Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622)

Taxonomy: cellular organisms; Bacteria; Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Geobacter; Geobacter bemidjiensis

Average proteome isoelectric point is 6.62

Get precalculated fractions of proteins

Acidic
pI < 6.8
6.8-7.4
pI > 7.4
Basic
    
All



Virtual 2D-PAGE plot for 4042 proteins (isoelectric point calculated using IPC2_protein)

Get csv file with sequences according to given criteria:
        -     Method 

     -  kDa    
                                                                                      

* You can choose from 21 different methods for calculating isoelectric point

Summary statistics related to proteome-wise predictions


    
Protein with the lowest isoelectric point:
>tr|B5EFX1|B5EFX1_GEOBB Metal-dependent hydrolase beta-lactamase superfamily OS=Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622) OX=404380 GN=Gbem_2426 PE=4 SV=1
MM1 pKa = 6.89EE2 pKa = 4.72TQPATKK8 pKa = 9.71RR9 pKa = 11.84LCSEE13 pKa = 3.47IQLFDD18 pKa = 3.97LCDD21 pKa = 5.01LDD23 pKa = 4.23TCTCKK28 pKa = 10.59DD29 pKa = 3.12GRR31 pKa = 11.84YY32 pKa = 7.04CTNPAILEE40 pKa = 3.9RR41 pKa = 11.84FEE43 pKa = 4.97AIKK46 pKa = 10.9EE47 pKa = 3.97EE48 pKa = 4.21DD49 pKa = 3.48EE50 pKa = 4.2RR51 pKa = 11.84THH53 pKa = 6.35YY54 pKa = 10.48VAEE57 pKa = 4.41EE58 pKa = 4.15YY59 pKa = 10.8EE60 pKa = 4.47EE61 pKa = 4.32EE62 pKa = 5.38DD63 pKa = 4.34EE64 pKa = 5.5DD65 pKa = 6.2AEE67 pKa = 5.2DD68 pKa = 6.01LDD70 pKa = 4.68GHH72 pKa = 6.9DD73 pKa = 5.31DD74 pKa = 4.61DD75 pKa = 6.04YY76 pKa = 12.16EE77 pKa = 4.24EE78 pKa = 6.22DD79 pKa = 3.68EE80 pKa = 4.36

Molecular weight: 9.43 kDa
Isoelectric point according different methods:





Protein with the highest isoelectric point:
>tr|B5EH00|B5EH00_GEOBB Acyl-CoA synthetase AMP-forming OS=Geobacter bemidjiensis (strain Bem / ATCC BAA-1014 / DSM 16622) OX=404380 GN=Gbem_1082 PE=4 SV=1
MM1 pKa = 7.45KK2 pKa = 9.61RR3 pKa = 11.84TFQPSNTSRR12 pKa = 11.84KK13 pKa = 7.49RR14 pKa = 11.84THH16 pKa = 6.14GFLVRR21 pKa = 11.84MATKK25 pKa = 10.45NGRR28 pKa = 11.84LVIKK32 pKa = 10.39RR33 pKa = 11.84RR34 pKa = 11.84RR35 pKa = 11.84AKK37 pKa = 9.58GRR39 pKa = 11.84KK40 pKa = 8.4RR41 pKa = 11.84LSVSIATKK49 pKa = 10.45

Molecular weight: 5.73 kDa
Isoelectric point according different methods:





Peptides (in silico digests for buttom-up proteomics)

Below you can find in silico digests of the whole proteome with Trypsin, Chymotrypsin, Trypsin+LysC, LysN, ArgC proteases suitable for different mass spec machines.

Try
ESI
ChTry
ESI
ArgC
ESI
LysN
ESI
TryLysC
ESI

Try
MALDI
ChTry
MALDI
ArgC
MALDI
LysN
MALDI
TryLysC
MALDI

Try
LTQ
ChTry
LTQ
ArgC
LTQ
LysN
LTQ
TryLysC
LTQ

Try
MSlow
ChTry
MSlow
ArgC
MSlow
LysN
MSlow
TryLysC
MSlow

Try
MShigh
ChTry
MShigh
ArgC
MShigh
LysN
MShigh
TryLysC
MShigh

General Statistics

Number of major isoforms

Number of additional isoforms

Number of all proteins

Number of amino acids

Min. Seq. Length

Max. Seq. Length

Avg. Seq. Length

Avg. Mol. Weight

4042

0

4042

1343640

26

3244

332.4

36.47

Amino acid frequency

Ala

Cys

Asp

Glu

Phe

Gly

His

Ile

Lys

Leu

10.079 ± 0.05

1.312 ± 0.02

4.985 ± 0.026

6.657 ± 0.052

3.957 ± 0.026

8.157 ± 0.038

1.971 ± 0.021

5.397 ± 0.036

5.012 ± 0.04

10.541 ± 0.059

Met

Asn

Gln

Pro

Arg

Ser

Thr

Val

Trp

Tyr

2.512 ± 0.018

3.138 ± 0.029

4.629 ± 0.031

3.403 ± 0.022

5.992 ± 0.037

5.947 ± 0.038

5.085 ± 0.046

7.468 ± 0.031

1.005 ± 0.014

2.752 ± 0.023
Note: For amino acid frequency statistics the error has been estimated with the bootstraping (x100) at the protein level

Most of the basic statistics you can see at this page can be downloaded from this CSV file

For dipeptide frequency statistics click here
See this proteome in: uniprot_link
Proteome-pI is available under Creative Commons Attribution-NoDerivs license, for more details see here

Reference: Kozlowski LP. Proteome-pI 2.0: Proteome Isoelectric Point Database Update. Nucleic Acids Res. 2021, doi: 10.1093/nar/gkab944 Contact: Lukasz P. Kozlowski