Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012976309.1 AZL_RS20130 amidase
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_000010725.1:WP_012976309.1 Length = 487 Score = 181 bits (458), Expect = 7e-50 Identities = 154/489 (31%), Positives = 224/489 (45%), Gaps = 39/489 (7%) Query: 10 ELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADRRIAAGEADV 69 +L ++++ EV+ EA + R+ + P +NA + E A E A RR +G+ Sbjct: 19 DLAERIQAGEVTPLEALDDAIARLERVNPTLNAVVEPLFETA---RETASRR-TSGDGP- 73 Query: 70 LTGIPLAVKDIFL-TEGTLTTCGSRILNNFIPPYSATSFEKLKQRGMVLLGKLNQDEFAM 128 G+P +KD+F+ G T GSR+ P A ++L+Q G+V+ G EF Sbjct: 74 FAGVPTFIKDLFMPVAGARMTNGSRLFEPVRAPVDADFVQRLRQAGIVIAGTTTSPEFGT 133 Query: 129 GSSNESSASGPCRNPWNTDCIPGGSSGGSAAAIAARQATVTLGTDTGGSIRQPASHCGCV 188 + ES G RNPW+ D PGGSSGG++A +AAR G D GGS+R PAS CG Sbjct: 134 SFATESQLFGATRNPWSPDHTPGGSSGGASALVAARVVPFAYGNDGGGSLRVPASCCGVF 193 Query: 189 GLKPTYGRVSRYGVIAYA-SSLDQVGPLTRDVTDCAIMLGALAGHDPKDSTSVDRPVPDY 247 GLKPT GRV +I + + +T V D A +L A AG+ D + P + Sbjct: 194 GLKPTRGRVPLGPMIGEGWAGMGVTHAITLSVRDSAALLDATAGYSAGDPYAAPTPDGRF 253 Query: 248 QAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLG--AEFTEISLPHTDYAV 305 A+T + LRIGL R PD A++D ++ LG E TE+ + D+ Sbjct: 254 LDAVTRPPKPLRIGLVRSLAPWPTHPDCLAAVDHSVRLCESLGHRVEETELPVSAADFYD 313 Query: 306 ASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRRIMLGTYAL 365 A + +I + +L G G A+ E +LE +R + G + YA Sbjct: 314 AIFTIIGA--QTRHLLEVVGAMTGRPAD--ESVLEPRTRVLLRAKGG-----VSGAAYAA 364 Query: 366 SSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIGEKVNDPLQMY--LS 423 + D+ + +++ L F D++LTP P IG + Q L Sbjct: 365 A---VDSIHALGRRMAGL--------FGRFDVLLTPTLAKPPVTIGALDMEDTQTLPELI 413 Query: 424 DIF------TIPVNLAGTCAMSLPAGISGQGLPIGVQLIGKPFGEETILRA-AHAFEQAT 476 D+F T N G AMS+P + GLPIG Q PFGEE++L A A E A Sbjct: 414 DLFHSFSPITPLFNATGQPAMSVPLHWNDAGLPIGTQ-FAAPFGEESLLFALAGQLEDAQ 472 Query: 477 EWHSLRAPL 485 W P+ Sbjct: 473 PWRDRVPPI 481 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: 551 Number of extensions: 31 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: 487 Length adjustment: 34 Effective length of query: 451 Effective length of database: 453 Effective search space: 204303 Effective search space used: 204303 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: 52 (24.6 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