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:C0QKZ5 (490 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3652 Length = 482 Score = 250 bits (638), Expect = 9e-71 Identities = 179/491 (36%), Positives = 251/491 (51%), Gaps = 51/491 (10%) Query: 5 ELTLEGARALLLSGEISSKDLTTCLLDRIKTHDADLGAFITVDAAGALEAATAADERIAR 64 EL + A A + G+ISS+ T LL R T +DLGAFIT+D A L AA A D A Sbjct: 16 ELGVAAAAAAIRRGDISSESYTAALLRRAHTF-SDLGAFITIDEAAVLAAARACDTARAT 74 Query: 65 GEDAPLLGIPLALKDLLCTSGVRTTCASKILENFVPTYDATAVTLLKQAGAVIVGKTNLD 124 G APLLG+P+A+KD T G+RTT + LENFVP DA V +K AG ++ GK NL Sbjct: 75 GSTAPLLGVPVAVKDSYLTQGLRTTLGIRSLENFVPARDAEVVRAIKDAGGIVFGKNNLV 134 Query: 125 EFGMGSSTENSAFHLTRNPWNLDHVPGGSSGGSAAAVAARMCTAALGTDTGGSIRQPASH 184 E G + NS F +NP N +HV GGSS G+ A+V A++ AALG DT GSIR PAS Sbjct: 135 EMSYGLTGHNSHFGQAKNPHNPEHVTGGSSSGAGASVGAQIVPAALGGDTVGSIRVPASF 194 Query: 185 CGVVGLKPSYGRVSRFGMVAYASSLDQIGPITRTVKDAALMMNVISGHDPKDSTSAAIDK 244 CGVVG KPS GR S G+ + +LD G RTV+D AL+ V++ Sbjct: 195 CGVVGFKPSPGRWSGDGIAPISHTLDTAGVFARTVEDCALIDQVVTK------------- 241 Query: 245 PDFTQAFAGFDAKGLAGMK-AGIPREYIGMKGLDPEVERSFKNACKVLEDLGVEVIDVSL 303 T + D GL G++ A PR++ ++ ++ EVE FK + L D G EV++V L Sbjct: 242 ---TTSTVHGDWTGLRGIRLAYAPRQH--LERINHEVEEHFKETIRRLCDAGAEVVEVDL 296 Query: 304 PHTNFAVA-----AYYVLAPSEASANLSRYDGVKYGFRQTGCDDLMDMYKQTRSSGFGPE 358 FA+ + + E+ A R + + F +D+ + K +G Sbjct: 297 GEDFFAMTERSTWSIFFHETMESVAGFLRKNRIPSSF-----EDIYNELKPGLKDAWGHL 351 Query: 359 VKRRIIMGTYALSAGYYDEYYGRASRVRTLIMADFSKAFDQ--CDIILSPVAPTPAFKI- 415 V + G +S ++ Y R I F+ AF ++ P P PA I Sbjct: 352 V---LPSGAGFIS---HETYQTALDHDRPEIQRRFNMAFSSSGAQALIMPTTPCPAPTIE 405 Query: 416 --------GENVDDPLTMYLGDIFTLSANMAGIPGLSVPCAMSTTGLPIGLQILGRRFDE 467 G+ VDD T++ ++AG+PG+S+P MS+ GLPIGL+I G+ D+ Sbjct: 406 QQTKFTIAGQEVDDLALAR----HTVAGSIAGLPGISIPMGMSSNGLPIGLEIDGKNGDD 461 Query: 468 MSVLKAGYGLE 478 +L+ +E Sbjct: 462 RKLLELARRVE 472 Lambda K H 0.319 0.136 0.397 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: 568 Number of extensions: 20 Number of successful extensions: 3 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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