Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate WP_011382489.1 AMB_RS00215 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_002444 (554 letters) >NCBI__GCF_000009985.1:WP_011382489.1 Length = 585 Score = 170 bits (431), Expect = 1e-46 Identities = 132/399 (33%), Positives = 199/399 (49%), Gaps = 47/399 (11%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSR-LMRHRGPDWSGIYASDNAI--LAHERLSIVDVN 57 MC + +F ++ A ++ L + R MR RGPD + + S + LAH RL+I+D++ Sbjct: 1 MCGLAAIFAYQSKAPPVQGDELAVVRDAMRLRGPDGAASWISPDGRVGLAHRRLAIIDLS 60 Query: 58 -AGAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQ-FQTGSDCEVILALYQEKGPEFL 115 AGAQP+ + L NGEIYN++ALRAE F++ +D EVIL ++ G + L Sbjct: 61 PAGAQPMTSADGRLALVFNGEIYNYRALRAELESLGTVFRSHTDTEVILEGWRHWGRDVL 120 Query: 116 DDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALV--------- 166 L+GMFA AL+D+E L+ RD LGI PLYM D+ G L VAS++KAL+ Sbjct: 121 SRLRGMFALALWDNEARGMLLARDPLGIKPLYMA-DQGGCLRVASQVKALLAGGSVDTTP 179 Query: 167 ------------------PVCRTIKEFPAGSYLWSQD--GEIRSYYHRDWFDYDAVKDNV 206 + R I+ PAGS+LW + G + + A + Sbjct: 180 DPAGHAGFFLWGHVPEPHTLYRAIQALPAGSWLWRDEAGGRDEGRFFDLGQELAAADEKS 239 Query: 207 TDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWP 266 D + L +AL DSVK+HL +DVP G+ LSGGLDS+ ++A+ ++ A V+ Sbjct: 240 FDIDILHEALADSVKAHLEADVPVGLFLSGGLDSTTLAALVREAAEGPVKSITLG----- 294 Query: 267 QLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRA 326 F G ++ A+ VA H H T + A ++ H++ V + Sbjct: 295 -FSEFQGG--AQDEVPLAERVAAHYRLNHTTSRVTAADFAQARDQLLAHMDQPSVDGVNT 351 Query: 327 STPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAP 365 + ++R G+K+ LSG G DE+F GY F + P Sbjct: 352 ----WFVARAAARSGLKVALSGLGGDELFAGYDSFAQIP 386 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: 697 Number of extensions: 42 Number of successful extensions: 6 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: 585 Length adjustment: 36 Effective length of query: 518 Effective length of database: 549 Effective search space: 284382 Effective search space used: 284382 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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