Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011648928.1 RL_RS33615 amidase
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_000009265.1:WP_011648928.1 Length = 457 Score = 167 bits (423), Expect = 7e-46 Identities = 147/481 (30%), Positives = 219/481 (45%), Gaps = 60/481 (12%) Query: 6 LTLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADRRIAAG 65 L++ +L ++ V +LD I + + FI++T ERA+AEA A+ +R+ G Sbjct: 8 LSIAQLSTLIQGGSVDPVTVAEQVLDAIESHDDKA-VFISLTRERAMAEAHASSKRLNDG 66 Query: 66 EA-DVLTGIPLAVKDIFLTEGTLTTCGSRILNNFIPPYS--ATSFEKLKQRGMVLLGKLN 122 + +L GIP+A KD+F G++T GSR+L P + A L GMV G++N Sbjct: 67 RSLGLLEGIPVAWKDLFDVAGSVTAAGSRLLLRDQAPAAVDAAVVSALASAGMVATGRVN 126 Query: 123 QDEFAMGSSNESSASGPCRNPWNTDC--IPGGSSGGSAAAIAARQATVTLGTDTGGSIRQ 180 EFA + G +NP +TD IPGGSS GS A+A+ V++G+DTGGS+R Sbjct: 127 MSEFAFSGLGINPHFGTPKNPRSTDVARIPGGSSSGSGVAVASALVPVSIGSDTGGSVRI 186 Query: 181 PASHCGCVGLKPTYGRVSRYGVIAYASSLDQVGPLTRDVTDC----AIMLGALAGHDPKD 236 PA+ G VG K T GR GV + SLD +GPL R V D A M GA+A Sbjct: 187 PAALNGIVGYKATRGRYPMTGVFPLSGSLDSLGPLCRSVQDAIWIDAAMRGAMA------ 240 Query: 237 STSVDRPVPDYQAALTNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEI 296 T+ RP + GL + +P + +P V A+ + A+E G FT + Sbjct: 241 PTASRRP-----------LAGLEVVIPTNVVFDDAEPGVVAAFEAAVERLSAAGVMFTRL 289 Query: 297 SLP---HTDYAVASYYLIATAEAS-ANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGS 352 +P +AS+ + TAEA + AR G GL++ SR++ FG Sbjct: 290 EIPAFAEILQLMASHGALVTAEAYWLHKARITG--------PDAGLIDPRVVSRTR-FGE 340 Query: 353 EVKRRIMLGTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIGE 412 E+ +YL R ++ + + G LI P A + Sbjct: 341 EITL---------------PHYLDILSARKRLI-EAVDRLVGDRLIAFPTVAHVAPLLEP 384 Query: 413 KVNDPLQMYLSDIFTIPVNLAGT----CAMSLPAGISGQGLPIGVQLIGKPFGEETILRA 468 D ++ T+ L G C +S+P G G+P+G L G G+E +L Sbjct: 385 LKTDDQLFVATNGKTLRNTLLGNFLDWCGVSIPCGAGDAGMPVGFLLSGLARGDERLLSV 444 Query: 469 A 469 A Sbjct: 445 A 445 Lambda K H 0.318 0.134 0.389 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: 433 Number of extensions: 19 Number of successful extensions: 5 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: 485 Length of database: 457 Length adjustment: 33 Effective length of query: 452 Effective length of database: 424 Effective search space: 191648 Effective search space used: 191648 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 (21.7 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