Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013092039.1 BC1002_RS21190 indole acetimide hydrolase
Query= curated2:Q1J0C2 (483 letters) >NCBI__GCF_000092885.1:WP_013092039.1 Length = 484 Score = 197 bits (502), Expect = 5e-55 Identities = 166/491 (33%), Positives = 236/491 (48%), Gaps = 51/491 (10%) Query: 6 TATDLARAVQARETTPQALLEAARRRAEAARDLNALISLNDRADEQAARVQVRLDAGET- 64 +AT A+Q+ + RA A LNAL +L+ AA+ L E Sbjct: 12 SATQAVEALQSGRLKASDYVATLLARAAALTQLNALTTLDFHGALAAAQRIDALPPAERA 71 Query: 65 -LPLAGVPIVVKDNLNVIGTRTTCGSRILANYVSPYDATAVERLTGAGAVIIGKANMDEF 123 LPL G+PIVVKDN+N G TT G+ LA++V A +V+RL AGAV++GKANM E Sbjct: 72 RLPLCGLPIVVKDNINTAGLPTTAGTPALASFVPTTSAPSVQRLVDAGAVVLGKANMHEL 131 Query: 124 AMG-SSTESSAW-GPTLNPWDRERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPAAF 181 A G +ST SA GP NP+D +PGGSSGG+AVA+AA + P LG+DTGGS R PAA Sbjct: 132 AFGITSTNLSAHAGPVRNPYDPSLMPGGSSGGTAVAIAARIAPAGLGTDTGGSTRIPAAL 191 Query: 182 TGIYGLKPTYGR---VSRY----GLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDA 234 TG GL+P+ G RY +V + + D +GP ARS ADLALL V+ G Sbjct: 192 TGTAGLRPSVGNGGAERRYHDPNAVVPISHTRDTVGPMARSVADLALLDGVITGDGALPE 251 Query: 235 TSLDAPPAFRPGTPDDLQGLRVGVIREALEGNTPGVEAALNATLDALRGAGATVREVSVP 294 +LD GLR+G+ + VE A L L AG T V++ Sbjct: 252 IALD--------------GLRIGLPAPLWDALERQVEDVARAALHKLEAAGVTFVPVAMT 297 Query: 295 SVQHAIAAYYLIATPEASSNLARYDGMVYGERVSAP-DAVSSMTLTREQGFGREVKRRIM 353 +++ ++ P A AR D + + AP V+ + + R + ++ Sbjct: 298 ELEYLNG---MVGGPLAIHE-ARDDVLAWLVANQAPVRTVADLAVRIASPDVRAIYDDVL 353 Query: 354 LGTYALSSGYYDAYYSKAMKVRRLIAQDFARAFGNVDVLVTPTSPFPAF----RRGEKTQ 409 L S Y A +++ +A FA A +D L+ PT+ A G T Sbjct: 354 AD--VLGSHYSAALNYWRPRLQNYVAATFANA--GLDALLFPTTRLVAVPIDDLNGSSTV 409 Query: 410 --------DPLAMYAADVDTVAINLAGLPALSVPAGFERVDGVRLPVGVQLIAPPLQDER 461 D + + + D + +G+P LS+PAG + LPVG++L P D R Sbjct: 410 TIDGGPPIDTMEAFLRNTDPA--STSGIPGLSLPAG---ISASGLPVGLELDGPLGSDRR 464 Query: 462 LVALAGGLEGI 472 L+A+ +E + Sbjct: 465 LLAIGVAIEQV 475 Lambda K H 0.316 0.132 0.375 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: 623 Number of extensions: 37 Number of successful extensions: 6 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: 483 Length of database: 484 Length adjustment: 34 Effective length of query: 449 Effective length of database: 450 Effective search space: 202050 Effective search space used: 202050 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: 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