Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate YP_001328648.1 Smed_2984 amidase
Query= curated2:Q8R679 (487 letters) >NCBI__GCF_000017145.1:YP_001328648.1 Length = 435 Score = 158 bits (399), Expect = 4e-43 Identities = 137/446 (30%), Positives = 215/446 (48%), Gaps = 47/446 (10%) Query: 44 KSFVSLRKDKALDEARKLDEKRKNGEKLGRLAGIPIAIKDNILMEGQKSTSCSKILENY- 102 ++FV L + A EA D +R+ LG L G +++KD + G+ + + S I Sbjct: 27 RAFVKLYPETARAEADAADRRRREKRSLGLLDGRIVSVKDLFDIAGEPTLAGSIIRRAAP 86 Query: 103 IGIYDATVVKKLKEEDAIIIGITNMDEFAMGSTTKTSFHHKTSNPWDLNRVPGGSSGGAA 162 DA +V++L+ A+IIG T+M EFA + + N D + +PGGSS GAA Sbjct: 87 SATADAAIVRRLRAAGAVIIGKTHMTEFAFTAVGLNPHYPVPGNATDRSLIPGGSSSGAA 146 Query: 163 ASVAAQEVPISLGSDTGGSVRQPASFCGVVGFKPTYGRVSRYGLMAFASSLDQIGTLAKT 222 S A I++GSD+GGSVR PA+ G+VGFKPT R+ G + SLD IG LA+T Sbjct: 147 VSAAEGTSEIAIGSDSGGSVRIPAALQGLVGFKPTARRIPLEGAFPLSPSLDSIGPLART 206 Query: 223 VEDIAICMNVIAGVDDYDATVSKKEVPDYTEFLNKDIKGLKIGLPKEYFIEGLNPEIKNV 282 V D A ++AG E P E + + G+K+G+PK +EGL EI Sbjct: 207 VADCAAADAIMAG-----------ETPRPLEPV--PLAGMKLGMPKGALLEGLATEIAAA 253 Query: 283 VDNSVKALKELGAEVVEISLPH--TKYAVPTYYVLAPAEASSNLARFDGIRYGYRAKDYT 340 + S++AL GA++ E + T++ A A A +LA + R D+ Sbjct: 254 FERSLQALSRAGAKLAECGIDDLLTRF--------AEATAIGSLAGLEASRV---HADWL 302 Query: 341 DLESLYVKTRSEGFGAEVKRRIMIGTYVLSAGFYDAYFKKAQKVRTLIKQDFENVLNEVD 400 E+ V R + ++RR+ I D+ + R + + + L D Sbjct: 303 RDENAPVDIRLK---FPLRRRLAIP---------DSAIHDLLRTRQGLMRAMDERLRPFD 350 Query: 401 VILTPVAPSVAFKLSDTKTPIELY--LEDIF---TISANLAGVPAISLP-GGLVDNLPVG 454 IL P P A ++ + Y +ED+ T AN + AI+LP G+ +LP G Sbjct: 351 FILMPATPIPAVSIASVEEDRAEYRRVEDLLLRNTQVANQFDLTAITLPMPGM--SLPAG 408 Query: 455 VQFMGKPFDEEILIKIADALEKKIGR 480 + MG+ + L+++A ++E+ + R Sbjct: 409 LMLMGRNGTDGALLRLAASVERLLQR 434 Lambda K H 0.316 0.135 0.376 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: 377 Number of extensions: 17 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: 487 Length of database: 435 Length adjustment: 33 Effective length of query: 454 Effective length of database: 402 Effective search space: 182508 Effective search space used: 182508 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