Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_015798864.1 AFER_RS07540 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000023265.1:WP_015798864.1 Length = 466 Score = 147 bits (370), Expect = 1e-39 Identities = 151/455 (33%), Positives = 214/455 (47%), Gaps = 55/455 (12%) Query: 33 PGLGAF-----LSLNERLLEEAEAV---DPGL----PLAGLVVAVKDNIATRGLRTTAGS 80 PG+GA L +++RL A A DP PLAG+ V VKD I T L TTAGS Sbjct: 21 PGIGAAWRAHALRIDDRLGLHALAAIADDPQPAAHGPLAGVPVLVKDTIDTADLSTTAGS 80 Query: 81 RLLENFVPPYEATAVARLKALGALVLGKTNLDEF----GMGSSTEHSAFFP-TKNPFDPD 135 +L P +A V L+A GA + KT E+ G GS + +A + +NP+DP Sbjct: 81 LVLPEEPPATDAWIVDALRAAGATIAAKTTCSEWANFRGEGSISGWNARYGLARNPYDPT 140 Query: 136 RVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYGLKPTYGRVSRFGLIAYAS 195 R GGSS GSA A+AA ++P+A+G++T GS+ PA+ GV G K R+ R G+I +S Sbjct: 141 RSAGGSSSGSAIAVAAGMSPIAIGTETDGSMLCPASLNGVIGFKTAPKRLDRSGVIPISS 200 Query: 196 SLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRFQEALEGPLPPLRLGVVREALA 255 + D +G A S DL L++ +V G ++AT+L P+RL VV E+L Sbjct: 201 TQDSLGIFATSADDL-LVVASVLG---IEATTL-------------TEPVRLCVVEESLN 243 Query: 256 GNSPGVERALEEALKVFRELGLSVREVSWP---SLPQALAAYYILAPAEASSNLARY--D 310 G P + L++ G+ V +S P +L + I+ E L RY Sbjct: 244 GFHPRTLARFHDVLELLSRAGVDVVTLSAPPRGTLEPSDEDELIVLRTELHVELDRYLDR 303 Query: 311 GTLYGRRAEGEEV---EGMMEATRALFGLEVKRRVLVGTFVLSSGYYEAYYGRAQAFRRR 367 + G R+ + V + + + A FG E L + Y A R + R Sbjct: 304 RAIPGLRSLADVVAANDALADRELAYFGQEHFVAALEAD--PADPAYRA--ARQRNLERT 359 Query: 368 LKAEAQALFREVDLLLLPTTPHPAFPFG-ARRDP--LAMYREDLYTVGANLTGLPALSFP 424 + +L L +L T A+P R DP A YR A + G ++S P Sbjct: 360 TEGIESSLAATDALAILAPTMDVAWPIDLLRGDPNSPAGYR------AAAVAGGTSVSVP 413 Query: 425 AGFEGHLPVGLQLLAPWGEDERLLRAALAFEEATA 459 AG GHLPVG+ L AP G +E +L E A A Sbjct: 414 AGRIGHLPVGVCLSAPAGHEETILELTALLERALA 448 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: 492 Number of extensions: 22 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: 471 Length of database: 466 Length adjustment: 33 Effective length of query: 438 Effective length of database: 433 Effective search space: 189654 Effective search space used: 189654 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: 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