GapMind for catabolism of small carbon sources

 

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

Align Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale)
to candidate H281DRAFT_01977 H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family

Query= uniprot:Q9KZP2
         (149 letters)



>FitnessBrowser__Burk376:H281DRAFT_01977
          Length = 854

 Score = 89.4 bits (220), Expect = 1e-22
 Identities = 50/144 (34%), Positives = 76/144 (52%), Gaps = 4/144 (2%)

Query: 6   SPLAGRAIGLAAVPDPVFSGAMVGPGTAIDPVREPSEAVAPVDGVIVSLHP--HAFVVVD 63
           +P+ G  + LA VPDPVFSG M G G  +DP+      VAP +G +  L    HA  +  
Sbjct: 12  APMTGPVVPLANVPDPVFSGGMFGDGIGVDPLE--GRLVAPCEGTVTHLARTGHAVTLAT 69

Query: 64  ESGHGVLTHLGIDTVQLNGEGFELLVNKGDTVVRGQGVVRWDPAAVEAAGKSPICPIVAL 123
             G  +L H+GIDTV+LNG+GF  ++ +G  V  G  ++ +D   +     S +  I   
Sbjct: 70  AEGAEILLHIGIDTVELNGKGFAPMIEQGAHVHAGDVLIEFDQDQIALHAPSLVSVIAIA 129

Query: 124 EATAEALADLREDGDVKAGESLFL 147
            + A  + +  + G +KAGE+  L
Sbjct: 130 NSDAFEIVERAQGGMLKAGETPLL 153


Lambda     K      H
   0.316    0.136    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: 341
Number of extensions: 18
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: 149
Length of database: 854
Length adjustment: 29
Effective length of query: 120
Effective length of database: 825
Effective search space:    99000
Effective search space used:    99000
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: 41 (21.6 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