Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012384300.1 BIND_RS06600 amidase
Query= curated2:Q8R679 (487 letters) >NCBI__GCF_000019845.1:WP_012384300.1 Length = 477 Score = 196 bits (497), Expect = 2e-54 Identities = 153/504 (30%), Positives = 256/504 (50%), Gaps = 54/504 (10%) Query: 6 LYELTAKELRDKFLSNELSAEEIVNSFYERIEKVEDKIKSFVSLRKDKALDEARKLDEKR 65 LY +LR + +LSA E+++ R +++ +++ + V+ D+A +A+ +D++R Sbjct: 4 LYSDAVDQLR-MLSTRQLSARELLDMVVARTDRLSERVNAVVARDLDRAYHDAQLIDDRR 62 Query: 66 KNGEKLGRLAGIPIAIKDNILMEGQKSTSCSKILENYIGIYDATVVKKLKEEDAIIIGIT 125 E +GRLAGIP+ +KD ++G +++ +IL N DA VV + + EDAII G T Sbjct: 63 ARSEPMGRLAGIPMTVKDTFDIDGLPASAGLRILLNRKA-KDAIVVSRARAEDAIIWGQT 121 Query: 126 NMDEFAMGSTTKTSFHHKTSNPWDLNRVPGGSSGGAAASVAAQEVPISLGSDTGGSVRQP 185 N A T + + T+NPW+L R PGGSSGG+AA++AA + +G+D GGS+R P Sbjct: 122 NTPTKAADWQTYNALYGTTNNPWNLERTPGGSSGGSAAALAAGLTALEIGADAGGSLRVP 181 Query: 186 ASFCGVVGFKPTYGRVSRYGLMA---FASSLDQ--IGTLAKTVEDIAICMNVIAGVDDYD 240 A+FCGV KPTYG +S+ GL+ FA+ +D +G +A++ D+ + M+VI+ D Sbjct: 182 ANFCGVFAHKPTYGLISQRGLVPPPNFAADVDLAVVGPMARSSRDLRLLMSVIS---DLP 238 Query: 241 ATVSKKEVPDYTEFLNKDIKGLKIGLPKEYFIEGLNPEIKNVVDNSVKALKELGAEVVEI 300 + VP IKGLK+ L + L+ ++++ + + L GA V + Sbjct: 239 LSAEAPPVP---------IKGLKVALWLDEPAFVLDADVRHRITVFAETLAANGAIVEPV 289 Query: 301 SLPHTKYAVPTYYVLAPAEASSNLARFDGIRY-----GYRAKDYTDLESLYVKTR-SEGF 354 +P EA + + + + Y G A++ T E L + + Sbjct: 290 R--------------SPIEADTLMFTYTMLLYPLSNAGMPAQERTLYELLRGPAKIALAL 335 Query: 355 GAEVKRRIMIGTYVLSAGFYDAYFKKAQKVRTLIKQDFENVLNEVDVILTPVAPSVAF-- 412 GA + + VL++ + +A ++R ++ + DV+L+P++P AF Sbjct: 336 GA---KPLSWAQGVLASTARHREWLRANEMRAGMQHTLQRFFTHYDVLLSPISPMPAFPH 392 Query: 413 --------KLSDTKTPIELYLEDIFTIS-ANLAGVPAISLPGGLVD-NLPVGVQFMGKPF 462 +L + YLE + I+ A G+PA +LP GL NLPVG Q +G Sbjct: 393 DHRPFLRRRLRGSDGRTFSYLELLNWIALATTCGLPATALPIGLTSQNLPVGAQLIGPRN 452 Query: 463 DEEILIKIADALEKKIGRLNLPKL 486 + + IA A+E+ IG +P L Sbjct: 453 SDARTLAIAQAMEEMIGGFQIPPL 476 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: 448 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 477 Length adjustment: 34 Effective length of query: 453 Effective length of database: 443 Effective search space: 200679 Effective search space used: 200679 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: 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