Table 2. Identified proteins putatively related to polysaccharide hydrolysis.

Identified proteinsa	Information based on public databases and publications				Mass spectrometry
Uniprot entry (gene)b [Reference]c	UniRef50 clusters: ID name taxonomic range	CAZyd	Domainse	Putative functions or activitiesd	Number of peptide ionsf	Coverage (%)g
Affiliated mainly to C. thermocellum strains (cellulolytic system based on a cellulosome)
O86999_CLOTM (slpA) A3DHX1_CLOTH	UniRef50_O86999 S-layer protein C. thermocellum		SLH signal	S-layer protein; functional partners: carbohydrate-binding protein A3DET8_CLOTH (STRING 9 network http://string-db.org/)	32	42
Q06851_CLOTH (cipA) [1] D1NHZ0_CLOTM E6UU82_CLOTL	UniRef50_Q06851 Cellulosomal-scaffolding protein A C. thermocellum	CBM3	Dockerin cohesin signal	Cellulosomal-scaffolding protein	20	15
A3DD30_CLOTH C7HDM6_CLOTM D1NI43_CLOTM E6USK3_CLOTL P71140_CLOTM (celJ) [1]	UniRef50_C7HDM6 Glycoside hydrolase family 9 domain protein, Ig domain protein cellulolytic Clostridiales	CBM30 CBM44 GH9 GH44	Dockerin Ig-like_fold signal	GH44: endoglucanase, xyloglucanase, active on many substances (GH9: endoglucanase)	11	9.3
A3DH67_CLOTH (celS) [1] P0C2S5_CLOTM (celS) C7HDZ8_CLOTM E6US41_CLOTL D1NQ73_CLOTM	UniRef50_P22534 Endoglucanase A mainly cellulolytic Clostridia	GH48	Dockerin signal	GH48: processive exoglucanase acting on reducing end, endo-processive cellulose, key component for enzymatic synergy, most abundant enzyme subunit	7	6.9
Q06852_CLOTH (olpB) [1] D1NHZ1_CLOTM E6UU83_CLOTL	UniRef50_Q06852 Cell surface glycoprotein 1 mainly C. thermocellum		Cohesin SLH signal	Cellulosome anchoring protein	6	4.8
C7HDC4_CLOTM E6URK4_CLOTL	UniRef50_D1NNW4 Type 3a cellulose-binding domain protein C. thermocellum	CBM3	signal	CBM3a	5	6.7
A3DBG8_CLOTH C7HH13_CLOTM E6UN62_CLOTL D1NKR6_CLOTM	UniRef50_A3DBG8 Ig domain protein group 2 domain protein mainly C. thermocellum		SLH Big_2 signal	Functional partners: carbohydrate-binding protein A3DET8 (STRING 9 network http://string-db.org/)	5	1.4
A3DC35_CLOTH C7HGL0_CLOTM E6ULX2_CLOTL	UniRef50_D2Q7C4 Cellobiose phosphorylase mainly cellulolytic Clostridiales, Actinobacteridae	CBM GH94		GH94: cellobiose phosphorylase	3	3.3
A3DDD5_CLOTH C7HD15_CLOTM D1NMI1_CLOTM E6URU4_CLOTL	UniRef50_C7HD15 Cellulosome protein dockerin type I mainly C. thermocellum		Dockerin signal	Cellulosome protein dockerin type I	2	3.4
A3DJQ6_CLOTH C7HEH9_CLOTM  D1NRB6_CLOTM E6UTK1_CLOTL Q93HT8_CLOTM (cdp-ym4)	UniRef50_D9SRI5 Glycosyltransferase 36(h) mainly C. thermocellum	GH94		GH94: cellodextrin phosphorylase	2	2.8
C7HJV5_CLOTM D1NR31_CLOTM D1NRP9_CLOTM O52779_CLOTM (xynV) E6UTI5_CLOTL O52780_CLOTM (xynU) O87118_CLOTM (xynB) O87119_CLOTM ( xynA) [1] E6UTI4_CLOTL A3DJP0_CLOTH Q8GJ44_CLOSR (xynA)	UniRef50_A3DJP0 Glycoside hydrolase family 11 mainly cellulolytic Clostridiales	CBM6 GH11 CE4	Dockerin signal	GH11: endo-β-1,4-xylanase	2	4.2
Affiliated mainly to Caldicellulosiruptor species (cellulolytic system based on multifunctional enzymes)
E4SCW4_CALK2	UniRef50_Q9KWY5 Beta-mannanase mainly thermophilic bacteria and archaea, including many Clostridia	GH3		GH3: removes single glycosyl residues from the non-reducing end, dual or broad substrate specificities, β-glucosidase	7	16
A4XM78_CALS8	UniRef50_F8F4V8 Esterase mainly Clostridia and Bacilli	CE7		CE7: acetyl xylan esterase	4	11
P22534_CALSA (celA) [2] A4XIF5_CALS8	UniRef50_P22534 Endoglucanase A mainly Clostridia and other bacteria	CBM3 GH9 GH48	Signal	GH48: processive exoglucanase acting on reducing end, endo-processive cellulose, key component for enzymatic synergy, most abundant enzyme subunit	3	1.3
E4S6B0_CALKI G2PWX9_9FIRM [2]	UniRef50_A4XIG8 Glycosyltransferase 36(h) Caldicellulosiruptor	GH94 CBM		GH94: cellobiose phosphorylase, membrane protein	2	3.9
G2PWE2_9FIRM	UniRef50_E4Q5G9 Endo-1,4-beta-xylanase mainly Caldicellulosiruptor	CBM9 CenC-like CBM GH10	SLH Signal	GH10: endo-beta-1,4-xylanase, membrane protein	2	1.3
A4XN28_CALS8 B9MLB5_ANATD D9TFV3_CALOO E4Q4G6_CALOW E4QE34_CALH1 E4S9M6_CALKI E4SEW2_CALK2 F7KFZ8 Lachno	UniRef50_P39130 Putative glucosidase lplD mainly Clostridia and Bacillales	GH4		GH4: distinct substrate specificities, unusual mechanism involving NAD+	2	6.7
B9MN93_ANATD D9TGX7_CALOO E4Q6A9_CALOW E4QAK4_CALH1	UniRef50_Q9KWY5 Beta-mannanase mainly thermophilic bacteria and archaea including many Clostridia	GH3		GH3: remove single glycosyl residues from the non-reducing end, dual or broad substrate specificities, β-glucosidase	2	7.1
Affiliated to Coprothermobacter proteolyticus strains (non-cellulolytic organisms)
B5Y6P8_COPPD	UniRef50_B5Y6P8 Amylopullulanase C. proteolyticus	GH13		GH13:amylopullulanase, α-amylase, pullulanase (etc), wide range of different preferred substrates and products	26	21
B5Y7R5_COPPD	UniRef50_B5Y7R5 Endoxylanase C. proteolyticus		SLH signal	Endoxylanase, pectin lyase	2	3.3

