GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SemiSWEET in Desulfovibrio vulgaris Miyazaki F

Align Sugar transporter SemiSWEET (characterized)
to candidate 8501181 DvMF_1915 hypothetical protein (RefSeq)

Query= SwissProt::B0SR19
         (85 letters)



>FitnessBrowser__Miya:8501181
          Length = 98

 Score = 66.2 bits (160), Expect = 8e-17
 Identities = 31/81 (38%), Positives = 48/81 (59%)

Query: 4  LIGYVAAFLTTVSFLPQVLRVVMTKQTRDISRNMYIMFFLGVVLWFVYGILRSDLPIILA 63
          +IGY A  LT++++LPQV+R+  T+   DIS   + +  +GV LW VYGI     P++ A
Sbjct: 17 IIGYAAGLLTSLAYLPQVVRIARTRSADDISLPTFRLLAVGVALWLVYGIGIGSWPVMAA 76

Query: 64 NVVTLFFVTIILYYKLTEGNQ 84
          N V L  +  +++ KL    Q
Sbjct: 77 NAVGLALILAVIWLKLRYSRQ 97


Lambda     K      H
   0.334    0.147    0.429 

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: 26
Number of extensions: 2
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: 85
Length of database: 98
Length adjustment: 9
Effective length of query: 76
Effective length of database: 89
Effective search space:     6764
Effective search space used:     6764
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 39 (19.6 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