GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Escherichia coli BW25113

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  216 bits (550), Expect = 8e-61
 Identities = 109/260 (41%), Positives = 173/260 (66%), Gaps = 14/260 (5%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           + L ++ K++   S+  +++ +L I   + +  +GPSGCGK+T LR+VAGLE  ++G++ 
Sbjct: 7   VELRNVTKRF--GSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIF 64

Query: 64  IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123
           IDGE V  ++ + RDI MVFQ+YAL+PHMS+ +N+ +GLK+    +  +  RVKEA  ++
Sbjct: 65  IDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMV 124

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183
            L  F +R    +SGGQ+QRVA+ RA++   KV L DEPLSNLDA LR SMR +I ++ +
Sbjct: 125 DLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQK 184

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243
           +   T++YVTHDQ+EA  ++D +++M+           G + Q+G+PQ+LY +PA++F+A
Sbjct: 185 QFDITSLYVTHDQSEAFAVSDTVLVMNK----------GHIMQIGSPQDLYRQPASRFMA 234

Query: 244 GFIGSPAMNFFDVTIKDGHL 263
            F+G    N F  T  DG++
Sbjct: 235 SFMGD--ANLFPATFSDGYV 252


Lambda     K      H
   0.318    0.135    0.375 

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: 315
Number of extensions: 11
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: 377
Length of database: 348
Length adjustment: 29
Effective length of query: 348
Effective length of database: 319
Effective search space:   111012
Effective search space used:   111012
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 (21.7 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