Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011157461.1 TX73_RS08850 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000195775.1:WP_011157461.1 Length = 477 Score = 194 bits (492), Expect = 7e-54 Identities = 149/471 (31%), Positives = 217/471 (46%), Gaps = 36/471 (7%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L + T + L GE++ +E+ D L RIA V+ + A + AR A A ++ Sbjct: 7 LVKETACAVVDKLKSGEVTPIEVLDVLEERIAEVDGAINALPTLCFDRARGHA-AELMKK 65 Query: 64 AAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLN 123 + L G+P+ IKD+ + G+ TT S + ++ P V L+ G V+ K N Sbjct: 66 PPAERGLLAGLPVPIKDLTAVAGVLTTQGSPIYKDNVPARSDLMVEHLEGNGGVVYAKSN 125 Query: 124 CDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPA 183 EF G++T N F TRNPW+L R GSSGG+AAA+A+G A A G+D GGS+R PA Sbjct: 126 TPEFGAGANTFNEVFGATRNPWDLSRSAAGSSGGAAAALASGTAWLAHGSDMGGSLRNPA 185 Query: 184 ALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDY 243 + CGI GL+P++GRV+ +L GPMAR V D A++L ++G D Sbjct: 186 SFCGIVGLRPSFGRVAHTPAAKIDRNLGVQGPMARNVEDVALLLDAMSGEYAADPLSIPS 245 Query: 244 PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTP 303 PA + AA + LR+ + + + P+V A R A E E G + E + P Sbjct: 246 PATSFLAAARSRQKPLRVAYSPDLGITPVDPEVAAVTRKAAERFAEAGV-IVEQAQPDLS 304 Query: 304 YALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGTY 363 A + + + + + A +L RT+ PEV I G Sbjct: 305 EAHECFQALRAFDFAISKA------------------DLLRTKRDLLKPEVIWNIEQG-- 344 Query: 364 ALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKI--------GAHTD 415 L D AQ+V R + F+ D++ P T T F + HT Sbjct: 345 -LKLSVDDLAKAEAQRVAMTART--IEFFKTYDLLLCPATITAPFPVEQRYLAECNGHTF 401 Query: 416 DPLAMYLEDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLL 465 +L V + L P L +PCGF A GLPIGLQ++ R +E LL Sbjct: 402 GNYVEWLGIV--YAITLVCCPALSLPCGFTATGLPIGLQMVARPRNEAGLL 450 Lambda K H 0.320 0.136 0.398 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: 507 Number of extensions: 26 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: 490 Length of database: 477 Length adjustment: 34 Effective length of query: 456 Effective length of database: 443 Effective search space: 202008 Effective search space used: 202008 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 (21.8 bits) S2: 52 (24.6 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