GapMind for catabolism of small carbon sources

 

Aligments for a candidate for crr in Paraburkholderia bryophila 376MFSha3.1

Align glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized)
to candidate H281DRAFT_01977 H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family

Query= CharProtDB::CH_088352
         (169 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01977 H281DRAFT_01977
           Phosphocarrier protein HPr /phosphoenolpyruvate--protein
           phosphotransferase /PTS system IIA component, Glc family
          Length = 854

 Score =  116 bits (290), Expect = 1e-30
 Identities = 59/152 (38%), Positives = 94/152 (61%), Gaps = 3/152 (1%)

Query: 19  GTIEIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAF 78
           G I ++AP++G +V + +VPD VF+  + GDGI + P   ++VAP +GT+  +  T HA 
Sbjct: 6   GHIVLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCEGTVTHLARTGHAV 65

Query: 79  SIESDSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTP 138
           ++ +  G E+ +H GIDTVEL G+GF  + E+G  V  GD +IEFD   +   A S ++ 
Sbjct: 66  TLATAEGAEILLHIGIDTVELNGKGFAPMIEQGAHVHAGDVLIEFDQDQIALHAPSLVSV 125

Query: 139 VVISNMD--EIKELIKLSGSVTVGETPVIRIK 168
           + I+N D  EI E  +  G +  GETP++ ++
Sbjct: 126 IAIANSDAFEIVERAQ-GGMLKAGETPLLLLR 156


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: 303
Number of extensions: 14
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: 854
Length adjustment: 30
Effective length of query: 139
Effective length of database: 824
Effective search space:   114536
Effective search space used:   114536
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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