Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_083930282.1 METMI_RS0111890 hypothetical protein
Query= BRENDA::P22106 (554 letters) >NCBI__GCF_000384075.1:WP_083930282.1 Length = 528 Score = 199 bits (505), Expect = 3e-55 Identities = 156/523 (29%), Positives = 256/523 (48%), Gaps = 32/523 (6%) Query: 1 MCSIFGVFDIKTDA-VELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAG 59 MC I G+ +A + + K E+ L+ HRG GI +N L RL ++ N G Sbjct: 1 MCGIAGIISKPNNADINISKLVNEMLELISHRGRGELGIKTGNNYSLGCYRLPVL-TNGG 59 Query: 60 AQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQ 119 QP+ N+ K+ +NGEIYN+ L ++ + D ++ LY+E G L L Sbjct: 60 EQPVSNELKSIFAVLNGEIYNYNELIDSLKLKHTIKGDCDTVILPHLYEE-GELSLRKLS 118 Query: 120 GMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCR-TIKEFPAG 178 GM+A ++D+ + ++ RD +GI PLY+ ++ + + ASE KA + + E G Sbjct: 119 GMYALCVHDTVSNETVLMRDLIGIKPLYI-FENNFFIAFASEKKAFSYLNHGKVSEVMPG 177 Query: 179 SYLWSQDGEIRSYYH--RDWFDYDAVKDNV--TDKNELRQALEDSVKSHLMSDVPYGVLL 234 L + G I S + + W + VK N D LR + +S+ L S+ P VL Sbjct: 178 ELLRLKHGLITSRANIVKPW-NKSLVKGNYQSVDYTGLRDEITNSLIQQLPSEWPVAVLC 236 Query: 235 SGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTV 294 SGG+DS I++ + KKY V+ ++ +G S D+KAA+ +HL Sbjct: 237 SGGIDSVILTYLAKKYHKHNVQ-------------AYVIGNENSADVKAARLACHHLDVN 283 Query: 295 HHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEV 354 EI +++E + + +VIYH+E+++ IR S YL+ R+I+ G ++ + GEG+DE+ Sbjct: 284 LKEIRISMEEIIKVLPEVIYHVESFESNLIRNSILSYLVFREIRKDGFRVAICGEGADEL 343 Query: 355 FGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAM 414 F GY F + E + L L R ++ A+ VE RVPFLD ++ A Sbjct: 344 FAGYGDFRLLSSIIEKQKFMKLLLDDLFKTQLQRVDRTSMAFNVETRVPFLDDNVIEYAC 403 Query: 415 RINPQDKMCGN--GK-MEKHILRECF-EAYLPASVAWRQKEQFSDGVGYSWID----TLK 466 I P +K CG G+ + K LR F +P + RQKE FS G G + ++ Sbjct: 404 NI-PIEKKCGKDFGRWLSKLPLRHAFANTQIPTEILLRQKETFSSGAGLGDLSMVGGPIE 462 Query: 467 EVAAQQVSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLP 509 ++A ++S + + + ++P + E LY + + F +P Sbjct: 463 KIAQSRISSNEFISMQSKYPVIDIKTYEQALYLSEYLKYFFVP 505 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: 597 Number of extensions: 25 Number of successful extensions: 5 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: 528 Length adjustment: 35 Effective length of query: 519 Effective length of database: 493 Effective search space: 255867 Effective search space used: 255867 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: 52 (24.6 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