GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-ABC in Escherichia coli BW25113

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= TCDB::Q1LZ59
         (655 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 =  337 bits (865), Expect = 8e-97
 Identities = 226/631 (35%), Positives = 337/631 (53%), Gaps = 48/631 (7%)

Query: 1   MKIQDLLNKDVMLLDLQATTKEAAIDEMVSKLVEQGIVTDFDTFKAGIMNREVQTSTGLG 60
           M +  L ++D + L+ + T++E AI  +  +L   G ++  + F   +  RE    T LG
Sbjct: 21  MNLTTLTHRDALCLNARFTSREEAIHALTQRLAALGKISSTEQFLEEVYRRESLGPTALG 80

Query: 61  DGIAMPHSKNKAVKEATVLFAKSNKGVDYEALDG-EPVDLFFMIAAPDG-ANDTHLAALA 118
           +G+A+PH K  AVKEA    A  ++ + +E +DG E VDL  ++A P   A  TH+  L 
Sbjct: 81  EGLAVPHGKTAAVKEAAFAVATLSEPLQWEGVDGPEAVDLVVLLAIPPNEAGTTHMQLLT 140

Query: 119 ELSQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPAAPVADSHDFLVAVTACTTG 178
            L+  L  D    +++  T PD++++      ++K    P+A  +++   +V VTAC  G
Sbjct: 141 ALTTRLADDEIRARIQSATTPDELLSAL----DDKGGTQPSASFSNAPT-IVCVTACPAG 195

Query: 179 IAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAV-EMDR 237
           IAHTYMA E L+K   ++GV + VE  GA+G+  +LTAD +  A   I AA+ A+ E +R
Sbjct: 196 IAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFAAEVAIKESER 255

Query: 238 FNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHL 297
           FNG P +S PVAE I+  E LI   L  K     +D +    + +   K+ + +   + L
Sbjct: 256 FNGIPALSVPVAEPIRHAEALIQQALTLKR----SDETRTVQQDTQPVKS-VKTELKQAL 310

Query: 298 MSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGF-M 356
           +SG+S  +P ++ GG ++A++ L+ Q  G+           +    ++ ++G    G  M
Sbjct: 311 LSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDL----FNEENSWLWMYRKLGGGLLGILM 366

Query: 357 IPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLG 416
           +PV AAY AYS+A+KP L  GF AG      LA N +                  SGFLG
Sbjct: 367 VPVLAAYTAYSLADKPALAPGFAAG------LAANMIG-----------------SGFLG 403

Query: 417 ALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLFV-NIPMAAINT 475
           A+ GG +AG ++  +K  L    +   G  +  LYP+LG L  G LMLFV   P+A IN 
Sbjct: 404 AVVGGLIAGYLMRWVKNHLRLSSK-FNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINN 462

Query: 476 ALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMAS 535
           +L  +L  LSG +A+LLG I+G M + D+GGP NKAAY F    +       G   + AS
Sbjct: 463 SLTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVY--GPYAIFAS 520

Query: 536 VMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPS 595
           V    MV    V  +T+L    F + E + G +  ++GL+ ITEGAIP    DP R I S
Sbjct: 521 VK---MVSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGS 577

Query: 596 FIVGSAVTGALVGLSGIKLMAPHGGIFVIAL 626
           F++GS VTGA+VG   I L  P  GIF + L
Sbjct: 578 FVLGSMVTGAIVGAMNIGLSTPGAGIFSLFL 608


Lambda     K      H
   0.320    0.137    0.381 

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: 934
Number of extensions: 41
Number of successful extensions: 10
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: 655
Length of database: 658
Length adjustment: 38
Effective length of query: 617
Effective length of database: 620
Effective search space:   382540
Effective search space used:   382540
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 (21.8 bits)
S2: 54 (25.4 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