Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_046009828.1 OLEAN_RS14555 amidase
Query= curated2:Q46E35 (475 letters) >NCBI__GCF_000967895.1:WP_046009828.1 Length = 498 Score = 178 bits (452), Expect = 3e-49 Identities = 140/450 (31%), Positives = 206/450 (45%), Gaps = 59/450 (13%) Query: 59 GPLAGVPIAIKDNI-SVVGLPNSCGSKILEDYIPPFNAYVIEKLLAAGAVILGKTNMDEF 117 GP +GVP +KD + S+ G P S GS + I P ++ ++++ ++G VI GKTN EF Sbjct: 64 GPFSGVPFLLKDLLGSLEGTPLSNGSAAFKGNISPSDSEMVKRYKSSGLVIFGKTNTPEF 123 Query: 118 AMGSSTETSYFGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSVRCPAAFCG 177 + TE FGPT NPW+L PGGSSGGS A +AAG P A G D GGS+R PAA CG Sbjct: 124 GLMGVTEPKAFGPTRNPWNLNHTPGGSSGGSGAAIAAGIVPMASGGDGGGSIRIPAACCG 183 Query: 178 VVGLKPTYGAVSRYGVVA-YANSLEQVGPLANNVTDIAVLMDVIAGYDRKDSTSIDSKTE 236 + GLKP+ G + Y + L +V D A ++DV+AG D + +T Sbjct: 184 LFGLKPSRGRTPTGPYFSEYWDGAAAEHVLTRSVRDSAAMLDVVAGPDGSSPYPVRKETG 243 Query: 237 YQKALIEDVKGLKIGVP-KEFFGEGIHPDVEKAVWNAIHKCEDLGASWEEVSMPHIKYAL 295 Y L E V+ LKI + FF + D K+V + + E LG + E V Sbjct: 244 YLTCLEEPVRPLKIAYTVQSFFDRPVTEDAIKSVQHTVKLLESLGHTVEAVHP------- 296 Query: 296 ASYYIIAMSEASSNLARFDGTRYGYRASGENWHAMVSKTRAEGFGTEVKRRILLGTYALS 355 YI A S L + YG+ A+ + A + + E +++ Sbjct: 297 ---YINANDLTDSYLTMY----YGHVAADLEFAAKLLNSNFSNLDVEDTTKLM------- 342 Query: 356 AGYHDK-----YYLKALKVRTLVKQDFDKALSKVDVLMAPTMPNPAFKIGE--------- 401 GY K ++ A + Q + D+L+ PT+ + +IGE Sbjct: 343 -GYIGKKISAEQFVTAKRRWNNFSQSMHALHQEYDLLLTPTLGSEPVRIGEFDLGLLDRI 401 Query: 402 --KIEDPLTLY-------------LSDVNTCPI----NLAGVPSLSVPCGFTD-GLPIGL 441 K+ + L L L ++ P NL G P++SVP +T+ GLP+G Sbjct: 402 GTKVVNALGLQNLLLKSGLTKKLALENLEKLPFTQLANLTGQPAMSVPLYWTESGLPLGS 461 Query: 442 QIMGKPFDEPAVLRAAYTFEQNTDYHTKRP 471 Q + DE +L+ A+ EQ + K P Sbjct: 462 QFIAPLGDEKTLLQLAHQLEQAQPWFDKTP 491 Lambda K H 0.315 0.133 0.391 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: 575 Number of extensions: 44 Number of successful extensions: 5 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: 475 Length of database: 498 Length adjustment: 34 Effective length of query: 441 Effective length of database: 464 Effective search space: 204624 Effective search space used: 204624 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: 42 (22.0 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