GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Brucella inopinata BO1

Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate WP_008509834.1 BIBO1_RS16195 carbohydrate ABC transporter permease

Query= reanno::Smeli:SM_b20327
         (276 letters)



>NCBI__GCF_000182725.1:WP_008509834.1
          Length = 275

 Score =  478 bits (1230), Expect = e-140
 Identities = 240/275 (87%), Positives = 262/275 (95%)

Query: 2   VVAIAKRTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSH 61
           ++   KR+AFY LVA+IILVAVFPFYYAI+TS KSGTALF++DYWP  +SL NY G+ + 
Sbjct: 1   MMRFVKRSAFYLLVALIILVAVFPFYYAIITSFKSGTALFQVDYWPKSLSLDNYTGVLTQ 60

Query: 62  GTFVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLA 121
           G+FVR+LGNSLLVAT+VVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLA
Sbjct: 61  GSFVRSLGNSLLVATVVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLA 120

Query: 122 GLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVI 181
           GLFELIRF+GIFNTPLAL+FSYMIF+LPFTVWVLTTFMRDLP+EIEEAAIVDGASPWV+I
Sbjct: 121 GLFELIRFLGIFNTPLALVFSYMIFSLPFTVWVLTTFMRDLPVEIEEAAIVDGASPWVII 180

Query: 182 TRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWG 241
           TRVFMPLMWPALVTTGLLAFI+AWNEFLFALTFTSS +QRTVPVAIALLSG SQFEIPWG
Sbjct: 181 TRVFMPLMWPALVTTGLLAFISAWNEFLFALTFTSSGSQRTVPVAIALLSGSSQFEIPWG 240

Query: 242 NIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276
           NIMAASVIVTVPLV+LVLIFQRRI+SGLTAGGVKG
Sbjct: 241 NIMAASVIVTVPLVILVLIFQRRIVSGLTAGGVKG 275


Lambda     K      H
   0.332    0.143    0.426 

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: 334
Number of extensions: 8
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: 276
Length of database: 275
Length adjustment: 25
Effective length of query: 251
Effective length of database: 250
Effective search space:    62750
Effective search space used:    62750
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: 40 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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