Paracoccus denitrificans (strain Pd 1222)

Taxonomy: cellular organisms; Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Paracoccus; Paracoccus denitrificans

Average proteome isoelectric point is 6.58

Get precalculated fractions of proteins

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



Virtual 2D-PAGE plot for 5019 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|A1AZI5|A1AZI5_PARDP Succinate dehydrogenase cytochrome b556 subunit OS=Paracoccus denitrificans (strain Pd 1222) OX=318586 GN=Pden_0567 PE=3 SV=1
MM1 pKa = 7.32AQTGRR6 pKa = 11.84ARR8 pKa = 11.84QFLLTSAAGSALFGAHH24 pKa = 5.95ISINLRR30 pKa = 11.84EE31 pKa = 4.2RR32 pKa = 11.84RR33 pKa = 11.84FMATITGTDD42 pKa = 3.16NSEE45 pKa = 4.34TLLGTANADD54 pKa = 4.18LINGLGGNDD63 pKa = 4.11TITGGSGNDD72 pKa = 3.38TMHH75 pKa = 6.9GGSGDD80 pKa = 3.64DD81 pKa = 3.33TFLIGGTDD89 pKa = 3.36IGHH92 pKa = 7.59DD93 pKa = 3.61IYY95 pKa = 11.52DD96 pKa = 4.21GGDD99 pKa = 3.28GADD102 pKa = 3.47QIRR105 pKa = 11.84LNGTLKK111 pKa = 10.73VSNLSLTSANVISTEE126 pKa = 3.83TLNFYY131 pKa = 10.92GYY133 pKa = 10.58GVEE136 pKa = 4.33GTGGNDD142 pKa = 2.92VFDD145 pKa = 4.28ISGMTYY151 pKa = 8.8VSGYY155 pKa = 9.13SRR157 pKa = 11.84IYY159 pKa = 10.12MFDD162 pKa = 3.4GNDD165 pKa = 3.12TFTGYY170 pKa = 10.97AGNDD174 pKa = 3.52NVDD177 pKa = 3.18GGAGNDD183 pKa = 3.73VLNGGAGNDD192 pKa = 3.79TLIGGSGNDD201 pKa = 3.71TLNGGSGNDD210 pKa = 3.25YY211 pKa = 10.73FYY213 pKa = 10.71IGGTNFGHH221 pKa = 7.19DD222 pKa = 3.76VYY224 pKa = 11.49NGGEE228 pKa = 4.09GSDD231 pKa = 4.04EE232 pKa = 3.58IRR234 pKa = 11.84LVGKK238 pKa = 8.02VTVSNLSLTSANVISTEE255 pKa = 3.83TLNFYY260 pKa = 10.92GYY262 pKa = 10.58GVEE265 pKa = 4.33GTGGNDD271 pKa = 2.92VFDD274 pKa = 4.28ISGMTYY280 pKa = 8.8VSGYY284 pKa = 9.13SRR286 pKa = 11.84IYY288 pKa = 10.12MFDD291 pKa = 3.4GNDD294 pKa = 3.12TFTGYY299 pKa = 10.97AGNDD303 pKa = 3.52NVDD306 pKa = 3.18GGAGNDD312 pKa = 3.73VLNGGAGNDD321 pKa = 3.79TLIGGSGNDD330 pKa = 3.71TLNGGSGNDD339 pKa = 3.25YY340 pKa = 10.62FYY342 pKa = 10.74IGGTDD347 pKa = 3.95FGHH350 pKa = 7.14DD351 pKa = 3.51VYY353 pKa = 11.6NGGEE357 pKa = 4.09GSDD360 pKa = 4.04EE361 pKa = 3.58IRR363 pKa = 11.84LVGKK367 pKa = 8.02VTVSNLSLTSANVIGTEE384 pKa = 3.86TLNFYY389 pKa = 10.93GYY391 pKa = 10.58GVEE394 pKa = 4.33GTGGNDD400 pKa = 2.92VFDD403 pKa = 4.28ISGMTYY409 pKa = 8.8VSGYY413 pKa = 9.13SRR415 pKa = 11.84IYY417 pKa = 10.12MFDD420 pKa = 3.4GNDD423 pKa = 3.12TFTGYY428 pKa = 10.97AGNDD432 pKa = 3.52NVDD435 pKa = 3.18GGAGNDD441 pKa = 3.73VLNGGAGNDD450 pKa = 3.79TLIGGSGNDD459 pKa = 3.71TLNGGSGNDD468 pKa = 3.25YY469 pKa = 10.62FYY471 pKa = 10.74IGGTDD476 pKa = 3.95FGHH479 pKa = 7.14DD480 pKa = 3.51VYY482 pKa = 11.6NGGEE486 pKa = 4.09GSDD489 pKa = 4.04EE490 pKa = 3.58IRR492 pKa = 11.84LVGKK496 pKa = 8.02VTVSNLSLTSANVISTEE513 pKa = 3.83TLNFYY518 pKa = 10.9GYY520 pKa = 10.45GIEE523 pKa = 4.3GTGGNDD529 pKa = 2.94VFDD532 pKa = 4.28ISGMTYY538 pKa = 8.8VSGYY542 pKa = 9.56SRR544 pKa = 11.84IYY546 pKa = 9.2MQDD549 pKa = 2.78GNDD552 pKa = 3.35RR553 pKa = 11.84FTGYY557 pKa = 10.85AGNDD561 pKa = 3.52NVDD564 pKa = 3.23GGAGNDD570 pKa = 3.82TLIGGAGNDD579 pKa = 3.87TLNGGSGIDD588 pKa = 3.32TAAYY592 pKa = 9.58GSATAGVTVNLALTTAQAVGGGQGVDD618 pKa = 3.22TLIDD622 pKa = 3.44IEE624 pKa = 4.42NVNGSAYY631 pKa = 10.56ADD633 pKa = 3.42ALLGNAAANLLQGAGGNDD651 pKa = 3.64TLDD654 pKa = 3.68GGAGNDD660 pKa = 3.95TLSGGAGMDD669 pKa = 3.18TAAYY673 pKa = 9.2GRR675 pKa = 11.84ASSGVTVNLGLTGAQLVGGGQGRR698 pKa = 11.84DD699 pKa = 3.29VLRR702 pKa = 11.84SIEE705 pKa = 4.45NIDD708 pKa = 3.28GSGFADD714 pKa = 3.92RR715 pKa = 11.84LTGNAGSNALRR726 pKa = 11.84GGAGNDD732 pKa = 3.51SLSGLGGNDD741 pKa = 2.99RR742 pKa = 11.84LFGGAGADD750 pKa = 3.53QLLGGAGNDD759 pKa = 3.86VLNGDD764 pKa = 4.8AGNDD768 pKa = 3.85LLNGGAGNDD777 pKa = 3.99TLNGGAGIDD786 pKa = 3.4TAAYY790 pKa = 9.06GGASSGVTVNLGLTVAQLIGGGQGRR815 pKa = 11.84DD816 pKa = 3.19VLRR819 pKa = 11.84NIEE822 pKa = 4.13NVNGSGFADD831 pKa = 3.51RR832 pKa = 11.84LTGNTGNNVLNGAAGNDD849 pKa = 3.99TLSGGAGRR857 pKa = 11.84DD858 pKa = 3.56QLLGGAGADD867 pKa = 3.55QLLGGAGNDD876 pKa = 3.89TLNGGAGNDD885 pKa = 3.99TLNGGAGIDD894 pKa = 3.4TAAYY898 pKa = 9.06GGASSGVTVNLGLTVAQLIGGGQGRR923 pKa = 11.84DD924 pKa = 3.19VLRR927 pKa = 11.84NIEE930 pKa = 4.13NVNGSGFADD939 pKa = 3.64RR940 pKa = 11.84LTGNAGNNVLNGAAGNDD957 pKa = 3.99TLSGGAGRR965 pKa = 11.84DD966 pKa = 3.68QLSGGAGADD975 pKa = 3.5RR976 pKa = 11.84LLGGAGNDD984 pKa = 3.89TLNGGAGNDD993 pKa = 3.71TLTGGVGADD1002 pKa = 3.01VFVFAVGNGADD1013 pKa = 5.63RR1014 pKa = 11.84ITDD1017 pKa = 3.48WQDD1020 pKa = 2.79GTDD1023 pKa = 3.63VIRR1026 pKa = 11.84IVSGNWQGEE1035 pKa = 4.51RR1036 pKa = 11.84YY1037 pKa = 10.36DD1038 pKa = 4.22SFDD1041 pKa = 4.54DD1042 pKa = 4.94LSITQSAGNAVVSFGGTTITLAGIGSGQLDD1072 pKa = 3.49ASDD1075 pKa = 4.75FIFVV1079 pKa = 3.67

