Query 031974
Match_columns 150
No_of_seqs 168 out of 460
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:54:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031974hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1616 Protein involved in Sn 100.0 1.4E-43 3E-48 297.3 8.8 148 1-150 121-289 (289)
2 PF04739 AMPKBI: 5'-AMP-activa 100.0 5.2E-38 1.1E-42 227.8 4.4 87 60-148 2-100 (100)
3 cd02859 AMPKbeta_GBD_like AMP- 99.5 3.6E-15 7.8E-20 103.1 3.7 39 2-40 41-79 (79)
4 cd02861 E_set_proteins_like E 98.8 4.3E-09 9.4E-14 72.6 4.0 38 2-39 42-81 (82)
5 cd02858 Esterase_N_term Estera 97.0 0.0011 2.4E-08 46.0 4.3 35 3-37 48-82 (85)
6 cd02688 E_set E or "early" set 94.9 0.019 4.1E-07 37.7 2.1 27 7-33 51-77 (83)
7 KOG0045 Cytosolic Ca2+-depende 79.0 2.2 4.9E-05 39.9 3.6 26 5-30 115-143 (612)
8 PF01378 IgG_binding_B: B doma 64.5 5.2 0.00011 26.0 1.7 13 15-27 38-50 (55)
9 cd00044 CysPc Calpains, domain 62.4 10 0.00022 31.9 3.6 25 4-28 106-133 (315)
10 PF02922 CBM_48: Carbohydrate- 59.4 4.2 9.1E-05 27.0 0.7 17 3-19 58-74 (85)
11 PF01491 Frataxin_Cyay: Fratax 58.1 12 0.00027 27.1 3.0 18 6-24 69-86 (109)
12 cd00503 Frataxin Frataxin is a 57.0 7.3 0.00016 28.3 1.7 19 5-24 65-83 (105)
13 TIGR03422 mito_frataxin fratax 56.5 8.8 0.00019 27.6 2.0 18 6-24 66-83 (97)
14 PRK00446 cyaY frataxin-like pr 56.2 8.1 0.00018 28.1 1.8 19 5-24 64-82 (105)
15 PF00648 Peptidase_C2: Calpain 55.5 11 0.00025 31.1 2.8 22 6-27 87-111 (298)
16 smart00230 CysPc Calpain-like 54.5 13 0.00028 31.6 3.0 24 5-28 99-125 (318)
17 cd02856 Glycogen_debranching_e 53.0 15 0.00032 25.7 2.7 14 4-18 54-67 (103)
18 cd05814 CBM20_Prei4 Prei4, N-t 51.8 18 0.00038 26.3 3.0 15 2-16 52-67 (120)
19 PF13954 PapC_N: PapC N-termin 47.7 20 0.00044 26.8 2.9 38 3-40 26-63 (146)
20 PF14645 Chibby: Chibby family 45.5 17 0.00036 27.0 2.0 16 4-20 45-60 (116)
21 cd05818 CBM20_water_dikinase P 45.1 34 0.00073 23.7 3.5 22 3-24 48-75 (92)
22 TIGR03421 FeS_CyaY iron donor 43.9 16 0.00035 26.4 1.7 20 5-25 62-81 (102)
23 cd05809 CBM20_beta_amylase Bet 40.4 26 0.00057 24.5 2.3 14 2-15 54-68 (99)
24 PF14347 DUF4399: Domain of un 39.0 25 0.00055 24.7 2.0 26 2-28 57-82 (87)
25 cd05807 CBM20_CGTase CGTase, C 38.2 49 0.0011 23.0 3.5 14 2-15 56-70 (101)
26 cd02852 Isoamylase_N_term Isoa 37.1 32 0.0007 24.5 2.4 16 4-20 58-73 (119)
