GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:14863 b0731 fused
           2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA
           component/IIB component/IIC component (NCBI)
          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 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