GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Escherichia coli BW25113

Align PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= TCDB::D2RXA8
         (392 letters)



>FitnessBrowser__Keio:14863
          Length = 658

 Score =  213 bits (541), Expect = 2e-59
 Identities = 129/325 (39%), Positives = 188/325 (57%), Gaps = 25/325 (7%)

Query: 16  VKEDLMTGVSFMIPFVTIGGIFLALAFMVAELPGTAGSTETVFEETGSLAWYLAQIGD-- 73
           +K+ L++G+SF +P +  GG  LA+A +++++ G     + +F E  S  W   ++G   
Sbjct: 306 LKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGL----QDLFNEENSWLWMYRKLGGGL 361

Query: 74  LGLTIMIPVLGGYIAYAVADKPGLAPGFILSWVIQQEAVIEAAGLVIGFEADGAVAGFLG 133
           LG+ +M+PVL  Y AY++ADKP LAPGF             AAGL     A+   +GFLG
Sbjct: 362 LGI-LMVPVLAAYTAYSLADKPALAPGF-------------AAGLA----ANMIGSGFLG 403

Query: 134 AIVAGLLAGYVARWMKGW-SVPSVVSQMMPILVIPVFTTLLLAPVVILGLGVPIAIVDDA 192
           A+V GL+AGY+ RW+K    + S  +  +   + PV  TL    +++  +G P+A ++++
Sbjct: 404 AVVGGLIAGYLMRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINNS 463

Query: 193 LTSALEGMQGSNALLLGAILGGMMAVDMGGPINKVAYVFGTVLVADQIFAPMAAVMIGGM 252
           LT+ L G+ GSNALLLGAILG M + D+GGP+NK AY F    +A+ ++ P A      M
Sbjct: 464 LTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVYGPYAIFASVKM 523

Query: 253 VPPLGLALSNFIAPQKYAAEMYENAKAAVPLGLAFITEGAIPYAAADPLRVIPSAVLGSA 312
           V    +  S  +AP+ +     E  K+   LGLA ITEGAIP A  DPLRVI S VLGS 
Sbjct: 524 VSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGSFVLGSM 583

Query: 313 TAGAAALWLGVTMPAPHGGIFVVFL 337
             GA    + + +  P  GIF +FL
Sbjct: 584 VTGAIVGAMNIGLSTPGAGIFSLFL 608


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: 631
Number of extensions: 30
Number of successful extensions: 5
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: 392
Length of database: 658
Length adjustment: 34
Effective length of query: 358
Effective length of database: 624
Effective search space:   223392
Effective search space used:   223392
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 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