GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Sphingomonas koreensis DSMZ 15582

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Ga0059261_2514 Ga0059261_2514 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::WCS417:GFF780
         (952 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2514 Ga0059261_2514
           phosphoenolpyruvate-protein phosphotransferase
          Length = 759

 Score =  279 bits (713), Expect = 6e-79
 Identities = 191/570 (33%), Positives = 295/570 (51%), Gaps = 22/570 (3%)

Query: 399 SQVQAIAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQ 458
           ++V       G+A G A     ++       E    ER R+++A   +R  I  +  +++
Sbjct: 183 ARVPGFKLVEGMAAGAAVFHQPRIIIEHTVAEDIEAERHRVYAAFDKMREQIDRMTSQAE 242

Query: 459 ---SKAIREIFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALL 515
                   E+  T++    D   +  ++  +  G +AEAA   V +    +   + D LL
Sbjct: 243 FGGGGEHEEVLETYKMFAYDEGWSRRINEAIDSGLTAEAAIERVQQRTRMRMRQIDDPLL 302

Query: 516 AERAADLRDIGRRVLAQLCG-VETSQEPS--EPYILVMDEVGPSDVARLDPARVAGILTA 572
            +R  DL D+  R+L  + G + T+ +    +  IL+   +GP+++   D  R+ G++  
Sbjct: 303 RDRMHDLEDLSNRLLRIVSGQLGTAAQLGLRQDSILIARNLGPAELLEYDRRRLKGVVLE 362

Query: 573 RGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVE 632
            G  TAH  IVARA+G+P L        L+A G  LL+D     L +   AA  +    +
Sbjct: 363 EGSLTAHVTIVARAMGVPVLGRVKDIRRLIAEGDRLLVDVTEDTLIIRPTAAMDEAFEAK 422

Query: 633 RDTREQRLQAASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFM 692
               ++R  A +A ++E  +T DGH + V  N G    VA+    GA+GIGL RTE  F+
Sbjct: 423 LLVTQKRRAAFAALKNEAPVTTDGHRLTVMVNAGLRDDVAALDLTGADGIGLFRTEFQFL 482

Query: 693 AHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYW---PIAEEENPFLGVRG 749
                P   +Q   Y+ VLD    RP+  RT+D+GGDK LPY       EEENP +G R 
Sbjct: 483 VSATLPQRDSQRRLYKDVLDAAGDRPVTFRTVDIGGDKALPYLDHDENGEEENPAMGWRA 542

Query: 750 IRLTLQRPQIMEAQLRALLRSADNRPLRIMFPMVGSVDEWRAARDM--TERLRLE----- 802
           +RL L R  +M+ Q RALL +A  R L +MFPMV    E+  AR +  T+R  LE     
Sbjct: 543 LRLALDREGLMKVQARALLEAAAGRTLNVMFPMVSEPWEFDEARTLFETQRAWLESRGHK 602

Query: 803 IPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLH 862
           +P+  ++ G M+EVP+ A +  +L   +DF SVGTNDLTQ+  A DR HP L+ + D L 
Sbjct: 603 LPL-HIRYGAMLEVPALAEVLDLLLPRLDFLSVGTNDLTQFLFAADRAHPKLAVRYDWLS 661

Query: 863 PAVLQLI-DITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARV 921
           P++L+ +  +T  AA A    + VCGE+   PL    L+GLG+D LS++  ++  +KA V
Sbjct: 662 PSILRFLRRVTAEAAEADVP-LAVCGEMGGRPLEAMALIGLGIDRLSITPAAVGPIKAMV 720

Query: 922 REFSLSEAQGL-AQKALAVGSPAEVRALVE 950
           R  SL  A+ + A + +    P ++RA +E
Sbjct: 721 R--SLDRAKLIAAMRGMLDRPPQDMRAALE 748


Lambda     K      H
   0.318    0.135    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: 1393
Number of extensions: 62
Number of successful extensions: 3
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: 952
Length of database: 759
Length adjustment: 42
Effective length of query: 910
Effective length of database: 717
Effective search space:   652470
Effective search space used:   652470
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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