Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106717548.1 CU100_RS15780 amidase
Query= curated2:C6BSE9 (487 letters) >NCBI__GCF_003010935.1:WP_106717548.1 Length = 473 Score = 147 bits (370), Expect = 1e-39 Identities = 140/479 (29%), Positives = 217/479 (45%), Gaps = 36/479 (7%) Query: 10 TEIHAMLMTKEVTATEAVKACLEQIAKSEPETKALLHICNDEALKQAEEMDAAGPDASKP 69 T + ++ +EVTA+E + A L +A + E A++ +EA + + + GP Sbjct: 12 TGLAELVAKQEVTASELLDAALAGVAAVDGELNAVIATFEEEARRFIAQELSDGP----- 66 Query: 70 LWGVPVVIKDALAT-NGIPTTAGSKILEGFTPFYDSTAVAKLKEAGAIIVGKANMDEFAM 128 GVP ++KD A G PT AG P DS V + K++G +I GK ++ E AM Sbjct: 67 FKGVPFLLKDLTAHYGGQPTGAGWPPRAAVRPAEDSELVRRFKKSGVVIFGKTSVPELAM 126 Query: 129 GSTTENSAYQTTTNPWDASRVPGGSSGGSGATVAAGQCYAALGTDTGGSIRLPASFCGCV 188 TT + A+ T NPWD +R G SSGG+ A VAAG G D GGSIR+P+S CGC Sbjct: 127 DWTTRSRAHGVTNNPWDTTRTAGTSSGGTAAAVAAGVVPMGHGNDGGGSIRVPSSACGCF 186 Query: 189 GVKPTYGR--VSRYGMIAYGSSLDQIGPMTRTVEDAARVLNVIGG-HDQRDSTSAEQPME 245 G+KP+ GR V+ G G ++ + ++R+V D+A +L+ G H + S P E Sbjct: 187 GLKPSRGRNPVAPSGSTWQGMLVEHV--LSRSVRDSAGMLDATQGLHVGQFFNS--PPGE 242 Query: 246 DFVAALEERKDLSGLTIGLPEEY-WGEGLSKEVSEACRAAIAKAEELGAKTVPVKLSMTE 304 F A E +D L IG+ + +G + A + E LG + + Sbjct: 243 GF--ASEVGRDPGKLRIGVSTKAPYGAATHPDCVTAIEETMKLLEGLGHICESHDIELPP 300 Query: 305 YAIATYYIIAMAEASSNLSRFDGVRYGHRTEDPKELAELYTKSRTEAFGDEVQRRIIIGT 364 + + +AE ++++ + V L K + F + I G Sbjct: 301 DGWSAFETFILAEYATDMRLEEDV--------------LGRKLTADDFPPMLWEMIDAGN 346 Query: 365 YVLSAGYYDAYYRKAAQIRRLLREDFNK--AFESCDIIASPACPTTAFPVGELTSDPLQM 422 + + A R A + + FN+ F S +A P AFP + + Sbjct: 347 GISAVDVNVATTRLHA-VASAVTSTFNRYDVFLS-PTLAQPPLAHDAFPQATSMREHYEF 404 Query: 423 YLQDI-FTISLNLVGMPGMSLPVAFGKETNMPVGLQFMAPAFDEKTMLQAAHVLEKNLP 480 YL + FT N+ G P MS+P+ + E +P+G+QF A E + + A LE P Sbjct: 405 YLSWMPFTHIFNVNGSPAMSVPLVWNAE-GLPIGVQFAAAPAAEGLLFRLASQLEMARP 462 Lambda K H 0.315 0.131 0.374 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: 497 Number of extensions: 30 Number of successful extensions: 4 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: 487 Length of database: 473 Length adjustment: 34 Effective length of query: 453 Effective length of database: 439 Effective search space: 198867 Effective search space used: 198867 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 Jul 26 2024. The underlying query database was built on Jul 25 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