Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013459025.1 SULKU_RS00835 amidase
Query= curated2:O66610 (478 letters) >NCBI__GCF_000183725.1:WP_013459025.1 Length = 449 Score = 148 bits (374), Expect = 3e-40 Identities = 133/474 (28%), Positives = 216/474 (45%), Gaps = 70/474 (14%) Query: 8 SELRELLKRGEVSPKEVVESFYDRYNQTEEKVKAYITPLYGKALKQAESLK-----EREL 62 +EL E LK +PKE+ +S +R + V A+ + +A +A+ K + Sbjct: 9 TELLERLKTNSTTPKEIAQSCIERIRAIDPMVNAW--EYFDEAAIEAQLAKIGTYNRDDY 66 Query: 63 PLFGIPIAVKDNILVEGEKTTCASKILENFVAPYDATVIERLKKAGALIVGKTNLDEFAM 122 PL+GIP+ VKD T S + +F DA +I L+++GA+++GKT EFA+ Sbjct: 67 PLYGIPVGVKDIYNTFDMPTQMGSPLWSDFTPGNDARMIHYLRRSGAVMLGKTVTAEFAV 126 Query: 123 GSSTEYSAFFPTKNPWDLERVPGGSSGGSAASVAVLSAPVSLGSDTGGSIRQPASFCGVI 182 + T+NP DL R PG SS GSA +VA PV+LGS T GSI +PAS+CG+ Sbjct: 127 HYQDK------TRNPHDLSRSPGTSSSGSAVAVATGMVPVALGSQTAGSISRPASYCGIY 180 Query: 183 GIKPTYGRVSRYGLVAFASSLDQIGVFGRRTEDVALVLEVISGWDEK-----DSTSAKVP 237 G KPT+G + R G++ SLD +G F R D+AL+ E E V Sbjct: 181 GFKPTFGVLPRIGVLKTTDSLDTLGFFARSVSDLALMFEASRVHGENYEFVHQYIDNYVS 240 Query: 238 VPEWSEEVKKEVKGLKIGLPKEFFEYELQPQVKEAFENFIKELEKEGFEIKEVSLPHVKY 297 VP+ K +IG+ K K AFE + L+ +++ V+LP Sbjct: 241 VPD---------KVYRIGIIKHPKWDLASESAKNAFEAWCARLKSPCLQVQTVTLPQFCD 291 Query: 298 SIPTYYIIAPSEASSNLARYDGVRYGYRAKEYKDIFEMYAR-TRDEGFGPEVKRRIMLGT 356 +I + ++ + + + ++ + + DI + R T++E Sbjct: 292 TIHATHQTIYDKSLAYYFKEEYAKHTLMSPIFYDIIQDGLRITKEE-------------- 337 Query: 357 FALSAGYYDAYYLKAQKVRRLITNDFLKAFEEVDVIASPTTPTLPFKFGERLENPIEMYL 416 Y DA ++++ T +F + D++ + T E PI + Sbjct: 338 ------YQDALEKQSRE-----TREFDAWMDSYDILITLATAD---------EAPIGLTT 377 Query: 417 SDILTVPANL----AGLPAISIPI-AWKDGLPVGGQLIGKHWDETTLLQ-ISYL 464 SDI ANL GLP ++P+ ++ LP+G + + +++ LL + YL Sbjct: 378 SDI--PDANLIWTYLGLPIATLPVLKGENHLPIGVSAVSRKYNDKLLLDFLQYL 429 Lambda K H 0.316 0.136 0.394 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: 559 Number of extensions: 33 Number of successful extensions: 2 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: 478 Length of database: 449 Length adjustment: 33 Effective length of query: 445 Effective length of database: 416 Effective search space: 185120 Effective search space used: 185120 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 (21.6 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