GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate 3607946 Dshi_1354 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::Phaeo:GFF1304
         (288 letters)



>FitnessBrowser__Dino:3607946
          Length = 416

 Score =  125 bits (315), Expect = 1e-33
 Identities = 75/236 (31%), Positives = 128/236 (54%), Gaps = 7/236 (2%)

Query: 54  DNYARFLSSSAFWPSVQATLVI-VGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPF 112
           +N+AR   +  FW  +  T+   V G L   ++ G+F ALLLN+   GQGI+R L + P+
Sbjct: 179 ENFARIFDADEFWGVLGVTMFYTVFGTLG-ALLFGLFAALLLNKSFRGQGILRGLYLFPY 237

Query: 113 FVMPTVSALVWKNMFMDPVNGLFAHLWKAFGA--EPVSWLSEASLQSIILIVS--WQWLP 168
                  A  W  +F DP +G    L    G   E +++  +  L  I++ V   W++ P
Sbjct: 238 VAPVIAVAFTWVTLF-DPFSGSANALLIQMGVTNEAINFFGQRPLALIMVTVFEIWRYFP 296

Query: 169 FATLILLTAIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFA 228
            + L +L  +QS+D++  EAA+MDGA P  +F Y++LP L   ++V+ L++ I+  + F 
Sbjct: 297 LSFLFILARMQSIDTDMYEAADMDGASPFQKFWYLSLPMLVGILSVLFLLRFIWTFNKFD 356

Query: 229 EIFVTTQGSFGTKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGK 284
           +IF+ T G+ GT+TLT  +Y++     N+G G+A  V       + ++   R + +
Sbjct: 357 DIFLLTGGNAGTRTLTVNVYEQAFAVSNIGAGAAVAVVIFGCLLLFSVLFFRFISR 412


Lambda     K      H
   0.328    0.140    0.430 

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: 318
Number of extensions: 17
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: 288
Length of database: 416
Length adjustment: 29
Effective length of query: 259
Effective length of database: 387
Effective search space:   100233
Effective search space used:   100233
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: 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