GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Paraburkholderia atlantica CCGE1002

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_013089330.1 BC1002_RS06830 homoserine dehydrogenase

Query= BRENDA::Q9WZ17
         (739 letters)



>NCBI__GCF_000092885.1:WP_013089330.1
          Length = 443

 Score =  206 bits (523), Expect = 3e-57
 Identities = 146/411 (35%), Positives = 222/411 (54%), Gaps = 22/411 (5%)

Query: 20  VRVGIAGLGTVGGSIYRILKERGNEIEKRIGEKFIISKVINRSPQKYEL-LGVPKEEIAF 78
           ++VG+ G GTVG   + +L+    EI++R G    I+++  R+P K    LG     +A 
Sbjct: 4   IKVGLLGFGTVGSGTFTVLRRNQEEIKRRAGRGIEIARIAVRNPAKATAALGAEAGSVAL 63

Query: 79  --DFDDLILNSDV--VVEAIGGTDVAVDLVRRALELGRIVVTPNKNLISEYGNEFSEYIK 134
             DF+ ++ +  +  V E IGGT +A DLV RA+  G+ VVT NK L++ +G E  E  +
Sbjct: 64  TDDFNAVVDDPSISIVAEMIGGTGIARDLVLRAINNGKHVVTANKALLAVHGTEIFEAAR 123

Query: 135 KRKLF--FEASVGGGIPIISLLQDYLIFQKVTRIRGIMNGTTNYILTEM-SKGRHFEEVL 191
              +   FEA+V GGIPII  L++ L   ++  I GI+NGTTNYIL+EM  +G  F   L
Sbjct: 124 ANGVMVAFEAAVAGGIPIIKALREGLTANRIQYIAGIINGTTNYILSEMRDRGLDFATAL 183

Query: 192 KEAQELGYAEADPTNDIEGYDVAYKVSVLAGVVTGRFPGINSVQFEGITR---IDPEYLK 248
           K AQELGYAEADPT DIEG D A+K ++++ +  G     +    EGI++   ID +Y +
Sbjct: 184 KAAQELGYAEADPTFDIEGVDAAHKATIMSAIAFGVPVQFDRAYVEGISKLAAIDIKYAE 243

Query: 249 EIVRSGKKLKLIGELDFSTNRYEVRLR-EVTPEDPFF-NVDGVDNAIEVSTDLAGDFLLK 306
           E+   G ++KL+G    +    E+R+   + PE     NV+G  NA+ V  D  G  L  
Sbjct: 244 EL---GYRIKLLGITRRTDKGIELRVHPTLIPEKRLLANVEGAMNAVVVHGDAVGTTLYY 300

Query: 307 GRGAGGYPTASAVIADLFRVAKYKVLGGAEKFSVVVMKFGGAAISDVEKLEKVAEKIIKR 366
           G+GAG  PTASAV+ADL  V +        +   +  +    + + +  +E+V      R
Sbjct: 301 GKGAGAEPTASAVVADLVDVTRLHTADPEHRVPHLAFQPDSLSNTPILPIEEVTSGYYLR 360

Query: 367 KK----SGVKPVV--VLSAMGDTTDHLIELAKTIDENPDPRELDLLLSTGE 411
            +    +GV   +  VL+  G + D L++    + +     E D+LL T E
Sbjct: 361 LRVADVTGVLADITRVLADTGISIDALLQKESELVDANGKGETDILLITHE 411


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: 747
Number of extensions: 35
Number of successful extensions: 6
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: 443
Length adjustment: 36
Effective length of query: 703
Effective length of database: 407
Effective search space:   286121
Effective search space used:   286121
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 25 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