^aRedundant protein list: all possibilities corresponding to a given set of peptides are shown. Italic font: entry showing 100% sequence identity with the above entry. The affiliation to distinct UniRef90 clusters is materialised by distinct paragraphs.

^bClostridium species: CLOTH, C. thermocellum strain ATCC 27405/DSM 1237; CLOTM, C. thermocellum strain YS; CLOTL, C. thermocellum strain DSM 1313/LMG 6656/LQ8; CLOSR, C. stercorarium; Lachnospiraceae species: Lachno, L. bacterium; Caldicellulsiruptor species: 9FIRM, C. lactoaceticus; ANATD, C. becscii; CALH1, C. hydrothermalis; CALK2, C. kronotskyensis; CALKI, C. kristjanssonii; CALS8, C. saccharolyticus; CALSA, C. saccharolyticus; CALOO, C. obsidiansis; CALOW, C. owensensis; and Coprothermobacter species: COPPD, C. proteolyticus.

^cReference indicating experimental evidence for the expression and/or activity of the corresponding protein or a closely related one. [1]=Gold and Martin, 2007; [2]=Lochner et al., 2011.

^dMore information at http://www.cazy.org/ and http://www.cazypedia.org (Cantarel et al., 2009). CBM, carbohydrate-binding module; GH, glycoside hydrolase; CE, carbohydrate esterase.

^eSLH, S-layer homology domain; Big, bacterial immunoglobulin-like, group 2; Ig, immunoglobulin-like; signal, signal sequence (secreted or membrane protein).

^fNumber of unique parent peptide ions matched (including different charge states, modifications).

^gPercentage of amino acid coverage to the matched protein.

^hGlycosyltransferase 36 was recently reclassified as glycoside hydrolase 94 (GH94) according to CAZy.