Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013259244.1 DEBA_RS12210 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000143965.1:WP_013259244.1 Length = 479 Score = 191 bits (484), Expect = 6e-53 Identities = 162/482 (33%), Positives = 237/482 (49%), Gaps = 42/482 (8%) Query: 10 VARGEVSPLEVAQAYLKRVQELDPGLGAFLS-LNERLLEEAEAVDPGLPLAGLVVAVKDN 68 V +GE++P E+ ++ + R ++L+P L A ++ L + + A P P G +KD Sbjct: 19 VRKGELTPSELLESAIARAEKLNPTLNAIITPLYDLARQTAAGPLPDGPFKGAPFLLKDI 78 Query: 69 IATR-GLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDEFGMGSSTEHSAFFP 127 +A + G+ G+ L+ P +AT AR KA G ++ G+TN EFG+ +TE F P Sbjct: 79 MAAQAGVPQACGTAALKGHAPKRDATLTARYKAAGLVIFGRTNTPEFGLLPTTEPRLFGP 138 Query: 128 TKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVYGLKPTYGRVSR 187 TKNP+ +R PGGSSGGSAAA+AA LAP+A +D GGS+R PA+ CG++GLKPT R + Sbjct: 139 TKNPWALERTPGGSSGGSAAAVAAGLAPMAHANDGGGSIRIPASCCGLFGLKPTRARNPK 198 Query: 188 FGLIAYA-SSLDQIGPMARSVRDLALLMDAVAGPDPLDA--TSLDLPPRFQEALEGPLPP 244 ++ A + + + RSVRD ALL+D +GP+P D P QEA P Sbjct: 199 GPVVGDAMGGMLEEHALTRSVRDSALLLDCTSGPEPGDPYWAPPKERPYIQEAATEP-GR 257 Query: 245 LRLGVVREALAGN--SPGVERALEEALKVFRELGLSVREVSWPSL--PQALAAYY-ILAP 299 LR+ + AG P A+E A K+ ELG V E + PSL Q + + IL Sbjct: 258 LRIAFSAKTAAGGPVHPDCLAAMESAAKLCAELGHIVEEDA-PSLRGQQDMGRLFTILWT 316 Query: 300 AEASSNLARYDGTLYGRRAEGEEVEGMMEATRALF--GLEVKRRVLVGTFVLSSGYYEAY 357 A N+ + G++ + + E + T AL+ GLEVK +G Y Sbjct: 317 AGLVGNIHAV-AMVTGKKPDPADYEPL---TWALYQRGLEVK-----------AGDYLNV 361 Query: 358 YGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGA----RRDPLAMYREDL----Y 409 Q + R++ A D+ L PT P P G+ P+ + Y Sbjct: 362 VAATQLWSRQM----AAFMARHDVWLTPTLAEPPLPLGSFDVVNNKPMDAWTRGAAFVPY 417 Query: 410 TVGANLTGLPALSFPAGFEGH-LPVGLQLLAPWGEDERLLRAALAFEEATARAHLKAPLG 468 T N TG PA+S P + LP+G + +G++ L R A E A A + PL Sbjct: 418 TPLQNCTGQPAMSVPLYWNDQGLPIGCHFVGRFGDEATLFRLAGQLERARPWAGRRPPLD 477 Query: 469 EA 470 A Sbjct: 478 AA 479 Lambda K H 0.319 0.137 0.395 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: 559 Number of extensions: 30 Number of successful extensions: 3 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: 471 Length of database: 479 Length adjustment: 33 Effective length of query: 438 Effective length of database: 446 Effective search space: 195348 Effective search space used: 195348 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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