GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Escherichia coli BW25113

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__Keio:14863
          Length = 658

 Score =  295 bits (754), Expect = 5e-84
 Identities = 183/494 (37%), Positives = 275/494 (55%), Gaps = 16/494 (3%)

Query: 90  RAFLQRAAALASVEVAGDEAGLVAPEAGA--APRIVAVTACPTGVAHTFMAAEALQLAAG 147
           RA +Q A     +  A D+ G   P A    AP IV VTACP G+AHT+MAAE L+ A  
Sbjct: 152 RARIQSATTPDELLSALDDKGGTQPSASFSNAPTIVCVTACPAGIAHTYMAAEYLEKAGR 211

Query: 148 QLGFALQVETQGSVGARNPLDPADIAAADVVLLAADIDV-DTARFAGKKIYRCGTGVALK 206
           +LG  + VE QG+ G    L    + +A   + AA++ + ++ RF G           ++
Sbjct: 212 KLGVNVYVEKQGANGIEGRLTADQLNSATACIFAAEVAIKESERFNGIPALSVPVAEPIR 271

Query: 207 QARATLERALAEGQVESAGAASAVV--ARDEKRGVYKHLLTGVSFMLPMVVAGGLLIA-- 262
            A A +++AL   + +            +  K  + + LL+G+SF +P++VAGG ++A  
Sbjct: 272 HAEALIQQALTLKRSDETRTVQQDTQPVKSVKTELKQALLSGISFAVPLIVAGGTVLAVA 331

Query: 263 --LSLAFGI-DAYKQPGSLAAVLRTVGDTAF-VLMVPMLAGYIAYSIADRPGLAPGMLGG 318
             LS  FG+ D + +  S   + R +G     +LMVP+LA Y AYS+AD+P LAPG   G
Sbjct: 332 VLLSQIFGLQDLFNEENSWLWMYRKLGGGLLGILMVPVLAAYTAYSLADKPALAPGFAAG 391

Query: 319 LLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKPILVIPLLASLVTGLLMLY 378
           L A  +G+GF+G +V G IAGY  R + + LRL +         + P+L +L  G LML+
Sbjct: 392 LAANMIGSGFLGAVVGGLIAGYLMRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLF 451

Query: 379 VVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGGPVNKAAYAFSVGLLSSHS 438
           VVG+PVA +  +LT +L+G+  SNA+LLG +LG M   DLGGPVNKAAYAF +G +++  
Sbjct: 452 VVGEPVAWINNSLTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGV 511

Query: 439 YAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASVLGLCFISEGAIPFAAKDP 498
           Y P A   +  MV    +  +T+LA R F E E + GK+  +LGL  I+EGAIP A +DP
Sbjct: 512 YGPYAIFASVKMVSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDP 571

Query: 499 LRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLV-----PNAINHALAYLLAIVAGS 553
           LRVI + + G  +TGA+       L  P  G+F + +        +  A+ +  A + G+
Sbjct: 572 LRVIGSFVLGSMVTGAIVGAMNIGLSTPGAGIFSLFLLHDNGAGGVMAAIGWFGAALVGA 631

Query: 554 LLTGLLYAVLKRGA 567
            ++  +  + +R A
Sbjct: 632 AISTAILLMWRRHA 645



 Score = 46.2 bits (108), Expect = 4e-09
 Identities = 31/98 (31%), Positives = 44/98 (44%), Gaps = 1/98 (1%)

Query: 3   LAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEAD-WVLL 61
           +  VTACP G   + +AA  L  A  +LG    VE    +  EG L+A+Q+  A   +  
Sbjct: 186 IVCVTACPAGIAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFA 245

Query: 62  VGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAAL 99
             V    + RF G P      AE +    A +Q+A  L
Sbjct: 246 AEVAIKESERFNGIPALSVPVAEPIRHAEALIQQALTL 283


Lambda     K      H
   0.321    0.137    0.392 

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: 778
Number of extensions: 32
Number of successful extensions: 5
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: 585
Length of database: 658
Length adjustment: 37
Effective length of query: 548
Effective length of database: 621
Effective search space:   340308
Effective search space used:   340308
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 (21.9 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