Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate YP_004144523.1 Mesci_5375 asparagine synthase
Query= BRENDA::P22106 (554 letters) >NCBI__GCF_000185905.1:YP_004144523.1 Length = 673 Score = 166 bits (419), Expect = 3e-45 Identities = 128/411 (31%), Positives = 200/411 (48%), Gaps = 71/411 (17%) Query: 1 MCSIFGVFDIKTDAVELRKKAL-ELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAG 59 MC I G+ + A + AL ++ + HRGPD SG+Y A LAH RLS++D++ G Sbjct: 1 MCGIAGIVALNAAAEPPSRAALLRMAAALSHRGPDESGVYRDRRAGLAHTRLSVIDLSTG 60 Query: 60 AQPLYNQQKTHVLAVNGEIYNHQALRAE-YGDRYQFQTGSDCEVILALYQEKGPEFLDDL 118 QPL + T + NGEI+N+ LR + ++F+T SD EVI+ Y+ G + L Sbjct: 61 QQPLADTGDTTWIVFNGEIFNYVELREQLMALGHRFRTRSDTEVIVHAYRAWGVAAFERL 120 Query: 119 QGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL------------- 165 G +A A++DS ++ RD GI PL++ + G+L+ ASE+KA+ Sbjct: 121 NGQWALAIWDSLTGRLVLSRDRFGICPLHL-CEHAGRLHFASEVKAIFAADPAIPRAFDP 179 Query: 166 ------------VP---VCRTIKEFPAGSYLWSQDGEIRSYYHRDWFD-YDAVKDNVTDK 209 VP V + +KE G +G +R H W Y + D Sbjct: 180 AGIDQTFTLWTVVPPQGVFQGVKELTPGHVRIYDNGSVRE--HAFWKPCYPEIADQAHGT 237 Query: 210 ---------NELRQALEDSVKSHLM-SDVPYGVLLSGGLDSSIISAITKKYA-------A 252 +E+R AL+ + ++ +DVP G LSGGLDSS+++ + +++A + Sbjct: 238 FTGSLDDAVDEVRSALQAATALRMVKADVPVGCYLSGGLDSSLVAMLGRRFAGAPFQTFS 297 Query: 253 RRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDV 312 R D E E + +L VA+ G HHE+ + + + DV Sbjct: 298 LRFADAEYDETRYQRL------------------VASASGGEHHEVMVSRGDIAEVFPDV 339 Query: 313 IYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHK 363 I H E + T A P++L+SR ++ GIK+VL+GEG+DE+F GY F + Sbjct: 340 IRHAERPILRT--APAPLFLLSRLVREHGIKVVLTGEGADEMFAGYDLFRE 388 Score = 38.9 bits (89), Expect = 6e-07 Identities = 25/89 (28%), Positives = 51/89 (57%), Gaps = 4/89 (4%) Query: 365 PNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCG 424 P A++ + E +R L++ ++ ++ ++ + A VE R PFLD + + +A + P K+ Sbjct: 488 PLAQDQYLE-IRTLMSGYLLS-SQGDRMLMAHSVEGRFPFLDDRLVALANSLPPDYKL-- 543 Query: 425 NGKMEKHILRECFEAYLPASVAWRQKEQF 453 EKH+L+ ++ +PA V R+K+ + Sbjct: 544 RILDEKHVLKRVAKSIVPAEVVARKKQPY 572 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: 788 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 554 Length of database: 673 Length adjustment: 37 Effective length of query: 517 Effective length of database: 636 Effective search space: 328812 Effective search space used: 328812 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