Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 17036 b2957 periplasmic L-asparaginase II (NCBI)
Query= curated2:O59132 (438 letters) >FitnessBrowser__Keio:17036 Length = 348 Score = 139 bits (350), Expect = 1e-37 Identities = 107/336 (31%), Positives = 167/336 (49%), Gaps = 22/336 (6%) Query: 91 LPDVTIIGTGGTIASRIDYETGAVYPA--FTAEELAKAVPEIFEIANIKPKLLFNIFSED 148 LP++TI+ TGGTIA D T + Y E L AVP++ +IAN+K + + NI S+D Sbjct: 23 LPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNAVPQLKDIANVKGEQVVNIGSQD 82 Query: 149 MKPKHWIKIAHEVAKSLNSGDSGVVVAHGTDTMGYTAAALSFMLRDLGKPVILVGAQRSS 208 M W+ +A ++ + D G V+ HGTDTM TA L ++ KPV++VGA R S Sbjct: 83 MNDNVWLTLAKKINTDCDKTD-GFVITHGTDTMEETAYFLDLTVK-CDKPVVMVGAMRPS 140 Query: 209 DRPSSDAAMNLICSVRMSTSDVAE----VMVVMHGETGDTYCLAHRGTKVRKMHTSRRDA 264 S+D NL +V ++ +D A V+VVM+ D G V K +T+ Sbjct: 141 TSMSADGPFNLYNAV-VTAADKASANRGVLVVMNDTVLD-------GRDVTKTNTTDVAT 192 Query: 265 FRSINDVPIAKVWPNGKIEFLRDDYRRRSDSEVWVDDKLEE--KVALVKVYPGISSEIIE 322 F+S+N P+ + NGKI++ R R+ + + KL E KV +V Y S + Sbjct: 193 FKSVNYGPLGYI-HNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAK 251 Query: 323 FFIDKGYRGIVIEGTGLGHTPNDIIPSIQRATEEGIAVCMTSQCIYGRVNLNVYATGRRL 382 +D GY GIV G G G+ + ++ A + G AV +S+ G + Sbjct: 252 ALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDD--- 308 Query: 383 LKAGVIPCEDMLPETAYVKLMWVLGHTQDLEEVRRM 418 K G + + P+ A V L L T+D ++++++ Sbjct: 309 AKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQI 344 Lambda K H 0.320 0.138 0.403 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: 335 Number of extensions: 20 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: 438 Length of database: 348 Length adjustment: 31 Effective length of query: 407 Effective length of database: 317 Effective search space: 129019 Effective search space used: 129019 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: 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