Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_036259701.1 DL86_RS06865 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000746085.1:WP_036259701.1 Length = 458 Score = 218 bits (555), Expect = 4e-61 Identities = 161/472 (34%), Positives = 233/472 (49%), Gaps = 42/472 (8%) Query: 7 LTVAQAREMLA---RGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 LT ARE++A +S +E+T A+L RI ++P A+ VVDA A AQARA++AR Sbjct: 5 LTQLSARELVALYRSKAVSPVEVTKAVLARIELLQPHFNAYRVVDAHSALAQARASEARW 64 Query: 64 AAGDASPLL-GIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKL 122 + G L G+P+G KD+++ QG T S + D+ ARL+ +GA+I+GK Sbjct: 65 SRGAPQGQLDGVPVGFKDLLNVQGFPTRKGSLATPDKVLAEDSPPAARLRESGAIIVGKT 124 Query: 123 NCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQP 182 EF + TE T N W+ + GGSSGG+A A A G P +GTD GGSIR P Sbjct: 125 QTAEFGLKGLTETRLAGITPNAWDRQYASGGSSGGAAVAAALGLGPLQVGTDGGGSIRNP 184 Query: 183 AALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTD 242 A++ G+ G KPT+GRV+ Y L IGP+ RTV D A++L VIA D D T Sbjct: 185 ASVNGVFGFKPTFGRVAGY---PHNGGLFHIGPITRTVTDAALLLNVIAAPDARDWTSIP 241 Query: 243 YPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHT 302 D+ A L G ++GLRIG R + P + A + A+ L + GA V E+ Sbjct: 242 GDVRDWTANLDGGVKGLRIGYSRSLGYLTVDPGIIAVIDRAVSWLTDAGAIVEEVD---- 297 Query: 303 PYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRI-MLG 361 P + +P + N R +R + G D P +R R+ L Sbjct: 298 ----PGFRDPSPIIDAINAERAIRLRREIGDAGLELVD-----------PTIRARVERLE 342 Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLAMY 421 YAL A +A +R ++ L+RR +Q Q D++ P + ++G + P A Sbjct: 343 RYAL-ADVVEANERRT-ELGILMRRFHQ----QYDLLVTPISSNPVPRVGTAPETPFA-- 394 Query: 422 LEDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLLRVGDAYQ 472 P N+ P VP GF GLP+GL ++G + + +LR A + Sbjct: 395 ------FPFNITQQPAASVPAGFDLNGLPVGLHIVGPQYGDAVVLRASRALE 440 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: 535 Number of extensions: 24 Number of successful extensions: 4 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: 458 Length adjustment: 33 Effective length of query: 457 Effective length of database: 425 Effective search space: 194225 Effective search space used: 194225 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: 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