GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Escherichia coli BW25113

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  235 bits (599), Expect = 2e-66
 Identities = 123/276 (44%), Positives = 177/276 (64%), Gaps = 8/276 (2%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           +   NL I  G+ + L+GPSGCGK+T LR++AGLE  ++G IFI  +DVTH + + RDI 
Sbjct: 22  IDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFIDGEDVTHRSIQQRDIC 81

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           MVFQ+YAL+PHM++GEN+G+ LK+ G  + E+  RV EA A + L  F +R    +SGGQ
Sbjct: 82  MVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDLEGFEDRFVDQISGGQ 141

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           +QRVA+ RA++  P+V L DEPLSNLDA LR   R +I  LQ++  +T++YVTHDQ+EA 
Sbjct: 142 QQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQFDITSLYVTHDQSEAF 201

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260
            + D + V+  G++ Q+G+P++LY +PA+ F+A F+G   +   TFS    D    H   
Sbjct: 202 AVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDANLFPATFSDGYVDIYGYHL-- 259

Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGEST 296
              P  L   T    G   +G RPEA+ +   GE +
Sbjct: 260 ---PRPLHFGT---QGEGMVGVRPEAITLSDRGEES 289


Lambda     K      H
   0.316    0.135    0.380 

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: 343
Number of extensions: 19
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: 376
Length of database: 348
Length adjustment: 29
Effective length of query: 347
Effective length of database: 319
Effective search space:   110693
Effective search space used:   110693
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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