Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate CA265_RS07955 CA265_RS07955 asparagine synthase (glutamine-hydrolyzing)
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__Pedo557:CA265_RS07955 Length = 613 Score = 154 bits (389), Expect = 1e-41 Identities = 124/412 (30%), Positives = 184/412 (44%), Gaps = 53/412 (12%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC I+G +D + +R+K +S RGPD++G+ D I AH RL+I+D++A + Sbjct: 1 MCGIYGTTIPYSDGI-VREKMARIS----FRGPDYTGVQRYDQVIFAHNRLAIIDLDARS 55 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDR-YQFQTGSDCEVILALYQEKGPEFLDDLQ 119 ++ H++ NGEIYN++ +R E + YQF T SD EVI A Y E G L Sbjct: 56 NQPFSYMHLHIV-FNGEIYNYKDIRRELERKNYQFNTSSDTEVICAAYLEYGAGCLTRFN 114 Query: 120 GMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGS 179 GMFAF +YD+ K+ RD G P Y +D + + + + ++ E Sbjct: 115 GMFAFVIYDTRKNELFGARDRFGKKPFYYAHDHSSFEFASQPSQINIDRGLSVNEEAINQ 174 Query: 180 YL-WSQDGEIRSYY---------HRDWFDYDAVKDNVTD-------------------KN 210 YL W E +S Y H +D + K +T+ K Sbjct: 175 YLIWGYVPEPQSIYAEVKQLPAAHYFKYDLKSHKLKITEYWTLDYGWKNKFEGSYEEAKE 234 Query: 211 ELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHS 270 L L D+VK + +DVP GV LSGG+DSS+I+A+ K E + S Sbjct: 235 ALALILADAVKIRMNADVPLGVFLSGGIDSSLIAALATK------------EIDHVKTFS 282 Query: 271 FAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPM 330 G + A +VA HLGT H+ I +G++ I + YD +S Sbjct: 283 IKFNEKGFDESAYASQVAKHLGTDHYTIECNYNDGIELIEN---FNRFYDEPFADSSAIP 339 Query: 331 YLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFH--KAPNAKELHEETVRKLLA 380 ++ K + + LSG+ DE F GY + K N+ VRK LA Sbjct: 340 TMLLSKNTRKHVTVALSGDAGDEAFLGYHRYKWIKQVNSLFYAPHGVRKALA 391 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: 777 Number of extensions: 33 Number of successful extensions: 6 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: 554 Length of database: 613 Length adjustment: 36 Effective length of query: 518 Effective length of database: 577 Effective search space: 298886 Effective search space used: 298886 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