GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Brucella inopinata BO1

Align ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate WP_134789831.1 BIBO1_RS17965 carbohydrate ABC transporter permease

Query= TCDB::G4FGN6
         (278 letters)



>NCBI__GCF_000182725.1:WP_134789831.1
          Length = 274

 Score =  166 bits (419), Expect = 7e-46
 Identities = 85/277 (30%), Positives = 160/277 (57%), Gaps = 3/277 (1%)

Query: 1   MSRSITQRILLYIAVVLILIWCVFPLYWAFISSIKPDRDLFEKNPSLFPKRITFENYVKV 60
           MS  + + ++ +  +  +++  +FP    F++++KP +++   +P+ +P    ++N+ ++
Sbjct: 1   MSAKLKRTVVAWAVLSPLIVLTLFPFAVMFLTAVKPAQEVL--SPNWWPSTFRWQNFSEM 58

Query: 61  FKERPFHINIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVS 120
           +    F   + NSI V+ I +V A+++   A YA++R +F         +L   M   + 
Sbjct: 59  WVATNFGNALLNSIYVSVIASVGAIIISIPAAYAMSRFRFAAHGAFRQFLLVSQMISPIV 118

Query: 121 ILGSLFLILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKL 180
           ++  LF +L    LI + + +   Y A N+  TVW+LQS+F  +P+++EE+++++GA + 
Sbjct: 119 LVLGLFRLLAAYGLIESVSAVGAVYMAFNIAFTVWMLQSYFDTIPRDLEEASWMEGAGRG 178

Query: 181 RTLWSIVLPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEI 240
           +TL  + LP+  P +  T + TFI AWNEF+ ALT +++   YT+P+ V     A +Y +
Sbjct: 179 KTLVKVFLPLCLPAIAVTAIFTFINAWNEFVVALTMLRRQESYTLPIQVFSLV-AGRYTV 237

Query: 241 PWGQLMAAAVIVTLPLVILVLVFQNRIIAGLSAGAVK 277
            W  +MAA  + TLP+ IL +  Q  +I GL+ GAVK
Sbjct: 238 EWHYVMAATFLATLPVAILFIWLQRYLIKGLALGAVK 274


Lambda     K      H
   0.329    0.142    0.424 

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: 190
Number of extensions: 10
Number of successful extensions: 3
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: 278
Length of database: 274
Length adjustment: 25
Effective length of query: 253
Effective length of database: 249
Effective search space:    62997
Effective search space used:    62997
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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