Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_066921215.1 ACG33_RS11140 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_001579945.1:WP_066921215.1 Length = 457 Score = 185 bits (469), Expect = 3e-51 Identities = 157/482 (32%), Positives = 216/482 (44%), Gaps = 46/482 (9%) Query: 1 MLSAARLNRLFLAGELSAVEIAESALSRIAQVEPA---VGAFITVAADHVIERAKKLDAR 57 M + A L R +G +A + E AL RI +PA FI V AD RA ++D Sbjct: 1 MPTLAELARRLDSGATNARSLVEEALERIQ--DPAGEGARVFIHVGADTARARADEIDRL 58 Query: 58 RKAGDTELGPLAGVPIAVKDNICTSGMETTCASRILKGY-VSPFDATVVERLRAAGAMII 116 R AG + L P AG+PI +KD G T SRIL+ + DA V RLR AG + I Sbjct: 59 RAAGQS-LPPWAGIPIGIKDLFDVEGEVTRAGSRILENAPAAREDAPAVARLRRAGFIFI 117 Query: 117 GKANMDEFAMGSSGESSAFGVTRNPWDLE--RVPGGSSSGSAAAVAAGEAPLALGTDTGG 174 G+ NM EFA G + +G NP+D R+PGGS+SG A AV G A +LGTDTGG Sbjct: 118 GRTNMTEFAYSGLGLNPHYGTPLNPFDRATGRIPGGSTSGGAVAVTDGMAVASLGTDTGG 177 Query: 175 SIRQPAAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRD 234 S R PAA TGIVG KPT V R G + + +LD VGP+ V A L ++ RD Sbjct: 178 SCRIPAALTGIVGFKPTADRVPRNGTIPLSPTLDSVGPLANSVACCATLDAIL-----RD 232 Query: 235 A-TNAGRTPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEE 293 A TPP + ++ RL +P + +D V E A+ L GA ++ Sbjct: 233 APMQLHETPPMV------AMKDQRLLLPTTFVLDDMDDTVACTFERAVDALARSGALIQR 286 Query: 294 CSLPSTEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVK 353 + E + + G AA+A H + E + V Sbjct: 287 APVYEFEVIPDINF-----------------KGGLAAAEAYAWHRQFLDRYAERYDPRVI 329 Query: 354 RRIMLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVD 413 RI+ G + R+ +Q R ++ F A + AL+ PT P A + Sbjct: 330 ARILKGQEPSAED-----IRQMRQARRRLIESFHAATREWHALIMPTVPVIAPPLSAVAL 384 Query: 414 DPVSMYLGDICTIPVNLAGL---PAVSVPCGFVDGLPVGMQLIGKPFADTQILQIAWAYQ 470 D + L + LA VS+P PVG+ LIG+ D Q+L +A + Sbjct: 385 DADYVRLNMLILRNPALANFLDGCGVSLPIHAPGDAPVGLMLIGRQGEDAQLLALAATIE 444 Query: 471 KV 472 +V Sbjct: 445 QV 446 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: 587 Number of extensions: 38 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: 488 Length of database: 457 Length adjustment: 33 Effective length of query: 455 Effective length of database: 424 Effective search space: 192920 Effective search space used: 192920 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: 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