Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011840779.1 RSPH17029_RS05425 amidase
Query= curated2:B8J405 (486 letters) >NCBI__GCF_000015985.1:WP_011840779.1 Length = 495 Score = 157 bits (398), Expect = 6e-43 Identities = 150/495 (30%), Positives = 221/495 (44%), Gaps = 51/495 (10%) Query: 10 TAVAQALQKKELSAVDVTTACLDRITATEPHLAALLYVNAENALARATTLDSEGPDAARP 69 T +A + +++ S ++ A LD + A P L A++ V E A GP Sbjct: 11 TGLAALVARRDTSPEELLDAALDAVAAVNPALNAVVLVQEETARRSIARGLPHGP----- 65 Query: 70 LWGVPVTLKD-AFSTRGMPTTAGSRMLEGYTPFYDAFAVQKLHEAGAVILGKTNLDEFAM 128 GVP LKD P+ GSR+L D+ +++ G V G+T E + Sbjct: 66 FRGVPFLLKDLGCEAVDFPSHNGSRLLADTRYARDSAIFERIRATGVVTFGRTTSPEGGI 125 Query: 129 GSSTENSAFK-VTRNPWNLNKVPGGSSGGSAASVTAGQCFASLGTDTGGSIRQPASFCGC 187 G +TE++ + TRNPWNL GGSSGG+ A+V AG + G+D GGS+R PAS CG Sbjct: 126 GPATESAVYGGPTRNPWNLEHTSGGSSGGAGAAVAAGIVAMAHGSDGGGSVRIPASSCGL 185 Query: 188 VGLKPTYGRVSRYGVIAYG-SSLDQVGPLTRSVEDCARVLTAIAGYDSRDNTCDPRPAED 246 G+KPT R+ G + + G LTRSV D A +L A G D P Sbjct: 186 FGMKPTRARLPDGPYAGEGWAGMAIDGFLTRSVRDTAHMLDACTGADPGAPYWAPPLLRS 245 Query: 247 YAATLSSRPLKGARLGI-PREFYGQGLSDEVRAACEAAIQAARNQDAELVEVSLPHTDAA 305 +A + RP + R+GI F G + EVRAA EAA + + V LP D A Sbjct: 246 HADAIG-RPPRRLRVGICDTTFTGAPIHPEVRAAVEAAGRLLESL-GHTVSPCLPRADVA 303 Query: 306 IATYYIIAMAEASSNLARFDGVRFGHRSADIKNLDDLYVHSRTEGFGPE-VKRRIMLGA- 363 + M EA +++ G G R A +G PE + + LGA Sbjct: 304 M-------MMEAWTDIVAC-GTALGIRKA-------------LKGRAPEGLVEPVSLGAM 342 Query: 364 ----------YVLSSGYYDAYYRKAAQVRRLIRDE-----LLAALGQCDALLAPVSPVTA 408 Y+ + G A+ R+ A V E L A L + A + + T Sbjct: 343 RRAAEIPGERYLEAVGQIHAFGRQMAAVFDPETGEGIDILLSATLAEPPARVGRFAHGTE 402 Query: 409 RDLGGNTADPLQIYLMDAYTLSLNLAGLPGLSLPVGLGAKSGMPVGMQIIGKPFEETQVL 468 + T P ++ +T N +G P SLP+G+ A G+P+G+ + + + +++ Sbjct: 403 DYVSFRTG-PESVFAYSPFTAVFNASGQPAASLPLGMSA-GGLPIGVHLAARFGADEELI 460 Query: 469 ALGHSLEQALPGIGR 483 AL +E+A P IGR Sbjct: 461 ALCAEIERAAPWIGR 475 Lambda K H 0.317 0.133 0.388 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: 579 Number of extensions: 43 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 495 Length adjustment: 34 Effective length of query: 452 Effective length of database: 461 Effective search space: 208372 Effective search space used: 208372 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 (21.7 bits) S2: 52 (24.6 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