GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Caldicellulosiruptor kronotskyensis 2002

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_013429770.1 CALKRO_RS03705 homoserine dehydrogenase

Query= BRENDA::D8WXQ1
         (432 letters)



>NCBI__GCF_000166775.1:WP_013429770.1
          Length = 418

 Score =  289 bits (740), Expect = 1e-82
 Identities = 159/426 (37%), Positives = 266/426 (62%), Gaps = 16/426 (3%)

Query: 5   QVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQ--LTT 62
           +V ++G G VGSGV +++  +   +  + G  + VK IL  D+   RD    PA+  +  
Sbjct: 3   KVAIMGFGVVGSGVWEVLTKNASSIAKRAGEEISVKYIL--DI---RDFPDHPAKDLMIK 57

Query: 63  NADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASAN 122
           + D IL DP++ +V+E +GG+E    Y  K L   KHVVT+NK+L+A +G ELL  A  N
Sbjct: 58  DFDIILNDPEVSIVVETIGGLEPAYTYTKKLLLNGKHVVTSNKELVARHGPELLKIAKEN 117

Query: 123 GCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKE 182
             + F+EASV GGIPI+R L + LA ++IT++ GI+NGTTNYILT+M K+  ++E+ LKE
Sbjct: 118 NINYFFEASVGGGIPIIRPLQNCLAGNQITEIAGILNGTTNYILTQMKKYSLSFEDALKE 177

Query: 183 AQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQL 242
           AQE GYAE +P++D+EG DA RK+AIL+++ +S  ++ + +  EGI++IT+ED++Y ++L
Sbjct: 178 AQEKGYAERNPSNDIEGHDACRKIAILSSIAYSHYVNYESIYTEGISKITKEDMEYAEEL 237

Query: 243 GYTMKLIGIAHR-EGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGA 301
           G T+KLI ++ + + ++V   V P ++S   P A+V+D +NA+ V G+A+G+ MFYG GA
Sbjct: 238 GCTIKLIAMSKKIDDKRVFARVSPLMISYKSPFANVDDVFNAILVKGDAIGDVMFYGQGA 297

Query: 302 GSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGV 361
           G LPTA+AVV D++ ++K++        A++   +  +   +    +FF+R+  KD    
Sbjct: 298 GKLPTASAVVGDIIDIVKHIDKSYVYTWAISGDIE--VVDIENTSCRFFVRVKYKDYTKA 355

Query: 362 FANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHEIK 421
              ++ IF+      + ++    +  G  E   VTH+    ++ + + +L  ++ V ++ 
Sbjct: 356 KDAVSLIFN------DCMIVNTHRPIGTNEFAFVTHELKESEFREKISQLEKISVVEKVL 409

Query: 422 SSYRVE 427
           S  R +
Sbjct: 410 SIVRYD 415


Lambda     K      H
   0.316    0.134    0.368 

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: 459
Number of extensions: 18
Number of successful extensions: 2
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: 432
Length of database: 418
Length adjustment: 32
Effective length of query: 400
Effective length of database: 386
Effective search space:   154400
Effective search space used:   154400
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 (21.6 bits)
S2: 51 (24.3 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