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Table 1 S. gordonii intracellular proteins and phosphoproteins, separated by 2DE and identified with LC-MS/MS

From: Intracellular Ser/Thr/Tyr phosphoproteome of the oral commensal Streptococcus gordonii DL1

Abbr Protein Geneb) Acc. No.c) pI
estimated from gel/theoreticald)
MW, Da
estimated from gel/ theoreticald)
LC-MS/MS Ser/Thr/Tyr
phosphory-lated
+/−
MASCOT
score
No. of peptidese) Coverage
Transmembrane transport
ABCa) ABC transporter ATP-binding protein SP1715 SGO_1342 A8AXW3 6.7/6.25 23,000/26325 1124 18 72%
Sugar transport
HPra) Phosphocarrier protein HPr ptsH (SGO_1556) A8AYH5 5.1/4.74 11,000/8935 124 2 55% +
Glycolysis
Tpi-1a) Triosephosphate isomerase tpiA (SGO_0762) A8AWA1 4.5/4.75 23,000/26524 652 9 52% +
Tpi-2a)     4.3/4.75 23,000/26524 540 9 52% -
pfk-1a) Phosphofructokinase pfkA (SGO_1340) A8AXW1 6.6/5.62 35,000/35346 1043 17 49% +
pfk-2     6.8/5.62 35,000/35346 1476 22 56% +
fba-1f) Fructose-1,6-bisphosphate aldolase, class II Fba (SGO_1745) A8AZ06 5.1/5.00 27,000/31394 - - - -
fba-2a)     5.2/5.00 27,000/31394 771 12 51% -
fba-3a)     5.3/5.00 27,000/31394 800 14 47% -
fba-4f)     5.4/5.00 27,000/31394 - - - -
fba-5a)     5.4/5.00 17,000/31394 164 3 11% -
gapdh-1a) Glyceraldehyde-3-phosphate dehydrogenase gap (SGO_0207) A8AUR7 5.5/5.37 39,000/35918 1153 20 51% +
gapdh-2a)     5.7/5.37 39,000/35918 1299 21 79% +
gapdh-3a)     5.9/5.37 39,000/35918 1304 22 58% +
gapdh-4     5.5/5.37 40,000/35918 89 2 8% -
gapdh-5     5.7/5.37 40,000/35918 276 4 14% -
gapdh-6     6.0/5.37 39,000/35918 84 2 6% -
gapdh-7     5.9/5.37 40,000/35918 325 5 16% -
gapdh-8     5.2/5.37 18,000/35918 141 2 8% -
pgk-1 Phosphoglycerate kinase pgk (SGO_0209) A8AUR9 4.9/4.88 45,000/42089 397 6 18% +
pgk -2a)     5.0/4.88 45,000/42089 1454 23 63% +
pgk -3a)     4.3/4.88 21,000/42089 340 5 17% +
pgk -4f)     5.1/4.88 45,000/42089 - - - -
pgk -5f)     5.2/4.88 45,000/42089 - - - -
pgk −6     4.3/4.88 45,000/42089 159 3 9% -
pgk -7a)     5.9/4.88 24,000/42089 431 7 18% -
pgk -8a)     4.2/4.88 20,000/42089 830 11 41% -
pgk -9a)     5.9/4.88 20,000/42089 561 9 28% -
pgm-1a) Phosphoglycerate mutase gpma (SGO_0704) A8AW46 5.9/5.41 22,000/26044 904 18 84% +
pgm-2a)     6.1/5.41 22,000/26044 933 18 87% +
eno-1 Enolase eno (SGO_1426) A8AY46 4.4/4.71 48,000/47062 1368 18 61% +
eno −2     4.5/4.71 48,000/47062 1260 13 52% +
eno −3     4.6/4.71 48,000/47062 1721 18 63% +
eno -4a)     4.7/4.71 48,000/47062 2245 31 77% +
eno −5     4.6/4.71 26,000/47062 1316 17 58% +
