Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_017600915.1 D471_RS0123665 amidase
Query= curated2:B8HY89 (482 letters) >NCBI__GCF_000341125.1:WP_017600915.1 Length = 307 Score = 89.4 bits (220), Expect = 2e-22 Identities = 102/330 (30%), Positives = 135/330 (40%), Gaps = 43/330 (13%) Query: 166 ALGSDTGGSIRQPASFCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGA 225 A GSD GGS+R PAS CG+ GLKPT G +S L L GP V DAALLL A Sbjct: 2 AHGSDGGGSLRIPASACGLFGLKPTRGRISGGPLKPDLVGLSTAGPLTHTVLDAALLLDA 61 Query: 226 IAGHDPQDSTSLNVPIPDYTQFLIPDLKGK---KIGIIQE--TYGEGLDPQVEQVTHKAI 280 +AG D P+P F + ++G + + + P V A Sbjct: 62 MAGARSGDLYGA-PPLPPGETFADHARRAPGRLRVGRYADAGSVDAPVHPHVRAAYDAAS 120 Query: 281 QQLEELGAEVREISCP---RFRYGLP-TYYIIAPSEASANLARYDGVKYGFRSPDPENLL 336 L ELG EV EI P F P + ++ + ASA+ PD E+ L Sbjct: 121 DLLVELGHEVEEIPTPGDAHFGGTFPEDFGVLWAAMASASPV----------DPDREHDL 170 Query: 337 SMYTRTRAEGFGPEVKRRIMIGTYALSAGYYDAYYLKAQK-VRTLIKQDFEAAFEQVDVL 395 TR E A Y A + Q+ VR+LI A E DVL Sbjct: 171 RPITRWLRE------------RARATPVPDYIAACARLQRGVRSLI-----TATEPYDVL 213 Query: 396 VCPT-----APTTAFAAGAKTADPLSMYLSDLMTIPVNLAGLPGLSLPCGFDQQGLPIGL 450 + PT P F G + M T N++G P +S+P + GLPIG+ Sbjct: 214 LSPTLALPPVPIGHFDQGGPEEEFRRMTEFTPFTSVYNVSGQPSVSVPLHWSPDGLPIGV 273 Query: 451 QLIGNVLREDLVFQVAYAYEQATPWHDRHP 480 L G + E + ++ E+A PW R P Sbjct: 274 MLTGRMGGEGTLLSLSAQMEEARPWAHRVP 303 Lambda K H 0.317 0.134 0.388 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: 365 Number of extensions: 21 Number of successful extensions: 3 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: 482 Length of database: 307 Length adjustment: 30 Effective length of query: 452 Effective length of database: 277 Effective search space: 125204 Effective search space used: 125204 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: 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