Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_066324795.1 BLR17_RS07430 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= curated2:B0KBN4 (488 letters) >NCBI__GCF_900100165.1:WP_066324795.1 Length = 465 Score = 328 bits (840), Expect = 3e-94 Identities = 185/446 (41%), Positives = 264/446 (59%), Gaps = 9/446 (2%) Query: 8 IHELRELLKKREVSALEVTKSYLERIKEVEPKIDALITITEDFALQRAKEADEKIKNGED 67 I ++ + L +++S + + L+ +K+ +++ ++ + AL+ A + D KI NGE Sbjct: 5 IKKIHQQLVSKQISCTALVQEKLDLLKQ--NTYNSVNSVLDTLALELAAKVDAKIANGET 62 Query: 68 TALT-GIPVIIKDNISTEGIKTTCSSKMLENYIPPYNATVVEKLLEEGVIILGKSNLDEF 126 L GIP IKD +G TT SS++L NY PY AT ++KLL+ G I L K N D F Sbjct: 63 IGLLEGIPFGIKDVYMVQGTYTTASSELLRNYKSPYTATAIQKLLDAGAIPLAKENCDSF 122 Query: 127 AMGSSTENSAFKTTKNPWDLSRVPGGSSGGSAAAIAADEAAFALGSDTGGSIRQPASLCG 186 GSS+EN+ F KN + V GGSSGGSA +A + F++G DTGGSIRQPA Sbjct: 123 GHGSSSENTIFGAVKNAINPELVGGGSSGGSAVNVAKEYTVFSIGGDTGGSIRQPAGYNH 182 Query: 187 VVGMKPTYGLVSRYGLVAFASSLDQIGPFTKDVTDCAIVLNTIIGHDPKDSTSLKIDKPD 246 + G+KPTYG +SRYGL+A+ASS D +GP K + D IVLN + G DPKD TS+ + Sbjct: 183 IYGLKPTYGRISRYGLMAYASSTDCVGPLAKSIEDIRIVLNVMSGKDPKDQTSIASTEIS 242 Query: 247 YTSYLKEDIKGLRIGVAKEFF-GEGIEEGVKETVQESIKVLQDLGAEIIDISIPYVEYAL 305 + ++K IG K F E I+ +K S++ ++ G E+ ++ + + Sbjct: 243 EDAIATSEVK--TIGYFKNFIESEAIDAQIKADFLASVEKIKAKGIEVKELDFFKSDILV 300 Query: 306 PAYYIIASAEASSNLARYDGIRYGH-IAGKYEDLIDMYMVTRSEGFGKEVKRRIMLGTYA 364 YY +A AE +SNL+R DG YG+ I G E+LID Y VTRSE F +E KRRI+ G Sbjct: 301 STYYTLAMAETASNLSRLDGTNYGNRIEG--ENLIDTYAVTRSENFSEETKRRIVGGNQV 358 Query: 365 LSSGYYDAYYKKALKVRTLIKNDFEKAFEKCDVIIGPTSPTVAFKIGERANDPLAMYLAD 424 LS G+ D Y K L +R I +F K F++ DVI+ P +P+ KIG+ DPLAMYL+D Sbjct: 359 LSQGFSDEIYLKGLALRDQISENFSKDFQEVDVILSPVTPSTPPKIGDSLKDPLAMYLSD 418 Query: 425 IYTVSVNIAGLPGISIPCGLSDGLPV 450 YTV ++ LP I++P G + GL + Sbjct: 419 AYTVGFSLGQLPTITVPQGTTTGLQI 444 Lambda K H 0.316 0.136 0.380 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: 544 Number of extensions: 27 Number of successful extensions: 3 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: 465 Length adjustment: 33 Effective length of query: 455 Effective length of database: 432 Effective search space: 196560 Effective search space used: 196560 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