GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Escherichia coli BW25113

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Keio:16645
          Length = 332

 Score =  187 bits (476), Expect = 2e-52
 Identities = 96/306 (31%), Positives = 171/306 (55%)

Query: 31  QQITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDL 90
           + I E  L+V+  +++   SL    F S+ N + +    + IG+ +  M   + S + D+
Sbjct: 22  RHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDV 81

Query: 91  SVGSTVAFAGVLCAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATM 150
           SVG  VAF  V  A +L       +A +  +  G ++G + G +     + + + TL   
Sbjct: 82  SVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLW 141

Query: 151 EIVRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRN 210
             +RG+G  +++   V +  +  +   G  F GV +   + ++ F +F  +  +T +GR+
Sbjct: 142 SALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAFGRS 201

Query: 211 TLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVI 270
             A+GGN  A++L GINV R R+ IF + G + A+ G++LA+R+ SG   AA G E +VI
Sbjct: 202 VFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVI 261

Query: 271 SACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQ 330
           +A V+GG +L GGR ++ G ++GVL++  + N + L+ I++F+Q +VRG I++ AVL + 
Sbjct: 262 AAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANI 321

Query: 331 LKNRGS 336
           L  + S
Sbjct: 322 LLTQRS 327


Lambda     K      H
   0.326    0.139    0.396 

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: 293
Number of extensions: 15
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: 338
Length of database: 332
Length adjustment: 28
Effective length of query: 310
Effective length of database: 304
Effective search space:    94240
Effective search space used:    94240
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