Align Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate WP_014149127.1 MEALZ_RS13110 asparagine synthase
Query= curated2:Q58456 (515 letters) >NCBI__GCF_000968535.2:WP_014149127.1 Length = 599 Score = 153 bits (387), Expect = 1e-41 Identities = 109/376 (28%), Positives = 179/376 (47%), Gaps = 30/376 (7%) Query: 44 YSIGLGHVRLAILDLSEKGHQP------MGYNVDEDKIIYRDDE--LDRADIIIVYNGEI 95 Y G+ + + L S KG P +G + E + DD+ L++ D + G Sbjct: 8 YGTGIDRNQASELAESLKGCAPESTKKTIGIRIAESLALVSDDKRSLEQGDCRLALTGHG 67 Query: 96 YNYLELKEKFNLETETGTDTEVILKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDR 155 + LE I++ Y G D +K+ G + +FD+ + + + DR Sbjct: 68 FGPLE----------------AIVENYKTKGDDFIKDMQGAFTLMLFDEYEKRLLLATDR 111 Query: 156 LGVKPFYYYWDGNEFIFSSELKGILAVKEINKKENINKDAVELYFALGFIPSPYSIYKNT 215 LG YY N +F S ++A E++ + I++ ++ Y PSP++IY+ Sbjct: 112 LGQNNLYYAQTLNGIVFGSTADSVVAHPEVSSE--ISRQSIYDYVYFHHCPSPHTIYRQV 169 Query: 216 FKLEARQNLIFDLDKREIRKYYYWELPDYKPIYDKKKLIEEGKKLLYDAVKIRMRSDVPV 275 KLE Q L + D + +YY+ + + Y ++ +E + + +AV+ Sbjct: 170 QKLEGGQVLTYQ-DGKIALQYYWMPVFSEQGAYSLEQSGQELRNEIIEAVRQSAADSNVT 228 Query: 276 GAFLSGGLDSSTVVGVMRE-FTDLSKLHTFSIGFEGKYDETPYIKIVVDYFKTQHHHYYF 334 GAFLSGGLDSS+V G + + + + +K T EG YDE Y +I VD FKT+ H YY Sbjct: 229 GAFLSGGLDSSSVAGALSKVYPEQAKTFTMGFPVEG-YDEIEYARIAVDCFKTRPHEYYV 287 Query: 335 KERDFEELIDKYSWIYDEPFGDYSGFPTYKVSEMARK-FVTVVLSGDGGDEVFGGYMTHL 393 D + K + YDEPFG+ S Y +++A++ + V+L+GDGGDE+F G + Sbjct: 288 TPEDTVAAVPKIAAFYDEPFGNSSALAAYYCAKLAKENGIQVMLAGDGGDELFAGNERYA 347 Query: 394 NGYRMDFIRKLPKFLR 409 D ++P F R Sbjct: 348 KQLLFDRYYRIPGFAR 363 Lambda K H 0.322 0.144 0.434 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: 801 Number of extensions: 44 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: 515 Length of database: 599 Length adjustment: 36 Effective length of query: 479 Effective length of database: 563 Effective search space: 269677 Effective search space used: 269677 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 (21.9 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 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