Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_007472835.1 CMTB2_RS00230 asparagine synthase (glutamine-hydrolyzing)
Query= BRENDA::P22106 (554 letters) >NCBI__GCF_000170735.1:WP_007472835.1 Length = 565 Score = 138 bits (347), Expect = 7e-37 Identities = 127/407 (31%), Positives = 190/407 (46%), Gaps = 81/407 (19%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC+IFG+ + VE+ K AL L M+HRG D+S I + RL+I ++ Sbjct: 1 MCAIFGMIG---ENVEVVKSALNL---MQHRGNDYSDIKTNKKYTFGFNRLAIENLEINN 54 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120 QPL + K V NGEIYN++ L +Y ++ EVI L+++ G EF+ L G Sbjct: 55 QPLKIEDKLFVF--NGEIYNYKELIK----KYNLNVKTEIEVIAKLWEKFGVEFVKYLDG 108 Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLY--------------------MGYDEHGQLYVAS 160 MFA A+YD K YL RD G PLY + + + + + Sbjct: 109 MFAIAIYD--KKLYLF-RDEFGKKPLYFTKNAFSSEINPLLKIVKKEINLNALSEFFAYN 165 Query: 161 EMKALVPVCRTIKEFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNE-----LRQA 215 A + + I + PAG Y DGEI+ W D++ + +NE + Sbjct: 166 SSIAPNTIYKGIFKLPAGCYF---DGEIKR-----WHDFEMKNEKCKMENEKVIFNIENL 217 Query: 216 LEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGL 275 L S++ LM DV G LLSGG+DSS+I A+ KY ++ +F++G Sbjct: 218 LTKSIEKRLMGDVEIGSLLSGGVDSSLIVALALKY---------------KKIDTFSIGY 262 Query: 276 PG---SPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYL 332 G + K A+ VANHLG + + T ++ + +V+ D S + Sbjct: 263 EGFENYDERKYAKVVANHLGIKNFDFVLTKKKFYENFENVL------DAMQEPISDSSFF 316 Query: 333 MSRKI-KAMGIKMVLSGEGSDEVFGGY------LYFHKA--PNAKEL 370 + ++ K + +K+VLSGEGSDE+F GY L F K+ PN K L Sbjct: 317 AAYELAKNIPLKVVLSGEGSDELFLGYRRYDEFLKFFKSYLPNKKWL 363 Score = 40.8 bits (94), Expect = 1e-07 Identities = 24/82 (29%), Positives = 46/82 (56%), Gaps = 6/82 (7%) Query: 387 ARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVA 446 ++ +K A +EAR PFLDK ++ ++ +++ GN +K I++E + YLP + Sbjct: 442 SKLDKMFMAHSIEARSPFLDKNLVNFVFSMS--EEIRGN---KKWIIKEIAKKYLPKEIV 496 Query: 447 WRQKEQFSDGVGYSWIDTLKEV 468 +R+K+ F+ Y W+ E+ Sbjct: 497 YRRKKGFALPF-YEWLKEENEL 517 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: 685 Number of extensions: 36 Number of successful extensions: 8 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: 565 Length adjustment: 36 Effective length of query: 518 Effective length of database: 529 Effective search space: 274022 Effective search space used: 274022 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