Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_069663619.1 BCR25_RS10830 amidase
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_001730305.1:WP_069663619.1 Length = 486 Score = 154 bits (389), Expect = 7e-42 Identities = 137/489 (28%), Positives = 229/489 (46%), Gaps = 61/489 (12%) Query: 18 KEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIG 77 K++ +++ +D+ +++ + ++ AF+ D E A+ K D +++G FG+PI Sbjct: 14 KKLSVTEWIDDREQQLNKRNPELNAFVDWDAEAAKKQYKAND------TQNGPFFGLPIP 67 Query: 78 VKD-NIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENS 136 +K KG++ + S++ + VQ L+ + +GK N EF + ++ Sbjct: 68 LKMLGQDKKGMKASSGSRLFKEQRATSTDHFVQGLERLGFIPLGKTNAPEFGFKNISDPL 127 Query: 137 AYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYG 196 Y KNPWNLD PGGSSGG+AAAVA+G P + SD GGSIR PASF G++GLKPT G Sbjct: 128 IYGPAKNPWNLDYSPGGSSGGAAAAVASGLFPIAGASDGGGSIRIPASFSGLIGLKPTRG 187 Query: 197 R--VSRYGLVAF-ASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLT 253 V G + +S+D +T ++ D L + G +K + V ++ Sbjct: 188 SMPVGPNGWRGWQGASID--FALTVSMRDTETLFYHLRGTEK--AAPYQVPKAEWSHQAA 243 Query: 254 GDIKGLKIA-VPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP-HSKYALATYYL 311 + K LKIA + + +G V EA ++V A+ LE G EVS P + + + +YYL Sbjct: 244 TEKKSLKIAFLTESPVGTPVSSEAVKAVHNAVDFLEKQGHQVTEVSYPVNGRQLIDSYYL 303 Query: 312 LSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYY 371 ++ +E + A F+GI+ + + ++L + G + Sbjct: 304 MNGAETA---AMFEGIQESLQRPLSKADMEL----------------MTWGIYQYGIQLS 344 Query: 372 DAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKI-----GENTKDPLT------ 420 + Y ++ ++ E +FE+YD+ + PT A KI E + L Sbjct: 345 ASQYTRSLQLWDQAAYKMEQLFEEYDLFLTPTAADTAPKIDAELQSEQIRKELAQAETLS 404 Query: 421 ----------MYANDILTIP----VNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTV 465 M+ + P NL G P IS+P +A+ GLPLG+Q + E + Sbjct: 405 QKQLQELIYDMFEKSLTITPFTQLANLTGQPAISLPTHVAESGLPLGVQFMASKGREDLL 464 Query: 466 YRVAHAFEQ 474 ++V FE+ Sbjct: 465 FQVGELFEK 473 Lambda K H 0.315 0.134 0.381 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: 470 Number of extensions: 16 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: 2 Length of query: 485 Length of database: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 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 Jul 26 2024. The underlying query database was built on Jul 25 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