Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011840201.1 RSPH17029_RS00740 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000015985.1:WP_011840201.1 Length = 441 Score = 164 bits (414), Expect = 7e-45 Identities = 159/480 (33%), Positives = 221/480 (46%), Gaps = 69/480 (14%) Query: 1 MLAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSL-----NERLLEEAEAVDPG 55 M A E+ + G + P+E+A+A+L + G + L + AE G Sbjct: 6 MTAAELGRGIEAGRIHPVELAEAFLAAAADHPEGTRIYARLCPTRARTEAMAAAERAKRG 65 Query: 56 L---PLAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLD 112 L PL G+ V+ KD T G+ T AGS LL+ VP +A + G + LGKT++ Sbjct: 66 LRRGPLDGVPVSWKDLFDTAGVATEAGSALLKGRVPEEDAAVLGTATLGGLVCLGKTHMS 125 Query: 113 EF---GMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQP 169 E G+G + +A P N DP V GGSS G+AA++A LAP A+GSDTGGSVR P Sbjct: 126 ELAFSGLGLNPV-TATPPCVN--DPAAVAGGSSSGAAASVAFGLAPAAIGSDTGGSVRIP 182 Query: 170 AAFCGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDPLDATSLD 229 AA+ + GLK T GR+S G + A+ D +GP+AR+V D ALL+ + G P D Sbjct: 183 AAWNDLAGLKTTAGRLSLAGTVPLAARFDTVGPLARTVEDCALLLAVLEGGRPADLRGAS 242 Query: 230 LPPRFQEALEGPLPPLRLGVVREALAGNSPGVERALEEALKVFRELGLSVREVSWPSLPQ 289 L R LE L L +REA A R EEA+ G + + P + + Sbjct: 243 LAGRRFLVLE----TLALEDLREAPA-------RGFEEAVARLARAGARIERGAAPEVVE 291 Query: 290 ALAAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTFVL 349 A+A L EA + A E +EG + L + R G + Sbjct: 292 AMAMAGPLFTGEAYATWA-------------EVIEGAPD----LMFPRILERFRSGASIT 334 Query: 350 SSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFGARRDPLAMYREDLY 409 + + A+ R +A R A D +L+PT+ P P A+R + ++ Y Sbjct: 335 AVEFVTAWQ-RLEALRAAWAARTAG----YDAVLVPTS--PILPPDAKR----LLTDESY 383 Query: 410 TVG-----------ANLTGLPALSFPAGFEGHLPVGLQLLA-PWGEDERLLRAALAFEEA 457 VG ANL GLPAL+ P G G+ L+ P GE ERLLR A E A Sbjct: 384 YVGENLLALRNTRIANLMGLPALTLPT---GQPSCGISLMGQPMGE-ERLLRLGAAAERA 439 Lambda K H 0.319 0.137 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: 500 Number of extensions: 27 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: 471 Length of database: 441 Length adjustment: 33 Effective length of query: 438 Effective length of database: 408 Effective search space: 178704 Effective search space used: 178704 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 16 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