Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_008804827.1 KVAR_RS12640 AtzE family amidohydrolase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000025465.1:WP_008804827.1 Length = 465 Score = 256 bits (655), Expect = 9e-73 Identities = 180/487 (36%), Positives = 244/487 (50%), Gaps = 34/487 (6%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADA-R 62 L+ T+A+ + L GE+S+ E+ L IA P++ A+ V A A+A + DA R Sbjct: 3 LHHFTIAEIQRALHEGELSAREIARQTLDDIARANPQINAWTEVTAQRMLAEADSIDALR 62 Query: 63 RAAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVY-DATAVARLKAAGAVILGK 121 R PL GIP +K++ G T +++L + P D+ AV +L +AGA++ G Sbjct: 63 REKRPLPPLAGIPYAVKNLFDVAGHTTLAGAELLSDRPPATSDSWAVRQLHSAGALLSGM 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 A V + G DP D Sbjct: 183 PASLCGIFGLKPTFGRLSRSGSHPFVASLDHIGPFARRVADLAAVYDALQGRDPADDFQA 242 Query: 242 DYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPH 301 D + L + GLR YF D AAV L GA+ E+ Sbjct: 243 DKASERTGNLLERGLEGLRCARLGGYFTTWCDDDARAAVDRVAHAL---GAD-SELQFAD 298 Query: 302 TPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLG 361 A ++I+ +E G Y +L R F P R R++ G Sbjct: 299 AALARSAAFIISASEG-----------------GNQYLTDL-RHSPERFEPHSRERLLAG 340 Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAH----TDDP 417 S A+Y +AQ+ R R+ + F Q DV+ AP TP A IGA P Sbjct: 341 AMIPS-----AWYLQAQRFRRHARQAMKSLFSQADVLIAPATPCSATPIGAEEMVINGQP 395 Query: 418 LAMYLE-DVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDAYQRVTD 476 L + + T P++ GLP + VP A G PIGLQLI F+E++ LR A + + Sbjct: 396 LPVRASMGMLTQPISFLGLPVVTVPLRTASGKPIGLQLIAAPFNEQACLRAARALEAMGI 455 Query: 477 WHTRMPE 483 R+ E Sbjct: 456 TDARVAE 462 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: 471 Number of extensions: 20 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: 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 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