Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate 5209024 Shew_1509 asparagine synthetase B (RefSeq)
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__PV4:5209024 Length = 552 Score = 800 bits (2066), Expect = 0.0 Identities = 388/554 (70%), Positives = 459/554 (82%), Gaps = 3/554 (0%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MCSIF + DI+TDA LR+ ALE+S+L+RHRGPDWSGIYASD AILAHERL+IVD+ GA Sbjct: 1 MCSIFAILDIQTDATPLRQVALEMSKLLRHRGPDWSGIYASDKAILAHERLAIVDIEHGA 60 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120 QPL ++ ++ +LAVNGEIYNH+ L+AE GD+Y +QT SDCEVILALYQE G EFLD L G Sbjct: 61 QPLLSEDESLILAVNGEIYNHKELKAELGDKYSYQTNSDCEVILALYQEYGTEFLDKLNG 120 Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180 +FAF LYD D+YLIGRDH+GIIPLY G+D G YVASEMKAL+PVC+T++ F G Y Sbjct: 121 IFAFVLYDKRSDSYLIGRDHMGIIPLYTGHDAEGNFYVASEMKALMPVCKTVETFKPGHY 180 Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240 L ++ GE YY RDW ++AV+DN ELR+ALE +VK LMSDVPYGVLLSGGLDS Sbjct: 181 L-TKSGETH-YYQRDWQSFEAVQDNAASVEELREALEAAVKRQLMSDVPYGVLLSGGLDS 238 Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300 S++SAIT+ +A RR+ED S+AWWPQLHSFAVGL G+PDL AAQ+VA+ +GT+HHEI F Sbjct: 239 SVVSAITQTFAKRRIEDDGASDAWWPQLHSFAVGLTGAPDLAAAQKVADAIGTIHHEITF 298 Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360 + QEGLDA++DVIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY Sbjct: 299 SFQEGLDALKDVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 358 Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420 FHKAPNA+ HEE VRKL LH++DC RANKAM+AWG+EARVPFLDK F+D AMRINP+ Sbjct: 359 FHKAPNAQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKAFIDTAMRINPEA 418 Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480 KM +G++EKHILR+ FE LP VAWRQKEQFSDGVGYSWID LKE AA QV D QL Sbjct: 419 KMSKDGRIEKHILRQAFEHKLPQEVAWRQKEQFSDGVGYSWIDGLKEHAAAQVDDLQLAN 478 Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540 A+FRFPYNTP +KEAY YR FEE FPLPSAAE VPGG SVACS+ +A+ WDE+ + + D Sbjct: 479 AKFRFPYNTPETKEAYFYRCFFEEHFPLPSAAETVPGGKSVACSTPEALAWDESLQGIID 538 Query: 541 PSGRAV-GVHQSAY 553 PSGRAV VH+SAY Sbjct: 539 PSGRAVQSVHESAY 552 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: 927 Number of extensions: 27 Number of successful extensions: 2 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: 552 Length adjustment: 36 Effective length of query: 518 Effective length of database: 516 Effective search space: 267288 Effective search space used: 267288 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