Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate GFF4005 Psest_4078 L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D
Query= curated2:Q9Y9T8 (427 letters) >FitnessBrowser__psRCH2:GFF4005 Length = 327 Score = 105 bits (262), Expect = 2e-27 Identities = 100/348 (28%), Positives = 157/348 (45%), Gaps = 35/348 (10%) Query: 74 ERVYIIGAGGTIASRVD----YETGAVKPYLDASELATTIPELQRYASIEAEQLFSILSE 129 ER+ ++ GGTI + + L A + T P L + E + L S Sbjct: 6 ERLLVLYTGGTIGMQQSAAGLMPASGFEARLRAQQALETGP-LPSWTFRELQPLLD--SA 62 Query: 130 DMKPSMWEAIVDRAAR-VLEAGYDGVVVAHGTDTMAFTASALSFAFHKGLPSPVILTGSQ 188 +M+PS W + V ++ D V++ HGTDT+A++A+ALSF L PV+LTG+ Sbjct: 63 NMQPSHWLQMATAVREAVAQSDCDAVLLLHGTDTLAYSAAALSFLL-LDLEIPVLLTGAM 121 Query: 189 RSSDRPSSDAAFNLTASVLAASRAPFAEVAVVMHGETGDTYALAHRGVRVKKMHSSRRDA 248 + P SDA NL ++ A V + +G L H G RV K+ S DA Sbjct: 122 LPAGSPGSDAWPNLFGAMRALQAGRVEGVRLFFNG------VLLH-GARVSKLRSDAFDA 174 Query: 249 FQSVNDKPLARIYPFEGRVEMLRDDYRRRGESGLEVDNGFEERVALVKHFPGLISEVIDA 308 F K A + GE + +V ++ +PG+ + + A Sbjct: 175 FAEAPRKRSATVV----------------GERPPMLLPQQPAQVVVLPLYPGVGAAQVQA 218 Query: 309 LLDRGFKGIVVE--GTGFGHVS-SDAIKSIERARDQGVPIVITTQTVFGRVNLNVYSTGR 365 L+ G + +++E G+G G + I+++ +A QGV + +Q G V+ VY+TG Sbjct: 219 LVASGAQALLLECYGSGTGPAGDAPFIEALRQAHRQGVVLAAISQCPGGHVDFGVYATGS 278 Query: 366 KMLAAGAIPAGDMTSEAAYAKLSWILARTRELEVVRKMFQRNLAGEVS 413 + AG + G MT EAA KL +L V F R+L GE++ Sbjct: 279 GLRDAGLVSGGGMTREAALGKLFALLTAGLNQAQVEHWFCRDLCGEMA 326 Lambda K H 0.318 0.136 0.385 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: 322 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: 427 Length of database: 327 Length adjustment: 30 Effective length of query: 397 Effective length of database: 297 Effective search space: 117909 Effective search space used: 117909 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: 50 (23.9 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