Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011320381.1 AVA_RS18630 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000204075.1:WP_011320381.1 Length = 464 Score = 280 bits (715), Expect = 1e-79 Identities = 186/459 (40%), Positives = 248/459 (54%), Gaps = 34/459 (7%) Query: 16 LARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAGDASPLL-GI 74 + G+++++E+T A L RIAA + ++ F V A A A D AAG+ S LL G+ Sbjct: 11 IGEGKVTAVEVTQAALARIAAQDVELNCFTAVTRETALADAARIDREIAAGNDSGLLAGV 70 Query: 75 PMGIKDVISTQGLRTTCASKM-LENYTPVYDATAVARLKAAGAVILGKLNCDEFAMGSST 133 P +K++ GL T +K+ EN DATAVA+LK AGAV++G LN DE+A G T Sbjct: 71 PFAVKNLFDLVGLTTLAGAKINAENPPASRDATAVAKLKQAGAVLVGALNMDEYAYGFVT 130 Query: 134 ENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAALCGITGLKP 193 ENS + TRNP +L+RV GGSSGGSA AVAAG P LG+DT GSIR PAALCG+ G KP Sbjct: 131 ENSHYGVTRNPHDLQRVAGGSSGGSAVAVAAGLVPFTLGSDTNGSIRVPAALCGVFGFKP 190 Query: 194 TYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYPAPDYEAALT 253 TYGR+SR G+ F+SS D IGP AR+V D A + ++ G D D CT PA L Sbjct: 191 TYGRLSRGGVTLFSSSFDHIGPFARSVGDIATIFDILQGGDDRDPICTQRPANPTLPQLH 250 Query: 254 GDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPYALPVYYLIA 313 DI +RI + +YF G AAV+ + L ++LP A ++I Sbjct: 251 QDISHIRIAIADDYFQKGATSAALAAVQQVADALNVTN----YVTLPEAHRARAAAFVIT 306 Query: 314 PAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGTYALSAGYYDAY 373 +E ANL + D+L RTR F P R R + G S + Sbjct: 307 ASE-GANL----------------HLDKL-RTRSQDFDPATRDRFLAGALIPS-----NW 343 Query: 374 YKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHT-----DDPLAMYLEDVCTL 428 Y +AQ+ R R ++ F+ VDVI APTTP A IG T ++ L + T Sbjct: 344 YIQAQRFRQWYRDRIREVFQNVDVILAPTTPITAPLIGQQTMILDGEEILVRPHLGLFTQ 403 Query: 429 PLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRV 467 PL+ GLP L VP LP+G+QLI ++E +L+V Sbjct: 404 PLSFIGLPVLSVPIQRPNTLPLGVQLIAAPYNEAFILQV 442 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: 502 Number of extensions: 28 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: 490 Length of database: 464 Length adjustment: 33 Effective length of query: 457 Effective length of database: 431 Effective search space: 196967 Effective search space used: 196967 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 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