Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_043828429.1 RSPH17029_RS15975 amidase
Query= curated2:A1ATL3 (485 letters) >NCBI__GCF_000015985.1:WP_043828429.1 Length = 477 Score = 207 bits (526), Expect = 8e-58 Identities = 152/484 (31%), Positives = 237/484 (48%), Gaps = 45/484 (9%) Query: 6 LTLHELHAKLKSKEVSSREATSAMLDRIAELEPRINAFITVTPERALAEAEAADRRIAAG 65 L+ +L A +++++S E + L RI +NA PE AL EA A+++R +G Sbjct: 9 LSAAQLTALYRARKISPVEVVTDALARIEASGDSLNAVCFTYPEEALEEARASEKRYMSG 68 Query: 66 --EADVLTGIPLAVKDIFLTEGTLTTCGSRILNNFIPPYSATSFEKLKQRGMVLLGKLNQ 123 + ++ GIP A+KD + G +TT GS + + + SA ++L + G V+ + Sbjct: 69 AQKPGMIDGIPTALKDETMMAGKVTTYGSLLYADHVAAKSAPVVQRLVEAGAVIHARTTT 128 Query: 124 DEFAMGSSNESSASGPCRNPWNTDCIPGGSSGGSAAAIAARQATVTLGTDTGGSIRQPAS 183 EF+ S G RNPWN PGGSSGGS AA+AA A + G+D GGSIR PAS Sbjct: 129 PEFSCAPFCHSRQWGVTRNPWNLAFTPGGSSGGSGAALAAGLAPLATGSDIGGSIRIPAS 188 Query: 184 HCGCVGLKPTYGRVSR---YGVIAYASSLDQVGPLTRDVTDCAIMLGALAGHDPKDSTSV 240 G VG KP YGRV + + Y + GP+ R V DC +M LAG P+D S+ Sbjct: 189 ASGVVGFKPPYGRVPSTPPFNLDPY----NHPGPMARTVEDCLLMQNVLAGPHPEDIASL 244 Query: 241 DRPVPDYQAAL-TNDIRGLRIGLPREYFIEGLDPDVQASMDQAIETYRRLGAEFTEISLP 299 P + L + ++G +I ++ +DP V+A+ A++ +R LGAE TE++LP Sbjct: 245 K---PKLELRLDRSGVKGWKIAYSLDFGFMEIDPAVRANTLAALDVFRALGAEVTEVALP 301 Query: 300 HTDYAVASYYLIATAEASANLARYDGVRFGHRAEQAEGLLEMYSRSRSQGFGSEVKRRIM 359 + + + A A+ + A + G ++ E L Y+R ++ Sbjct: 302 WS-------WEVYRAAATHHKALF-GAWLAEYLDEREERLTSYARRFARD---------- 343 Query: 360 LGTYALSSGYYDAYYLKAQKVRTLIMADFIQAFEGVDLILTPVAPTPAFRIGEKVNDPL- 418 AL++ D YL ++ I + F EG DL L P PA +DPL Sbjct: 344 ----ALATTTRD--YLAGMEIEGRIWSHFGPMMEGFDLFLCPTLAIPAVPAEFDFSDPLI 397 Query: 419 ------QMYLSDIFTIPVNLAGTC-AMSLPAGISGQGLPIGVQLIGKPFGEETILRAAHA 471 YL P N+ C +S+P+G + G+P G+QL+G+ + ++++ A A Sbjct: 398 INGEEIDSYLGWTMAWPFNMLSRCPVLSVPSGHAPNGVPTGIQLVGRTYEDQSVFTAGLA 457 Query: 472 FEQA 475 +E A Sbjct: 458 YETA 461 Lambda K H 0.318 0.134 0.389 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: 482 Number of extensions: 26 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: 485 Length of database: 477 Length adjustment: 34 Effective length of query: 451 Effective length of database: 443 Effective search space: 199793 Effective search space used: 199793 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: 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