GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Escherichia coli BW25113

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  212 bits (540), Expect = 1e-59
 Identities = 114/288 (39%), Positives = 181/288 (62%), Gaps = 10/288 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           + + N++K F  G   V  +DN+++TI  G    +LGPSG GKTT LRL+AGLE+P+ G 
Sbjct: 7   VELRNVTKRF--GSNTV--IDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQ 62

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           I+ D E V+       S ++R I MVFQ++AL+P+M++ +N+ + LK+  VP+ +++ +V
Sbjct: 63  IFIDGEDVTH-----RSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARV 117

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
           KE    + L G  +R+  ++SGGQ QR A+ARAL+  PKVLL DEP SNLDA +R S R 
Sbjct: 118 KEALAMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRD 177

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            +R++Q++  +T+L V+HD ++ FA+++   V+  G   QIG+P ++Y  PA+  +A   
Sbjct: 178 KIRELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFM 237

Query: 244 GEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSD 291
           G+ NL  A   +    I    +P   +    Q   ++G+RP+ +TLSD
Sbjct: 238 GDANLFPATFSDGYVDIYGYHLP-RPLHFGTQGEGMVGVRPEAITLSD 284


Lambda     K      H
   0.317    0.136    0.374 

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: 264
Number of extensions: 11
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: 371
Length of database: 348
Length adjustment: 29
Effective length of query: 342
Effective length of database: 319
Effective search space:   109098
Effective search space used:   109098
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