Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate N515DRAFT_1546 N515DRAFT_1546 asparagine synthase (glutamine-hydrolysing)
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__Dyella79:N515DRAFT_1546 Length = 559 Score = 674 bits (1739), Expect = 0.0 Identities = 340/560 (60%), Positives = 412/560 (73%), Gaps = 10/560 (1%) Query: 1 MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNA 58 MCSIFG+FD++ D LR++ALELS+ RHRGPDWSG++ IL HERL+IVD + Sbjct: 1 MCSIFGMFDLQPGDDLAGLRRQALELSQRQRHRGPDWSGVFVDAGVILVHERLAIVDPAS 60 Query: 59 GAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEF---- 114 G+QPL ++++T LAVNGEIYNH+ LRA G Y F TGSDCEVI ALY+E GPE Sbjct: 61 GSQPLRSREETLALAVNGEIYNHRELRAASG--YDFTTGSDCEVINALYRELGPEEFLAR 118 Query: 115 -LDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIK 173 + L G+FAFAL+DS YLI RD +G+ PLY G+D G+L VASEMKALV VC + Sbjct: 119 GIKQLNGIFAFALWDSATQRYLIARDPIGVCPLYWGHDGEGRLCVASEMKALVGVCADVS 178 Query: 174 EFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVL 233 FP G S GE+ YY + W Y+ + + LR A E +V LM+DVPYGVL Sbjct: 179 AFPPGHVYDSATGEVTRYYRKHWRSYEVTHGQQLEPSALRGAFEQAVHRQLMTDVPYGVL 238 Query: 234 LSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGT 293 LSGGLDSS+++A ++A R+ED +RSEAWWP+LHSFA+GL GSPDL AAQ A+ LGT Sbjct: 239 LSGGLDSSLVAACAARFARERIEDDDRSEAWWPRLHSFAIGLEGSPDLAAAQVAADALGT 298 Query: 294 VHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDE 353 VHH +T EGLDA+ +VI HIETYDVTTIRASTPM+L++R+IKAMG+KMVLSGEGSDE Sbjct: 299 VHHGFVYTFWEGLDALPEVIRHIETYDVTTIRASTPMFLLARRIKAMGVKMVLSGEGSDE 358 Query: 354 VFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVA 413 +FGGYLYFHKAP+ + HEETVRKL ALH +DC RANKAM AWGVEARVPFLD +FLDVA Sbjct: 359 IFGGYLYFHKAPSPEAFHEETVRKLDALHSFDCLRANKAMMAWGVEARVPFLDLEFLDVA 418 Query: 414 MRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQV 473 M ++ + KM G+G++EK +LRE F+ LP S+ WRQKEQFSDGVGY WID LK A Q V Sbjct: 419 MGLDARYKMAGHGRIEKAVLREAFQGALPDSILWRQKEQFSDGVGYGWIDGLKAHAEQVV 478 Query: 474 SDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDE 533 SD++ A RFP+N P +KEAYLYR IFE+ FP + A VPGG S+ACSS A+ WD Sbjct: 479 SDREFAAASTRFPHNPPATKEAYLYRRIFEQHFPGEACAATVPGGKSIACSSPAALAWDP 538 Query: 534 AFKKMDDPSGRAV-GVHQSA 552 AF DPSGRAV GVHQ A Sbjct: 539 AFAAAADPSGRAVRGVHQQA 558 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: 919 Number of extensions: 24 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: 559 Length adjustment: 36 Effective length of query: 518 Effective length of database: 523 Effective search space: 270914 Effective search space used: 270914 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