Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_234007488.1 SARO_RS19950 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000013325.1:WP_234007488.1 Length = 435 Score = 159 bits (403), Expect = 1e-43 Identities = 146/456 (32%), Positives = 201/456 (44%), Gaps = 59/456 (12%) Query: 13 AGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTELGPLAGVP 72 A AV + + R+ Q G AA V A + A + D G L Sbjct: 15 AASADAVPEDQGIMGRVEQESGMQGD----AAAGVTTEADRFGALVRPCDLGKGTLR--- 67 Query: 73 IAVKDNICTSGMETTCASRILKGYVSPF-DATVVERLRAAGAM-IIGKANMDEFAMGSSG 130 +A+KD I +G +T S +L +A VV + + IIGKA M EFA G SG Sbjct: 68 VAIKDCIDIAGWQTRQGSAVLADVPPAIANAEVVTCILSDPRWRIIGKARMHEFAYGVSG 127 Query: 131 ESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKP 190 + A G NP+ +R+PGGSSSGSA AVA+G A +A+GTDTGGS+R PAA G++G KP Sbjct: 128 LNPACGTPINPFWPDRIPGGSSSGSAVAVASGLADVAIGTDTGGSVRMPAACCGVIGFKP 187 Query: 191 TYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTPPALKFGGE 250 T+G VSR G SSLD +G R++ V + E IA G P L Sbjct: 188 TFGLVSRRGAHPAKSSLDCIGIFAREMGLVEAMMETIA---------PGFVPATL--SRS 236 Query: 251 PSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEYALSAYYVIA 310 P+L L+ PG G+ + AIA G +L E A +A I Sbjct: 237 PTLG---------LVTPGTSNGIAGYLAAAIA---GAGIANRSTALDGMEAAFAAGMTII 284 Query: 311 VAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLSAGHYDA 370 E + LA F G G +V+ R+M + + D Sbjct: 285 GRETWAALAPF---------------------VSHPGMGDDVRTRLMRASALT-----DE 318 Query: 371 YYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPVSMYLGDICTIPVNL 430 A+ VR + A E DALV PT P + E D + L + P NL Sbjct: 319 DLGAAEDVRAAFRDGVDAALEGVDALVLPTLPVVPPLLSEAEDAAALLPLTRLVR-PFNL 377 Query: 431 AGLPAVSVPCGFVDGLPVGMQLIGKPFADTQILQIA 466 +G PA+++P G+PV +QL+G+ D + +A Sbjct: 378 SGHPAIALPLRAAHGVPVSLQLVGRHGGDAALCAVA 413 Lambda K H 0.318 0.135 0.391 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: 564 Number of extensions: 32 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: 488 Length of database: 435 Length adjustment: 33 Effective length of query: 455 Effective length of database: 402 Effective search space: 182910 Effective search space used: 182910 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 09 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