Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_043536994.1 SACCYDRAFT_RS02120 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000244975.1:WP_043536994.1 Length = 493 Score = 152 bits (384), Expect = 3e-41 Identities = 152/524 (29%), Positives = 212/524 (40%), Gaps = 86/524 (16%) Query: 4 AARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDT 63 A L L E+S E+ E+A+ R V + A + D AR++A Sbjct: 11 AVGLAELVARREVSPAELLEAAIRRAEHVNGHLNAIVYPMYDI---------ARQRAATE 61 Query: 64 ELGPLAGVPIAVKDNICT-SGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMD 122 GP AGVP +KD + +G+ T SR ++ +V+ + VV R AG ++ G+ Sbjct: 62 LSGPFAGVPFLLKDLMQDYAGVPTGSGSRAMRRHVATRHSEVVRRWLDAGLVVFGRTATP 121 Query: 123 EFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAF 182 EF ES A G TRNPW+L PGGSS GSAAAVAAG P+A +D GGSIR PAA Sbjct: 122 EFGTKGITESDATGPTRNPWNLAHTPGGSSGGSAAAVAAGVVPVAGASDGGGSIRIPAAC 181 Query: 183 TGIVGLKPTYGYV-SRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAG------------ 229 G+ GLKP G V + S G + R V D A + +V+A Sbjct: 182 CGVFGLKPGRGLVPAGPDHAEHLSGAATDGVVSRTVRDTAAMLDVLARNPDPGGPYLAAV 241 Query: 230 PDRRDATNAGRTPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGA 289 PD A RTPP L+ G + LG + A VE A L++LG Sbjct: 242 PDTPYVELARRTPPRLRIG----------FTTRSPLGTPVHADAVAAVEHAATLLDKLGH 291 Query: 290 TVEECSLPSTEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFG 349 VE AL+ ++ + A A + + T Sbjct: 292 DVEPAEPDIDGVALARDFMTM-----------------WSAQTAVTIATIKRNTGARDRE 334 Query: 350 TEVKRRIMLGT--YVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWK 407 EV R++ + V +A H A R R L ERYD L+TP + Sbjct: 335 FEVDNRLLAASAHTVRAADHAAARARWNGYTRALA-----EFHERYDLLLTPAIARPPVR 389 Query: 408 IGEKVDDPV------------------------SMYLGDICTIP----VNLAGLPAVSVP 439 IGE P+ L ++ +P N+ G PA+SVP Sbjct: 390 IGELTTPPLLRLGGELLLRLRLTGPLTRTRVWNEQILANLAPVPFTQLANITGRPAMSVP 449 Query: 440 C-GFVDGLPVGMQLIGKPFADTQILQIAWAYQKVTKHHEARPAL 482 GLP+G+Q +G ++ +L +A + E P L Sbjct: 450 LYRTAGGLPLGVQFVGGLGGESTLLALATQLEAEHPWAEEEPEL 493 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: 648 Number of extensions: 46 Number of successful extensions: 6 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: 493 Length adjustment: 34 Effective length of query: 454 Effective length of database: 459 Effective search space: 208386 Effective search space used: 208386 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