Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AZOBR_RS22750 AZOBR_RS22750 glutamyl-tRNA(Gln) amidotransferase
Query= curated2:Q2IH94 (492 letters) >FitnessBrowser__azobra:AZOBR_RS22750 Length = 470 Score = 268 bits (685), Expect = 3e-76 Identities = 199/495 (40%), Positives = 252/495 (50%), Gaps = 46/495 (9%) Query: 1 MSTPAKELCRLGLREAGAGVAAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAA 60 MSTP +L RL E GV + + +LV ASL RI A DG L +F+ V D A AAA Sbjct: 1 MSTP--DLFRLSAAEMAEGVRNRRFRARDLVAASLERIAALDGGLKSFITVAPDAALAAA 58 Query: 61 KAADARAARGERRSELDGVPVAVKDLFVTKGVPTTAGSRILEGYLPPYDATVVERLEAAG 120 +AAD R G L GVPV VKDL +T G+ TT GS + +P D V RL+AAG Sbjct: 59 EAADRRVEAGAPLGPLHGVPVGVKDLTLTAGLRTTYGSTLYADLIPDTDDLSVARLKAAG 118 Query: 121 AVIVGKLNMDEFAMGSSNENSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDT 180 A+IVGK N EF G+ N P NP+DL +T GGSSGGSAA+VAAG V + GTD Sbjct: 119 AIIVGKTNTPEFGFGAITGNELCGPTANPYDLDKTSGGSSGGSAAAVAAGLVPLAQGTDF 178 Query: 181 GGSIREPAAFCGVVGVKPTYGRVSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDP 240 GGS+R PA+FCGVVG++PT GR+ G L G LAR++ DAAL L ++G DP Sbjct: 179 GGSVRTPASFCGVVGLRPTPGRIPSPGRALAWDGLATQGFLARDIADAALALAAVSGPDP 238 Query: 241 RDMTSSTRPVDDYLGPLEEGARGLRVGVPREWLSGGLDAGVEAAIRAALDTYRRLGATLV 300 RD TS P EW LDA ++R A T LG+ L+ Sbjct: 239 RDPTSLPVP---------------------EWTVPDLDALDPLSLRVAWST--DLGSALI 275 Query: 301 DVSLPHSKYGI--GAYYLIAPAEASSNLARYDGVRYG-LRAEGAKGLKEMYAESREQ-GL 356 D+ L + G ++ R G +G LR A + Y + EQ G Sbjct: 276 DLGLAERFEAVMRGLEGRFGDFVEATPDCREAGAAFGTLR---AAHIFHTYGRTLEQDGD 332 Query: 357 GAEPKRRIMLGTYALSSGYYDAYYLRAQKVRTLIRRDFDEAFRGCDVI-----AGPVTPS 411 P + A G A YLRA+ R+ + R F FR D++ + P P+ Sbjct: 333 RLSPS---VAWNIARGKGLSAADYLRAEAQRSALYRRFAAFFRDHDILMTLSASVPPFPN 389 Query: 412 VAFALGERTGDPLQM---YLADIFTITCNLAALPGLSVPCGLEAASGLPVGLQLVGRPFD 468 + E G L YLA T T +L P LS+PCG A GLP+GLQL+ RP++ Sbjct: 390 AQGDVTEINGFRLSTIIDYLA--ITYTVSLIGFPCLSIPCGW-TADGLPIGLQLIARPYE 446 Query: 469 EATLFRAARALEREL 483 E L R AR LEREL Sbjct: 447 EDRLLRCARFLEREL 461 Lambda K H 0.317 0.135 0.393 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: 657 Number of extensions: 41 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 492 Length of database: 470 Length adjustment: 34 Effective length of query: 458 Effective length of database: 436 Effective search space: 199688 Effective search space used: 199688 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 (21.6 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