eno -6a)     4.5/4.71 24,000/47062 460 8 26% +
eno -7a)     4.1/4.71 22,000/47062 809 9 30% +
eno -8a)     4.2/4.71 21,000/47062 673 9 28% +
eno -9a)     4.3/4.71 21,000/47062 595 10 32% +
eno -10a)     4.4/4.71 21,000/47062 989 11 34% +
eno -11a)     4.4/4.71 28,000/47062 1485 15 55% -
eno -12a)     4.8/4.71 25,000/47062 950 14 47% -
eno -13a)     4.4/4.71 23,000/47062 460 8 26% -
eno -14a)     4.2/4.71 23,000/47062 746 11 36% -
eno -15a)     4.8/4.71 23,000/47062 627 9 32% -
eno -16a)     4.8/4.71 22,000/47062 631 9 31% -
eno -17a)     4.9/4.71 22,000/47062 636 9 31% -
eno -18a)     4.4/4.71 17,000/47062 230 4 11% -
eno −19     4.5/4.71 14,500/47062 931 9 41% -
eno − 20     4.6/4.71 14,000/47062 533 7 23% -
eno -21a)     5.0/4.71 13,000/47062 437 7 23% -
eno -22a)     4.7/4.71 12,500/47062 722 9 33% -
eno -23a)     4.3/4.71 11,000/47062 418 6 20% -
eno -24a)     5.4/4.71 18,000/47062 684 9 27% -
pyk-1a) Pyruvate kinase pyk (SGO_1339) A8AXW0 5.15/4.94 58,000/54799 150 3 6% +
pyk-2a)     5.2/4.94 58,000/54799 1474 29 62% +
pyk-3f)     5.1/4.94 58,000/54799 - - - -
pyk-4f)     5.3/4.94 58,000/54799 - - - -
Cofactor biosynthesis
nadea) NH(3)-dependent NAD(+) synthetase nadE (SGO_0583) A8AVT9 5.4/5.11 35,000/30248 268 3 16%
Acetoin catabolism  
aced-1 Acetoin dehydrogenase butA (SGO_1096) A8AX75 5.4/5.20 26,000/26547 1008 15 77% -
aced-2a)     5.7/5.20 26,000/26547 1247 17 75% -
aced-3a)     5.7/5.20 24,000/26547 809 13 62% -
Carbohydrate catabolism
deraa) Deoxyribose-phosphate aldolase deoC (SGO_1080) A8AX59 4.9/4.84 20,000/23380 691 8 49%
Pyruvate conversion
ldh-1a) L-lactate dehydrogenase ldh (SGO_1232) A8AXK9 5.4/5.24 36,000/35267 327 6 28% +
ldh-2     5.6/5.24 36,000/35267 436 6 28% +
ldh-3     5.8/5.24 36,000/35267 641 8 32% -
adha) Alcohol dehydrogenase adhA (SGO_0565) A8AVS1 5.2/4.94 39,000/35958 911 13 69%
pox Pyruvate oxidase spxB (SGO_0292) A8AV01 5.3/5.06 65,000/65283 161 3 5%
Pentose phosphate pathway  
deob Phosphopentomutase deoB (SGO_1264) A8AXN8 5.3/4.96 47,000/44508 172 3 9% +
Amino acid metabolism
alad Alanine dehydrogenase ald (SGO_0708) A8AW50 6.1/5.29 45,000/38960 1378 19 63%
dapha) 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase dapH (SGO_0158) A8AUL9 5.2/5.06 22,000/24255 291 5 25%
glya Serine hydroxymethyltransferase glyA, (SGO_1151) A8AXC8 5.4/5.07 48,000/45566 583 8 28%
sed Homoserine dehydrogenase hom (SGO_0801) A8AWE0 5.0/4.86 45,000/46154 245 3 11%
Nucleotide metabolism
adka) Adenylate kinase adk (SGO_1964) A8AZK4 5.2/4.95 22,000/ 23,857 318 6 38%
aprta) Adenine phosphoribosyltransferase apt (SGO_1001) A8AWY0 5.0/4.90 17,000/18840 875 12 74%
