GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuG in Dinoroseobacter shibae DFL-12

Align Sugar ABC transporter permease (characterized, see rationale)
to candidate 3608007 Dshi_1415 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= uniprot:A0A161ZE72
         (280 letters)



>lcl|FitnessBrowser__Dino:3608007 Dshi_1415
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 294

 Score =  155 bits (391), Expect = 1e-42
 Identities = 96/292 (32%), Positives = 145/292 (49%), Gaps = 14/292 (4%)

Query: 2   NLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWI---------- 51
           N+   +   LRL  W ++ + L+ A FPF + +  S K     F    W           
Sbjct: 4   NIATRRSMPLRLFLWGVVLLWLMLAAFPFLWTLWGSFKVQGDFFSREDWTNALTGVRTLA 63

Query: 52  ENPDF---SNYAAVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTV 108
           E   +     YA    Q  F RA  N+++V L VV ++L       YAL R  F+    +
Sbjct: 64  ETGGYFTGGGYAGAWVQEEFWRAGLNTMIVTLSVVAISLTFGTLGGYALSRSSFKYTFWI 123

Query: 109 LMMVLGVSMFPQVAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPH 168
           LM  L     P + ++SG       L ++      I+       PFT+W+L +F   +P 
Sbjct: 124 LMAALIFRAMPHITLVSGYLLPFFELNIWGILPTTIIVLVAINQPFTLWMLRSFFMNIPK 183

Query: 169 ELEEAAIMDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVP 228
           +L+E+A++DG + +    RV++P++WP ++TTGL +F+ A+N+F    T    D Q  +P
Sbjct: 184 DLDESAMVDGCTRFQAFRRVIIPVMWPGVITTGLFSFLLAYNDFAVTATLLSQDNQTMIP 243

Query: 229 VAIALISGGSPHELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG 280
             IA   G +  E      ++A V  T PL ILVL FQR+IVSGLTAGA+KG
Sbjct: 244 -KIASFLGTTQQEGNVMFAVSAVVSATAPLFILVLFFQRQIVSGLTAGAVKG 294


Lambda     K      H
   0.329    0.141    0.433 

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: 248
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: 280
Length of database: 294
Length adjustment: 26
Effective length of query: 254
Effective length of database: 268
Effective search space:    68072
Effective search space used:    68072
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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