GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Escherichia coli BW25113

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 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Keio:15248
          Length = 378

 Score =  120 bits (300), Expect = 5e-32
 Identities = 78/253 (30%), Positives = 130/253 (51%), Gaps = 20/253 (7%)

Query: 4   PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63
           P+++++G+   F G   +  ++L +   + ++++GP+G GKTTV   + G      G I 
Sbjct: 16  PLVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75

Query: 64  LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAF 123
           LD E+I  +P      + V   FQ+  LF  MT  EN+           F   + KTPA 
Sbjct: 76  LDNEDITHVPAEN---RYVNTVFQSYALFPHMTVFENVA----------FGLRMQKTPAA 122

Query: 124 RRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
             + R  ME     L  V L  FA R    L+ GQQ+R+ IAR ++ +PR+L+LDE  + 
Sbjct: 123 EITPR-VMEA----LRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSA 177

Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243
           L+ K    ++  +  L+ +  +T + + HD +  +++SD IVV+  G    DGTP +I +
Sbjct: 178 LDYKLRKQMQNELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYE 237

Query: 244 NPD--VIKAYLGE 254
            P    +  ++GE
Sbjct: 238 EPKNLFVAGFIGE 250


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: 223
Number of extensions: 12
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: 255
Length of database: 378
Length adjustment: 27
Effective length of query: 228
Effective length of database: 351
Effective search space:    80028
Effective search space used:    80028
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: 48 (23.1 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 (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