Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 15885 b1767 cytoplasmic asparaginase I (NCBI)
Query= curated2:A5UK11 (436 letters) >FitnessBrowser__Keio:15885 Length = 338 Score = 160 bits (404), Expect = 7e-44 Identities = 112/343 (32%), Positives = 176/343 (51%), Gaps = 20/343 (5%) Query: 90 KQNISIISTGGTVS---SIIDYRTGAVHPKFTAADLIKAN-PELLDYANYNVKALYNILS 145 K++I + TGGT+ S Y + H + A + + + PE+ D+ + L + S Sbjct: 3 KKSIYVAYTGGTIGMQRSEQGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYTPLMD--S 60 Query: 146 ENMQPKYWVEAAESIANDISDGSDGIVIAHGTDTLHYTAAALSFMLKT-PVPIVITGAQR 204 +M P+ W AE I D DG VI HGTDT+ YTA+ALSFML+ P+++TG+Q Sbjct: 61 SDMTPEDWQHIAEDIKAHYDD-YDGFVILHGTDTMAYTASALSFMLENLGKPVIVTGSQI 119 Query: 205 SSDRPSSDANMNLIDSV-VAAKSDIAEVSVCMHGSLNDSYTYLHKGTKVRKMHTSRRDTF 263 SD +NL++++ VAA I EV++ + L ++G + K H D F Sbjct: 120 PLAELRSDGQINLLNALYVAANYPINEVTLFFNNRL-------YRGNRTTKAHADGFDAF 172 Query: 264 RSINYEPIAKIENHSVDINPNYRYTKRNENELEVNSAVEEKVGLIKSFPGICEELIEYHI 323 S N P+ + H +N E EL V+ + +G++ +PGI +++ + Sbjct: 173 ASPNLPPLLEAGIHIRRLNTPP--APHGEGELIVHPITPQPIGVVTIYPGISADVVRNFL 230 Query: 324 DKGYKGLVIEGTGLGHVPDK--LITPLARAHDENIPVVMTSQCLYGRVNMNVYSTGREIL 381 + K L++ G+G+ P + L A D I VV +QC+ G+VNM Y+TG + Sbjct: 231 RQPVKALILRSYGVGNAPQNKAFLQELQEASDRGIVVVNLTQCMSGKVNMGGYATGNALA 290 Query: 382 NAGVISGRDMTPETAYVKLSWVLGQTNDIGEVAKLMNKNIAGE 424 +AGVI G DMT E KL ++L Q D + K M++N+ GE Sbjct: 291 HAGVIGGADMTVEATLTKLHYLLSQELDTETIRKAMSQNLRGE 333 Lambda K H 0.313 0.132 0.373 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: 375 Number of extensions: 24 Number of successful extensions: 5 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: 436 Length of database: 338 Length adjustment: 30 Effective length of query: 406 Effective length of database: 308 Effective search space: 125048 Effective search space used: 125048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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