GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Escherichia coli BW25113

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Keio:14980
          Length = 377

 Score =  212 bits (540), Expect = 1e-59
 Identities = 130/343 (37%), Positives = 195/343 (56%), Gaps = 8/343 (2%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           L++  + K+Y     + +++L I +GE+   +G SGCGKSTLLRM+AG E+ + G + +D
Sbjct: 20  LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  ++ VPP  R I M+FQSYAL+PHMTV +N++F LK  K  +AEI + V      + +
Sbjct: 80  GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
            ++  R P  LSGGQRQRVA+ RS+ + PK+ L DEP+  LD  LR   +LE+  + E +
Sbjct: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
              T V VTHDQ EAMT+A RI ++  G   Q+G P E+YE P   + A+FIGS  +N+ 
Sbjct: 200 -GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS--VNVF 256

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLM-GAAVNVGVRPEDMV---EAAPGGDYVF 299
            G +        V  + G        +D S++    V+V +RPE ++   E    G    
Sbjct: 257 EGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFA 316

Query: 300 EGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVT 342
            G+V     LG++++ +    SG+     +LQ  H+  KG  T
Sbjct: 317 VGEVIHIAYLGDLSVYHVRLKSGQ-MISAQLQNAHRHRKGLPT 358


Lambda     K      H
   0.316    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: 348
Number of extensions: 13
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: 373
Length of database: 377
Length adjustment: 30
Effective length of query: 343
Effective length of database: 347
Effective search space:   119021
Effective search space used:   119021
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: 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