27 cd05820 CBM20_novamyl Novamyl 36.4 57 0.0012 23.0 3.6 14 2-15 56-70 (103)
28 PRK01379 cyaY frataxin-like pr 35.8 20 0.00043 26.1 1.1 14 6-20 66-79 (103)
29 cd02860 Pullulanase_N_term Pul 35.7 38 0.00082 23.4 2.5 24 5-29 57-85 (100)
30 TIGR00481 Raf kinase inhibitor 32.3 30 0.00066 26.1 1.7 11 5-15 94-104 (141)
31 PF06573 Churchill: Churchill 32.0 32 0.0007 25.5 1.7 14 7-20 69-82 (112)
32 TIGR01159 DRP1 density-regulat 31.6 54 0.0012 26.0 3.0 21 123-143 87-107 (173)
33 smart00155 PLDc Phospholipase 30.5 60 0.0013 17.4 2.3 17 6-22 2-19 (28)
34 smart00107 BTK Bruton's tyrosi 30.0 19 0.0004 21.5 0.1 19 8-26 7-25 (36)
35 TIGR03769 P_ac_wall_RPT actino 29.3 79 0.0017 19.1 2.9 11 5-15 11-21 (41)
36 PF08308 PEGA: PEGA domain; I 29.2 48 0.001 21.3 2.0 17 3-19 31-47 (71)
37 PF00686 CBM_20: Starch bindin 29.1 26 0.00057 24.1 0.8 13 3-15 55-68 (96)
38 PF05738 Cna_B: Cna protein B- 28.7 70 0.0015 20.2 2.8 31 3-33 33-65 (70)
39 PF07495 Y_Y_Y: Y_Y_Y domain; 27.4 45 0.00097 20.8 1.6 21 6-26 5-28 (66)
40 cd05808 CBM20_alpha_amylase Al 26.7 69 0.0015 21.6 2.6 14 2-15 49-63 (95)
41 PF09829 DUF2057: Uncharacteri 26.7 60 0.0013 25.2 2.6 24 2-25 30-53 (189)
42 PF02751 TFIIA_gamma_C: Transc 26.5 77 0.0017 20.4 2.6 21 9-30 13-33 (52)
43 TIGR01160 SUI1_MOF2 translatio 26.3 75 0.0016 23.4 2.8 20 124-143 25-44 (110)
44 cd05815 CBM20_DPE2_repeat1 Dis 25.5 1E+02 0.0022 21.3 3.4 13 3-15 52-65 (101)
45 COG5227 SMT3 Ubiquitin-like pr 25.2 70 0.0015 23.2 2.4 25 9-33 63-87 (103)
46 PF01253 SUI1: Translation ini 24.3 88 0.0019 21.2 2.7 21 124-144 4-24 (83)
47 PHA02639 EEV host range protei 23.5 85 0.0018 26.8 3.0 33 15-50 194-228 (295)
48 COG3316 Transposase and inacti 22.9 20 0.00043 29.5 -0.8 32 11-42 128-164 (215)
49 PF14321 DUF4382: Domain of un 22.2 65 0.0014 23.8 1.9 16 2-17 63-79 (139)
50 cd05810 CBM20_alpha_MTH Glucan 21.9 1.3E+02 0.0029 20.9 3.4 14 2-15 50-64 (97)
51 cd07429 Cby_like Chibby, a nuc 20.4 74 0.0016 23.5 1.8 18 6-24 47-64 (108)
52 PF14416 PMR5N: PMR5 N termina 20.3 80 0.0017 20.4 1.8 17 15-31 7-23 (55)
53 PF03072 DUF237: MG032/MG096/M 20.2 1.1E+02 0.0023 23.6 2.7 19 6-24 87-108 (137)
No 1
>KOG1616 consensus Protein involved in Snf1 protein kinase complex assembly [Carbohydrate transport and metabolism]
Probab=100.00 E-value=1.4e-43 Score=297.32 Aligned_cols=148 Identities=40% Similarity=0.641 Sum_probs=135.6
