Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012591599.1 MSIL_RS13285 allophanate hydrolase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000021745.1:WP_012591599.1 Length = 601 Score = 193 bits (490), Expect = 2e-53 Identities = 172/472 (36%), Positives = 224/472 (47%), Gaps = 41/472 (8%) Query: 1 MLSAARLNRLFLAGELSAVEIAESALSRI-AQVEPAVGAFITVAADHVIERAKKLDARRK 59 ML A L + LS ++A L RI A +PAV AD V RA +L+ Sbjct: 5 MLQIAILREAYRQKTLSPKDVALEMLRRIDAYDDPAVWICRVKDAD-VFARAHELE--ED 61 Query: 60 AGDTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKA 119 AG E PL GVP AVKDNI +G+ TT A Y ATVV RL AAGAM+IGK Sbjct: 62 AGALERLPLYGVPFAVKDNIDVAGLPTTAACPSF-AYTPEVHATVVARLLAAGAMLIGKT 120 Query: 120 NMDEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQP 179 N+D+FA G +G S +G R +D + GGSSSGSA AVAAG +LGTDT GS R P Sbjct: 121 NLDQFATGLNGTRSPYGAPRCVFDNRYISGGSSSGSAVAVAAGLVAFSLGTDTAGSGRVP 180 Query: 180 AAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAG 239 AAF +VG+KPT G +S GV SLD V D + E+ G D D + Sbjct: 181 AAFNNLVGVKPTKGLISTAGVTPACRSLDCVSLFAASAADAQAVAEIAQGFDASD--DYS 238 Query: 240 RTPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGA-TVEECSLPS 298 R PA++ E GV +E G D A E AI +L LG V P Sbjct: 239 RQGPAVRLPLEKFRFGVLAVEQREFFG---DEEAGALYEAAIGRLGALGGQAVAFDYAPF 295 Query: 299 TEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIML 358 + A Y VAE R G+ + AAQA + V+ I Sbjct: 296 RDAAALLYEDAFVAE------RLAGIE-AFFAAQA------------QDMDPNVRAIIRK 336 Query: 359 GTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPV-- 416 G +A + A Y+ R E + ++D ++ PT P T + + + +DP+ Sbjct: 337 GQNFSAADAFKAAYK-----LRAFARKAEGEWAKFDFMLLPTAP-TIFTVAQMAEDPIGN 390 Query: 417 SMYLGDICTIPVNLAGLPAVSVPCGF--VDGLPVGMQLIGKPFADTQILQIA 466 + LG + T VNL AV+VP GF LP G+ LIG F+D+ +L +A Sbjct: 391 NSRLG-LYTNFVNLLDYAAVAVPAGFRPASKLPFGVTLIGPAFSDSDLLVLA 441 Lambda K H 0.318 0.135 0.391 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: 781 Number of extensions: 48 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: 488 Length of database: 601 Length adjustment: 35 Effective length of query: 453 Effective length of database: 566 Effective search space: 256398 Effective search space used: 256398 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 (21.7 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