GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Novosphingobium barchaimii LL02

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_059152208.1 V474_RS14540 aspartate kinase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_001046635.1:WP_059152208.1
          Length = 419

 Score =  270 bits (691), Expect = 8e-77
 Identities = 156/414 (37%), Positives = 252/414 (60%), Gaps = 18/414 (4%)

Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400
           +VMKFGG +++  E++ +VA  + +++++G +  VV+SAM   TD L+   +  +   DP
Sbjct: 4   IVMKFGGTSMAGSERIRRVAGIVKRQQEAGHEVAVVVSAMSGETDRLVNFCREANALYDP 63

Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460
            E D+++++GE  +  L+++ L+  G KA S+ G Q+ I TD  +  ARI +I+ D +  
Sbjct: 64  AEYDVVVASGEQVTSGLLALTLQAIGCKARSWQGWQVPIKTDDAHAKARIEEIDADALIA 123

Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520
            +    I V+ GFQG++  G +TTLGRGGSD +A+A+A ++ AD C++Y DVDGVYT DP
Sbjct: 124 SMAAGEIAVIPGFQGVSPEGRVTTLGRGGSDTSAVAVAAAVKADRCDIYTDVDGVYTTDP 183

Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKN--------AHKET 572
           RIV  AR +  +++EEM+EL+  G++VLQ R+   A K  V+V + +        A    
Sbjct: 184 RIVAKARKLPLVTYEEMLELASVGSKVLQTRSVSLAMKEKVRVQVLSSFIDETAPAADTI 243

Query: 573 RGTLI-----WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNID 627
            GTLI      EG+ +E  ++  +  +   AKV L  VPD+PG  A I   L++  +N+D
Sbjct: 244 PGTLIVSDEELEGSDMERQLITGIAADKNEAKVTLTRVPDRPGAVASIFAPLAESNINVD 303

Query: 628 MIIQGMKSGEYNT-VAFIVPESQLGKLDIDLLKTRSEA---KEIIIEKGLAKVSIVGVNL 683
           MIIQ +   +  T V F VP+S L +    +L+ R ++     +I +  +AK+S+VGV +
Sbjct: 304 MIIQNVAKDKGETDVTFTVPQSDLARAQA-MLEERKDSIGYYRLIADGNVAKISVVGVGM 362

Query: 684 TSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737
            S   +++T+F+TLA+ GINI  IS S  ++SV+ID    E AV+ +H+ + LD
Sbjct: 363 RSHAGVASTMFKTLADRGINIIAISTSEIKVSVLIDTDETELAVRVLHTAYGLD 416


Lambda     K      H
   0.318    0.137    0.377 

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: 616
Number of extensions: 24
Number of successful extensions: 4
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: 739
Length of database: 419
Length adjustment: 36
Effective length of query: 703
Effective length of database: 383
Effective search space:   269249
Effective search space used:   269249
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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