Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate Echvi_0080 Echvi_0080 L-asparaginases, type I
Query= curated2:O59132 (438 letters) >FitnessBrowser__Cola:Echvi_0080 Length = 358 Score = 166 bits (419), Expect = 1e-45 Identities = 115/346 (33%), Positives = 191/346 (55%), Gaps = 22/346 (6%) Query: 94 VTIIGTGGTIASRIDYETGAVYPAFTAEELAKAVPEIFEIANIKPKLLFN--IFSEDMKP 151 V II TGGT+ D E+GA+ P F ++ + +P + + + F I S ++ Sbjct: 20 VLIIYTGGTLGMAYD-ESGALVP-FNFGQIMEKIPNLGNLNIAITVISFPEPIDSSNVNM 77 Query: 152 KHWIKIAHEVAKSLNSGDSGVVVAHGTDTMGYTAAALSFMLRDLGKPVILVGAQRSSDRP 211 +HW+ +A+ + ++ ++ D G VV HGTDTM Y+A+ LSFML+ L KPVI GAQ Sbjct: 78 QHWVDMAYIIYENYDTYD-GFVVLHGTDTMAYSASMLSFMLKGLSKPVIFTGAQLPISAM 136 Query: 212 SSDAAMNLICSVRMSTSDVAEVMVVMHGETGDTYCLAHRGTKVRKMHTSRRDAFRSINDV 271 SDA NL+ S+ ++ S +V + L RG + +KM + DAF S N Sbjct: 137 RSDARENLMTSLEIAISQANGKPIVPEVCIFFNHMLL-RGNRAKKMQSVHFDAFESENYP 195 Query: 272 PIAKVWPNGKIEFLRDDYRR------RSDSEVWVDDKLEEKVALVKVYPGISSEIIEF-F 324 P+A+ + DY + ++ +KL+++V ++K++PGI++E+I+ F Sbjct: 196 PLAE-------SGIVIDYNYAAIKPYKEGVQLKYLNKLDKRVMILKLFPGITAEVIDSCF 248 Query: 325 IDKGYRGIVIEGTGLGHTPND--IIPSIQRATEEGIAVCMTSQCIYGRVNLNVYATGRRL 382 KG RG+V+E G G++P + I ++++A + GI + SQC GRV Y T + L Sbjct: 249 SIKGLRGVVLETYGSGNSPTEPWFIETVRKAVDRGIIILNVSQCNGGRVIQGRYETSKEL 308 Query: 383 LKAGVIPCEDMLPETAYVKLMWVLGHTQDLEEVRRMMLTNYAGEIT 428 + GV+ D+ E A K+M++L + D +E+RR ++T AGE++ Sbjct: 309 KRLGVLSGGDITSEAAICKMMFLLANETDEDEIRRKLITPLAGEMS 354 Lambda K H 0.320 0.138 0.403 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: 350 Number of extensions: 19 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: 438 Length of database: 358 Length adjustment: 31 Effective length of query: 407 Effective length of database: 327 Effective search space: 133089 Effective search space used: 133089 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: 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