GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_2514
          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 (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