GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Escherichia coli BW25113

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)

Query= curated2:C4Z566
         (557 letters)



>FitnessBrowser__Keio:14407
          Length = 655

 Score =  248 bits (634), Expect = 4e-70
 Identities = 175/499 (35%), Positives = 253/499 (50%), Gaps = 47/499 (9%)

Query: 46  GHMNIDKIVNAVKLGVAEAGGVPVVFPAIAVCDGIAMGHVGMKYSLVTR-DLIADSTECM 104
           GH  I   + A    +   GG+P        CDG + G  GM  SL  R D        +
Sbjct: 88  GHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLI 147

Query: 105 AIAHQFDGLVMVPNCDKNVPGLLMAAARLN-LPTVFVSGG---PMLAGHVKGKKRSLSSM 160
                   ++ V  CDK +P  ++A A ++ LPT+ V GG   P   G   GK +++ + 
Sbjct: 148 RSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQTIGAR 207

Query: 161 FEAVGSYAAGTMTEEDVLEFEEKVCPTC----GSCSGMYTANSMNCLTEALGMGLRGNGT 216
           F            E  + E  E  C  C    G C  + TA +   + EALG+ L  +  
Sbjct: 208 F---------ANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSAL 258

Query: 217 IPAVYSERIKLAKHAGMAVMDMVNKGITARDIITKDSIMNALTVDMALGCSTNSMLHLPA 276
            P+  +  +++A+ +  AV ++ ++GIT RDI++  +I NA+ +  A G STN +LH+PA
Sbjct: 259 APSGQAVWLEIARQSARAVSELDSRGITTRDILSDKAIENAMVIHAAFGGSTNLLLHIPA 318

Query: 277 IAHEIGFDF-DIKFANPISEKTPNLCHLAPAGPTYMEDLNE--AGGVYAVMKELADIGLL 333
           IAH  G    D++    I+ K P L  + P GP Y   +    AGGV  VM  L D+GLL
Sbjct: 319 IAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLHLRDLGLL 378

Query: 334 NTDCLTVSGKTIGE----------------CIATAYNRDPE-VIRTVDNAYSK--TGGLA 374
           + D +TV+G+T+GE                C+      +P+ VI   + A +K  T  + 
Sbjct: 379 HLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEKAKAKGLTSTVC 438

Query: 375 VLSGNLAPDGSVVKRSAVVPEMLV------HEGPARVFDSEEDAIAAIKGGKIVEGDVVV 428
             +GN+AP+GSV+K +A+ P ++       H G  RVF SE  AI AIK  +IV+GD++V
Sbjct: 439 FPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMV 498

Query: 429 IRYEGPKGGPGMREMLNPTSAIAGMGLGSSVALITDGRFSGASRGASIGHVSPEAAVGGP 488
           +   GP G  GM E    TSA+  +  G +V+LITD RFSG S GA  GHVSPEA  GGP
Sbjct: 499 VIGGGPSG-TGMEETYQLTSALKHISWGKTVSLITDARFSGVSTGACFGHVSPEALAGGP 557

Query: 489 IALVEEGDIISIDIPGLKL 507
           I  + + DII I +  L L
Sbjct: 558 IGKLRDNDIIEIAVDRLTL 576


Lambda     K      H
   0.317    0.134    0.385 

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: 924
Number of extensions: 50
Number of successful extensions: 8
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: 557
Length of database: 655
Length adjustment: 37
Effective length of query: 520
Effective length of database: 618
Effective search space:   321360
Effective search space used:   321360
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: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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