Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011814761.1 HHAL_RS09980 amidase
Query= curated2:B8HY89 (482 letters) >NCBI__GCF_000015585.1:WP_011814761.1 Length = 470 Score = 208 bits (530), Expect = 3e-58 Identities = 162/480 (33%), Positives = 224/480 (46%), Gaps = 33/480 (6%) Query: 6 ELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGTEIG 65 EL ++ S S E T+ AL +I+ V+AF + LA A R +Q+ + +G Sbjct: 15 ELLRRYRSGSLSPVEATEAALARIRAHNETVNAFCLVDETTTLAAARRAEQRYLNTSPMG 74 Query: 66 LLAGIPIAIKDNLCTKGIPTTCGSKILQGFIP-PYESTVTSRLAAAGAVMVGKTNLDEFA 124 L G+P+AIKD T+G P GSK + P ++ S L G V +GKT E Sbjct: 75 ELDGVPVAIKDVFLTRGWPNLKGSKTVDPAGPWEQDAPAVSALRRHGFVPLGKTTTPELG 134 Query: 125 MGSSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFCGV 184 T+ Y +T NP+D + GGSSGGSA++V G +ALG+D GGSIR PA F G+ Sbjct: 135 WKGVTDCPCYGVTRNPFDPDKTAGGSSGGSASSVVLGMGPLALGTDAGGSIRIPAGFSGL 194 Query: 185 VGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVPIPDY 244 VG KPT G V + + L GP VEDAA L+ IA DP+D T L DY Sbjct: 195 VGHKPTQGRVPLWPASPF-GQLAHPGPMTWTVEDAARLMNVIAETDPRDPT-LPAAGGDY 252 Query: 245 TQFLIPDLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRYGLPT 304 L + G ++ +D ++ + +A + E LGA V E+ P F Sbjct: 253 VAALAGGVGGLRVAFSPNLGYVQVDAEIARSVAEAARMFEALGARVEEVD-PGF------ 305 Query: 305 YYIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIGTYALSA 364 A + +L + G RS PE + E G V+ M+ Sbjct: 306 ----ADPREAFDLLFFGGAANALRS-IPEERHAEMDPCLIEAAG-SVRDASMLD------ 353 Query: 365 GYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAAGAKTA----DPLSMYLS 420 YL A R + + +Q D+L+ PT P AF AG + DP + Sbjct: 354 ------YLAAMNERAALIERTSLFHQQYDLLLTPTLPIPAFTAGREVPEGWHDPRWPSWT 407 Query: 421 DLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQATPWHDRHP 480 T P N+ G P S+PCGF QGLPIGLQ++G + LV + A+AY+QA P D P Sbjct: 408 P-FTYPFNMTGQPACSVPCGFTGQGLPIGLQIVGPRHADALVLRAAHAYQQAAPLTDHRP 466 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: 558 Number of extensions: 31 Number of successful extensions: 4 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: 470 Length adjustment: 33 Effective length of query: 449 Effective length of database: 437 Effective search space: 196213 Effective search space used: 196213 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: 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