GapMind for catabolism of small carbon sources

 

Alignments for a candidate for crr in Pseudomonas fluorescens FW300-N1B4

Align glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= CharProtDB::CH_088352
         (169 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833
          Length = 844

 Score =  120 bits (302), Expect = 4e-32
 Identities = 57/141 (40%), Positives = 91/141 (64%)

Query: 21  IEIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSI 80
           ++++APLSG ++ ++ VPD VF+ +++GDG+ I PT   + AP+ G I  +  + HA SI
Sbjct: 7   LQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVSGHAVSI 66

Query: 81  ESDSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTPVV 140
             D+GV++ +H G+DTV L G+GF R+ EEGQRV VG  +IEFD   +   A+S LT ++
Sbjct: 67  TDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARSLLTLML 126

Query: 141 ISNMDEIKELIKLSGSVTVGE 161
           + + +    L   +G V  G+
Sbjct: 127 VVSGEPFTWLAPETGVVESGQ 147


Lambda     K      H
   0.315    0.138    0.374 

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: 286
Number of extensions: 12
Number of successful extensions: 1
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: 169
Length of database: 844
Length adjustment: 30
Effective length of query: 139
Effective length of database: 814
Effective search space:   113146
Effective search space used:   113146
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: 42 (21.9 bits)
S2: 49 (23.5 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