GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Escherichia coli BW25113

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)

Query= reanno::psRCH2:GFF857
         (371 letters)



>FitnessBrowser__Keio:14980
          Length = 377

 Score =  229 bits (583), Expect = 1e-64
 Identities = 116/289 (40%), Positives = 181/289 (62%), Gaps = 4/289 (1%)

Query: 6   LRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQ 65
           +R++ KSYDG      + L I  GE    +G SGCGKSTLLR++AG E  ++G +++D  
Sbjct: 22  IRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGV 81

Query: 66  RVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDK 125
            ++ +PP  R + M+FQSYAL+PHMTV +N+AFGLK   + K EI  RV  +  ++ + +
Sbjct: 82  DLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQE 141

Query: 126 LLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRS 185
             +RKP  LSGGQRQRVA+ R++ + PK+ L DEP+  LD  LR +M++E+  + +R+  
Sbjct: 142 FAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGV 201

Query: 186 TMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVR 245
           T + VTHDQ EAMT+A +I ++N G+  Q+G+P  +Y +P  R+ A F+GS  +N  E  
Sbjct: 202 TCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS--VNVFEGV 259

Query: 246 AISASPETVTIELPS-GYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDE 293
                 + + ++ P   +PL +  D S V    P+ + +RPE  ++ +E
Sbjct: 260 LKERQEDGLVLDSPGLVHPLKVDADASVVD-NVPVHVALRPEKIMLCEE 307


Lambda     K      H
   0.322    0.139    0.405 

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: 340
Number of extensions: 11
Number of successful extensions: 1
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: 371
Length of database: 377
Length adjustment: 30
Effective length of query: 341
Effective length of database: 347
Effective search space:   118327
Effective search space used:   118327
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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