GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 3606947 Dshi_0375 ABC transporter related (RefSeq)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Dino:3606947
          Length = 273

 Score =  196 bits (498), Expect = 4e-55
 Identities = 89/251 (35%), Positives = 155/251 (61%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           ++E+  +T++FGG+ A+  ++  + E ++ ++IGPNGAGK+++ N ++GFY P  G +  
Sbjct: 21  LMEMRNITLKFGGVTAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGQVMF 80

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
            G     +  +++AR+G+ RTFQN+ LF+ M+ ++N++  +  H+ +N L         +
Sbjct: 81  RGAPRPKMKPYQVARQGIARTFQNIALFEGMSVLDNIMTGRLTHMKSNMLDQAIWWGKAQ 140

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
           + E E  E     ++ + +        G L YG ++R+E+AR +   P++L+LDEP AG+
Sbjct: 141 KEETENREKVEKIIDFLEIQNIRKTPVGRLPYGLKKRVELARALAAEPKLLLLDEPMAGM 200

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           N +E +D+   I     E   T+ LIEHDM +VM +SD +VV++ G  + DGTP+++R+N
Sbjct: 201 NVEEKEDMSRYILDTNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEVRNN 260

Query: 245 PDVIKAYLGEA 255
            DVI AYLG A
Sbjct: 261 QDVIDAYLGVA 271


Lambda     K      H
   0.320    0.137    0.391 

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: 172
Number of extensions: 5
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: 255
Length of database: 273
Length adjustment: 25
Effective length of query: 230
Effective length of database: 248
Effective search space:    57040
Effective search space used:    57040
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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