Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013520042.1 ALIDE2_RS06025 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000204645.1:WP_013520042.1 Length = 487 Score = 210 bits (535), Expect = 8e-59 Identities = 165/494 (33%), Positives = 235/494 (47%), Gaps = 37/494 (7%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVA-ADHVIERAKKLDARRKA 60 +SA L+R A E+S VE+ ++ ++I ++ P V A + A D + + A+ LD R Sbjct: 16 MSAVALSRAIHAREVSCVEVLDACYAQIDRLNPVVNALVAFADRDAMRQLARALDERLAR 75 Query: 61 GDTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKAN 120 G++ LGPL G P A KD + +GM TT S + G VS D V ER+RA G + + ++N Sbjct: 76 GES-LGPLHGFPQAPKDIMPAAGMVTTKGSPLFAGQVSQADCVVFERMRAGGCLFVARSN 134 Query: 121 MDEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPA 180 EF +G + +G TRN WD R GGSS G+A AVA P+A G+D GS+R PA Sbjct: 135 SPEFGLGGHTYNPVYGTTRNAWDTTRSAGGSSGGAAVAVALSMLPVADGSDMMGSLRTPA 194 Query: 181 AFTGIVGLKPTYGYVSR-YGVVAFASSLDQVGPMGRDVEDVARLFEVIAG-PDRRDATNA 238 AF + GL+ + G V G F GPM RD+ D+A L V AG DR T Sbjct: 195 AFNNVYGLRTSVGCVPHGPGEEVFFQQFSVAGPMARDIPDLALLLSVQAGFDDRLPLTRR 254 Query: 239 GRTPPALKFGGEPSLSGVRLGVPKELLGP-GIDPGVKARVEEAIAQLEELGATVEECSLP 297 G P G R+G +L G +PGV A+ ++G TV++ Sbjct: 255 GEGPRDWGAALARDFRGARIGWLGDLKGHLPTEPGVLDTCRAALRHFTDIGCTVDD---- 310 Query: 298 STEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIM 357 AL A+ ++ A +L F A G L+E + + E I Sbjct: 311 ----ALPAFDFESLWRAWLDLRSFS------VAGANGALYE--NPEKRALLKPEALWEIE 358 Query: 358 LGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTT---PFTA---W--KIG 409 G + + YD A +VR+ R F YD LV P PF A W +G Sbjct: 359 RGRALCAMRVYD-----AARVRSAWYEALRRLFATYDFLVLPAAQVFPFDAALDWPHAVG 413 Query: 410 EKVDDPVSMYLGDICTIPVNLAGLPAVSVPCGF-VDGLPVGMQLIGKPFADTQILQIAWA 468 + D ++ + +P +AGLPA++ P GF GLP G+Q+IG AD +LQI A Sbjct: 414 GREMDTYHRWMQAV--VPATMAGLPALAAPAGFGPQGLPAGLQIIGPAQADLAVLQIGHA 471 Query: 469 YQKVTKHHEARPAL 482 Y + + + R L Sbjct: 472 YDQASGYARRRSPL 485 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: 593 Number of extensions: 36 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: 488 Length of database: 487 Length adjustment: 34 Effective length of query: 454 Effective length of database: 453 Effective search space: 205662 Effective search space used: 205662 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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