imdh-1 Inosine-5′-monophosphate dehydrogenase guaB (SGO_0008) A8AU70 5.4/5.19 58,000/52717 116 2 5% +
imdh-2     5.5/5.19 56,000/52717 252 4 12% -
pyrb Aspartate carbamoyltransferase pyrB (SGO_1109) A8AX88 5.6/5.04 35,000/34741 54 1g) 4%
xprt Xanthine phosphoribosyltransferase xpt (SGO_1158) A8AXD5 6.2/5.79 17,000/20849 684 12 77%
Molecular chaperone activity and/or protein folding
Dnak-1 Molecular chaperone DnaK dnaK (SGO_0402) A8AVA8 4.4/4.69 68,000/64724 266 4 9% +
DnaK-2a)     4.5/4.69 68,000/64724 1557 26 50% +
DnaK-3a)     5.2/4.69 25,000/64724 134 2 3% +
DnaK-4f)     4.6/4.69 68,000/64724 - - - -
DnaK-5     4.1/4.69 44,000/64724 254 4 10% -
DnaK-6a)     5.3/4.69 36,000/64724 345 6 14% -
GroEL-1 Molecular chaperone GroEL groEL (SGO_1885) A8AZE1 4.2/4.66 64,000/56754 776 13 34% +
GroEL-2     4.3/4.66 64,000/56754 1500 22 47% +
GroEL-3     4.4/4.66 64,000/56754 794 13 32% -
GroES Co-chaperone GroES groES (SGO_1886) A8AZE2 5.4/5.11 64,000/9681 65 1g) 2%
grpEa) Molecular chaperone GrpE grpE (SGO_0401) A8AVA7 4.8/4.83 23,000/20265 186 3 18%
hyda) Hydrolase, haloacid dehalogenase family/ peptidyl-prolyl cis-trans isomerase, cyclophilin type SGO_0604 A8AVW0 4.2/4.74 22,000/51936 516 10 30%
tiga) Trigger factor (chaperone) tig (SGO_0412) A8AVB8 4.2/4.53 55,000/47242 531 10 31% +
Transcription
GreA Transcription elongation factor GreA greA (SGO_0519) A8AVM5 4.9/4.85 15,500/17515 581 9 68%
rpoAa) DNA-directed RNA polymerase subunit alpha rpoA (SGO_1959) A8AZJ9 4.5/4.70 41,000/34502 578 7 29%
rpoZ DNA-directed RNA polymerase subunit omega rpoZ (SGO_0595) A8AVV1 6.7/5.82 12,000/11851 231 5 44%
y454 Probable transcriptional regulatory protein   A8AVG0 4.6/4.45 30,000/25722 227 4 26%
Translation
ef-G Elongation factor G fusA (SGO_0206) A8AUR6 4.7/4.88 50,000/76785 53 1g) 2%
ef-Ts Elongation factor Ts tsf (SGO_2000) A8AZP0 4.9/4.84 41,000/37284 326 5 20%
ef-tu-1a) Elongation factor tu tuf (SGO_0761) A8AWA0 4.1/4.86 55,000/44011 519 8 31% +
ef-tu-2     5–6/4.86 55,000/44011 1253 22 63% +
ef-tu-3a)     4.2/4.86 34,000/44011 532 6 23% +
ef-tu-4a)     4.3/4.86 25,000/44011 167 3 8% +
ef-tu-5a)     4.3/4.86 29,000/44011 553 6 25% -
ef-tu-6a)     4.7/4.86 23,000/44011 420 6 18% -
ef-tu-7a)     5.3/4.86 20,000/44011 433 6 16% -
rL1a) 50S ribosomal protein L1 rplA (SGO_1455) A8AY74 5.5/9.22 23,000/24399 202 3 16%
rL4-1a) 50S ribosomal protein L4 rplD (SGO_1984) A8AZM4 5.2/10.03 19,000/22279 285 4 26% -
rL4-2a)     5.5/10.03 19,000/22279 327 4 24% -
