Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate CA265_RS25090 CA265_RS25090 L-asparaginase 1
Query= curated2:Q8TV84 (458 letters) >FitnessBrowser__Pedo557:CA265_RS25090 Length = 339 Score = 155 bits (393), Expect = 1e-42 Identities = 114/352 (32%), Positives = 179/352 (50%), Gaps = 24/352 (6%) Query: 96 LPNVSVMSTGGTIACRVDYETGAVKPAFTAEELVGAVPELLDVINIVDARAVLDLL-SEN 154 + + ++ TGGTI D G + P F +++ VPEL + +D + +L S N Sbjct: 1 MTKILIIYTGGTIGMVNDPTNGMLIP-FDFQQIKENVPELSRLDYDLDVHSFNPVLDSSN 59 Query: 155 MEPKHWMKIAEEVVDALSDPDVEGVVIGHGTDTMAFTAAALSFVIEGLNGPVVLVGAQRS 214 M+P+ W +AE V D G VI HG+DTMAFTA+ALSF++E L PVVL G+Q Sbjct: 60 MDPEIWKTLAELVYHKYDAYD--GFVILHGSDTMAFTASALSFMLENLAKPVVLTGSQLP 117 Query: 215 SDRPSSDAASNLIAACAFAGDGEVGEVTVCMHGWTSDEVCL-----VHRGVRVRKMHTSR 269 +DA NLI A A E G+ EVC+ + RG R K ++ + Sbjct: 118 IGEIRTDAKENLITALEIAATKEDGKALF-------PEVCIYFDAQLFRGNRSIKYNSEK 170 Query: 270 RDAFRSVESIPIAKVDVKDLRNPKIEFLRSDYRRPEDGEPEISGGFEEKVALVKFAPGMD 329 +AFRS +A+ V ++F R+ + +GE ++ F + ++K PG+ Sbjct: 171 FEAFRSPNYPILAEAGV------HLQFHRNYILKATEGELKLHTNFNSNIGVLKLYPGIT 224 Query: 330 PEVLDFYVDRGYRGIVLEGTGLGH-VSEQW-LESIERAVDDGIAVVMTSQCLYGRVNMNV 387 P+ + D I+LE G G+ + QW L+S+ +A+ +G ++ SQC G V + Sbjct: 225 PQAVQAITDSKVDAIILETFGSGNTTTAQWFLDSLRQAILNGKIIIDISQCKKGSVQLGR 284 Query: 388 YRTGRLLRAVGVIPGEDMLPEVAYVKLMYVLDRTDDIKEVERLMRTNIAGEI 439 Y T R L +G++ G D+ E KLM+V+ I+E +LM ++ GE+ Sbjct: 285 YETSRELLKMGILSGYDLTFEATVTKLMFVMGLGLSIEESRKLMEESLRGEL 336 Lambda K H 0.318 0.139 0.404 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: 350 Number of extensions: 24 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: 458 Length of database: 339 Length adjustment: 31 Effective length of query: 427 Effective length of database: 308 Effective search space: 131516 Effective search space used: 131516 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 09 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