Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate YP_001329069.1 Smed_3413 hypothetical protein
Query= curated2:Q2LXM9 (485 letters) >NCBI__GCF_000017145.1:YP_001329069.1 Length = 453 Score = 183 bits (464), Expect = 1e-50 Identities = 150/477 (31%), Positives = 217/477 (45%), Gaps = 42/477 (8%) Query: 5 QLTIHELQNKIRQGGVTSTAIVNSVFGRIDAVEENVHSYITLMRESALEEAQKADEQIRT 64 Q T+ L +++ G + +V I + + ++ L RE A EAQ A E++R Sbjct: 4 QQTLASLAVRVQSGQLDPITLVEETLTEIGSHPDK-SIFVALTRERATREAQAASERMRA 62 Query: 65 GE-INALTGIPVALKDIYCTRGVRTTCGSLILDNFIPPY-DATVVVKLREAGAVFTGKTN 122 G + L G+PVA KD++ G TT GS +L+N DA VV KL AG V G+TN Sbjct: 63 GRSLGLLDGLPVAWKDLFDLAGSVTTAGSAVLENRSRAVTDAAVVAKLASAGMVSIGRTN 122 Query: 123 MDEFAMGSSTETSYYGFTRNP--WDLERIPGGSSGGSAAAVAADECIAALGSDTGGSIRQ 180 + EFA +YG RNP D RIPGGSS GSAAAVAA A+G+DTGGS+R Sbjct: 123 LSEFAFSGLGINPHYGTPRNPRSTDAHRIPGGSSSGSAAAVAAGLVPLAIGTDTGGSVRI 182 Query: 181 PAALCGVVGMKPTYGRVSRFGLIAFASSLDQIGPFTKDVEDCAILLNVIAGYDLRDSTSV 240 PAA+ G+VG K T GR + G+ A SLD +GP + V+D V A + T+ Sbjct: 183 PAAMNGIVGYKATRGRYAMRGVFPLARSLDSLGPLCRTVQDA-----VWADAAMHGLTAP 237 Query: 241 PVDVPDYRDYLNRGIEGWTVGIPKEYFIEGIDPEVRGAIEQAIRTVEGLGARCREISLPH 300 + + D ++ I + +PE+ A E AI+ +E G + R + P Sbjct: 238 VIRRAELADL--------SIVIADTIVFDDAEPEIVTAFEGAIKRLEAAGVKIRRQAFP- 288 Query: 301 TDYCVAVYYIIAPAEASSNLARYDGVKYGFRAADCRDLLDMYKKTRSAGFGTEVKRRVML 360 + AE AR+ + A R+ L +A V R L Sbjct: 289 -----------SFAEIFELTARHGALVTAEAYALHRERL---AGAEAANMDPRVVARTRL 334 Query: 361 GTYSLSSGYYDAYYKKASQVRGLIKRDFEEALKDCNVILTPTTPTPAFTIGEKTDDPMQM 420 G S Y + R + + E++ +I PT P A + D Sbjct: 335 GEKITVSDYI-----ALLEARDRLIHEAGESISAGELIAHPTLPHVAPLLDPLLADYDLF 389 Query: 421 YLSDIFTIS----ANLAGIPGISVPCGYTQSGLPVGIQFLAGHFEEGKLLQIASAYE 473 + ++ T+ N G+S+PCG +G+PVG Q A H ++ +LL A A E Sbjct: 390 FKTNARTLRNTSIGNFLDFCGVSIPCGTGGAGMPVGFQLSAPHHQDDRLLSAALAAE 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: 425 Number of extensions: 21 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