Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012115219.1 XAUT_RS16305 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000017645.1:WP_012115219.1 Length = 474 Score = 277 bits (708), Expect = 7e-79 Identities = 177/493 (35%), Positives = 249/493 (50%), Gaps = 37/493 (7%) Query: 1 MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAAD 60 M+ + L V + + +A G +SS L + L R+ + P+ A + ++ AR ARA D Sbjct: 1 MSGFFTLGVVEMADAVADGSVSSEALAEEALQRLETLGPRYNAVMQIEPERAREAARAVD 60 Query: 61 ARRAAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVIL 119 RA GD PL G+P+ KD++ G T S + +++ P ++ + RL AAGA+ L Sbjct: 61 LARARGDKLGPLAGVPLAHKDLLYRAGRVATGGSLIRKDFVPDVTSSVLERLDAAGALDL 120 Query: 120 GKLNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSI 179 G L+ EFA+ + N + +PWN GGSS GS AAVAA P ALG+DTGGSI Sbjct: 121 GSLHLAEFALSPTGFNVHYGHGLSPWNTAYGAGGSSSGSGAAVAARMVPGALGSDTGGSI 180 Query: 180 RQPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDAT 239 R P+A+CG+TGLKPT+G V YG + A SLD IGP+ RT RD A ++ IAG DP D Sbjct: 181 RHPSAMCGVTGLKPTHGLVPLYGAMPLAPSLDTIGPLTRTARDAARMMTAIAGPDPRDGA 240 Query: 240 CTDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISL 299 P D+E L GD++GL I VP Y+ P++ A + + VL++ GA++ E S Sbjct: 241 TLPAPRLDFEGGLKGDLKGLTIAVPSGYYRELATPEIAALMDDSRAVLKDAGAQLIETSP 300 Query: 300 PHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIM 359 P + ++ E S R+ R + +VR R++ Sbjct: 301 PDMALVNALMQVVMLVEMSTLHRRW------------------LTERPQDYSLQVRARML 342 Query: 360 LGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLA 419 G + Y +A RA R + A D++ PT P I T P Sbjct: 343 PGLALPATRYAEALMMRASVTRDWLATTMGAA----DMVHMPTLPVAVPSIAETTAGP-- 396 Query: 420 MYLEDVC---------TLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLLRVGD 469 ED+ T +N GLP L VPCGF A GLP QL+GR + + LL+ GD Sbjct: 397 --PEDIAAVVGRLAAFTRGINYLGLPSLSVPCGFTANGLPAAFQLVGRPYADPVLLKAGD 454 Query: 470 AYQRVTDWHTRMP 482 AYQR TD+H +P Sbjct: 455 AYQRRTDFHALLP 467 Lambda K H 0.320 0.136 0.398 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: 546 Number of extensions: 23 Number of successful extensions: 3 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: 490 Length of database: 474 Length adjustment: 34 Effective length of query: 456 Effective length of database: 440 Effective search space: 200640 Effective search space used: 200640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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