Molecular weight: 106.85 kDa
Isoelectric point according different methods:





Protein with the highest isoelectric point:
>tr|A1B0I1|A1B0I1_PARDP Transcriptional regulator MarR family OS=Paracoccus denitrificans (strain Pd 1222) OX=318586 GN=Pden_0914 PE=4 SV=1
MM1 pKa = 7.74SKK3 pKa = 8.95RR4 pKa = 11.84TYY6 pKa = 10.2QPSNLVRR13 pKa = 11.84ARR15 pKa = 11.84RR16 pKa = 11.84HH17 pKa = 4.37GFRR20 pKa = 11.84ARR22 pKa = 11.84MATKK26 pKa = 10.13GGRR29 pKa = 11.84RR30 pKa = 11.84VINARR35 pKa = 11.84RR36 pKa = 11.84AKK38 pKa = 10.0GRR40 pKa = 11.84KK41 pKa = 6.51TLSAA45 pKa = 4.15

Molecular weight: 5.17 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

5019

0

5019

1561797

36

2779

311.2

33.68

Amino acid frequency

Ala

Cys

Asp

Glu

Phe

Gly

His

Ile

Lys

Leu

13.254 ± 0.046

0.883 ± 0.011

5.644 ± 0.028

5.71 ± 0.027

3.461 ± 0.021

9.075 ± 0.037

2.1 ± 0.015

5.015 ± 0.025

2.47 ± 0.026

10.442 ± 0.042

Met

Asn

Gln

Pro

Arg

Ser

Thr

Val

Trp

Tyr

2.705 ± 0.017

2.281 ± 0.019

5.601 ± 0.026

3.229 ± 0.019

7.805 ± 0.035

4.854 ± 0.021

4.946 ± 0.023

7.021 ± 0.026

1.475 ± 0.014

2.03 ± 0.017
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