Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_083784660.1 M446_RS10150 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000019365.1:WP_083784660.1 Length = 499 Score = 242 bits (617), Expect = 2e-68 Identities = 193/490 (39%), Positives = 251/490 (51%), Gaps = 59/490 (12%) Query: 3 AHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNE-RLLEEAEAVDPGL----- 56 A I RVAR E+ V A L R+ LDP +GAF + R L AEA+D L Sbjct: 44 AAAIAGRVARRELGARAVVAAALDRIAALDPRVGAFTDVTAARALAAAEALDARLDRGEA 103 Query: 57 --PLAGLVVAVKDNIATRGLRTTAGSRLLENFVPPY-EATAVARLKALGALVLGKTNLDE 113 PLAG+ AVK+ I GL T AGSR+ VP + V RL+A GA+++G N+ E Sbjct: 104 AGPLAGVPFAVKNLIDVAGLPTRAGSRINRERVPAARDGALVRRLEAAGAILVGALNMGE 163 Query: 114 FGMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFC 173 + + E+ P++NP + GGSSGGS AALAA L PL LGSDT GS+R P+AFC Sbjct: 164 YAYDFTGENVHDGPSRNPHALAHMSGGSSGGSGAALAAGLVPLTLGSDTNGSIRVPSAFC 223 Query: 174 GVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPR 233 GV+GLKPTYGR++R G + SLD +GPMARSV DLAL DA+ GPDP D + PP Sbjct: 224 GVFGLKPTYGRLTRAGSFPFVGSLDHLGPMARSVADLALAYDAMQGPDPEDPVATRRPPE 283 Query: 234 FQEALEGPLPPLRLG----VVREALAGN---SPGVERALEEALKVFRELGLSVREVSWPS 286 P+ PL LG +R A+AG G A E +V R LG V P Sbjct: 284 -------PVTPL-LGRGAEGLRVAVAGGYFARGGDPEAFEAVARVARALGADA-TVEIPE 334 Query: 287 LPQALAAYYILAPAE-ASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVG 345 +A AA Y+++ AE A+ +L R + A F V+ R+L G Sbjct: 335 AARARAAAYLISAAEGAALHLDR------------------LRARPGDFDPAVRDRLLAG 376 Query: 346 TFVLSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGARR----DPL 401 + + + RAQ FRR +F VD +L P TP A P G D + Sbjct: 377 AMIPA-----PHVERAQRFRRWYAGAVAEVFAGVDAILAPATPCRA-PRGGETVLVLDGV 430 Query: 402 AM-YREDL--YTVGANLTGLPALSFPAGFEGHLPVGLQLL-APWGEDERLLRAALAFEEA 457 AM R +L +T + GLP + P + LP+G+Q++ APW ED LR A A E+A Sbjct: 431 AMPLRPNLGVFTQPISFVGLPVAAVPVWLDDGLPLGVQVIAAPWREDV-ALRIAHALEQA 489 Query: 458 TARAHLKAPL 467 APL Sbjct: 490 GVARAPVAPL 499 Lambda K H 0.319 0.137 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: 659 Number of extensions: 41 Number of successful extensions: 5 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: 471 Length of database: 499 Length adjustment: 34 Effective length of query: 437 Effective length of database: 465 Effective search space: 203205 Effective search space used: 203205 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 (21.7 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