Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012331585.1 M446_RS07915 amidase
Query= curated2:Q72L58 (471 letters) >NCBI__GCF_000019365.1:WP_012331585.1 Length = 480 Score = 215 bits (547), Expect = 3e-60 Identities = 180/479 (37%), Positives = 235/479 (49%), Gaps = 47/479 (9%) Query: 2 LAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLN--ERLLEEAEAVDPGL--- 56 LA IR R VS EV +A+L R+ +P A + L E LLEEA D L Sbjct: 15 LARAIRDRT----VSAREVMRAHLDRIARANPAANAIVGLRDPEILLEEAACADRDLAAG 70 Query: 57 ----PLAGLVVAVKDNIATRGLRTTAGSRLLENFVPPYEATAVARLKALGALVLGKTNLD 112 PL GL AVKD GL T GS L V +A VARL+ GA+++GKTN+ Sbjct: 71 RWRGPLHGLPHAVKDTSPAAGLIWTQGSPLFAGRVAEADAPHVARLRQAGAILIGKTNVP 130 Query: 113 EFGMGSSTEHSAFFPTKNPFDPDRVPGGSSGGSAAALAADLAPLALGSDTGGSVRQPAAF 172 EFG+GS T + F T+N +DP R GGSSGG+A ALA + PLA GSD GS+R PAA+ Sbjct: 131 EFGLGSHTVNPVFGATRNAYDPARSAGGSSGGAAVALALRMLPLADGSDHAGSLRNPAAW 190 Query: 173 CGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAVAGPDP-LDATSLDLP 231 GV GL+P+ GRV + L GPMAR DL LL+ +AGPDP L + + P Sbjct: 191 NGVLGLRPSPGRVPMRTDEVFLPDLTVAGPMARCTADLGLLLSVLAGPDPRLPHSLTEDP 250 Query: 232 PRFQEALEGPLPPLRLGVVREALAGN---SPGVERALEEALKVFRELGLSVREVSWPSLP 288 F L LR+G + + L G+ PG+ E AL VF G V ++ Sbjct: 251 SAFAAPAPLALAGLRIGWLGD-LGGHLPVEPGILALCERALAVFAGEGARVAPLALGFDA 309 Query: 289 QAL-AAYYILAPAEASSNLARYDGTLYGRRAEGEEVEGMMEATRALFGLEVKRRVLVGTF 347 +A+ A+ +L +A + LA + R A + ALF E+ R + + Sbjct: 310 EAVFRAWRVLRAWQAGAALAPHARDPAARAALKPD---------ALF--EIDERARLDAY 358 Query: 348 VLSSGYYEAYYGRAQAFRRRLKAEAQALFREVDLLLLPTTPHPAFPFG-------ARRDP 400 + + A A R R A LF DLL LP FP G A R Sbjct: 359 AVQA---------ASALRSRWFAHLLDLFARCDLLALPAAQVFPFPIGEMWPRAIAGRPM 409 Query: 401 LAMYREDLYTVGANLTGLPALSFPAG-FEGHLPVGLQLLAPWGEDERLLRAALAFEEAT 458 + +R + A + G PA+S PAG G LP+GLQL+AP + RLL A A+E AT Sbjct: 410 DSYHRWMEVAIPATMGGCPAISLPAGRGPGGLPMGLQLIAPHRGEGRLLAVAAAYEAAT 468 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: 630 Number of extensions: 33 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: 480 Length adjustment: 33 Effective length of query: 438 Effective length of database: 447 Effective search space: 195786 Effective search space used: 195786 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 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