Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate YP_002827683.1 NGR_c31970 amidase
Query= curated2:A6TTJ8 (491 letters) >NCBI__GCF_000018545.1:YP_002827683.1 Length = 435 Score = 172 bits (437), Expect = 2e-47 Identities = 149/466 (31%), Positives = 228/466 (48%), Gaps = 52/466 (11%) Query: 23 KDVVQGYIDRIKELDGKINAFITLCEESALMEAAVLDEKLSRGEEIGLLGGIPVAIKDNM 82 +D ++ + R+ F+ L ESA EAA D + G+ +G L G V+IKD Sbjct: 9 RDRLEAVLARLAGRCDDERVFMKLYAESARAEAAAADRRQQEGKSLGPLDGRIVSIKDLF 68 Query: 83 CTQGIKTSCASEMLADFIPPY--DATIVKKLRAAGAIIIGKTNMDEFAMGSSTENSAFKV 140 G T A ++ PP DATIV++LRAAGA+IIGKT+M EFA + N + V Sbjct: 69 DIAGEPT-LAGSIIRRMAPPASADATIVRRLRAAGAVIIGKTHMTEFAFTAVGLNPHYPV 127 Query: 141 TKNPWDLTKVPGGSSGGSAAALAAGFAPLTIGSDTGGSIRQPAAFCGTVGLKPTYGLVSR 200 N D +PGGSS G+ ++A G + + IGSDTGGS+R PAA G VG KPT V Sbjct: 128 PGNAVDPMLIPGGSSSGAGVSVAEGTSDIAIGSDTGGSVRIPAALQGLVGFKPTARRVPL 187 Query: 201 FGLIAFASSLDQIGPFTKTVKDCALSLQVMQGNDPLDSTSIQQEPMDDYVKDLDKGVKGL 260 G + SLD IGP +V DCAL+ VM G+ P T + P+D GL Sbjct: 188 DGAFPLSPSLDSIGPLALSVADCALADAVMAGDRPEPLTPL---PVD-----------GL 233 Query: 261 KVGIPKEFFQEGLNIEISDSIKEAIKVLEQLGAVVEEFSLPVTDSGLSAYYIISSAEASS 320 K+GIPK E L +++ + + ++ L + GA + E + D L+ + + A A Sbjct: 234 KLGIPKGVLLEELAPDVAKAFEAGLQRLSRAGARLAELEI---DDLLARF---AEATAIG 287 Query: 321 NLARYDGVRYGHRAAVYEGIEEMMLNSRSEGFGKEVKRRIMLGTYVLSSGYYDAYYKKAM 380 +LA G+ A + +E ++ R + ++RR+ A A+ Sbjct: 288 SLA---GLEASRIHADWLVDDEAPVDPRVK---SPLRRRL-------------AVPDTAL 328 Query: 381 DFRKKTRNVFKKAFES----YDVILTPTSPVLPFTIGEKTGDPLE-MYLADIYTVNVNIA 435 + KTR+ +A + +D++L PT+P+ I D E + + N +A Sbjct: 329 ENLLKTRHALARAMDGRLAPFDLVLLPTTPIPAVRIAAVEEDKREYRRIEGLLLRNTEVA 388 Query: 436 G---VPAISIPCGFSKEKLPIGLQLIGDHYSEKKLLQAAYGLEQEL 478 + AI++P LP GL L+G + +++ LL+ A +E+ L Sbjct: 389 NQFDLTAITLP--MPGAALPAGLMLMGRNGTDRTLLRLAACVERLL 432 Lambda K H 0.317 0.136 0.382 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: 431 Number of extensions: 21 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: 491 Length of database: 435 Length adjustment: 33 Effective length of query: 458 Effective length of database: 402 Effective search space: 184116 Effective search space used: 184116 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: 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