Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_028998310.1 H537_RS0113260 indole acetimide hydrolase
Query= curated2:B2A5W7 (491 letters) >NCBI__GCF_000430725.1:WP_028998310.1 Length = 481 Score = 211 bits (538), Expect = 3e-59 Identities = 155/504 (30%), Positives = 247/504 (49%), Gaps = 68/504 (13%) Query: 2 KLHELTLMEVKRGLEQGDFSSEELVTSVYDRIEETEDHIKAYITLTKEQALAQSKEIDSQ 61 ++ LT + + G ++E V ++ R + + + A+ITL + A+A +K ID++ Sbjct: 5 QMFSLTASQAVDSIASGQMTAEAYVRALLSRAQSLSN-LGAFITLNADGAIAAAKAIDAK 63 Query: 62 RAKGEELGPLAGIPVAIKDNICTKDVTTSCASKILEDFVPPYNATVISKLAEAGAIIVGK 121 R G+ LG LAG+P+ +KDNI TKD+ T+ A+ L F P NA V+ L +AGAII+GK Sbjct: 64 RQAGQPLGALAGLPIVVKDNINTKDLPTTGATPGLAGFRPSANAAVLQPLLDAGAIIIGK 123 Query: 122 TNMDEFAMGSSTENSAFF--VTSNPWDTERVPGGSSGGSAASVASAQVPLALGSDTGGSI 179 NM E A G + N A F V N + + +PGGSSGGS A++ + VP LGSDTGGS+ Sbjct: 124 ANMHELAFGITNTNFAPFAGVARNAYKSTHIPGGSSGGSGAAIGARIVPAGLGSDTGGSV 183 Query: 180 RQPASFCGVVGMKPTYG------RVSRYGLVAFASSLDQIGPLSKNVEDTALALDIISGH 233 R PA+ G+ GM+P+ G R S G++ + + D +GP+ + V D AL +I+G Sbjct: 184 RIPAALNGIAGMRPSVGNGGAERRYSGKGVIPLSHTRDTVGPMGRTVADIALLDAVITG- 242 Query: 234 DHMDSTSVDLEVPNHTDFLNQDIDELTIGIPKEYYELVDNDVKSLVESSLQSIEPEAGNY 293 TS +P + L GIP Y++LVDN+V +++E++ + + Sbjct: 243 -----TSRPAPLP---------LRGLRFGIPTAYWDLVDNEVLAMMEAAKAKLAAAGVVF 288 Query: 294 RQVSLPTTEHAL-SAYYLIAPAEASSNLARF------DGV---RYGQRFATDDLKTMYNQ 343 Q LP L + I EA +L + GV Q+ A ++++ + Sbjct: 289 VQAELPNVRELLEKTGFPIVLHEAGVDLPVYLAESGATGVTVASLAQQAANPEVRSAFQA 348 Query: 344 TRKEGFGNEVKQRVMLGTYALSAGYYDALYLKALKVRSLIKQEFEQVFSECDVLIAPTTP 403 + FG + Y DAL + ++R+L F D + PTTP Sbjct: 349 VVTDAFGPQ---------------YPDALNVYRPQMRALYDNYFSS--QGIDAIFFPTTP 391 Query: 404 -------------TVPFREGENVDDPLTMYKNDICTAPVNLAGLPSISIPCGFS-NGLPV 449 TV G +D+ T +N P + GLP I++P G + +GLPV Sbjct: 392 LPAVPIDPIKGTSTVTVNGGAPLDEFETFIRN---CDPGSTTGLPGITLPIGLTKDGLPV 448 Query: 450 GLQVIGKAFDEGKVIQVAHKIEQM 473 G+ + G + +++ + E + Sbjct: 449 GMALDGPVGSDQRLLSIGMSAEAL 472 Lambda K H 0.314 0.132 0.372 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: 535 Number of extensions: 28 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: 491 Length of database: 481 Length adjustment: 34 Effective length of query: 457 Effective length of database: 447 Effective search space: 204279 Effective search space used: 204279 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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