GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Escherichia coli BW25113

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= SwissProt::Q9YGA6
         (372 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  238 bits (607), Expect = 2e-67
 Identities = 139/320 (43%), Positives = 197/320 (61%), Gaps = 23/320 (7%)

Query: 4   VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63
           V L +V K FG  T +  ++L +  G+ + LLGPSGCGKTT LR++AGLE+PS GQI+I 
Sbjct: 7   VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFI- 65

Query: 64  DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123
                D E       + RDI MVFQSYAL+PHM++ +N+ + LK+  VPR E+  RV+E 
Sbjct: 66  -----DGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEA 120

Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183
             ++ L    +R   ++SGGQ+QRVAL RA++ KP+V L DEPLSNLDA LR  MR +++
Sbjct: 121 LAMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIR 180

Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243
           +LQ+Q  +T++YVTHDQ EA  + D + VMN+G + Q+GSP ++Y +PA+ F+A F+G  
Sbjct: 181 ELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD- 239

Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGYVGREVIFGIRPEDLYDAMFAQVR 303
             N   A  + DG+VD   + L   P  F   GE G V      G+RPE +       + 
Sbjct: 240 -ANLFPATFS-DGYVDIYGYHLP-RPLHFGTQGE-GMV------GVRPEAI------TLS 283

Query: 304 VPGENLVRAVVEIVENLGSE 323
             GE   R V+  V  +G +
Sbjct: 284 DRGEESQRCVIRHVAYMGPQ 303


Lambda     K      H
   0.323    0.142    0.406 

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: 352
Number of extensions: 14
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: 372
Length of database: 348
Length adjustment: 29
Effective length of query: 343
Effective length of database: 319
Effective search space:   109417
Effective search space used:   109417
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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