Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_028997171.1 H537_RS0106055 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000430725.1:WP_028997171.1 Length = 465 Score = 211 bits (538), Expect = 3e-59 Identities = 170/470 (36%), Positives = 236/470 (50%), Gaps = 49/470 (10%) Query: 6 IRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNER--LLEEAEAVDP----GLPLA 59 +RA A G + P +A L R+ ++ P L AF +L + LL+EAEA G PL Sbjct: 13 LRAGYAEGRLDPPAAMRACLARIAQVQPALNAFTALRAQAQLLQEAEASAARWRAGRPLG 72 Query: 60 ---GLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLDEFGM 116 G+ +AVKDN+ T L T+ G F + AVAR +A GA+V+GKTN+ EF + Sbjct: 73 ALDGIPLAVKDNLPTADLPTSWGCA--PGFRGDRDELAVARARAAGAIVVGKTNVPEFTL 130 Query: 117 GSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAFCGVY 176 T + AF T+NP++ + PGGSSGG+ AA+AA PLALG+D GGS+R+PA+ + Sbjct: 131 EGYTSNRAFGTTRNPWNRELTPGGSSGGAVAAVAAGCVPLALGTDGGGSIRRPASHTNLV 190 Query: 177 GLKPTYGRVSRF-GLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLDLPPRFQ 235 GLKP+ G V R L + +GP+AR+V D LL DA+ GPD D SL + Sbjct: 191 GLKPSIGMVPRVDALPPLLLDFEVVGPIARNVEDAQLLFDALRGPDTRDRRSLAATAACR 250 Query: 236 EALEGPLPPLRLGVVREALAGNSP---GVERALEEALKVFRELGLSVREVSWPSLPQALA 292 E P PLR V+ A +P V R EA +G +V E +LP LA Sbjct: 251 ER---PARPLR--VLHVATLDGAPVDAQVRRCTAEAAARLARMGHAVEE---GALPLELA 302 Query: 293 AYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVLSSG 352 A P LA L+ + E G A A G ++ Sbjct: 303 ALNRDWPRVGQIGLA----WLFAQHPHWHEAAGARYAALARQG--------------AAQ 344 Query: 353 YYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTT---PHPA---FPFGARRDPLAMYRE 406 A +G +A +L+ + ALF VDL+L+P P PA FP +P+ Sbjct: 345 PASALWGMLEAV-EQLRRDCAALFERVDLVLMPAAAALPWPADESFPPLIDGEPVGPRGH 403 Query: 407 DLYTVGANLTGLPALSFPAGFEGH-LPVGLQLLAPWGEDERLLRAALAFE 455 ++T N GLPAL+ PAGF LP+G+QL+A +G D+ LL LA++ Sbjct: 404 AVFTGWVNAAGLPALALPAGFSDEGLPIGIQLVAGYGRDDDLLDLGLAWQ 453 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: 558 Number of extensions: 38 Number of successful extensions: 7 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: 465 Length adjustment: 33 Effective length of query: 438 Effective length of database: 432 Effective search space: 189216 Effective search space used: 189216 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