GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asnB in Methylobacterium nodulans ORS 2060

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.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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