GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Escherichia coli BW25113

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__Keio:16258 b2149 fused methyl-galactoside
           transporter subunits of ABC superfamily: ATP-binding
           components (NCBI)
          Length = 506

 Score =  338 bits (868), Expect = 2e-97
 Identities = 183/477 (38%), Positives = 296/477 (62%), Gaps = 11/477 (2%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           ++ M GI   FPGVKALD V+L + P  +HALMGENGAGKST++K L G+Y+ ++G+I+ 
Sbjct: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126
            GK   F+   +A   GI+ V+QE+NL    SV +N+ LG        +D  K +   K 
Sbjct: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
              ++ ++ IDP   + ++S++  Q++ IA+A   NAK++I+DEPTSSL   EV  LF I
Sbjct: 133 IFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246
           +RK+++ G  I+++SH +++I+++ D +T+LR+GQ+I          D++I MM+G+S  
Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS-- 249

Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLG--KKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
               +  +   +E  PGE  I++V+ L   ++ +I  V  D++KGE++G AGL+G+ RT+
Sbjct: 250 ----LNQRFPDKENKPGE-VILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTD 304

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
           +   L+G  +  +GT TL+GK++N  +   A+ +  A  TE RR  GI   L +  N LI
Sbjct: 305 IVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLI 364

Query: 365 A-LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           + ++  +     +      +     +  + V+       + +LSGGNQQKV+IGRWL T 
Sbjct: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
           PE+L+LDEPTRGID+GAK EI Q++ +LA +G G++ ISSE+ E++ ++D I V+ +
Sbjct: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 55/218 (25%), Positives = 112/218 (51%), Gaps = 6/218 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           V   L+ GE+  + G  GA ++ +++ L G+ + +AG+I + GK    +   +A N G A
Sbjct: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341

Query: 86  TVYQE---VNLCTNLSVGENVMLGHEK--RGPFGI-DWKKTHEAAKKYLAQMGLESIDPH 139
            V +E     +   L +G N ++ + +  +   G+ D  +     +  +  M +++    
Sbjct: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHR 401

Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199
           T + S+S   QQ V I R ++   ++L+LDEPT  +D     +++ ++ ++   G  I+ 
Sbjct: 402 TQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIII 461

Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           +S  + ++  ITDR+ ++ NG     V TK T ++E++
Sbjct: 462 ISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEIL 499



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 59/225 (26%), Positives = 114/225 (50%), Gaps = 14/225 (6%)

Query: 267 IVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTL 322
           ++++ G+ K       ++ V++ +    +    G  G+G++ L + L+G  + DSGT   
Sbjct: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72

Query: 323 NGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPK--KE 380
            GK+++      AL+N I+      ++  ++   +V  N+ +    T+GMF    K  +E
Sbjct: 73  QGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRE 129

Query: 381 ADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGA 440
             AI D    EL++   DP   V  LS    Q + I +  + + +++I+DEPT  +    
Sbjct: 130 TKAIFD----ELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKE 184

Query: 441 KAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIA 485
              +  ++  L  +G G+V+IS ++EE+ +L D++ VL+D   IA
Sbjct: 185 VNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIA 229


Lambda     K      H
   0.316    0.135    0.376 

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: 654
Number of extensions: 29
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 513
Length of database: 506
Length adjustment: 34
Effective length of query: 479
Effective length of database: 472
Effective search space:   226088
Effective search space used:   226088
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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