GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Escherichia coli BW25113

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 17739 b3679 predicted transporter (NCBI)

Query= SwissProt::P96169
         (543 letters)



>FitnessBrowser__Keio:17739
          Length = 571

 Score =  225 bits (573), Expect = 4e-63
 Identities = 159/549 (28%), Positives = 272/549 (49%), Gaps = 47/549 (8%)

Query: 8   LSFIDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISA 67
           ++ + I+ F  +  ++  +  W  R  K    S + YFLAG+SL    + ASL+  N+S 
Sbjct: 1   MNSLQILSFVGFTLLVAVITWWKVR--KTDTGSQQGYFLAGRSLKAPVIAASLMLTNLST 58

Query: 68  EQFIGMSGSGYSIGLAIASYEWMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           EQ +G+SG  Y  G+++  +E  SA+TLI +   FLP ++++GI TIP+F+E+R++K  +
Sbjct: 59  EQLVGLSGQAYKSGMSVMGWEVTSAVTLIFLALIFLPRYLKRGIATIPDFLEERYDKTTR 118

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETIL----------GIPLMYSILGLALFALVYS 177
            I+   ++       L  VLY G LAL ++           G  +   ++ L L  ++Y+
Sbjct: 119 IIIDFCFLIATGVCFLPIVLYSGALALNSLFHVGESLQISHGAAIWLLVILLGLAGILYA 178

Query: 178 IYGGLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILD 237
           + GGL A+   D I    LV+GG M     +  + G   +  G+ ++          I  
Sbjct: 179 VIGGLRAMAVADSINGIGLVIGGLMVPVFGLIAM-GKGSFMQGIEQLTTVHAEKLNSIGG 237

Query: 238 QSNPQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIV 297
            ++P    LP I     GL + N +YW  NQ I+QRTLA+KS++E QKG +  A LK++ 
Sbjct: 238 PTDP----LP-IGAAFTGLILVNTFYWCTNQGIVQRTLASKSLAEGQKGALLTAVLKMLD 292

Query: 298 PFLVVLPGIAAYVITSDPQLMASLGDIAATNLPSAANADKAYPWL-TQFLPVGVKGVVFA 356
           P ++VLPG+ A+ +  D              LP    AD AYP L    LPV + G   A
Sbjct: 293 PLVLVLPGLIAFHLYQD--------------LP---KADMAYPTLVNNVLPVPMVGFFGA 335

Query: 357 ALAAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPM 416
            L  A++S+    LNS +T+F+M IY+  I+ ++   +LV VGR       I++ L+AP 
Sbjct: 336 VLFGAVISTFNGFLNSASTLFSMGIYRRIINQNAEPQQLVTVGRKFGFFIAIVSVLVAPW 395

Query: 417 LGGIGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFALFLKFMPL 475
           +    Q  + ++++  G+ +  ++ + ++G F+ +  +  A + +   I   + + ++  
Sbjct: 396 IANAPQGLYSWMKQLNGIYNVPLVTIIIMGFFFPRIPALAAKVAMGIGIISYITINYL-- 453

Query: 476 SMPFMDQMLYTLLFTMVVIAFTSLSTSINDDDPKGISVT-SSMFVTD----RSFNIAAYG 530
            + F    LY L  T  +     L   I    P+    T    F  D    ++  IA+ G
Sbjct: 454 -VKFDFHFLYVLACTFCINVVVML--VIGFIKPRATPFTFKDAFAVDMKPWKNVKIASIG 510

Query: 531 IMIVLAVLY 539
           I+  +  +Y
Sbjct: 511 ILFAMIGVY 519


Lambda     K      H
   0.326    0.141    0.421 

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: 857
Number of extensions: 60
Number of successful extensions: 4
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: 543
Length of database: 571
Length adjustment: 36
Effective length of query: 507
Effective length of database: 535
Effective search space:   271245
Effective search space used:   271245
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 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