Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011427567.1 RHE_RS22530 amidase
Query= curated2:Q21RH9 (493 letters) >NCBI__GCF_000092045.1:WP_011427567.1 Length = 470 Score = 123 bits (309), Expect = 1e-32 Identities = 145/489 (29%), Positives = 205/489 (41%), Gaps = 53/489 (10%) Query: 14 QLASLLRARKVSALETAQHFLARAQANASLGAFLDFNEEVTLRQARAADLAL-AADSGGA 72 +LA+ +R +SA E L A +A LGA + + L A A D A Sbjct: 7 ELAAAIRHGSLSAAEAMHISLEAAALHAPLGAIAYLDGAMGLAAAHACDRERQTVPRRFA 66 Query: 73 TPTLLGVPMAHKDIFVT-RDFISTAGSRMLAGYRSPFDATVVSKLAAQGVVTLGKLNCDE 131 GVP KD+ R TAGSR+ D+ + S+ G G E Sbjct: 67 ARPFAGVPTLAKDLGGPFRGLPVTAGSRLFERKGGEADSDLASRFRDAGFCLFGLTTSPE 126 Query: 132 FAMGSANENSAFGPV-RNPWDLTRTPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPASF 190 F + A+E A GPV RNP D TRT GGSSGG+AAAVAA ++ A TD GGSIR PA+ Sbjct: 127 FGLSLASE-PAIGPVCRNPLDPTRTAGGSSGGAAAAVAAGIVAIAHATDAGGSIRVPAAC 185 Query: 191 CGVTGIKPTYGR---ASRYG--MVAFASSLDQAGPMARTAQDCALLLSAMCG------PD 239 CG+ G+KPT G +G + AS L + R+ +D AL+ + G PD Sbjct: 186 CGLVGMKPTRGAIPGGPSFGNHLAGIASEL----AVCRSVRDTALIFDRLSGNARGPVPD 241 Query: 240 P---DRDSTSLDLPAEDFTRSLTESIEGLRIGVPAEFFGEGLADDVRAAVDGALKELEKL 296 P D D+ L + T T S EG R+ AAV+ A + LE Sbjct: 242 PSPADIDNGRLRIGLLTDT-GPTYSTEGSRL----------------AAVEDAARMLESD 284 Query: 297 GARLVPISLPRTELSIPVYYIIAPAEASSNLSRFDGVKFGHRAAQYADLTDMYKKTRAEG 356 G +VP++ E S+ S NLS G ++ LT + R Sbjct: 285 GHVIVPLAWADFEWSVAASGRAFADIVSVNLSALIEAA-GLEESRAEPLTQAF-AARGRA 342 Query: 357 FGDEVKRRIMIGTYVLSHGYYDAYYLQAQKIRRMIADDFQQAYLQCDVIAGPVAPTVAWK 416 + + ++SH + + K+ M+ A L A T Sbjct: 343 LSASMLWNTLNAAVLVSHALWALF----DKVDCMVMSMLASAPLAIGSFPSDHADTDLHL 398 Query: 417 LGGHGNDPLADYLADIFTLPGSLAGLPGMSLPVGFGANHMPVGLQLIGNYLQEAKLLNVA 476 PLA LA+I +G P ++LP G + MP+ +QL+ + E +LL++A Sbjct: 399 ERMTAFAPLA-CLANI-------SGFPALTLPFGQDEHAMPLPVQLMMSMGDEPRLLSLA 450 Query: 477 HRFQQATHW 485 R + W Sbjct: 451 ARLEAEGRW 459 Lambda K H 0.319 0.134 0.395 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: 532 Number of extensions: 34 Number of successful extensions: 3 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: 493 Length of database: 470 Length adjustment: 34 Effective length of query: 459 Effective length of database: 436 Effective search space: 200124 Effective search space used: 200124 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