Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO353_15115 AO353_15115 amidase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15115 Length = 462 Score = 199 bits (506), Expect = 2e-55 Identities = 158/480 (32%), Positives = 233/480 (48%), Gaps = 48/480 (10%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61 L+AA L F + +L+ ++ + L+ I + EP + A V ++A+ R G Sbjct: 7 LTAAELLARFASRQLTPIDYYDQLLTHIDRWEPQINALYAFDPQQVRQQAQASTERWNKG 66 Query: 62 DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANM 121 G L GVP+ +K+ I T G S + + DA RLR AGA+I+ K + Sbjct: 67 QPN-GALDGVPVTLKELIATEGQPIPLGSAATRLTPALKDAPPAARLREAGAIILAKTTV 125 Query: 122 DEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181 +F M SSG SS G+TRNPW+ PGGSS+G+AAA AAG PL +GTD GGS+R PAA Sbjct: 126 PDFGMLSSGLSSFHGITRNPWNTANNPGGSSAGAAAAAAAGYGPLHVGTDIGGSVRLPAA 185 Query: 182 FTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRT 241 + G+VG KPT G R + + + GPM R V+D L + +A PD RDAT+ Sbjct: 186 WCGLVGFKPTLG---RIPIDPYYTG-RTAGPMTRTVDDCVLLMQHLARPDSRDATSL--P 239 Query: 242 PPALKFGGEP-SLSGVRLGVPKELLGPGIDPG--VKARVEEAIAQLEELGATVEECSLPS 298 P + +P S+ G+R+G+ E G G+ P V VE+A E GA V Sbjct: 240 PLTTPWSNQPLSVKGLRVGLMLE-PGAGLAPEAFVCNAVEQAARLFEAHGAKV------- 291 Query: 299 TEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIML 358 V + A+ DG+ +RA Q L + S E R++ Sbjct: 292 -----------TVIAPIMDRAQLDGLDQFWRARQWAELSALSS---------EQFDRVL- 330 Query: 359 GTYVLSAGHYDAYYRRAQQVRTL-----VVRDFERAFERYDALVTPTTPFTAWKIG--EK 411 Y+ A + VR + R + F+ +D +++PT A+ Sbjct: 331 -PYIRDWAAPGADITGVEAVRGFNQTFEMRRRAAQLFDTFDLVLSPTNQINAFAADWPSP 389 Query: 412 VDDPVSMYLGDICTIPVNLAGLPAVSVPCGF-VDGLPVGMQLIGKPFADTQILQIAWAYQ 470 +DP + + T+P N+ PA+S+ CGF DG+P+G+Q+I FAD +LQIA Y+ Sbjct: 390 SNDPQQPFEHIVFTVPWNMGEQPALSINCGFAADGMPIGLQMIAPRFADQWLLQIAKTYE 449 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: 547 Number of extensions: 37 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: 2 Length of query: 488 Length of database: 462 Length adjustment: 33 Effective length of query: 455 Effective length of database: 429 Effective search space: 195195 Effective search space used: 195195 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 09 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