GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Escherichia coli BW25113

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  207 bits (526), Expect = 4e-58
 Identities = 112/313 (35%), Positives = 185/313 (59%), Gaps = 16/313 (5%)

Query: 6   VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65
           ++NV+K F  G    +DN+N+ I  G+   +LGPSG GKTT +R++AGL+ PS G+++ D
Sbjct: 9   LRNVTKRF--GSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66

Query: 66  DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125
              V          + R I MVFQ++AL+P+++  EN+ + L  + + + E++ RV+E  
Sbjct: 67  GEDVTHRSI-----QQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEAL 121

Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185
            ++D+    + F  ++SGGQQQRVALARAL+  P +LL DEP SNLDA +R S R  ++E
Sbjct: 122 AMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRE 181

Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245
           +Q +  +T L V+HD ++ FA++D V V+ KG ++Q+G P+DLY  P S  +AS +G+ N
Sbjct: 182 LQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGDAN 241

Query: 246 ELEGKVTNEGVVIGSLRFPVSV---SSDRAIIGIRPEDVKLSKDVIKDDSWILVGKGKVK 302
                 ++  V I     P  +   +    ++G+RPE + LS    +    +      ++
Sbjct: 242 LFPATFSDGYVDIYGYHLPRPLHFGTQGEGMVGVRPEAITLSDRGEESQRCV------IR 295

Query: 303 VIGYQGGLFRITI 315
            + Y G  + +T+
Sbjct: 296 HVAYMGPQYEVTV 308


Lambda     K      H
   0.319    0.139    0.390 

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: 290
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: 353
Length of database: 348
Length adjustment: 29
Effective length of query: 324
Effective length of database: 319
Effective search space:   103356
Effective search space used:   103356
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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