Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO356_18110 AO356_18110 amidase
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18110 Length = 471 Score = 181 bits (459), Expect = 5e-50 Identities = 158/486 (32%), Positives = 224/486 (46%), Gaps = 56/486 (11%) Query: 7 LTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFL-VVDAAGARAQARAADARRAA 65 LT+ + +L RG ++S+ L + L RIA ++ A + + R QAR AD Sbjct: 7 LTLREMAGLLRRGVLTSVTLLEFYLQRIAERNRQINALIQLAPVEDLRRQAREADEMARI 66 Query: 66 GDAS-PLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNC 124 G S PL GIP+ +KDV+ +G + + L DATAVARL+ AGA+ILG N Sbjct: 67 GQISGPLHGIPITVKDVLHVRGFKMSRGVGELMGDVSQEDATAVARLRQAGAIILGISNV 126 Query: 125 DEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAA 184 E M TEN + +T NP +L R GGSSGG AAA+AAG +PA L +D GS+R PA Sbjct: 127 PELCMAFETENLIYGRTLNPHDLLRSAGGSSGGEAAAIAAGCSPAGLASDACGSVRIPAH 186 Query: 185 LCGITGLKPTYGRV--------SRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPF 236 GI GLK T GRV R GL S+ G M R V D A++ +I+GAD Sbjct: 187 FNGICGLKLTQGRVPLTGQFPNDRSGLFHLTSA---FGVMGRYVDDLALLGPLISGADGH 243 Query: 237 DATCTDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIE----VLREQGA 292 D D P A + + LRI + F A + V AAV ++ L Sbjct: 244 DPDTVDVP-----FAASEPLADLRIAL----FSASSRTPVSAAVSQVLQQVERCLSPVVT 294 Query: 293 EVCEISLPHTPYALPVYY--LIAPAEASANLAR-FDGVRYGLRVPGESYFDELERTRGAG 349 +V E++ P A V + I A+A R F+ + P + ++ Sbjct: 295 QVSEVAPPMLDEACDVLWRVFITGADAGRGWRRLFESMNKRSFTPAIAQLLDMSEAVELS 354 Query: 350 FGPEVRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFK 409 R IM+ T+ R + F+Q D+ P P VAF+ Sbjct: 355 VDEVKRDWIMIDTF---------------------RYQLAKFFKQHDLFICPVFPDVAFR 393 Query: 410 IGAHTDDPLAMYLEDVCTLPLNLAGLPGLVVPCGF--AEGLPIGLQLIGRAFDEESLLRV 467 GA +D + P +L+G P +V+ G + G+PIG+Q++G + EE LL V Sbjct: 394 HGASLED----RDQYAFVFPFSLSGSPAVVIRAGVDPSTGMPIGIQIVGPHWQEERLLAV 449 Query: 468 GDAYQR 473 +R Sbjct: 450 AAFLER 455 Lambda K H 0.320 0.136 0.398 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: 527 Number of extensions: 31 Number of successful extensions: 4 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: 490 Length of database: 471 Length adjustment: 34 Effective length of query: 456 Effective length of database: 437 Effective search space: 199272 Effective search space used: 199272 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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