Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011321194.1 AVA_RS22975 amidase
Query= curated2:B8FCK9 (485 letters) >NCBI__GCF_000204075.1:WP_011321194.1 Length = 467 Score = 204 bits (520), Expect = 4e-57 Identities = 144/475 (30%), Positives = 220/475 (46%), Gaps = 43/475 (9%) Query: 18 KEISSQDLTKAVLDRIEAVEPQVDAYLTVSKEEAM-EAAQKADKALAQGETAPLCGIPLA 76 +E+S +L + L RIE + P++ +Y TV+ E A +A K + E P G+P++ Sbjct: 21 REVSPLELVEIYLQRIELLNPELGSYFTVTAELASADAKAKTELLTTTSELPPFFGVPIS 80 Query: 77 IKDVMCTKGVLTTCASKILGNFVPPYDATSITKLKEAGAVLVGKTNMDEFAMGSSTENSA 136 IKD+ GV T + L N +P +D +T++K+AG ++GKT E TE + Sbjct: 81 IKDLNAVAGVPCTYGNPALLNNIPEFDDGVVTRIKQAGFTILGKTATSELGSFPYTEPTG 140 Query: 137 FKTTKNPWDLTRTPGGSSGGSAAAVAADMCLGAFGSDTGGSIRQPGSHCSVVGLKPTYGR 196 F +NPW+L TPGGSSGG+AAAVAA +C A GSD GGSIR P + C VVG+KP GR Sbjct: 141 FVPARNPWNLEYTPGGSSGGAAAAVAAGLCAIAQGSDGGGSIRGPAACCGVVGIKPARGR 200 Query: 197 VSRYGLVAFASSLDQIGPFAKTVEDAAILLQAVAGYDPSDSTSVNVEVPDYTTAIQEDVK 256 VS+ + + + GP A+TV DAA LL A++GY D + P + TA Q Sbjct: 201 VSKAPVGDRLAGISTNGPIARTVADAAALLDAMSGYVTGDPYWLPDPEPSFLTAAQTPPT 260 Query: 257 GMRVGMPKEYFEMGGLTPDVKNSVDQAIKTLESQGVEVMDVSLPHSKYCVAVYYVIAPAE 316 +R+ + +G + + V +K LE G + SL S ++ P + Sbjct: 261 QLRIAFATDIPPLGEADANCQQGVLTTVKLLEQLGHHIEQKSLDLSG-------LVEPFQ 313 Query: 317 ASSNLARYDGVKYGMREERDSLIDMYHATRSSGFGPEVQR---RIIIGTYALSAGYYDAY 373 I SG PE+ + R ++ A Y A Sbjct: 314 ----------------------IVWQSGVAGSGLPPEILQPVNRWLLARTGTVADYIQAV 351 Query: 374 YGKASQVRTLIMEDYKKAFEKCDAIISPVAPTPAFKLGE----NTDDPLTMYLSDIFTLS 429 Y R ++ F+ D ++ PV ++GE + +D ++ + Sbjct: 352 YKMQIVARQIV-----AFFDNIDVLVLPVYLHSPIRVGEWAALSPEDTFQQIINWVAPCP 406 Query: 430 -ANLAGVCGVSVPCGFSSEGLPIGLQLQGSHFQEEKILRLGHHFQKATDFHTKRP 483 AN G +++P GF GLPI +QL G E ++ L + A ++ RP Sbjct: 407 LANATGQPAIALPAGFDRNGLPISVQLIGRPAAEATLISLAAQIEAANPWNKDRP 461 Lambda K H 0.315 0.132 0.378 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: 503 Number of extensions: 22 Number of successful extensions: 4 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: 467 Length adjustment: 33 Effective length of query: 452 Effective length of database: 434 Effective search space: 196168 Effective search space used: 196168 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: 51 (24.3 bits)
This GapMind analysis is from Jul 25 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