Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate N515DRAFT_4323 N515DRAFT_4323 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A (EC 6.3.5.-)
Query= curated2:O27955 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_4323 Length = 469 Score = 209 bits (532), Expect = 2e-58 Identities = 155/451 (34%), Positives = 234/451 (51%), Gaps = 41/451 (9%) Query: 9 KVESQGCYDAVSEMLERIEKSRLNAYITVCKD---EALKMAEKYDRGELKGRLAGIPVAV 65 +V +G + E +ER+ +LNAY+ + E + A+ R + GRL G+PVA+ Sbjct: 28 RVHPEGLAEVYLEAIERLNP-QLNAYVGLSAGLLREQARAAQHRRRDGVLGRLDGLPVAI 86 Query: 66 KDNISTKGILTTCASKMLSNYRPVF-DAHVVEKLKQEGAIIIGKANMDEFAMGTTTETSY 124 KDN G T + +P DAH V +L+ GA+++GK NMDE A+G +T+ + Sbjct: 87 KDNFDVAGWPTRAG--LPGRAQPAQGDAHAVARLRASGAVLLGKTNMDEGALGASTDNPH 144 Query: 125 FGVVRNPHDEARVAGGSSGGSGAVIAADEAVLSLGSDTGGSIRCPASFCGVYGLKPTYGL 184 G NPH AGGSSGG+ A +AA AV ++GSD+ GSIR PAS+CGVY LKPT+G Sbjct: 145 TGPTHNPHRHGYTAGGSSGGAAAAVAAGMAVAAIGSDSLGSIRIPASYCGVYALKPTHGE 204 Query: 185 VSRYGLIPYANSLEQIGPMADSIEDLALLLEVIAGKDTRDSTNAGREFRFEPED---RKL 241 +S GL+P A L+ +G +A S DL +LL+V+AG D D+ + R F P D L Sbjct: 205 ISARGLVPAARRLDAVGLLARSANDLTVLLQVLAGYDADDARSRRRRVAFAPPDWEPGNL 264 Query: 242 RVGI---IAEMGGNDDVMKRFNEAVEVI-REKHEVGEVSMPSFKYALAAYYIIAMSEASS 297 R G+ +A +G V+ F +A+ + RE E +V + +A + + EA Sbjct: 265 RCGLLPDLAAVGVEAAVIDVFEDALSRLPRELGERRQVDFSDWDFARTRRAGLFLMEAE- 323 Query: 298 NLARYDGVRYGFALEKLDSWRRYFSKVRAEGFGDEVKRRIMLGSYALSAGYYGKYYLKAQ 357 + FA + D AE E RR++ SYA + Y A Sbjct: 324 -------MLSTFAADLDD----------AEHPASERFRRML--SYAATKS--AADYAVAD 362 Query: 358 KVRTLVIRDFKKAFEEYDVLISPTMPALPFKIGELADPLTMYKADVNTVPVNLAGLPALS 417 +V ++ F + DVL+ PT P F +G + +AD+ + +LAG PA+S Sbjct: 363 RVLDAATLKMRRLFAQIDVLVLPTTPQGAFPLG---GAVPDSQADLTSF-ASLAGCPAVS 418 Query: 418 VPVG-MVKGLPVGLQVIGNYFSENTLLNFGK 447 +P+G + G+PVG+Q++G S+ LL + Sbjct: 419 IPMGTLPDGMPVGMQLVGARGSDLRLLELAE 449 Lambda K H 0.318 0.136 0.392 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: 498 Number of extensions: 25 Number of successful extensions: 5 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: 457 Length of database: 469 Length adjustment: 33 Effective length of query: 424 Effective length of database: 436 Effective search space: 184864 Effective search space used: 184864 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