Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BWI76_RS10550 BWI76_RS10550 AtzE family amidohydrolase
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__Koxy:BWI76_RS10550 Length = 465 Score = 251 bits (640), Expect = 5e-71 Identities = 176/482 (36%), Positives = 242/482 (50%), Gaps = 36/482 (7%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L ++T+ + LA GE+S+ E+ L IA V P++ A+ + A+A D R Sbjct: 3 LPEMTIHDIQRALASGELSAKEIARHTLENIARVNPQINAWTHISEKRMLAEAENIDTLR 62 Query: 64 AAGDASPLL-GIPMGIKDVISTQGLRTTCASKML-ENYTPVYDATAVARLKAAGAVILGK 121 P L G+P +K++ G T +++L + V D+ AV +L +AGA++ G Sbjct: 63 REKKPLPALAGVPYAVKNLFDVAGHTTLAGAQLLGDRPAAVADSWAVRQLLSAGALLSGM 122 Query: 122 LNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQ 181 LN D +A G +TENS + TRNP +L R+ GGSSGGSAAAVAAG +LG+DT GSIR Sbjct: 123 LNMDAYAYGFTTENSHYGATRNPHDLSRIAGGSSGGSAAAVAAGLVHFSLGSDTNGSIRV 182 Query: 182 PAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCT 241 PA+LCGI GLKPT+GR+SR G F +SLD IGP AR V D + V + G DP D Sbjct: 183 PASLCGIFGLKPTFGRLSRSGSHPFVASLDHIGPFARCVSDLSAVYDALQGRDPGDGFQA 242 Query: 242 DYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPH 301 D + L+ + GLR YF D AAV L A E+ P Sbjct: 243 DKASERTANLLSRGLEGLRCATLGGYFTTWCDNDARAAVARVAGAL----AAHEELIFPE 298 Query: 302 TPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLG 361 A ++I+ AE G Y L R++ F P R R++ G Sbjct: 299 AELARSAAFIISAAEG-----------------GNQYLPAL-RSQAERFEPNSRERLLAG 340 Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAH----TDDP 417 S A+Y +AQ+ R ++ ++ F DV+ AP TP A IGA P Sbjct: 341 AMIPS-----AWYLQAQRFRRHAQQAFKALFAHADVLIAPATPCSATLIGAQNMEINGQP 395 Query: 418 LAMYLE-DVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDAYQR--V 474 L + + T P++ GLP + VP A G PIGLQLI F+E++ LRV A + V Sbjct: 396 LPIRASMGMLTQPISFLGLPVVTVPLRTASGQPIGLQLIAAPFNEQACLRVARALEETGV 455 Query: 475 TD 476 TD Sbjct: 456 TD 457 Lambda K H 0.320 0.136 0.398 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: 480 Number of extensions: 24 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: 1 Length of query: 490 Length of database: 465 Length adjustment: 34 Effective length of query: 456 Effective length of database: 431 Effective search space: 196536 Effective search space used: 196536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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