Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate 201902 SO2767 asparagine synthetase B, glutamine-hydrolyzing (NCBI ptt file)
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__MR1:201902 Length = 554 Score = 809 bits (2089), Expect = 0.0 Identities = 392/554 (70%), Positives = 461/554 (83%), Gaps = 1/554 (0%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MCSIF + DI++DA ELR+ ALE+S+LMRHRGPDWSGIYASD AILAHERL+IVD+ GA Sbjct: 1 MCSIFSILDIQSDAKELRQVALEMSKLMRHRGPDWSGIYASDKAILAHERLAIVDIEHGA 60 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120 QPL + + +LAVNGEIYNH+ L+A+ GD+Y +QT SDCEVILALYQE G EFLD L G Sbjct: 61 QPLLTEDGSLILAVNGEIYNHKELKAQLGDKYSYQTNSDCEVILALYQEYGTEFLDKLNG 120 Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180 +FAF LYD KDAYLIGRDH+GIIPLY G D G LYVASEMKAL+PVC+T++EF G Y Sbjct: 121 IFAFVLYDKAKDAYLIGRDHMGIIPLYTGRDAAGNLYVASEMKALMPVCKTVEEFQPGQY 180 Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240 L+S D YY RDW YDAVKDN + ELR+ALE +VK LMSDVPYGVLLSGGLDS Sbjct: 181 LYSSDAAAVKYYTRDWQQYDAVKDNGASQEELREALEAAVKRQLMSDVPYGVLLSGGLDS 240 Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300 S+ISAIT+ +A RR+ED + AWWPQLHSFAVGL G+PDL AA++VA+ +GT+HHEI+F Sbjct: 241 SVISAITQTFAKRRIEDDGETGAWWPQLHSFAVGLKGAPDLIAAKKVADAIGTIHHEINF 300 Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360 T QEGLDAI++VIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY Sbjct: 301 TFQEGLDAIKEVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360 Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420 FHKAPNA+ HEE VRKL LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMRINP+ Sbjct: 361 FHKAPNAQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRINPEA 420 Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480 KM +G++EKHILR+ FE LP VAWRQKEQFSDGVGYSWID LK AA+QV D QL Sbjct: 421 KMSKDGRIEKHILRQAFEHKLPKEVAWRQKEQFSDGVGYSWIDGLKAHAAEQVDDLQLAN 480 Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540 A+FRFPYNTP +KEAY YR FEE +PLPSAAE VPGG SVACS+ +A+ WDE+ + + D Sbjct: 481 AKFRFPYNTPETKEAYFYRCFFEEHYPLPSAAETVPGGKSVACSTPEALAWDESLRGIID 540 Query: 541 PSGRAV-GVHQSAY 553 PSGRAV VH ++Y Sbjct: 541 PSGRAVRSVHAASY 554 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: 924 Number of extensions: 27 Number of successful extensions: 1 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: 554 Length adjustment: 36 Effective length of query: 518 Effective length of database: 518 Effective search space: 268324 Effective search space used: 268324 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