Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_015933298.1 MNOD_RS33010 asparagine synthetase B
Query= BRENDA::Q9SP20 (591 letters) >NCBI__GCF_000022085.1:WP_015933298.1 Length = 470 Score = 160 bits (405), Expect = 1e-43 Identities = 141/467 (30%), Positives = 213/467 (45%), Gaps = 46/467 (9%) Query: 1 MCGILAVLGCSDDSQAKRVRVLELSRRLKHRGPDWSGLYQHGDNYLSHQRLAIIDPASG- 59 MCGI+ + R+ +L HRGPD SG+ G H RL+++D S Sbjct: 1 MCGIIGSFNLPGFDVSSRLE------QLAHRGPDGSGVLSAGPAVHGHVRLSLVDLTSAS 54 Query: 60 DQPLFNEDQTIVVTVNGEIYNHEELRKRLTAAGHKFRTGSDCDVIAHLYEEHGEDFVDML 119 DQP D V+T NGEI+N++E+R +L A G +FRT D +V+A + G + L Sbjct: 55 DQPFRYGDA--VLTFNGEIWNYQEVRAQLQAEGVRFRTAGDTEVLAAVLHRWGVHGLARL 112 Query: 120 DGMFSFVLLDTRNNTYIAARDAIGITSLYIGWGLDGSVWISSELKGLNDDCEHFEVFPPG 179 +GMF+F ++ +I RD G LY+ +G W SSE KGL DC + PPG Sbjct: 113 EGMFAFAW--SKGEMHILVRDRFGEIPLYVHRKGNGFAW-SSERKGLGRDCPAAPL-PPG 168 Query: 180 HLYSSKTGGFKRWYNPLWFAETIPSTPYDPLVLRCAFENAVIKRLMTDVPFGVLLSGGLD 239 + G + WY P P L + V +RL+ D P L+SGGLD Sbjct: 169 CVLDLPNGEVRPWYER-------PEHPGINDRLISLVRDGVERRLVADAPLCCLISGGLD 221 Query: 240 SSLVASITARYLAGTKAAKQWGAQLHSFCVGLEG-SPDLKAAREVADYLGTVHHEFHFTV 298 SSLV LA KA K + ++ L+G S DL+AAR + D E Sbjct: 222 SSLV-------LALAKARK---PDVVAYTAVLDGESADLRAARRLCDEFEVPLVEVPVPA 271 Query: 299 QDGIDAIEDVIYHIETYDVTTIRASTPMFLMSRKIKSLGVKMVISGEGSDEIFGGY-LYF 357 G DA+E IE + + ++ I S G K +SGE +DE+FGGY Sbjct: 272 PTG-DALEAAARAIEIDSKAQVEIAALCIPLAHAIASDGFKACLSGEAADELFGGYGNMC 330 Query: 358 HKALNREEFHQETCR--KIKALHQYDCLRANKSTSAWGLEARVPFLDKEFINVAMSIDPE 415 K + + R ++ + + + +R NK+ A G+E R+PF+++ + +++ Sbjct: 331 IKGASASDIGWREIRVAQLLKMARGNFVRCNKAFMAAGVECRLPFIERRLVEAVIAM--- 387 Query: 416 AKMINMDQKRIEKWVLRRAFEDEEHPYLPKHILYRQKEQFSDGVGYS 462 + E + A + +P ++ R K+ F G G S Sbjct: 388 --------TKAECPPGKGALKQAAAGIVPGWVVKRPKDTFQGGAGMS 426 Lambda K H 0.320 0.137 0.421 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: 584 Number of extensions: 29 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: 591 Length of database: 470 Length adjustment: 35 Effective length of query: 556 Effective length of database: 435 Effective search space: 241860 Effective search space used: 241860 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 Apr 10 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