Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013136498.1 ARNIT_RS13600 allophanate hydrolase
Query= curated2:O66610 (478 letters) >NCBI__GCF_000092245.1:WP_013136498.1 Length = 598 Score = 162 bits (411), Expect = 2e-44 Identities = 138/467 (29%), Positives = 227/467 (48%), Gaps = 47/467 (10%) Query: 7 LSELRELLKRGEVSPKEVVESFYDRYNQTEEKVKAYITPLYGKALKQAESLKEREL---P 63 + + + K+G V+PK++V Y+R + + Q SL+E L P Sbjct: 9 IKSIHDSYKKG-VTPKDIVTEVYNRIKKVNDDGIFIHLQAIEDIFAQISSLEEMNLSEKP 67 Query: 64 LFGIPIAVKDNILVEGEKTTCASKILENFVAPYDATVIERLKKAGALIVGKTNLDEFAMG 123 L+GIP VKDNI VEG TT A E ++A DA +++ LK+AGA+ +GKTNLD+FA G Sbjct: 68 LWGIPFTVKDNIDVEGIPTTAACPAYE-YIAKEDAFIVKVLKQAGAICIGKTNLDQFATG 126 Query: 124 SSTEYSAFFPTKNPWDLERVPGGSSGGSAASVAVLSAPVSLGSDTGGSIRQPASFCGVIG 183 + + KN D + +PGGSS GSA +V+ SLG+DT GS R PA+ ++G Sbjct: 127 LVGIRTPYGAPKNALDEKIIPGGSSCGSAVAVSHQLFSFSLGTDTAGSGRIPAALNNLVG 186 Query: 184 IKPTYGRVSRYGLVAFASSLDQIGVFGRRTEDVALVLEVISGWDEKDSTSAKVPVPEWSE 243 +KPT G S+ G+V ++D + VF ED + E+ S DEKD S K P ++ Sbjct: 187 LKPTLGAFSKRGVVPACLTVDTVSVFALNIEDAYDIFEIASKHDEKDPYSKKRPKNKY-- 244 Query: 244 EVKKEVKGLKIGLPKE----FFEYELQPQVKEAFENFIKELEKEGFEIKEVSLPHVKYSI 299 K+ + + + +P F + E+Q +++++ I ++++GF+ E+ L Sbjct: 245 ---KDTQNVVVAIPNSKSQIFIDDEIQ---RKSYQETISLIKEKGFKTIEIDL------- 291 Query: 300 PTYYIIAPSEASSNLARYDGVRYGYRAKEYKDIFEMYARTRDEGFGPEVKRRIM--LGTF 357 ++ +A Y+G + A+ Y I +M + ++ R ++ TF Sbjct: 292 KPFFEVAQ-------LLYEGT---WLAERYTVIGDMIKNQPADIL--DITRTLIQKAETF 339 Query: 358 ALSAGYYDAYYLKAQKVRRLITNDFLKAFEEVDVIASPTTPTLPFKFGERLENPIEMYLS 417 + S Y D Y K + E+ D++ P+ P + E ++PI+ Sbjct: 340 SASDVYRDIYRFNELK------KEIEPVLEQFDILCLPSMPRVA-SVKEIEDDPIKANSR 392 Query: 418 -DILTVPANLAGLPAISIPI-AWKDGLPVGGQLIGKHWDETTLLQIS 462 I T NL L AI+IP+ +DG G +I ++E L + + Sbjct: 393 LGIYTNFVNLLDLSAIAIPVNKREDGFAGGVTIIANAFEELKLAKFA 439 Lambda K H 0.316 0.136 0.394 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: 661 Number of extensions: 33 Number of successful extensions: 2 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: 478 Length of database: 598 Length adjustment: 35 Effective length of query: 443 Effective length of database: 563 Effective search space: 249409 Effective search space used: 249409 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: 52 (24.6 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