Q ss_pred CcccCCeeEEEEEEeCCEEEEcCCCCeeeCCCCCccceeecccCC--CCccccccCC----------CCCCCC-------
Q 031974 1 MKVLPSGVYQYRFLVDGLWKYAPDLPSTQDDDGNVYNILDLQEYV--PDDLESISSF----------EPPQSP------- 61 (150)
Q Consensus 1 i~~Lp~G~~~yKFiVDG~W~~d~~~p~~~d~~G~~nN~i~v~~~~--p~~~~~~~~~----------~~~~sp------- 61 (150)
+++|++|.|+|||+|||+|+||+++|+++|+.|++||+|+|.+.. .+.++.+.++ +.+..+
T Consensus 121 ~~dL~~g~~~~kf~vdge~~~s~~~pta~d~~Gn~~N~i~v~~~~~v~~~~~~l~~~~~~~~~~~s~e~~~~~~~~~~~~ 200 (289)
T KOG1616|consen 121 ILDLPPGEHEYKFIVDGEWRHDPDLPTAEDSLGNLNNILEVQDPDEVFEVFQALEEDLPSSNHSESSEVPNLPEELEAKP 200 (289)
T ss_pred eEecCCceEEEEEecCCceecCCCCcccccccCCcccceEecCccccchhhhhhhhhccccccccccccCCCcccccccc
Confidence 478999999999999999999999999999999999999999888 7777766555 444444
Q ss_pred CCCCccccCCcccccCC--CCCCCccccccccCCCCCCCCCCCCCCCCCeeeeceeEEeccccCCcEEEEeeeeeeCcee
Q 031974 62 ETSYNNLQLTAEDFAKE--PPLVPPHLQMTLLNVPASYMEIPPPLSRPQHVVLNHLYMQKGKSGPSVVALGSTHRFLAKY 139 (150)
Q Consensus 62 ~~~Y~~~~p~~~~~~~~--PP~LPphL~~~iLN~~~~~~~~~~~Lp~P~HVvLNHLy~~si~~~~~vl~l~~T~Ryk~Ky 139 (150)
.++|+|+.|..+++.+. ||.|||||.++|||+.+..+|+++.|++|+||+|||||+++| +++++++++||||++||
T Consensus 201 ~~~y~~~~~~~~~~~~~~~~p~lpp~l~~v~lnk~~~~~~~~~~~~~p~hv~lnhl~~~si--k~~~~~~~~~~r~~~k~ 278 (289)
T KOG1616|consen 201 LGSYTQEKPAVEDEEKAMAPPVLPPHLLQVILNKDTQVSCDPALLPEPNHVALNHLYALSI--KDGVMVLSFTHRYKKKY 278 (289)
T ss_pred ccccccccchhhcchhcccCCCCCcchheeeccccccccccccccCCccchhhhhhhhhcc--CCCeeEecceecccccc
Confidence 89999999998877665 999999999999999999999999999999999999999998 58999999999999999
Q ss_pred eEEEEEeeccC
Q 031974 140 VTVVLYKSMQR 150 (150)
Q Consensus 140 vTtvlYkp~~~ 150 (150)
||++||||+++
T Consensus 279 vt~~lyk~~~~ 289 (289)
T KOG1616|consen 279 VTTGLYKPLQL 289 (289)
T ss_pred eeEEeeeeccC
Confidence 99999999975
No 2
>PF04739 AMPKBI: 5'-AMP-activated protein kinase beta subunit, interation domain; InterPro: IPR006828 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This interaction domain is found in the beta subunit of the 5-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex []. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known []. The isoamylase domain (IPR004193 from INTERPRO) is sometimes found associated with proteins that contain this C-terminal domain.; GO: 0005515 protein binding; PDB: 2QRE_D 2OOY_B 2OOX_B 2QRD_D 2QR1_D 2QRC_D 1Z0N_C 4EAK_B 4EAL_B 4EAG_B ....
