GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaS in Escherichia coli BW25113

Align RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate 15637 b1516 AI2 transporter (NCBI)

Query= TCDB::Q7BSH5
         (331 letters)



>FitnessBrowser__Keio:15637
          Length = 340

 Score =  187 bits (474), Expect = 4e-52
 Identities = 111/336 (33%), Positives = 186/336 (55%), Gaps = 17/336 (5%)

Query: 5   KTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTG 64
           K +AL  AL +A ++    A + +I  + K +G GFF +   GAQ+A KELG V+V Y G
Sbjct: 7   KKIALLSALGIAAISMNVQAAE-RIAFIPKLVGVGFFTSGGNGAQQAGKELG-VDVTYDG 64

Query: 65  PTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGR 124
           PT  +  GQ+++IN+ + QG +AI VSA  PD L PALK+A QRG++V++WDS   PE R
Sbjct: 65  PTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVRVLTWDSDTKPECR 124

Query: 125 ILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQL-KDFPG 183
              +N  +   +G M + +A   +   K   A   ++ T T+QN W+ + K ++ K+ PG
Sbjct: 125 SYYINQGTPAQLGGMLVDMAARQVNKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEHPG 184

Query: 184 LNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVT 243
             +VTT +G + + KS + AEG+LK+  ++  I+AP    + AA++  E+     KV + 
Sbjct: 185 WEIVTTQFGYNDATKSLQTAEGILKAYSDLDAIIAPDANALPAAAQAAENL-KNDKVAIV 243

Query: 244 GLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKI 303
           G   P+ M   ++ G  KEF +W+ +  G  +  +A  L+K +   K G +++   +G++
Sbjct: 244 GFSTPNVMRPYVERGTVKEFGLWDVVQQGKISVYVADALLK-KGSMKTGDKLDIKGVGQV 302

Query: 304 KVG------------DNGEAAMADPFVYNASNIDQF 327
           +V              NG   + +  ++N  NI ++
Sbjct: 303 EVSPNSVQGYDYEADGNGIVLLPERVIFNKENIGKY 338


Lambda     K      H
   0.313    0.131    0.365 

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: 286
Number of extensions: 14
Number of successful extensions: 5
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: 331
Length of database: 340
Length adjustment: 28
Effective length of query: 303
Effective length of database: 312
Effective search space:    94536
Effective search space used:    94536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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