GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Sm in Escherichia coli BW25113

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= TCDB::Q8DT25
         (377 letters)



>lcl|FitnessBrowser__Keio:14400 b0262 putative ATP-binding component
           of a transport system (VIMSS)
          Length = 348

 Score =  214 bits (544), Expect = 4e-60
 Identities = 127/329 (38%), Positives = 195/329 (59%), Gaps = 26/329 (7%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           ++L N+ KR+    +  ++N NL I   + +  +GPSGCGK+T LR++AGLE  +EG ++
Sbjct: 7   VELRNVTKRF--GSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIF 64

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
           ID + +   S + RDI MVFQ+YAL+PHMS+ EN+ +GLK+    + ++  RV EA  ++
Sbjct: 65  IDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMV 124

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

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

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALP-----QGQEKILEEKGYLGKKVTLGIRPE 298
            F+G    N F  T   +  V+  G  L  P     QG+  +    G   + +TL  R E
Sbjct: 235 SFMGD--ANLFPATF-SDGYVDIYGYHLPRPLHFGTQGEGMV----GVRPEAITLSDRGE 287

Query: 299 DISSDQIVHETF--PNASVTADILVSELL 325
           +     I H  +  P   VT +    E+L
Sbjct: 288 ESQRCVIRHVAYMGPQYEVTVEWHGQEIL 316


Lambda     K      H
   0.318    0.135    0.379 

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: 330
Number of extensions: 10
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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