Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_068166836.1 HTA01S_RS01780 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_001592305.1:WP_068166836.1 Length = 504 Score = 226 bits (576), Expect = 1e-63 Identities = 168/487 (34%), Positives = 236/487 (48%), Gaps = 53/487 (10%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L L+ + R + EIS +EL +A + RI AV P V A D ARA AR A+A+ Sbjct: 3 LVHLSAVELRRRIGNKEISPVELLEACIARIEAVNPAVNAICATDHERARAAARTAEAQV 62 Query: 64 AAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKL 122 G+A L G+P+G+KD+ T GL TT + P D VARL+AAGA++ K Sbjct: 63 LRGEALGALHGLPLGVKDLQDTAGLLTTSGNVGRRGNVPQQDNALVARLRAAGAIVTAKT 122 Query: 123 NCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQP 182 N + G++T N + T NP+N GGSSGGSAAA+A P G+DTGGS+R P Sbjct: 123 NVPDMGAGANTRNPVWGATGNPFNPLLNAGGSSGGSAAALATDMLPLCTGSDTGGSLRIP 182 Query: 183 AALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFD----- 237 AALCG+ GL+P+ G V+ S + +GPM RTV D A++L G P D Sbjct: 183 AALCGVVGLRPSPGVVANDARPLGWSVISVLGPMGRTVADTALMLSASVGRHPMDPLSVS 242 Query: 238 ATCTDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVL--REQGAEVC 295 C +P + D+ LRIG ++ + P + R + L + E Sbjct: 243 GVCQGWPVREL------DLASLRIGTVEDFGACAVDPSIRRTFRQRVAALARHTRSCEPL 296 Query: 296 EISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESY---FDELERTRGAGFGP 352 ++SLP DG R + ES+ F + R GP Sbjct: 297 DLSLP------------------------DGHRCFDILRAESFVAAFADTYRQDPQSLGP 332 Query: 353 EVRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAF---K 409 VR + + +A++ G D + +Q R I R +++AFEQVD+I AP TP F + Sbjct: 333 NVRANVEM-AHAITLG--DRAWAHLEQTR--IARRFERAFEQVDLIVAPVTPISPFPWSE 387 Query: 410 IGAHTDDPLAM--YLEDV-CTLPLNLAGLPGLVVPCGFAE-GLPIGLQLIGRAFDEESLL 465 + A D AM Y E + T + LA P L +PCG E G+P GLQLI ++ LL Sbjct: 388 LYAECIDGQAMRNYYEWLGLTYMVTLATNPALSLPCGVDEQGMPFGLQLIAPLRADDRLL 447 Query: 466 RVGDAYQ 472 + A + Sbjct: 448 AMASAIE 454 Lambda K H 0.320 0.136 0.398 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: 577 Number of extensions: 27 Number of successful extensions: 4 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: 490 Length of database: 504 Length adjustment: 34 Effective length of query: 456 Effective length of database: 470 Effective search space: 214320 Effective search space used: 214320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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