: 451 Effective length of database: 443 Effective search space: 199793 Effective search space used: 199793 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