Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate YP_002828014.1 NGR_c35370 hypothetical protein
Query= curated2:Q2LXM9 (485 letters) >NCBI__GCF_000018545.1:YP_002828014.1 Length = 453 Score = 187 bits (475), Expect = 6e-52 Identities = 152/475 (32%), Positives = 215/475 (45%), Gaps = 42/475 (8%) Query: 7 TIHELQNKIRQGGVTSTAIVNSVFGRIDAVEENVHSYITLMRESALEEAQKADEQIRTGE 66 T+ L ++ G + A+ RI+ + ++ L RE A EA+ A E+I+ G Sbjct: 6 TLASLAVLVQSGQLDPVALAGDTLTRIETHADQ-SIFVGLTRERAEREAKAASERIKAGR 64 Query: 67 -INALTGIPVALKDIYCTRGVRTTCGSLIL-DNFIPPYDATVVVKLREAGAVFTGKTNMD 124 + L G+PVA KD++ G TT GS++L DN DA VV L AG V G+TNM Sbjct: 65 SLGLLDGLPVAWKDLFDMAGSVTTAGSVVLKDNPPASSDAAVVAALGSAGMVSVGRTNMS 124 Query: 125 EFAMGSSTETSYYGFTRNPW--DLERIPGGSSGGSAAAVAADECIAALGSDTGGSIRQPA 182 EFA +YG RNP D+ RIPGGSS GSAAAVAA A+G+DTGGS+R PA Sbjct: 125 EFAFSGLGVNPHYGTPRNPASPDVHRIPGGSSSGSAAAVAAGLVPLAIGTDTGGSVRIPA 184 Query: 183 ALCGVVGMKPTYGRVSRFGLIAFASSLDQIGPFTKDVEDCAILLNVIAGYDLRDSTSVPV 242 A+ G+VG K T GR + G+ A SLD +GP V+D V A + T+ + Sbjct: 185 AMTGIVGYKATRGRYTMKGVFPLAQSLDSLGPLCHSVQDA-----VWADAAMHSLTAPVI 239 Query: 243 DVPDYRDYLNRGIEGWTVGIPKEYFIEGIDPEVRGAIEQAIRTVEGLGARCREISLPHTD 302 + D ++ IP+ + + EV A E AI+ +E G R R + P Sbjct: 240 RRAELADL--------SLVIPETIVFDEAEAEVVAAFETAIKRLEAAGVRVRRQAFPS-- 289 Query: 303 YCVAVYYIIAPAEASSNLARYDGVKYGFRAADCRDLLDMYKKTRSAGFGTEVKRRVMLGT 362 ++ +IA A N Y + +D +A V R LG Sbjct: 290 -FAEIFELIARHGALVNAEAYALHRERLAGSD------------AARMDQRVVVRTRLGE 336 Query: 363 YSLSSGYYDAYYKKASQVRGLIKRDFEEALKDCNVILTPTTPTPAFTIGEKTDDPMQMYL 422 Y Y R + + E+LK +I PT P A + D + Sbjct: 337 KITVGDYIALLY-----ARDRLIHETVESLKPGELIAHPTVPHVAPPVDPLLADDDLFFK 391 Query: 423 SDIFTIS----ANLAGIPGISVPCGYTQSGLPVGIQFLAGHFEEGKLLQIASAYE 473 + T+ N G+S+PCG +G+PVG A H ++ +LL A A E Sbjct: 392 VNAKTLRNTSIGNFLDFCGVSIPCGTGAAGMPVGFLLSAPHHQDDRLLSAALALE 446 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: 427 Number of extensions: 14 Number of successful extensions: 5 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: 485 Length of database: 453 Length adjustment: 33 Effective length of query: 452 Effective length of database: 420 Effective search space: 189840 Effective search space used: 189840 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