GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Dinoroseobacter shibae DFL-12

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3606947 Dshi_0375 ABC transporter related (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Dino:3606947
          Length = 273

 Score =  202 bits (515), Expect = 5e-57
 Identities = 105/254 (41%), Positives = 155/254 (61%), Gaps = 1/254 (0%)

Query: 4   KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63
           K   V++++  I+ +FGG+ A+ D+   I+ G++  +IGPNGAGK++  NVI+G Y P  
Sbjct: 16  KIGGVLMEMRNITLKFGGVTAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQE 75

Query: 64  GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123
           G     G P      ++VA+ GIARTFQNI LF  M+ L+N+M GR     S +      
Sbjct: 76  GQVMFRGAPRPKMKPYQVARQGIARTFQNIALFEGMSVLDNIMTGRLTHMKSNMLDQAIW 135

Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183
               + EE    ++ ++++D++ I          L YG ++R+E+ARALA +P+L+ LDE
Sbjct: 136 WGKAQKEETENREKVEKIIDFLEIQNIRKTPVGRLPYGLKKRVELARALAAEPKLLLLDE 195

Query: 184 PAAGMNATEKVQL-RELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPA 242
           P AGMN  EK  + R ++D       TI LIEHD+ +VM L DRV V+DYGK+I +G P 
Sbjct: 196 PMAGMNVEEKEDMSRYILDTNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPD 255

Query: 243 EVQKNEKVIEAYLG 256
           EV+ N+ VI+AYLG
Sbjct: 256 EVRNNQDVIDAYLG 269


Lambda     K      H
   0.319    0.137    0.384 

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: 202
Number of extensions: 6
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: 260
Length of database: 273
Length adjustment: 25
Effective length of query: 235
Effective length of database: 248
Effective search space:    58280
Effective search space used:    58280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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