Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_057507873.1 ABB28_RS06540 asparagine synthase B
Query= BRENDA::P22106 (554 letters) >NCBI__GCF_001431535.1:WP_057507873.1 Length = 563 Score = 671 bits (1732), Expect = 0.0 Identities = 336/561 (59%), Positives = 410/561 (73%), Gaps = 9/561 (1%) Query: 1 MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA 58 MCSIFG+F ++ D LR+ ALE S+ RHRGPDWSG+Y D A+L HERL+IVD Sbjct: 1 MCSIFGIFGLQAGDDLPALRRHALESSQRQRHRGPDWSGVYLDDGALLVHERLAIVDPAG 60 Query: 59 GAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGP-EFLDD 117 G+QPL ++ LAVNGEIYNHQ L+A Y FQTGSDCEVI ALY++ P ++L+ Sbjct: 61 GSQPLLSEDGGLALAVNGEIYNHQQLKAGLDQPYAFQTGSDCEVINALYRQGEPSQWLER 120 Query: 118 LQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPA 177 L G+FAFAL+D L+ RD +G++PLY G+D G+L VASE+KALV C +FP Sbjct: 121 LNGIFAFALWDKAAGRVLVARDPIGVVPLYWGHDAQGRLRVASELKALVDTCADAAQFPP 180 Query: 178 GSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGG 237 G Y S G + YY + W +YDAV+ D ELR+A E +V+ LMSDVPYGVLLSGG Sbjct: 181 GHYYDSATGALVRYYQQSWREYDAVQGKPVDLAELREAFERAVERQLMSDVPYGVLLSGG 240 Query: 238 LDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHE 297 LDSS+++A+ +YA RR+ED SEAWWP+LHSFA+GL GSPDL AA A LGTVHH Sbjct: 241 LDSSLVAAVAARYARRRIEDGGESEAWWPRLHSFAIGLKGSPDLAAAAIAAEALGTVHHG 300 Query: 298 IHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGG 357 +T +EGLD + +VI HIETYDVTTIRASTPM+L++R+IKAMG+KMVLSGEGSDE+FGG Sbjct: 301 FEYTFEEGLDVLPEVIRHIETYDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDEIFGG 360 Query: 358 YLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRIN 417 YLYFHKAP+A+E H E VRKL ALH YDC RANK+M AWGVE RVPFLD++FLDVAMR + Sbjct: 361 YLYFHKAPDAREFHSELVRKLDALHNYDCLRANKSMMAWGVEPRVPFLDREFLDVAMRFD 420 Query: 418 PQDKMCGN-----GKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQ 472 KM G+ ++EK +LR FE YLP S+ WRQKEQFSDGVGY WID LK A Q Sbjct: 421 AAHKMVGSEASGGRRVEKGVLRAAFEGYLPESILWRQKEQFSDGVGYGWIDGLKAHAEAQ 480 Query: 473 VSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWD 532 VSD+ L A RFP+N P +KEAY YR +FE+ FP +AAE VPGG S+ACSS AI WD Sbjct: 481 VSDRVLAAADKRFPHNPPQTKEAYYYRHVFEQYFPSHAAAETVPGGKSIACSSPAAIAWD 540 Query: 533 EAFKKMDDPSGRAV-GVHQSA 552 +F DPSGRA+ GVH++A Sbjct: 541 ASFAAAADPSGRAIAGVHEAA 561 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: 932 Number of extensions: 30 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: 554 Length of database: 563 Length adjustment: 36 Effective length of query: 518 Effective length of database: 527 Effective search space: 272986 Effective search space used: 272986 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 24 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