Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BPHYT_RS10730 BPHYT_RS10730 Glu-tRNA amidotransferase
Query= curated2:C0R074 (482 letters) >FitnessBrowser__BFirm:BPHYT_RS10730 Length = 374 Score = 155 bits (392), Expect = 2e-42 Identities = 128/411 (31%), Positives = 192/411 (46%), Gaps = 58/411 (14%) Query: 75 GVPLAIKDNLCYKDHLMTASSKML-EGYKAPYTAPTVQRLIDNGAIIIGRTNMDEFAMGG 133 G +AIKD + + TA+S+ L + A A V+RLI +G I+G+ NM E A G Sbjct: 14 GPSIAIKDTIDIAGYATTAASRALADTPPAQQHAEVVERLIASGWHIVGKANMHELAFGM 73 Query: 134 TTETSNYGVTRNPKNRAHVPGGSSGGSAAAVAANFAFGALGSDTGGSIRQPASFCGIVGV 193 T G +NP++ A +PGGSS GSAAAV A ALG+DTGGSIR PA+ CG++G+ Sbjct: 74 TGINDYTGTPQNPQDAARIPGGSSSGSAAAVGLKLADAALGTDTGGSIRGPAACCGVIGL 133 Query: 194 KPTYGRVPRLGCIAMASSLDQVGPLTKDVKD-AALMTKIIAGFDPKESTTLNIPVPDYVA 252 KPT+GRV RLG S+LD VGP +D++ A M I FD + Sbjct: 134 KPTFGRVSRLGVAPRESTLDCVGPFARDMRMLVAAMQAIAVNFDANTA-----------H 182 Query: 253 ALDGNIKGMKIGLAKEYYDTDLIAADVKENVMDAIGKLKDQGAEIVDISLPNAKYGSR-- 310 A G K+G ++ A+ +++A+ + D+ A V +LP A + Sbjct: 183 AWQG---ACKVG---------IVQAEAAAEIVEAVTRAADK-ASCVAHTLPLAGLAAAFD 229 Query: 311 VYTAVMDVEVASNMGRYDGIRYGYHPKGDFNLDEYYYTSRSVGLAFETRARILFGTLMTG 370 V++VE + G + S +G + R R T Sbjct: 230 AGLTVINVETSRAFG-------------------HLVASGKLGADLDARLRAAANTTA-- 268 Query: 371 KRFFYSHYQHALKVRKLMQMDFDNAFKNVDVIVSPTSPVTAGLLGTRDQTDSALSFLA-D 429 + A +VR+ D+A NVDV++ PT P L T +Q S S +A Sbjct: 269 -----AQLDAAEQVRRDFTAAVDHALDNVDVLILPTLP---ALPITLEQARSGTSVIAMS 320 Query: 430 SYVSNINLVGLPAMSVPCGVDKNNMPIGIQFITKQFNEVDMFRMAYAHELA 480 S + NL G PA+S+P + + + G+Q + ++ + + +A E A Sbjct: 321 SLIRPFNLSGHPALSLPLPISGSPLKAGLQIVGRKGQDEQVCAIAARFEAA 371 Lambda K H 0.317 0.135 0.385 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: 400 Number of extensions: 15 Number of successful extensions: 3 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: 482 Length of database: 374 Length adjustment: 32 Effective length of query: 450 Effective length of database: 342 Effective search space: 153900 Effective search space used: 153900 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