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 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Keio:18063
          Length = 371

 Score =  339 bits (870), Expect = 6e-98
 Identities = 191/368 (51%), Positives = 244/368 (66%), Gaps = 6/368 (1%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA ++L  V KA+G+V V  +INLDI +GE +VFVGPSGCGKSTLLRMIAGLE IT G L
Sbjct: 1   MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            I    +ND PPA+RG+ MVFQSYALYPH++V ENMSF LK+A   +  I+  V   AE 
Sbjct: 61  FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           LQL   LDR PKALSGGQRQRVAIGR++V +P V+L DEPLSNLDAALRV  R+EI++L 
Sbjct: 121 LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +   TM+YVTHDQVEAMTLA +IVVL  G +AQVG PLELY  P + FVA FIGSPKM
Sbjct: 181 KRLGR-TMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKM 239

Query: 241 NLLPGKIIGTGA-QTTVEMTDGGRAVSDYP--SDDSLMGAAVNVGVRPEDMVEAAPGGDY 297
           N LP K+  T   Q  VE+    R     P  S D  +GA +++G+RPE ++  +   D 
Sbjct: 240 NFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLL-PSDIADV 298

Query: 298 VFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFK-D 356
           + EG+V + E LG  T ++ + PS     + +   +    +G    +   P + H+F+ D
Sbjct: 299 ILEGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFRED 358

Query: 357 GVSLHYPH 364
           G +    H
Sbjct: 359 GTACRRLH 366


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: 390
Number of extensions: 15
Number of successful extensions: 3
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: 371
Length adjustment: 30
Effective length of query: 343
Effective length of database: 341
Effective search space:   116963
Effective search space used:   116963
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: 49 (23.5 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