Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BPHYT_RS00200 BPHYT_RS00200 amidase
Query= curated2:A0L5G0 (485 letters) >FitnessBrowser__BFirm:BPHYT_RS00200 Length = 467 Score = 212 bits (539), Expect = 3e-59 Identities = 149/491 (30%), Positives = 233/491 (47%), Gaps = 50/491 (10%) Query: 7 TLREAADKLATKEISSVELTQACLDQIAKHNPTINAFVTVDAEKALAAAQ-----AADAR 61 T+ +AA + E++ VEL Q CLD I HNPT++AF V AE+AL A+ A + R Sbjct: 3 TVADAAASIRCGELTPVELVQRCLDSIKTHNPTLHAFGDVYAEEALRYAETLTREAKENR 62 Query: 62 IAAGNGAPLTGIPIAHKDIFNTTDMRTTCSSRMLENFIPPFDATITTHLRQAGAVILGKT 121 G L G+P A KD+F T +RTT S N++P DA + L++AGA++LGK Sbjct: 63 TRGG----LHGVPFAIKDLFATAGLRTTRGSLTAMNWVPQEDAPVIRRLKEAGAILLGKA 118 Query: 122 NLDEFAMGSSTETSYFGASRNPWDTQRTPGGSSGGSSAAIAANMAICATGTDTGGSIRQP 181 EF ++ + FG NPWD + T GGSS GS+ ++AA M + G+D GGS+R P Sbjct: 119 ATTEFGWSGASYSRVFGNGCNPWDARLTSGGSSSGSAISVAARMVPASLGSDGGGSVRIP 178 Query: 182 ASLTNLTGLKPTYGRCSRYGIIAFASSLDQAGPMTRTAEDAAMLLNVMVSYDPKDSTSIQ 241 ++ + +K ++GR + A L AGP+TRT D+A+L +V+ D +D ++ Sbjct: 179 SAFCGVFAMKGSHGRIPTWPWSA-TEMLSHAGPITRTVRDSALLFDVLAGPDSRDHQALP 237 Query: 242 SPAPDFTQALTGDVKGLKIGIAAEYFGDGLNDEVRAAIETAQQQYQAMGAELVPISL--P 299 + + +K +++ FG ++ E+ + A ++ A +PI L P Sbjct: 238 AATGSYLARCEEPLKRVRVAFCPTLFGVDVDPEISRVVGAAVERI----ARALPIDLEMP 293 Query: 300 NSGY--AIPTYYIISPAECSSNLARYDGVKFGYRCEEPKDIRDLYFRSRSEGFGDEVKRR 357 G+ +PT+ + A G+ +G + D D GF + R Sbjct: 294 VLGWHDPLPTFETLWVAG--------RGIVYGQTLKNCADQLD-------PGFARLIGR- 337 Query: 358 IMLGTYVLSSGYYDAYYRKAQQARRLIADEFKAAFEKVDLILTPTSPTTAF--------K 409 +S Y Y A Q R A + A F+ D +LTPT P F + Sbjct: 338 --------ASDYSLEDYLTAIQRRATFACQVHALFDTYDFLLTPTLPILPFDADLIAPPE 389 Query: 410 FGEKDDPVQMYLSDIYTINVNLAGLPGISVPCGFDSKGLPIGMQLIGRPLDEETLLRSAD 469 D + +T NL+G P S+PCG+ GLP+G+Q++G + +L+ Sbjct: 390 LDTHDSALPWACWTPFTYPFNLSGNPAASLPCGWSDTGLPVGLQVVGPRFADADVLQFCS 449 Query: 470 AYQRQTDWHKR 480 A + W R Sbjct: 450 AIEAIMPWAHR 460 Lambda K H 0.317 0.132 0.383 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: 497 Number of extensions: 34 Number of successful extensions: 5 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: 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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