GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Thermophagus xiamenensis HS1

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010527681.1 GQW_RS0109190 homoserine dehydrogenase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_000220155.1:WP_010527681.1
          Length = 399

 Score =  146 bits (368), Expect = 2e-39
 Identities = 97/314 (30%), Positives = 173/314 (55%), Gaps = 18/314 (5%)

Query: 18  RKVRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYELLGVPKEEIA 77
           +K+ +G+ G G VG  +Y +LK +   ++ ++ EK  + + I RS        +P+    
Sbjct: 4   QKLTLGLFGFGVVGQGLYDVLK-KSPALDVKV-EKICVKRKIKRS--------LPEHFFC 53

Query: 78  FDFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIKK 135
           ++ DD++ N  +  +VE I   D A  +V++AL  G+ VV+ NK +++E   E     K+
Sbjct: 54  YNPDDILENDRINTIVELIDNADEAYFIVKKALLKGKNVVSANKKMLAENLAELVSLAKE 113

Query: 136 RK--LFFEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVLK 192
           +   L +EAS  G IP+I  L++Y     +  + GI+NG++NYIL+++    + +EE LK
Sbjct: 114 KNVSLLYEASACGSIPVIRNLEEYYDNDLLLSVTGILNGSSNYILSKIFDNNQSYEEALK 173

Query: 193 EAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITRIDPEYLKEIVR 252
           EAQ LG+AE++P+ D++G+D  YK+ +L     G     N V   GI+ I    +     
Sbjct: 174 EAQNLGFAESNPSFDVDGFDSLYKLIILTMHSFGVIVPPNDVLNYGISNISDFDINFAKE 233

Query: 253 SGKKLKLIGELDFSTNR---YEVRLREVTPEDPFFNVDGVDNAIEVSTDLAGDFLLKGRG 309
            G K+KL+G+++   ++     V  R V+ +   ++V+   N + +         + G+G
Sbjct: 234 KGYKIKLVGQVERLHDKKITLFVLPRFVSKDKYIYSVEDEFNGVVIKGLAYDKQFMFGKG 293

Query: 310 AGGYPTASAVIADL 323
           AGG+PT SAV++D+
Sbjct: 294 AGGHPTGSAVLSDI 307


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: 650
Number of extensions: 31
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: 739
Length of database: 399
Length adjustment: 35
Effective length of query: 704
Effective length of database: 364
Effective search space:   256256
Effective search space used:   256256
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: 52 (24.6 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