Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_3652 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3652 Length = 482 Score = 228 bits (582), Expect = 3e-64 Identities = 170/480 (35%), Positives = 238/480 (49%), Gaps = 46/480 (9%) Query: 6 QLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAA 65 +L VA A + RG+ISS T ALL R A + AF+ +D A A ARA D RA Sbjct: 16 ELGVAAAAAAIRRGDISSESYTAALLRR-AHTFSDLGAFITIDEAAVLAAARACDTARAT 74 Query: 66 GDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCD 125 G +PLLG+P+ +KD TQGLRTT + LEN+ P DA V +K AG ++ GK N Sbjct: 75 GSTAPLLGVPVAVKDSYLTQGLRTTLGIRSLENFVPARDAEVVRAIKDAGGIVFGKNNLV 134 Query: 126 EFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAAL 185 E + G + NS F Q +NP N E V GGSS G+ A+V A PAALG DT GSIR PA+ Sbjct: 135 EMSYGLTGHNSHFGQAKNPHNPEHVTGGSSSGAGASVGAQIVPAALGGDTVGSIRVPASF 194 Query: 186 CGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYPA 245 CG+ G KP+ GR S G+ + +LD G ARTV DCA++ +V+ T T Sbjct: 195 CGVVGFKPSPGRWSGDGIAPISHTLDTAGVFARTVEDCALIDQVVT-----KTTST---- 245 Query: 246 PDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPYA 305 TG +RG+R+ + + +VE + I L + GAEV E+ L +A Sbjct: 246 --VHGDWTG-LRGIRLAYAPRQHLERINHEVEEHFKETIRRLCDAGAEVVEVDLGEDFFA 302 Query: 306 LP-----VYYLIAPAEASANLARFDGVRYGLRVPG--ESYFDELERTRGAGFGPEVRRRI 358 + + E+ A R + R+P E ++EL+ +G V + Sbjct: 303 MTERSTWSIFFHETMESVAGFLRKN------RIPSSFEDIYNELKPGLKDAWGHLV---L 353 Query: 359 MLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQ--VDVIAAPTTPTVA--------F 408 G +S ++ Y R I+R + AF + PTTP A F Sbjct: 354 PSGAGFIS---HETYQTALDHDRPEIQRRFNMAFSSSGAQALIMPTTPCPAPTIEQQTKF 410 Query: 409 KIGAHTDDPLAMYLEDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLLRV 467 I D LA+ T+ ++AGLPG+ +P G + GLPIGL++ G+ D+ LL + Sbjct: 411 TIAGQEVDDLALARH---TVAGSIAGLPGISIPMGMSSNGLPIGLEIDGKNGDDRKLLEL 467 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: 515 Number of extensions: 26 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: 482 Length adjustment: 34 Effective length of query: 456 Effective length of database: 448 Effective search space: 204288 Effective search space used: 204288 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: 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