Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_010530226.1 ON01_RS06595 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= curated2:B8HY89 (482 letters) >NCBI__GCF_000224785.1:WP_010530226.1 Length = 462 Score = 325 bits (832), Expect = 3e-93 Identities = 196/472 (41%), Positives = 268/472 (56%), Gaps = 27/472 (5%) Query: 6 ELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGTEIG 65 EL + SK+ S E+T L +I ++P +H+++T E AL QA +Q I G G Sbjct: 11 ELAPLIESKQLSPVELTNHLLTRIDTIDPTIHSYITPLPELALKQAREAEQNIMHGRYKG 70 Query: 66 LLAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDEFAM 125 L GIP+ IKDN TKGI TT GSK+ FIP + +L AAG +M+GK N+ E A+ Sbjct: 71 PLHGIPVGIKDNYYTKGIRTTAGSKLFVDFIPNKTAPAAEKLLAAGGIMLGKLNMHELAL 130 Query: 126 GSSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFCGVV 185 GS+ N + T NPW++ +PGGSSGGS+AA+AAG T +A G+DT GSIR PA+ CGV Sbjct: 131 GSTGTNLTFGTTRNPWNIHHMPGGSSGGSSAALAAGLTTLATGTDTFGSIRLPAAMCGVY 190 Query: 186 GLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVPIPDYT 245 GLKPTYGLVS + A SLD GP A +V D AL+L +AG D D SL V PDY Sbjct: 191 GLKPTYGLVSTSNMFPSAWSLDTAGPMARSVSDLALMLNDMAGFDANDPASLRVSTPDYA 250 Query: 246 QFLIPDLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRYGLPTY 305 + L ++G +IG I Y EGLD +VE++ AI+ L+ LGAE+REI P + Sbjct: 251 EDLNKGIRGIRIG-IPTYYLEGLDTEVERLFKNAIETLQNLGAEIREIVIPELSMSTFSG 309 Query: 306 YIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIGTYALSAG 365 Y I EASA Y+ + +T +E +G + + ++ GT + Sbjct: 310 YSIVAGEASA--FHYE-----------------WLQTHSEDYGADNRIFLLSGTLTNT-- 348 Query: 366 YYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAP--TTAFAAGAKTADPLSMYLSDLM 423 + +KAQ+ R + + F A E VD+++ PT P T AFA + + Sbjct: 349 ---PHCVKAQQARRKMIEAFHNALESVDIMLGPTIPITTPAFAQNWVEQNLEVIRRCLPF 405 Query: 424 TIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQATPW 475 T PVNL G P LS+P G D +GLP G+Q IGN L E + QVA+A+E+ P+ Sbjct: 406 TSPVNLLGTPSLSMPMGLDLRGLPAGMQFIGNHLSEKQLLQVAHAWERINPF 457 Lambda K H 0.317 0.134 0.388 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: 518 Number of extensions: 29 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: 482 Length of database: 462 Length adjustment: 33 Effective length of query: 449 Effective length of database: 429 Effective search space: 192621 Effective search space used: 192621 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 Jul 26 2024. The underlying query database was built on Jul 25 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