Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_052664645.1 NITAL_RS03165 amidase
Query= curated2:Q7UT33 (499 letters) >NCBI__GCF_000969705.1:WP_052664645.1 Length = 446 Score = 182 bits (463), Expect = 2e-50 Identities = 155/458 (33%), Positives = 214/458 (46%), Gaps = 69/458 (15%) Query: 14 SGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAGKTLGPLAGLPV 73 +G T+ EV+A L I + ++A+ HV E A+ A DA G PL G+PV Sbjct: 21 AGTTTSEEVVASCLELIAEREDELHAWVHVDAELALAEARRRDAQEPRG----PLHGVPV 76 Query: 74 AIKDVLCTSDMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMDEFAMGASTETS 133 +KD++ T+D PT S + +G P DAT VARL+ AGA+++GKT EFA+ Sbjct: 77 GVKDLIDTADQPTAYGSPIYDGHRPATDATAVARLREAGAVILGKTVTTEFAVFTP---- 132 Query: 134 AMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAAFCGITGLKPTYG 193 G T +P D T+TPGGSS G+AAAVAAG VPL+LGT T GS+ +PA+FCG+ G K T G Sbjct: 133 --GPTAHPADPTRTPGGSSSGSAAAVAAGGVPLALGTQTAGSVVRPASFCGVFGGKATIG 190 Query: 194 RVSRYGLVAFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTSVNAEVPDFTPAMAAED 253 + G+ A +++LD G G + DVA+ L MAG ++ F P Sbjct: 191 AIPTDGVKACSTTLDHVGAFGRDIRDVAVALGVMAG-----------DLDRFAPIDLG-- 237 Query: 254 VRGMRIGVLREGLDQDGISPAVRDAL-ATAESVFREQGAEIVEVELPHS-KYWVPTYYVI 311 R G R D + + R A+ A AE + R A+++EV LP V VI Sbjct: 238 -TRPRFGFCRTPW-WDALDASTRVAVEAGAEHLAR--FADVIEVTLPPDFAGLVDAQQVI 293 Query: 312 APCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYSLSRAGGFGSEVKRRIMVGTYA 371 E NL DAE D G L +++R Y Sbjct: 294 MAVELRRNL-------------DAE--RRDHGDL-----------LSDQLRR------YL 321 Query: 372 LSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVTPSPAFALNEKTDDPIAMYLCD 431 G Y+ AL + R F ++L P A + + T DP+ LC Sbjct: 322 DEAGASADRYDDALALADRCRAQLTDVFADARVVLAPSVLGEAPPI-DTTGDPL---LCR 377 Query: 432 LFTVGANLAGVPAISLPGGFDAVGLPVGVQLQAPVMEE 469 +T L G P S+PG GLP+G Q+ A E+ Sbjct: 378 AWT----LLGTPTTSVPGLTGPAGLPIGTQVIAAPGED 411 Lambda K H 0.316 0.132 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: 615 Number of extensions: 33 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: 499 Length of database: 446 Length adjustment: 33 Effective length of query: 466 Effective length of database: 413 Effective search space: 192458 Effective search space used: 192458 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 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