Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 351932 BT2404 L-asparaginase I (NCBI ptt file)
Query= curated2:O59132 (438 letters) >FitnessBrowser__Btheta:351932 Length = 327 Score = 147 bits (370), Expect = 6e-40 Identities = 108/330 (32%), Positives = 169/330 (51%), Gaps = 22/330 (6%) Query: 111 TGAVYPAFTAEELAKAVPEIFEIANIKPKLLFN--IFSEDMKPKHWIKIAHEVAKSLNSG 168 TGA+ F E+L + +PE+ + F+ + S DM+P W K+ H + ++ + Sbjct: 7 TGAL-ENFNFEQLQRHIPELQKFNFPIDTYQFDPPMDSSDMEPDMWRKLVHIIHENYDLY 65 Query: 169 DSGVVVAHGTDTMGYTAAALSFMLRDLGKPVILVGAQRSSDRPSSDAAMNLICSVRMSTS 228 G V+ HGTDTM YTA+ALSFML L KPVIL G+Q +D NL+ S+ ++ + Sbjct: 66 H-GFVILHGTDTMAYTASALSFMLEGLDKPVILTGSQLPIGVLRTDGKENLMTSIEIAAA 124 Query: 229 D-------VAEVMVVMHGETGDTYCLAHRGTKVRKMHTSRRDAFRSINDVPIAKVWPNGK 281 V EV + RG + KM+ +AFRS N +A+ + K Sbjct: 125 QDKDGKALVPEVCIFFENHL-------MRGNRTTKMNAENFNAFRSFNYPVLAEAGIHIK 177 Query: 282 IEFLRDDYRRRSDSEVWVDDKLEEKVALVKVYPGISSEIIEFFID-KGYRGIVIEGTGLG 340 + + +S E+ L+ + ++K++PGI +I + KG + +V+E G G Sbjct: 178 YNQAQI-HVNKSKQELVPHYLLDTNIVVLKLFPGIQENVIATMLGTKGLKAVVLETYGSG 236 Query: 341 HTPND--IIPSIQRATEEGIAVCMTSQCIYGRVNLNVYATGRRLLKAGVIPCEDMLPETA 398 + P I + +A+ +GI + +QC G V + Y TG +LL+AGV+ D E+A Sbjct: 237 NAPRKEWFIRRLCQASAQGIVIVNVTQCNAGMVEMERYETGYQLLQAGVVSGYDSTTESA 296 Query: 399 YVKLMWVLGHTQDLEEVRRMMLTNYAGEIT 428 KLM++LGH +EVR M + AGEIT Sbjct: 297 VTKLMFLLGHGYTPDEVRDCMNRSIAGEIT 326 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: 343 Number of extensions: 13 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: 438 Length of database: 327 Length adjustment: 30 Effective length of query: 408 Effective length of database: 297 Effective search space: 121176 Effective search space used: 121176 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