Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011906849.1 SARO_RS18885 amidase
Query= curated2:Q21RH9 (493 letters) >NCBI__GCF_000013325.1:WP_011906849.1 Length = 501 Score = 162 bits (410), Expect = 3e-44 Identities = 147/488 (30%), Positives = 216/488 (44%), Gaps = 40/488 (8%) Query: 15 LASLLRARKVSALETAQHFLARAQANASLGAFLDFNEEVTLRQARAADLALAADSGGATP 74 LA L+R RKVSA E + +ARA+A + +F + R A +A G T Sbjct: 40 LAELVRKRKVSAAELLEAAIARAEA---MNPRFNFMAQKHYDYGRKA-IAQGLPEGPFT- 94 Query: 75 TLLGVPMAHKDI--FVTRDFISTAGSRMLAGYRSPFDATVVSKLAAQGVVTLGKLNCDEF 132 GVP KD+ ++ + ++ GSR+ G R+ + +V ++ G GK EF Sbjct: 95 ---GVPWLLKDLNTYIAGE-VTENGSRLYKGQRASVTSELVRRIERAGFAIFGKTTTPEF 150 Query: 133 AMGSANENSAFGPVRNPWDLTRTPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPASFCG 192 + E+ GP RNPW+ R GGSSGG+AAAVAA ++PAA TD GGSIR PAS CG Sbjct: 151 GLTGTTESVLMGPTRNPWNPGRIAGGSSGGAAAAVAAGVIPAAHATDGGGSIRIPASACG 210 Query: 193 VTGIKPTYGRASR-YGMVAFASSLDQAGPMARTAQDCALLLSAMCGPDPDRDSTSLDLPA 251 + G+KP+ GR + + RT +D A +L A G +P P Sbjct: 211 LFGLKPSRGRVPMGPSRTEGWGGMSVHHAVTRTVRDSAAILDATHGVEPG-SRYGAPTPE 269 Query: 252 EDFTRSLTESIEGLRIGVP-AEFFGEGLADDVRAAVDGALKELEKLGARLVPISLPRTEL 310 F + LR+ + + F G + +V AA GA + LE LG V + P+ + Sbjct: 270 RPFLAEVGRDPGKLRVALMLSPFSGAPVDPEVIAATQGAARLLETLGHH-VEEAAPKIDF 328 Query: 311 SIPVYYIIAPAEASSNLSRFDGVKFGHRAAQYADLTDMYKKTRAEGFGDEVKRRIMIGTY 370 AS S F + ++ AD D K E G +V R + Sbjct: 329 ------------ASIGASSFALM----ASSVAADCVDRAKALGIE-LGPDVLERTTLDFV 371 Query: 371 VLSHGYYDAYYLQAQKIRRMIADDFQQAYLQCDVIAGPVAPTVAWKLGGHGND---PLAD 427 + Y + + + A Q DVI P LG G D +AD Sbjct: 372 AMGKAYTGMDFARGNSAYQAAAVSIAQFMEGYDVILSPTLSAPPLPLGRVGLDTGRSMAD 431 Query: 428 YLADI-----FTLPGSLAGLPGMSLPVGFGANHMPVGLQLIGNYLQEAKLLNVAHRFQQA 482 + ++ FT + G P MSLP+G + +P+G+ G Y +EA LL +A + ++A Sbjct: 432 WGREVGAFTAFTGIYNGTGQPSMSLPLGMSKDGLPIGIMATGRYGEEALLLRLAGQVEKA 491 Query: 483 THWHLAKP 490 W +P Sbjct: 492 APWAARRP 499 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: 552 Number of extensions: 21 Number of successful extensions: 3 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: 501 Length adjustment: 34 Effective length of query: 459 Effective length of database: 467 Effective search space: 214353 Effective search space used: 214353 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