Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_092993132.1 BLP65_RS04690 amidase
Query= curated2:A0L5G0 (485 letters) >NCBI__GCF_900102855.1:WP_092993132.1 Length = 478 Score = 249 bits (637), Expect = 1e-70 Identities = 175/486 (36%), Positives = 249/486 (51%), Gaps = 55/486 (11%) Query: 5 ELTLREAADKLATKEISSVELTQACLDQIAKHNPTINAFVTVDAEKALAAAQAADARIAA 64 ++T E A + +S VE +A LD+I ++NP +NAF VD E L AA+AA+ R Sbjct: 7 DMTAAEMAAMFRHRLLSPVEAAEAALDRIRRYNPAVNAFCLVDEETTLKAARAAEERHLR 66 Query: 65 GNG-APLTGIPIAHKDIFNTTDMRTTCSSRMLENFIP-PFDATITTHLRQAGAVILGKTN 122 G L G+P+A KD+F T + T SR + P DA LR+ GAV +GKT Sbjct: 67 GESLGELDGVPVAIKDVFLTREWPTLKGSRTITPHQPWRTDAPAVAALRRHGAVPVGKTT 126 Query: 123 LDEFAMGSSTETSYFGASRNPWDTQRTPGGSSGGSSAAIAANMAICATGTDTGGSIRQPA 182 EF T+ G +RNPWD RT GGSSGGS+AAI M + A GTD GGSIR PA Sbjct: 127 TPEFGWKGVTDNPVDGITRNPWDISRTAGGSSGGSAAAIPLGMGVLALGTDAGGSIRIPA 186 Query: 183 SLTNLTGLKPTYGRC-----SRYGIIAFASSLDQAGPMTRTAEDAAMLLNVMVSYDPKDS 237 + L G KPT+GR S +G++A GPMT+T EDAA+L+NV+ D +D Sbjct: 187 GFSGLFGHKPTHGRIPMWPGSPFGVLA------HPGPMTKTVEDAALLMNVLTEPDRRD- 239 Query: 238 TSIQSPAPDFTQALTGDVKGLKIGIAAEYFGDGLNDEVRAAIETAQQQYQAMGA--ELVP 295 S+ D+ QAL G + GL I +A++ ++ E+ A+ A + ++++GA E V Sbjct: 240 PSLPPDHTDYVQALGGRIAGLHIAFSADFGFVDVDPEIADAVAEAARVFESLGATVEAVD 299 Query: 296 ISLPNSGYAIPTYYIISPAECSSNLARYDGVKFGYRCEEPKDIRDLYFRSRSEGFGDEVK 355 PN P E ++ + FG +DI D + Sbjct: 300 PGFPN------------PEE------SFERLFFGGAANALRDI-------------DTDQ 328 Query: 356 RRIMLGTYVLSSGYYDAY----YRKAQQARRLIADEFKAAFEKVDLILTPTSPTTAFKFG 411 RR+M V S+ Y AQ R + ++ E+ DL+LTPT P AF+ G Sbjct: 329 RRLMDAGLVESAEAAAKMPLLEYLAAQNVRNELLEQMSRFHERFDLLLTPTLPIAAFEAG 388 Query: 412 EKDD---PVQMYLS-DIYTINVNLAGLPGISVPCGFDSKGLPIGMQLIGRPLDEETLLRS 467 + P + + S +T N+ G P SVPCGF S+GLPIG+QL+G + +LR+ Sbjct: 389 REVPPGWPKRRWPSWTPFTFPFNMTGQPASSVPCGFTSEGLPIGLQLVGARHQDALVLRA 448 Query: 468 ADAYQR 473 A A+++ Sbjct: 449 AHAFEQ 454 Lambda K H 0.317 0.132 0.383 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: 538 Number of extensions: 19 Number of successful extensions: 6 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: 485 Length of database: 478 Length adjustment: 34 Effective length of query: 451 Effective length of database: 444 Effective search space: 200244 Effective search space used: 200244 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