Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate H281DRAFT_02970 H281DRAFT_02970 aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A
Query= curated2:Q2IH94 (492 letters) >FitnessBrowser__Burk376:H281DRAFT_02970 Length = 473 Score = 267 bits (682), Expect = 7e-76 Identities = 195/480 (40%), Positives = 242/480 (50%), Gaps = 47/480 (9%) Query: 21 AAKAISSTELVEASLARIQATDGKLGAFLAVCADRARAAAKAADARAARGERRSELDGVP 80 A A S+ EL+EA+LARI A D ++ AF V +RA A A A DAR A G L GVP Sbjct: 19 AQGAFSARELIEATLARIDAYDTQVNAFTTVTRERALAEADALDARRASGHNLPPLAGVP 78 Query: 81 VAVKDLFVTKGVPTTAGSRILEGYLPPY-DATVVERLEAAGAVIVGKLNMDEFAMGSSNE 139 A K+LF GV T AGSR+L P DAT+VERL A GA+++G LNMDEFA G + E Sbjct: 79 FAAKNLFDISGVTTLAGSRVLADAPPAAADATLVERLCAQGAILIGALNMDEFAYGFTTE 138 Query: 140 NSAYKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDTGGSIREPAAFCGVVGVKPT 199 N PC NP DL+RT GGSSGGSAA+VAAG V +LGTDT GS+R PA+ CGV GVKPT Sbjct: 139 NHHAGPCRNPHDLTRTAGGSSGGSAAAVAAGFVPLTLGTDTNGSVRVPASLCGVFGVKPT 198 Query: 200 YGRVSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDPRDMTSSTR---PVDDYLGP 256 YGR+SR+G F +SLD +G AR V D A V + G + D + R VD GP Sbjct: 199 YGRLSRHGTWPFVASLDHMGAFARTVDDLAAVYDALQGTEALDPACAQRGFESVDTRPGP 258 Query: 257 LEEGARGLRVGVPREWLSGGLDAGVEAAIRAALDTYRRLGATLVDVSLPHSKYGIGAYYL 316 L R R+G G D R A + V P + GA +L Sbjct: 259 L----RVARLG-------GYFDTYANDDAREASHAAAHALSATHTVEYPDADAARGAAFL 307 Query: 317 IAPAEASSNLARYDGVRYGLRAEGAKGLKEMYAESREQGLGAEPKRRIMLGTYALSSGYY 376 I AE YG R EP R L AL Sbjct: 308 ITAAEGGQLHMENLRTHYGAR---------------------EPLSRDRLIAGALLPA-- 344 Query: 377 DAYYLRAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAFALGERTGDPLQMYLA-----DI 431 A+ ++AQ+VR +RR E F DV+ P TP VA +G+ + LA + Sbjct: 345 -AWVVQAQRVRAALRRRVLELFERYDVLIAPATPVVAPRIGDEFMEVNGERLAVRPNLGM 403 Query: 432 FTITCNLAALPGLSVPCGLEAASGLPVGLQLVGRPFDEATLFRAARALE-RELGPLPAPP 490 T + LP ++ P + GLPVG+QL+ P+ E F AAR LE +L P PP Sbjct: 404 LTQPVSCLGLPVVAAP--MRTRGGLPVGVQLIAAPWREDLAFEAARRLEAAQLAVSPPPP 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: 620 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: 492 Length of database: 473 Length adjustment: 34 Effective length of query: 458 Effective length of database: 439 Effective search space: 201062 Effective search space used: 201062 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: 52 (24.6 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