Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate SM_b20652 SM_b20652 asparagine synthetase
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__Smeli:SM_b20652 Length = 645 Score = 176 bits (447), Expect = 2e-48 Identities = 137/399 (34%), Positives = 196/399 (49%), Gaps = 54/399 (13%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC G D L ++ ++ + HRGPD GI+ + A L H RLSIV + G Sbjct: 1 MCGFGGYLGSIRDGKPLLER---MTAAIGHRGPDERGIFTAPGAGLGHVRLSIVGLGDGQ 57 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDR-YQFQTGSDCEVILALYQEKGPEFLDDLQ 119 QP+ N +A NGEI+N+ LR E R QF+T SD EVIL LY+E G + L L Sbjct: 58 QPMSNPSGELTIAFNGEIFNYVELRDELRARGRQFRTSSDTEVILHLYEEMGEDCLSLLN 117 Query: 120 GMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPV----------- 168 G FAFA++D+ + ++ RD +G+ PL+ + G LY ASE+KAL+ V Sbjct: 118 GDFAFAIWDARRRRMMLARDRMGVRPLFHTL-KGGTLYFASEVKALLEVPGVSAEIDPIA 176 Query: 169 ----------------CRTIKEFPAGSYLWS-QDGEI-RSYYHRDWFDYD---AVKDNVT 207 R I E G + + Q+G R Y+ D+ D D A + Sbjct: 177 LDQIFTLWAPIAPRTPFRDIHELEPGHLMIADQNGTTTRPYWQLDYPDRDERPAYAEESR 236 Query: 208 DKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQ 267 ELR L D+ + + +DVP G LSGGLDSSIISA+ ++ Sbjct: 237 AAEELRALLTDATRIRMRADVPVGAYLSGGLDSSIISALAAGMTSQG------------- 283 Query: 268 LHSFAVGLPGSPDLKAA--QEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIR 325 L +F+V + ++A +E+A LGT H + + DVI E + T Sbjct: 284 LRTFSVTFDSAEHDESAFQEEMAAALGTEHRAVACRAGDIARDFPDVIRFTEKPIIRT-- 341 Query: 326 ASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKA 364 A P+Y +S ++ G+K+VL+GEG+DEVF GY F +A Sbjct: 342 APAPLYKLSGLVREAGLKVVLTGEGADEVFAGYDIFKEA 380 Score = 48.5 bits (114), Expect = 8e-10 Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 2/67 (2%) Query: 387 ARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVA 446 ++ ++ A G+E R PFLD + ++ A ++ P+ K+ G +EKHILRE + LP ++ Sbjct: 499 SQGDRMAMAHGIEGRFPFLDHRLVEFAAKLPPEMKL--RGLVEKHILREATKDLLPPAIG 556 Query: 447 WRQKEQF 453 R K+ + Sbjct: 557 RRTKQPY 563 Lambda K H 0.319 0.135 0.407 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: 784 Number of extensions: 43 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 554 Length of database: 645 Length adjustment: 37 Effective length of query: 517 Effective length of database: 608 Effective search space: 314336 Effective search space used: 314336 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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