GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Escherichia coli BW25113

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  133 bits (334), Expect = 8e-36
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 12/250 (4%)

Query: 7   EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66
           E +L++ GI K F G++ALS   + +  G+V  L+G NGAGK+T   V+TG+YT DAGT 
Sbjct: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61

Query: 67  ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126
              GK    T      +AGI    Q + L  ++T  EN+ +GR            F  + 
Sbjct: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGRE-----------FVNRF 110

Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186
            K +   +   A +LL  + +   +D     LS GDQ+ +EIA+ L+ + ++I +DEP  
Sbjct: 111 GKIDWKTMYAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTD 170

Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246
            +  TE   L  +I  +++  R I+ I H +K +  +CD VTV   G+ IAE   A + +
Sbjct: 171 ALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTE 230

Query: 247 NEKVIEAYLG 256
            + +IE  +G
Sbjct: 231 -DSLIEMMVG 239



 Score = 75.9 bits (185), Expect = 2e-18
 Identities = 53/214 (24%), Positives = 103/214 (48%), Gaps = 15/214 (7%)

Query: 25  LSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYEPTAVHEVAKA 84
           ++DV  T+++G++ G+ G  GAG+T    V+ G     +G   L G        HEV   
Sbjct: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDG--------HEVVTR 319

Query: 85  GIARTFQN-IRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAIAKRAQELLD 143
                  N I   +E    + +++G  ++    L    + ++         A   Q + D
Sbjct: 320 SPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA--GGSLKHADEQQAVSD 377

Query: 144 YVGIGKFA----DYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKVQLREL 199
           ++ +        +     LS G+Q+++ IAR L T P+++ LDEP  G++   K ++ +L
Sbjct: 378 FIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQL 437

Query: 200 IDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYG 233
           I++ + D  +I+L+  ++  V+G+ DR+ V+  G
Sbjct: 438 INQFKADGLSIILVSSEMPEVLGMSDRIIVMHEG 471


Lambda     K      H
   0.319    0.137    0.384 

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: 281
Number of extensions: 18
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: 260
Length of database: 501
Length adjustment: 29
Effective length of query: 231
Effective length of database: 472
Effective search space:   109032
Effective search space used:   109032
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