Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate YP_001313780.1 Smed_5068 amidase
Query= curated2:Q21RH9 (493 letters) >NCBI__GCF_000017145.1:YP_001313780.1 Length = 473 Score = 211 bits (536), Expect = 6e-59 Identities = 153/489 (31%), Positives = 231/489 (47%), Gaps = 61/489 (12%) Query: 5 TALHDLTVAQLASLLRARKVSALETAQHFLARAQANASLGAFLDFN---EEVTLRQARAA 61 T L L + +LA+++R+RK+SA+E +FL R A A FN E + AR Sbjct: 2 TVLETLPIRKLAAMVRSRKISAVEVTSYFLNRIMAFDD--AICGFNVPAPETAMGAARDL 59 Query: 62 DLALAADSGGATPTLLGVPMAHKDIFVTRDFISTAGSRMLAGYRSPFDATVVSKLAAQGV 121 D LAA GG L G+P++ KDI S S AG + DATVV+++ G Sbjct: 60 DKQLAA--GGEAGALAGIPLSIKDIADVAGLPSAGASASRAGRMASTDATVVARMKIAGG 117 Query: 122 VTLGKLNCDEFAMGSANENSAFGPVRNPWDLTRTPGGSSGGSAAAVAARLLPAATGTDTG 181 + LGK NC E A G + + + P RNPW+ R PGGSS GS VAA L + TDT Sbjct: 118 IALGKANCHELAFGGPSFDLPYPPARNPWNRDRFPGGSSSGSGVTVAAGLCLGSLATDTA 177 Query: 182 GSIRQPASFCGVTGIKPTYGRASRYGMVAFASSLDQAGPMARTAQDCALLLSAMCGPDPD 241 GSIR PA+ CGV G+KP G+ A+++D GP+ARTA D +L M G P Sbjct: 178 GSIRLPATMCGVFGLKPGRDTLPLDGIAVLAATMDHVGPVARTADDTRILFDVMAGRSPG 237 Query: 242 RDSTSLDLPAEDFTRSLTESIEGLRIGVPAEFFGEG--LADDVRAAVDGALKELEKLGAR 299 + S+ GLRIGVP++ +G G + DV+ ++ A+ GA Sbjct: 238 PPCSG--------------SLHGLRIGVPSDDWGVGSLMHPDVQTGLESAIDVARSEGAE 283 Query: 300 LVPISLPRTELSIPVYYIIAPAEASSNLSRFDGVKFGHRAAQYADLTDMYKKTRAEGFGD 359 +VP+ LP + I+ AE ++ H A+ + + FG Sbjct: 284 IVPLELPSLDDFHAPATILMMAEIAAE----------HAAS---------VRAAWDKFGA 324 Query: 360 EVKRRIMIGTYVLSHGYYDAYYLQAQKIRRMIADDFQQAYLQCDVIAGPVAPTVAWKLGG 419 + R ++G + + Y A L+ RR+ + + C ++AG +AP Sbjct: 325 IFRARALVGEGITAEDYRLAERLRPVLTRRLFD---AISSVDCLLVAGALAPP------- 374 Query: 420 HGNDPLADYLADIF------TLPGSLAGLPGMSLPVGFGANHMPVGLQLIGNYLQEAKLL 473 PLA + F + + G P ++ P G + MP+G+Q++G E +LL Sbjct: 375 ---GPLASVDSFYFMKEPIPNIVANYTGFPALAFPAGVSSEGMPIGVQIMGVPGSEHRLL 431 Query: 474 NVAHRFQQA 482 ++A +++A Sbjct: 432 DIAENYERA 440 Lambda K H 0.319 0.134 0.395 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: 599 Number of extensions: 42 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: 493 Length of database: 473 Length adjustment: 34 Effective length of query: 459 Effective length of database: 439 Effective search space: 201501 Effective search space used: 201501 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: 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