GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylHsa in Escherichia coli BW25113

Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= uniprot:Q4J711
         (356 letters)



>FitnessBrowser__Keio:16645
          Length = 332

 Score =  123 bits (309), Expect = 6e-33
 Identities = 90/303 (29%), Positives = 145/303 (47%), Gaps = 12/303 (3%)

Query: 11  EFQLFLVNVIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPPA 70
           E  L +V  I+ L F      + S NN   + +  A IGI A    ++++ GEID+S   
Sbjct: 26  EIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGP 85

Query: 71  LANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTV 130
           +  FV +    +       +     + V+ LL L L +L+G + G++     V S + T+
Sbjct: 86  MVAFVSVCLAFL-------LQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATL 138

Query: 131 GTLFLFNGIALIYSGGYP---ESFPYFRFLGGTVSILPVPFIWSLGALVFLILLLHYTKI 187
           G      G+ L  +   P   +      +LGG    +PV  +  +      + +   T  
Sbjct: 139 GLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAF 198

Query: 188 GVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTADVV 247
           G    A G N T A   G+ V RV+I+ F +   + A+ GI+  +R L  G       + 
Sbjct: 199 GRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAAR-LGSGNAGAANGLE 257

Query: 248 LEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVVVM 307
            + IAA V+GGT+L GG+GSL G  LG + I+ + NG  +LGIN++ F  ++ G I+VV 
Sbjct: 258 FDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSF-FQQVVRGVIIVVA 316

Query: 308 VLS 310
           VL+
Sbjct: 317 VLA 319


Lambda     K      H
   0.325    0.143    0.404 

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: 323
Number of extensions: 16
Number of successful extensions: 4
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: 356
Length of database: 332
Length adjustment: 29
Effective length of query: 327
Effective length of database: 303
Effective search space:    99081
Effective search space used:    99081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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