rL10a) 50S ribosomal protein L10 rplJ (SGO_1192) A8AXG9 5.2/5.06 15,000/17462 1002 15 86%
rL17 50S ribosomal protein L17 rplQ (SGO_1958) A8AZJ8 5.3/9.86 13,000/14511 141 2 17%
rrfa) Ribosome recycling factor frr (SGO_1451) A8AY70 6.8/5.90 18,000/20640 421 8 46%
rS1 30S ribosomal protein S1 rpsA (SGO_1234) A8AXL0 4.5/4.91 52,000/44149 130 2 5% +
rS2 30S ribosomal protein S2 rpsB (SGO_2001) A8AZP1 4.6/5.07 33,000/29125 515 8 35%
rS5-1a) 30S ribosomal protein S5 rpsE (SGO_1968) A8AZK8 5.1/9.69 14,000/17079 335 4 33% -
rS5–2     5.3/9.69 14,000/17079 283 4 33% -
rS8a) 30S ribosomal protein S8 rpsH (SGO_1971) A8AZL1 5.3/9.48 12,500/14753 120 2 25%
rS17 30S ribosomal protein S17 rpsQ (SGO_1976) A8AZL6 5.0/9.92 11,000/10010 58 1g) 10%
sys-1 Serine tRNA-ligase serS (SGO_1683) A8AYV0 5.4/5.11 48,000/48110 342 7 21% -
sys-2a)     5.7/5.11 21,000/48110 95 1g) 2% -
Protein catabolism
clpp ATP-dependent Clp protease proteolytic subunit clpP (SGO_1632) A8AYP9 4.3/4.72 18,000/21363 200 3 12%
pept Peptidase T pepT (SGO_1312) A8AXT3 4.2/4.59 49,000/45200 332 4 13%
Vitamin B biosynthesis
pxka) Pyridoxine kinase SGO_0409 A8AVB5 5.3/5.16 23,000/27598 583 10 52%
Cell envelope biosynthesis
murda) UDP-N-acetylmuramoylalanine D-glutamate ligase murdD (SGO_0671) A8AW14 5.4/5.07 46,000/48257 253 4 12%
pgama) Phosphoglucosamine mutase glmM (SGO_0889) A8AWM5 4.6/4.71 52,000/48396 592 7 26% +
rmla-1 Glucose-1-phosphate thymidylyltransferase rfbA-1 (SGO_1009) A8AWY8 5.1/4.92 28,000/32213 42 1g) 3% +
rmla-2a)     5.3/4.92 28,000/32213 136 2 7% +
rmlb dTDP-glucose 4,6-dehydratase rfbB-1 (SGO_1011) A8AWZ0 6.3/5.55 40,000/39314 168 3 12%
Cell division
SepF Cell division protein SepF sepF (SGO_0677) A8AW20 6.6/5.61 19,000/21654 367 6 41%
Antioxidant activity
soda) Superoxide dismutase sodA (SGO_1599) A8AYL7 4.9/4.78 19,000/22446 474 8 46%
tox Thiol peroxidase Tpx (SGO_1803) A8AZ62 4.2/4.52 16,000/18015 349 6 59%
Protein dephosphorylation
pppa) Phosphoprotein phosphatase SGO_0599 SGO_0599 A8AVV5 4.3/4.62 23,000/26870 696 11 61% +
  1. a) Two or more proteins were identified from this spot
  2. b) Gene name in the UniProt database as entered for S. gordonii DL1 proteins
  3. c) Accession number in the UniProt database for S. gordonii DL1
  4. d) Theoretical values for S. gordonii DL1 proteins
  5. e) The sequenced peptides identified by LC-MS/MS can be found in supplemental material (Additional file 1)
  6. f) Protein identity deduced from adjacent identified spot
  7. g) Proteins identified by only one peptide are given when only a single match was yielded from the database search