Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_022948201.1 H035_RS0106605 amidase
Query= curated2:Q2LXM9 (485 letters) >NCBI__GCF_000421465.1:WP_022948201.1 Length = 473 Score = 234 bits (597), Expect = 5e-66 Identities = 157/491 (31%), Positives = 249/491 (50%), Gaps = 35/491 (7%) Query: 2 ELYQLTIHELQNKIRQGGVTSTAIVNSVFGRIDAVEENVHSYITLMRESALEEAQKADEQ 61 ++ ++T EL R+G ++ ++ +I+ ++ +V+++ + E+ L A++++E+ Sbjct: 4 DVLRMTAVELLEAYRKGSLSPVEATRAMLDQIERLDPHVNAWCLVDSETTLRYARESEER 63 Query: 62 IRTGEINA-LTGIPVALKDIYCTRGVRTTCGSLILD-NFIPPYDATVVVKLREAGAVFTG 119 + GE L G+PVA+KD++ T T GS +++ N ++ V L+ G V G Sbjct: 64 YQQGEPKGWLDGVPVAVKDVFLTPMWPTVKGSKVIEPNSTLGKESPAVAALKRNGYVPLG 123 Query: 120 KTNMDEFAMGSSTETSYYGFTRNPWDLERIPGGSSGGSAAAVAADECIAALGSDTGGSIR 179 KT EF T++ +G TRNPW+ E+ GGSSGGS AAVA ALG+D GGSIR Sbjct: 124 KTTTPEFGWKGVTDSPIHGVTRNPWNPEKTSGGSSGGSGAAVALGMGPLALGTDAGGSIR 183 Query: 180 QPAALCGVVGMKPTYGRVSRFGLIAFASSLDQIGPFTKDVEDCAILLNVIAGYDLRDSTS 239 PAA CG+VG+KPT+G V + F +L GP T V+DCA+++NV+ DLRDS + Sbjct: 184 IPAAFCGIVGLKPTFGEVPHWPASPF-GTLAHAGPMTWTVQDCALMMNVLTEPDLRDSQA 242 Query: 240 VPVDVPDYRDYLNRGIEGWTVGIPKEYFIEGIDPEVRGAIEQAIRTVEGLGARCREISLP 299 P +Y L+RG++ W + +DPE+ A +QA+ E LGA E+ Sbjct: 243 APRRGVNYLAELDRGVKRWKIAYTPNLGHVNVDPEIEAAFKQAVAVFESLGAEVMEVDPS 302 Query: 300 HTDYCVAVYYIIAPAEASSNLARYDGVKYGFRAADCRDLLDMYKKTRSAGFGTEVKRRVM 359 +D A ++ A N R G K RA +L+ + +K R M Sbjct: 303 FSDPVGAFGHLFYGGAA--NAMRDIGTKK--RALMDPELVKVAEK---------ASRLSM 349 Query: 360 LGTYSLSSGYYDAYYKKASQVRGLIKRDFEEALKDCNVILTPTTPTPAFTIGEKTDDPMQ 419 L Y A +R + + +++LTPT P AF G + P Sbjct: 350 LD------------YLGAVNIRMALSERMAVFHRKYDLLLTPTLPITAFKAGREV--PED 395 Query: 420 MYLS-----DIFTISANLAGIPGISVPCGYTQSGLPVGIQFLAGHFEEGKLLQIASAYER 474 Y + FT N+ G P +SVPCG++ GLP+G+Q + F + ++L+ AY++ Sbjct: 396 WYSTRWPSWTPFTYPFNMTGQPALSVPCGFSTDGLPIGLQIVGPRFSDERVLRAGYAYQQ 455 Query: 475 NAHIEKRRPIL 485 A + + RP L Sbjct: 456 AAPLTENRPEL 466 Lambda K H 0.319 0.137 0.402 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: 548 Number of extensions: 31 Number of successful extensions: 6 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: 485 Length of database: 473 Length adjustment: 34 Effective length of query: 451 Effective length of database: 439 Effective search space: 197989 Effective search space used: 197989 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