GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Streptococcus oralis 7747

Align PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate WP_000701472.1 HK29_RS06445 PTS transporter subunit EIIA

Query= TCDB::D2RXA8
         (392 letters)



>NCBI__GCF_000382825.1:WP_000701472.1
          Length = 650

 Score =  259 bits (663), Expect = 1e-73
 Identities = 149/351 (42%), Positives = 212/351 (60%), Gaps = 16/351 (4%)

Query: 20  LMTGVSFMIPFVTIGGIFLALAFMVAELPGTAGSTETVFEETGS---LAWYLAQIGDLGL 76
           LM+GVS M+PFV  GGI +ALAF++    G  G  +      GS   LA    +IG    
Sbjct: 295 LMSGVSQMLPFVIGGGIMIALAFLI---DGAFGVPQDSLGNLGSYHELASMFMKIGGAAF 351

Query: 77  TIMIPVLGGYIAYAVADKPGLAPGFILSWVIQQEAVIEAAGLVIGFEADGAVAG----FL 132
            +M+PV  GY+AY++A+KPGL  GF+   + ++           G EA   +AG    FL
Sbjct: 352 GLMLPVFAGYVAYSIAEKPGLVAGFVAGAIAKEGFAFGKIPYAAGGEATSTLAGVSSGFL 411

Query: 133 GAIVAGLLAGYVARWMKGW-SVPSVVSQMMPILVIPVFTTLLLAPVVILGLGVPIAIVDD 191
           GA+V G +AG +   +K +  VP  +     IL++P+  T+L    V+L + +P+A ++ 
Sbjct: 412 GALVGGFIAGALVLAIKKYVKVPRSLEGAKSILLLPLLGTILTG-FVMLAVNIPMAAINT 470

Query: 192 ALTSALEGMQGSNALLLGAILGGMMAVDMGGPINKVAYVFGTVLVADQIFA----PMAAV 247
           A+   L G+ G +A+LLG +LGGMMAVDMGGP+NK AYVFGT  +A  + +     MAAV
Sbjct: 471 AMNDFLGGLGGGSAVLLGIVLGGMMAVDMGGPVNKAAYVFGTGTLAATVSSGGSVAMAAV 530

Query: 248 MIGGMVPPLGLALSNFIAPQKYAAEMYENAKAAVPLGLAFITEGAIPYAAADPLRVIPSA 307
           M GGMVPPL + ++  +   K+  E   +    + +GL+FITEGAIP+ AADP R IPS 
Sbjct: 531 MAGGMVPPLAIFVATLLFKDKFTKEERNSGLTNIIMGLSFITEGAIPFGAADPARAIPSF 590

Query: 308 VLGSATAGAAALWLGVTMPAPHGGIFVVFLSSSALLFLACIALGTIVTATV 358
           +LGSA AG      G+ + APHGGIFV+ L+S+ALL+L  + +G IV+  V
Sbjct: 591 ILGSAVAGGLVGLAGIKLMAPHGGIFVIALTSNALLYLVFVLIGAIVSGVV 641


Lambda     K      H
   0.322    0.138    0.402 

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: 717
Number of extensions: 44
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 392
Length of database: 650
Length adjustment: 34
Effective length of query: 358
Effective length of database: 616
Effective search space:   220528
Effective search space used:   220528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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