Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_085772734.1 B1812_RS17510 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_002117405.1:WP_085772734.1 Length = 396 Score = 147 bits (370), Expect = 8e-40 Identities = 129/401 (32%), Positives = 179/401 (44%), Gaps = 48/401 (11%) Query: 57 PLAGLVVAVKDNIATRGLRTTAGSR--LLENFVPPYEATAVARLKALGALVLGKTNLDEF 114 PLAGL VK+NI GL +T G + A V L A GA ++GKT++DE Sbjct: 21 PLAGLAFVVKENIDVEGLVSTNGHPEFAASHMAARANAPVVEALLAAGATLVGKTHMDEM 80 Query: 115 GMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCG 174 ++ + N PDR PGGSS GSAA +AA LA ALG+DT GS R PA+FCG Sbjct: 81 AYSLMGANAHYGTPVNGRAPDRHPGGSSSGSAAVVAAGLADFALGTDTAGSCRAPASFCG 140 Query: 175 VYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRF 234 V+G +P++ +S G++ A S D +G AR LA + D + DP Sbjct: 141 VFGFRPSHDALSLAGIVPLAPSFDVVGFFARDAATLAKVGDILLPQDP------------ 188 Query: 235 QEALEGPLPPLRLGVVREALAGNSPGVERALEEALKVFRELGLSVREVSWPS--LPQALA 292 PL G+V + + P E A A L +REV+ + PQAL Sbjct: 189 ------DRRPLAQGLVLADVFADCPQAEGARFVAAMTALAPELPMREVALDASFWPQALT 242 Query: 293 AYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVLSSG 352 + EA R+ G +E R FG + R F ++ Sbjct: 243 HFRNYQAFEA-------------WRSHG----AWIEQRRPGFGPGIGER-----FAYAAT 280 Query: 353 YYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGARRDPLAMYREDLYTVG 412 +A A+AFR + + +AL E LL+LPTTP A + L R ++ + Sbjct: 281 VTQAQRLEAEAFREEARPKIEALLGEDGLLVLPTTPFFAPRLDESAEALDAKRYQMFRLF 340 Query: 413 --ANLTGLPALSFPAGFEGHLPVGLQLLAPWGEDERLLRAA 451 A+ GLP +S P + P+GL L+ G D LL A Sbjct: 341 LIASFFGLPQVSLPLASDP--PLGLSLIGRRGTDRALLALA 379 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: 483 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: 471 Length of database: 396 Length adjustment: 32 Effective length of query: 439 Effective length of database: 364 Effective search space: 159796 Effective search space used: 159796 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