Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011882484.1 amidase
Query= curated2:Q2IH94 (492 letters) >NCBI__GCF_000016205.1:WP_011882484.1 Length = 493 Score = 219 bits (558), Expect = 2e-61 Identities = 172/494 (34%), Positives = 239/494 (48%), Gaps = 41/494 (8%) Query: 2 STPAKELCRLGLREAGAGVAAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAAK 61 S P L RL E + + KA+S E + A L I+ +G + A +++ DRA A+ Sbjct: 12 SIPVDPLVRLSAGELASAIRRKAVSCVETMRAYLDHIERVNGAVNALISL-RDRATLLAE 70 Query: 62 AA--DARAARGERRSELDGVPVAVKDLFVTKGVPTTAGSRILEGYLPPYDATVVERLEAA 119 AA DA ARGE L G+P A KDL +TKG+ TT GS I ++P D+ V R+ AA Sbjct: 71 AAEKDAALARGEYHGWLHGMPQAPKDLAMTKGLRTTYGSPIFRDHVPQADSIGVGRMRAA 130 Query: 120 GAVIVGKLNMDEFAMGSSNENSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTD 179 GA+ +GK N EF +GS N + NP+DL+R+ GGSSGGSAA++AA + + G+D Sbjct: 131 GAIFIGKTNTPEFGLGSHTFNDVHGATRNPYDLTRSAGGSSGGSAAALAARMLPVADGSD 190 Query: 180 TGGSIREPAAFCGVVGVKPTYGRVSRYGVV-AFASSLDQVGPLAREVGDAALVLRTIAGH 238 GGS+R PAAFC V G++P+ GRV R+ V F L GP+ R VGD A +L AG+ Sbjct: 191 FGGSLRNPAAFCNVYGMRPSQGRVPRWPAVDVFMQQLGTEGPMGRTVGDVAQLLAIQAGY 250 Query: 239 DPRDMTSSTRPVDDYLGPLEEGARGLRVGVPREWLSGGL--DAGVEAAIRAALDTYRRLG 296 D D S + PL+ RG R+ +W G L + GV A L T R +G Sbjct: 251 DANDPLSLAEQPLVFATPLDTDLRGRRIAWVGDW-DGYLATEPGVLAQCEQGLATLREIG 309 Query: 297 ATLVDVSLPHSKYGIGAYYLIAPAEASSNLARYDGVRYGLRAEGAKGLKEMYAESREQGL 356 VD +LP A A + R L A G GL Y + + L Sbjct: 310 CD-VDAALP--------------AFAPERIWRLWLAHRHLLAGG--GLLAHYRDPARRAL 352 Query: 357 GAEPKRRIMLGTYALS-SGYYDAYYLRAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAF- 414 + G A+ + +DA R + ++R F D IA P F Sbjct: 353 LKPEAIYEVEGLLAMGGAAVFDASVERTAWHQAVLR-----FFDRYDFIAAPSAQVFPFD 407 Query: 415 -------ALGERTGDPLQMYLADIFTITCNLAALPGLSVPCGLEAASGLPVGLQLVGRPF 467 A+ R D ++ + T LA P +SVP G GLP+G+QL+GRP Sbjct: 408 VELRWPQAIAGRQMDTYHRWMETVVPWT--LAGCPVISVPVGFND-DGLPMGMQLIGRPR 464 Query: 468 DEATLFRAARALER 481 + + + AR E+ Sbjct: 465 ADLAVLQLARGYEQ 478 Lambda K H 0.317 0.135 0.393 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: 587 Number of extensions: 22 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: 492 Length of database: 493 Length adjustment: 34 Effective length of query: 458 Effective length of database: 459 Effective search space: 210222 Effective search space used: 210222 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 (21.6 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