Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011798409.1 PNAP_RS23690 amidase
Query= curated2:Q2IH94 (492 letters) >NCBI__GCF_000015505.1:WP_011798409.1 Length = 506 Score = 214 bits (545), Expect = 6e-60 Identities = 164/496 (33%), Positives = 237/496 (47%), Gaps = 36/496 (7%) Query: 5 AKELCRLGLREAGAGVAAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAAKAAD 64 A++L L E + A+ +S EL+ A +ARI+A + + A A C DRAR A+AA+ Sbjct: 3 AEDLIALPATEMRRMIGARQLSPVELLNACIARIEAVNPYVNAVTATCFDRARTEARAAE 62 Query: 65 ARAARGERRSELDGVPVAVKDLFVTKGVPTTAGSRILEGYLPPYDATVVERLEAAGAVIV 124 A G L G+P+ VKDL T+G+ TT GS I G +P D +V RL AAGA++ Sbjct: 63 AAVMAGGPLGLLHGLPLGVKDLEDTEGLLTTHGSPIYRGNVPTRDNVLVARLRAAGAIVT 122 Query: 125 GKLNMDEFAMGSSNENSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDTGGSI 184 GK N+ E G+++ N + NP++ + GGSSGGSAA++A + G+DTGGS+ Sbjct: 123 GKTNVPEMGAGANSRNPVWGATGNPFNPNLNAGGSSGGSAAALALDMLPVCTGSDTGGSL 182 Query: 185 REPAAFCGVVGVKPTYGRVSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDPRD-M 243 R PAA CGVVG +P+ G V + + VGP+ R V DA L L AG D + Sbjct: 183 RIPAAKCGVVGFRPSPGVVPSSRKPLGWTPISVVGPMGRTVADACLQLAATAGVSATDPL 242 Query: 244 TSSTRPVDDYLGPLEEGARGLRVGVPREWLSGGLDAGVEAAIRAALDTYRRLGATLVDVS 303 T P+ +L P + GLRVG ++ + +D G+ R + R L + ++ Sbjct: 243 TYEVDPL-SFLLPQDLDLGGLRVGYTEDFGACAVDDGIRGVFREKIAAMRHLFRSCEPLA 301 Query: 304 LPHSKYGIGAYYLIAPAEASSNLARYDGVRYGLRAEG-AKGLKEMYAESREQGLGAEPKR 362 L +L LRAE G++ Y E LG P+ Sbjct: 302 L--------------------DLGEVHHCFDVLRAEAFVAGMRSAY-ERDPSSLGPNPRA 340 Query: 363 RIMLGTYALSSGYYDAYYLRAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAF--ALGERT 420 +G + D + +A++ R L R F A+ D+I P TP F L T Sbjct: 341 NYEMGA---AMSLLDCAWAQAEQTRILAR--FQAAYCDVDIILAPTTPVSPFPWMLAHAT 395 Query: 421 ---GDPLQMYLADI-FTITCNLAALPGLSVPCGLEAASGLPVGLQLVGRPFDEATLFRAA 476 G+ + Y + T L P LS+PCG + A G+P GLQ+VGR + A Sbjct: 396 HINGEQQENYYRWLSLTYVTTLTTHPSLSLPCGTDHA-GMPFGLQIVGRFRADRHTLGVA 454 Query: 477 RALERELGPLPAPPEP 492 +A+ER A P Sbjct: 455 QAMERAFASSEALRRP 470 Lambda K H 0.317 0.135 0.393 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: 591 Number of extensions: 35 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: 492 Length of database: 506 Length adjustment: 34 Effective length of query: 458 Effective length of database: 472 Effective search space: 216176 Effective search space used: 216176 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 (21.6 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