Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_086508811.1 BZY95_RS04655 amidase
Query= curated2:A0L5G0 (485 letters) >NCBI__GCF_002151265.1:WP_086508811.1 Length = 468 Score = 208 bits (530), Expect = 3e-58 Identities = 145/457 (31%), Positives = 229/457 (50%), Gaps = 33/457 (7%) Query: 21 SSVELTQACLDQIAKHNPTINAFVTVDAEKALAAAQAADARIAAGNG-APLTGIPIAHKD 79 S +E T+A L++I + N +NA+V VD E A AA+A++ R G + + GIP++ KD Sbjct: 24 SPLEATRAALERIERFNEAVNAYVLVDREGAETAAEASNKRWQQGRPLSAIDGIPVSLKD 83 Query: 80 IFNTTDMRTTCSSRMLENFIPPFDATITTHLRQAGAVILGKTNLDEFAMGSSTETSYFGA 139 + + + S + + D+ LR+AGAVILGKTN EF + T+ FGA Sbjct: 84 LTESVGLPARKGSLTVSDAPCERDSPPARMLREAGAVILGKTNTPEFGWKAITDNRVFGA 143 Query: 140 SRNPWDTQRTPGGSSGGSSAAIAANMAICATGTDTGGSIRQPASLTNLTGLKPTYGRCSR 199 + NPWDT+ TPGGSSGG++ A A NM + G D+GGSIR PAS T + G KPT+G Sbjct: 144 TANPWDTRLTPGGSSGGAAVAAALNMGVLHQGGDSGGSIRIPASFTGVFGFKPTFGWVPE 203 Query: 200 YGIIAFASSLDQAGPMTRTAEDAAMLLNVMVSYDPKDSTSIQSPAPDFTQALTGDVKGLK 259 + + ++L GP+TRT EDA +LNVM YD +D +++ D+ + L ++G++ Sbjct: 204 WP-RSKEATLSHLGPLTRTVEDAVRMLNVMGRYDYRDPYALRGQPADWGEELGQGIEGMR 262 Query: 260 IGIAAEYFGDGLNDEVRAAIETAQQQYQAMGAELVPISLPNSGYAIPTYYIISPAECSSN 319 I + + EV + A + +A+GA + + + G+ P I + +++ Sbjct: 263 IAFSPTLGYARVEPEVAECVRQAAHRLEALGAVVEEV---DPGFESP-IRIFNTLWFTAS 318 Query: 320 LARYDGVKFGYRCEEPKDIRDLYFRSRSEGFGDEVKRRIMLGTYVLSSGYYDAYYRKAQQ 379 LA Y ++ + R G + KR L D +Y + Sbjct: 319 LAVY------------REHSERQRRLLDSGLVADAKRAERLSA-------LDMFYALRDR 359 Query: 380 ARRLIADEFKAAFEKVDLILTPTSPTTAFKFGEKDDPVQMYLSD-----IYTINVNLAGL 434 AR + + + ++ L++TP+ F D P + D ++ NL+ Sbjct: 360 AR--LTESLEHFNQRYHLVMTPSVAVRPFPL-HHDVPPGSGMRDWEEWAPFSYPFNLSQQ 416 Query: 435 PGISVPCGFDSKGLPIGMQLIGRPLDEETLLRSADAY 471 P S+PCGF GLP+G QL G D+ +LR + AY Sbjct: 417 PAASIPCGFTPDGLPVGFQLAGGKHDDARVLRVSQAY 453 Lambda K H 0.317 0.132 0.383 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: 501 Number of extensions: 21 Number of successful extensions: 3 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: 468 Length adjustment: 33 Effective length of query: 452 Effective length of database: 435 Effective search space: 196620 Effective search space used: 196620 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