GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3606947 Dshi_0375 ABC transporter related (RefSeq)

Query= TCDB::Q8DQH8
         (254 letters)



>lcl|FitnessBrowser__Dino:3606947 Dshi_0375 ABC transporter related
           (RefSeq)
          Length = 273

 Score =  218 bits (555), Expect = 1e-61
 Identities = 104/249 (41%), Positives = 162/249 (65%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           L+E++ +T  FGG+TA+ D++ ++ EGE+  +IGPNGAGK+++ N+++G Y P EG V  
Sbjct: 21  LMEMRNITLKFGGVTAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGQVMF 80

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
            G       PY++A  G+ RTFQNI LF+ ++VLDN++     H K ++    +      
Sbjct: 81  RGAPRPKMKPYQVARQGIARTFQNIALFEGMSVLDNIMTGRLTHMKSNMLDQAIWWGKAQ 140

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
           K E E + K  +++   ++    +T    L YG ++R+E+ RALA EPK+L LDEP AGM
Sbjct: 141 KEETENREKVEKIIDFLEIQNIRKTPVGRLPYGLKKRVELARALAAEPKLLLLDEPMAGM 200

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242
           N +E  +++  I    DEF  TI LIEHDM +VM++++R+ V++YG+ I  GTPDE++ N
Sbjct: 201 NVEEKEDMSRYILDTNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEVRNN 260

Query: 243 KRVIEAYLG 251
           + VI+AYLG
Sbjct: 261 QDVIDAYLG 269


Lambda     K      H
   0.319    0.139    0.385 

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: 186
Number of extensions: 6
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: 254
Length of database: 273
Length adjustment: 25
Effective length of query: 229
Effective length of database: 248
Effective search space:    56792
Effective search space used:    56792
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 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