Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012116626.1 XAUT_RS23580 AtzE family amidohydrolase
Query= curated2:Q2IH94 (492 letters) >NCBI__GCF_000017645.1:WP_012116626.1 Length = 482 Score = 258 bits (659), Expect = 3e-73 Identities = 181/485 (37%), Positives = 252/485 (51%), Gaps = 36/485 (7%) Query: 5 AKELCRLGLREAGAGVAAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAAKAAD 64 A L E VA+ A+++ ++EA+LARI A D K+ AF + A+RARA+A D Sbjct: 15 AASLATASAAEIATAVASGAVTARAMIEATLARIAAVDPKVNAFTDLTAERARASADRID 74 Query: 65 ARAARGERRSELDGVPVAVKDLFVTKGVPTTAGSRILEGYLPPY-DATVVERLEAAGAVI 123 AR A G L G P AVK+LF KG+PT AGS+I P DAT++ +LEAA AV+ Sbjct: 75 ARRAAGAPLGPLAGAPFAVKNLFDVKGLPTRAGSKINRDLSPADGDATLIAKLEAADAVL 134 Query: 124 VGKLNMDEFAMGSSNENSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDTGGS 183 VG LNM E+A + EN NP DL+R GGSSGGS A+VAAG V +LG+DT GS Sbjct: 135 VGALNMGEYAYDFTGENVHDGASRNPHDLTRMTGGSSGGSGAAVAAGLVPIALGSDTNGS 194 Query: 184 IREPAAFCGVVGVKPTYGRVSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDPRDM 243 IR P++ CG G+KPTYGR++R G F ++LD +GPL R V D A + G D RD Sbjct: 195 IRVPSSLCGTFGLKPTYGRLTRGGSFPFVTALDHLGPLGRSVADLAAFYDAMQGEDARDP 254 Query: 244 TSSTRPVDDYLGPLEEGARGLRVGVPREWLSGGLDAGVEAAIRAALDTYRRLGATLVDVS 303 + RP + G + +GA GLR+ + W + A A LG T V V Sbjct: 255 GQTPRPFEPVSGLIGQGADGLRIAIAGGWFR---SRALPEAFAAVDHVAASLGVTQV-VD 310 Query: 304 LPHSKYGIGAYYLIAPAEASSNLARYDGVRYGLRAEGAKGLKEMYAESREQGLGAEPKRR 363 +P + + ++I AE +S AR R RAE + R Sbjct: 311 IPDAARARASAFIITAAEGASLHAR----RLAARAE---------------DFDPAVRDR 351 Query: 364 IMLGTYALSSGYYDAYYLRAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAFALGERTG-- 421 + G A+ + + DA AQ+ R + + F+ DV+ P TPS A LG++T Sbjct: 352 LFAG-LAIPASWVDA----AQRFRRHFHGEMMKLFQTHDVLLAPTTPSRAPKLGQKTFVL 406 Query: 422 DPLQMYL---ADIFTITCNLAALPGLSVPCGLEA--ASGLPVGLQLVGRPFDEATLFRAA 476 D +M + +FT + LP ++VP ++A A LP+ +Q++ P+ E R A Sbjct: 407 DGEEMLVRPNMGLFTQPISFIGLPVVAVPVRVDAGDAPELPLAVQVIAPPWREDLALRVA 466 Query: 477 RALER 481 LER Sbjct: 467 ATLER 471 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: 584 Number of extensions: 37 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: 482 Length adjustment: 34 Effective length of query: 458 Effective length of database: 448 Effective search space: 205184 Effective search space used: 205184 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