GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Escherichia coli BW25113

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__Keio:18115
          Length = 510

 Score =  129 bits (324), Expect = 1e-34
 Identities = 80/253 (31%), Positives = 141/253 (55%), Gaps = 10/253 (3%)

Query: 1   MSQPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60
           M+ P +S+ G+   FG + A+ +VNL +YP EI +L+G NGAGK+T+   L+G ++PT G
Sbjct: 1   MATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKG 60

Query: 61  TILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120
           TI + +     L  +  A++G+   +Q + +  E+TV+ENL + +H   K     G +  
Sbjct: 61  TITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKK---ICG-VNI 116

Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180
             +R    E   RAA  L R+GL    + + +NL+   ++ LEIA+ ++   +++++DEP
Sbjct: 117 IDWR----EMRVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEP 172

Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240
            + L  KE   L  ++ +LR    T I+ I H +  +  I DR  V+  G+ + +G    
Sbjct: 173 TSSLTNKEVDYLFLIMNQLRK-EGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSD 231

Query: 241 IRNNPDVIRAYLG 253
           + +N D++R  +G
Sbjct: 232 V-SNDDIVRLMVG 243



 Score = 64.3 bits (155), Expect = 5e-15
 Identities = 49/214 (22%), Positives = 103/214 (48%), Gaps = 11/214 (5%)

Query: 21  VNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLPGQQIARM 80
           V +++  +   EI+   G  G+G+T + NCL G  K  GG I L  + +         + 
Sbjct: 279 VRDISFSVCRGEILGFAGLVGSGRTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKK 338

Query: 81  GVVRTFQHVR---LFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSEALDRAATW 137
           G+    +  R    F   ++ +N+ +++   LK G + G +    F     +    A   
Sbjct: 339 GMAYITESRRDNGFFPNFSIAQNMAISR--SLKDGGYKGAMGL--FHEVDEQRT--AENQ 392

Query: 138 LERIGLLEHA-NRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKELDELI 196
            E + L  H+ N+  + L+ G+Q+++ I++ +   PE+++ DEP  G++     E+ +++
Sbjct: 393 RELLALKCHSVNQNITELSGGNQQKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVM 452

Query: 197 AELRNHHNTTILLIEHDMKLVMGISDRIYVVNQG 230
            +L +     IL++  ++  ++ + DRI V  +G
Sbjct: 453 RQLAD-DGKVILMVSSELPEIITVCDRIAVFCEG 485


Lambda     K      H
   0.320    0.137    0.395 

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: 277
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 510
Length adjustment: 29
Effective length of query: 226
Effective length of database: 481
Effective search space:   108706
Effective search space used:   108706
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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