Table 3

Identified carbohydrate-modifying enzymes from hypoxia-acclimated (Hyp) and normoxia-acclimated (Norm) Daphnia pulex

Spot no.

Specificity

Hyp: Norm

Matched peptide

sequencesa)

Sequence

coverageb)

Mascot

scorec)

Mr predicted/Mr geld)

pI predicted/

pI gele)

SP

Length

Functionf)

Model name [Protein ID, Reference ID]


1

7.2

MFQLLNR

WINGLANSK

DGCDFASYR

MNDHTFYGPGSTFK

FYVQNGVR

GLFGDLDDHK

GLFGDLDDHKNK

13.3%

284

48.2/58

4.73/4.72

19

Cellubiohydrolase (CEL7A) PIR_PASA_GEN_1000209 [347598, 300366]


19

1.4

GNPTVEVDLTTEK

MGTETYHHLKK

NGKYDLDFK

NPASDPATYLESNK

RIQMAVDCK

ACNCLLLK

VNQIGTVTESIAAHK

LAKYNQILR

IEEELGAAAK

22.6%

468

46.8/51

5.98/6.01

Enolase (ENO) PIR_PASA_GEN_1500033 [347595, 301844]


29

1.2

KSILFYEAQR

SILFYEAQR

NAYTAAGELDNGLAALR

QLYDFAK

MAGISVLLSR

ILGDQKYK

QQIDYALGSTGR

SYVVGFGNNPPVK

17.7%

355

47.3/53

5.09/5.00

18

Endo-β-1,4-Glucanase (CEL9A)

PIR_estExt_fgenesh1_kg.C_70001

[347602, 230437]

VQLEEEAEAR

LTHELDKTR

KLGDENAELK

LKTEIQR

4.1%

124

103.7/53

5.42/5.00

Myosin

estExt_Genewise1.C_2380001

[219409, 219409]


30

0.8

DSILHIKPTLTEDR

GGGNTINPAMAAR

YGRVEVNAK

SSTPGYNSAFHR

YQLEWTPDYLK

FSIDDVETGR

19.8%

327

38.5/39

4.76/4.77

19

β-1,3-Glucan-binding protein

(gram-negative bacteria-binding protein)

PASA_GEN_0200102 [303036, 303036]

SFLDFAQSK

FVNWQADGVK

NYYTDSCLVAAGGK

9.1%

88

39.0

4.75

19

Endo-β-1,4-Mannanase (MAN5A)

PASA_GEN_8600009 [347627, 308762]


34

0.3*

YLGHEVGDAR

LKDYYLR

DLINDCIMDPK

7.3%

160

43.1/44

4.75/4.76

19

Exo-β-1,3-Glucanase (EXG5)

PIR_PASA_GEN_1000289

[347606,300436]


35

0.5

WDDIAAECER

YQPVSYK

SGDENAFKSMVDR

GKILEFLNK

ILEFLNK

LTSYGVAGFR

HMWPGDLK

KLSDVFHK

LSDVFHK

LSDVFHKK

GHGGGGDLLTFR

QIYNMAK

17.2%

536

54.9/62

6.03/6.30

19

α-Amylase (AMY)

PASA_GEN_2100059 [303445, 303445]


Identification was based on 2D gel electrophoresis and nano-HPLC-ESI-MS/MS analysis of trypsin-digested proteins matched against the "Frozen Gene Catalog" of the D. pulex protein database [26], which contains all manual curations as of July 3, 2007 as well as automatically annotated models chosen from the "Filtered Models" v1.1 reference set. The compiled information includes the spot number (Figure 1A, B), the hypoxia-to-normoxia expression ratio, the number and sequences of matched peptides, the sequence coverage, the Mascot score as a statistical measure of identification probability, the theoretical and experimental molecular weight (Mr) and isolectric point (pI) of the mature protein (without signal peptide), the predicted length of the N-terminal signal peptide (SP) in extracellular proteins, the putative function of the protein, as well as the gene model name and protein identification number for the locus. The protein IDs may differ from those contained in the "Filtered Models v1.1" reference set. The Reference ID can be used to retrieve the corresponding models from this reference set. Underlined and bold-printed sequences indicate peptides that are specific for a globin gene.

a) Matched peptide sequences: tryptic peptide sequences identified via nano-HPLC-ESI-MS/MS.

b) Sequence coverage %: percentage of predicted protein sequence covered by matched peptides.

c) Probability based Mascot score: -10*Log(P), where P is the probability that the observed match is a random event. Scores > 38 indicate identity or extensive homology (p < 0.05). Protein scores are derived from ions scores as a non-probabilistic basis for ranking protein hits. The Mascot-score calculation was performed using whole-protein sequence (including the N-terminal signal peptide in case of extracellular proteins).

d) Mr predicted/Mr gel: molecular mass of predicted protein/of protein on gel.

e) pI predicted/pI gel: isoelectric point of predicted proteins/of proteins on gel.

f) Function of identified proteins was obtained either via automated blastp search provided by JGI or after manual curation of a gene model.

* p < 0.05 (t-Test)

Zeis et al. BMC Physiology 2009 9:7   doi:10.1186/1472-6793-9-7

Open Data