GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01115 in Escherichia coli BW25113

Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)

Query= reanno::Burk376:H281DRAFT_01115
         (357 letters)



>FitnessBrowser__Keio:17810
          Length = 321

 Score =  134 bits (338), Expect = 3e-36
 Identities = 100/305 (32%), Positives = 158/305 (51%), Gaps = 17/305 (5%)

Query: 19  LLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVG 78
           L+ + VL+ +V+T      F  I+NL ++  Q     ++A+G+ L +++   GIDLS   
Sbjct: 23  LIALLVLIAIVSTLSPN--FFTINNLFNILQQTSVNAIMAVGMTLVILTS--GIDLSVGS 78

Query: 79  LANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPILCT 138
           L  L+G VAA +V   VN          +  A  L +G   G + GV++A+ R+   + T
Sbjct: 79  LLALTGAVAASIVGIEVNA--------LVAVAAALALGAAIGAVTGVIVAKGRVQAFIAT 130

Query: 139 LGTQLLFTGFAVVISNGASVHVDYVEPLSDI----GNGTVLQVPIAFCIFLAAVIVLGWL 194
           L   LL  G  +V +NG+ V+  + E  +D+    G G  L VP    I     +   ++
Sbjct: 131 LVMMLLLRGVTMVYTNGSPVNTGFTEN-ADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYM 189

Query: 195 LKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDY 254
           L  +  G  +Y +G N  A   +GI   ++ I  Y++CG+LASLAG+I     SSA+   
Sbjct: 190 LHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTA 249

Query: 255 GNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFL 314
           G  Y L AI   V+GG + AGG GRI+     A +L FL++  NLLGVS ++       +
Sbjct: 250 GTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVV 309

Query: 315 LLLSL 319
           +LL++
Sbjct: 310 ILLAV 314


Lambda     K      H
   0.327    0.143    0.429 

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: 287
Number of extensions: 18
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: 357
Length of database: 321
Length adjustment: 28
Effective length of query: 329
Effective length of database: 293
Effective search space:    96397
Effective search space used:    96397
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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