GapMind for catabolism of small carbon sources

 

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

Align Putative PTS IIA-like nitrogen-regulatory protein PtsN, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate 17275 b3204 sugar-specific enzyme IIA component of PTS (NCBI)

Query= TCDB::D2RXA7
         (156 letters)



>FitnessBrowser__Keio:17275
          Length = 163

 Score = 75.5 bits (184), Expect = 4e-19
 Identities = 49/148 (33%), Positives = 75/148 (50%), Gaps = 2/148 (1%)

Query: 7   EIDAVLTPELITLEEPPAEKAAAIEFLLDRAVDAGRVTDREAALEALLAREEETTTGVGM 66
           ++ +VL  E          K  A+E + + A     +   +   EA+L RE+  +TG+G 
Sbjct: 9   QLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPP-QVVFEAILTREKMGSTGIGN 67

Query: 67  GIGIPHAKTDAVAEPTI-VFARSSAGIDFDAMDDQPATLLFLLLVPAEGGEEHLELLSSL 125
           GI IPH K +      + VF +    I FDA+D+QP  LLF LLVPA+  + HL  LS +
Sbjct: 68  GIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLV 127

Query: 126 SRALMHDDVRERLHEADSKAAIEETITE 153
           ++ L    +  RL  A S   + + IT+
Sbjct: 128 AKRLADKTICRRLRAAQSDEELYQIITD 155


Lambda     K      H
   0.313    0.130    0.347 

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: 42
Number of extensions: 2
Number of successful extensions: 2
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: 156
Length of database: 163
Length adjustment: 17
Effective length of query: 139
Effective length of database: 146
Effective search space:    20294
Effective search space used:    20294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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