Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate WP_086509657.1 BZY95_RS09260 asparaginase
Query= curated2:Q9HJJ5 (409 letters) >NCBI__GCF_002151265.1:WP_086509657.1 Length = 350 Score = 117 bits (294), Expect = 4e-31 Identities = 96/333 (28%), Positives = 146/333 (43%), Gaps = 35/333 (10%) Query: 67 DRKISVLATGGTIASRVDYETGAVSPVSDPELIFGGSDILTRFTVAVKPILNEF------ 120 DR + VL TGGT+ E + P D E + L + + L EF Sbjct: 8 DRPVLVLYTGGTLGMMPSAE--GLVPAGDIETRLRNA--LDGLPPSRQSQLPEFVVHTVA 63 Query: 121 ----SENLKPADWIRIGQAVADESSEADGVVVAHGTDTMAYTSSALAFMFERMRVPVVFV 176 S P DW R+ +AD + G+VV HGTDT+A+++S+LAF + + PVV Sbjct: 64 SPIDSSAATPHDWQRLAATIADRIGQHAGIVVLHGTDTLAWSASSLAFQLQGLDRPVVVT 123 Query: 177 GAQRSSDRPSSDSRENMQAAINFAG-TDLGEVGISMHASTSDGHVSLLRSVRSRKMHTSR 235 GA + SD+ N++ A+ FA +L E+ ++ LLR RS K H+ Sbjct: 124 GAMHPLEAEGSDALANIELALRFAARPELQEIAVAFAG-------RLLRGARSSKTHSEN 176 Query: 236 RDAFESIGIPPLAEYDGSVKFLIDYRRVS---------DTVEFRPDLDDRVSMIYFHPGL 286 DAF S P L E G L R + + ++ P V + PG+ Sbjct: 177 DDAFASPNYPLLGEQVGDDVVLYPARCLETQQRGAPRFELPDYSPLAKGGVVRLALWPGI 236 Query: 287 NAGDLENMIAEKHA----VVILGTGLGHMAKDLIPVVKKYTADGNYAIMASQCIYGSTDL 342 A LE + + + + G G ++I V+ K + +G SQC +G Sbjct: 237 QAWQLEAWLGDDRVQGALLEVWGGGNIPPDPEVIGVLAKASGEGKLIAAISQCRWGGIAP 296 Query: 343 NVYSTGRELLAAGVIEAGNMVPEVAYVKAMYLL 375 Y+ G+ L+ AGV+ +M PE A K ++LL Sbjct: 297 GRYAAGQGLIEAGVLSGDDMTPEAAITKLVHLL 329 Lambda K H 0.317 0.135 0.376 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: 303 Number of extensions: 15 Number of successful extensions: 4 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: 409 Length of database: 350 Length adjustment: 30 Effective length of query: 379 Effective length of database: 320 Effective search space: 121280 Effective search space used: 121280 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: 50 (23.9 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