Probab=100.00 E-value=5.2e-38 Score=227.84 Aligned_cols=87 Identities=55% Similarity=0.865 Sum_probs=66.4
Q ss_pred CCCCCCccccCCc------------ccccCCCCCCCccccccccCCCCCCCCCCCCCCCCCeeeeceeEEeccccCCcEE
Q 031974 60 SPETSYNNLQLTA------------EDFAKEPPLVPPHLQMTLLNVPASYMEIPPPLSRPQHVVLNHLYMQKGKSGPSVV 127 (150)
Q Consensus 60 sp~~~Y~~~~p~~------------~~~~~~PP~LPphL~~~iLN~~~~~~~~~~~Lp~P~HVvLNHLy~~si~~~~~vl 127 (150)
+++++|++++|.. ++|+++||.||+||+++|||++....|+++.||+|+||||||||+++| ++|||
T Consensus 2 ~p~~~ys~~iP~~~~~~~~~~~~~~~~~~~~PP~lPp~L~~~iLN~~~~~~~~~~~Lp~P~HV~LNHL~~~~i--k~~v~ 79 (100)
T PF04739_consen 2 SPESSYSSEIPENLQDDDEFEEQPEEEFAKEPPSLPPHLQKTILNKPSSSTDDPSVLPIPNHVVLNHLYTSSI--KDGVL 79 (100)
T ss_dssp -----EESS--HCCCSCCCCCHHH--TCCCS--BS-GGGCSEECCSCTCHHSHTTB-----GGGTTBEEEEEE--BTTEE
T ss_pred CCCcCccccCCccccchhhhhhhhcccccCCCCCCChhhCeeccCCCCcccCccccCCCCCEEEecceEEccc--CCCeE
Confidence 5778899888753 588999999999999999999988889999999999999999999998 57999
Q ss_pred EEeeeeeeCceeeEEEEEeec
Q 031974 128 ALGSTHRFLAKYVTVVLYKSM 148 (150)
Q Consensus 128 ~l~~T~Ryk~KyvTtvlYkp~ 148 (150)
|+|+|||||+||||||||||+
T Consensus 80 al~~T~Ryk~KyVT~vlYkP~ 100 (100)
T PF04739_consen 80 ALGTTHRYKSKYVTTVLYKPI 100 (100)
T ss_dssp EEEEEEEETTEEEEEEEEEE-
T ss_pred EEEEEEEecceEEEEEEecCC
Confidence 999999999999999999996
No 3
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=99.54 E-value=3.6e-15 Score=103.12 Aligned_cols=39 Identities=56% Similarity=1.157 Sum_probs=37.5
Q ss_pred cccCCeeEEEEEEeCCEEEEcCCCCeeeCCCCCccceee
Q 031974 2 KVLPSGVYQYRFLVDGLWKYAPDLPSTQDDDGNVYNILD 40 (150)
Q Consensus 2 ~~Lp~G~~~yKFiVDG~W~~d~~~p~~~d~~G~~nN~i~ 40 (150)
+.||+|.|+|||+|||+|++|+++|++.|+.|+.||+|+
T Consensus 41 ~~L~~g~y~YkF~Vdg~w~~d~~~~~~~d~~G~~NN~i~ 79 (79)
T cd02859 41 LRLPPGKYQYKFIVDGEWRHSPDLPTETDDEGNVNNVID 79 (79)
T ss_pred EEcCCCCEEEEEEECCEEEeCCCCCccCCCCCcEeeeEC
Confidence 579999999999999999999999999999999999985
No 4
>cd02861 E_set_proteins_like E or "early" set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=98.82 E-value=4.3e-09 Score=72.60 Aligned_cols=38 Identities=32% Similarity=0.669 Sum_probs=34.1
Q ss_pred cccCCeeEEEEEEeCCEEE-EcCCCCe-eeCCCCCcccee
Q 031974 2 KVLPSGVYQYRFLVDGLWK-YAPDLPS-TQDDDGNVYNIL 39 (150)
Q Consensus 2 ~~Lp~G~~~yKFiVDG~W~-~d~~~p~-~~d~~G~~nN~i 39 (150)
+.|++|.|+|||+|||.|. .||..+. ..|..|+.||+|
T Consensus 42 ~~l~~G~y~Ykf~vdg~~~~~DP~~~~~~~~~~g~~n~v~ 81 (82)
T cd02861 42 VELRPGRYEYKFVVDGEWVIVDPNAAAYVDDGFGGKNAVF 81 (82)
T ss_pred EeCCCCcEEEEEEECCEEeeCCCCCCceecCCCCccceEc
Confidence 4689999999999999999 9999985 788889999987
No 5
>cd02858 Esterase_N_term Esterase N-terminal domain. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the first class of substrate. The N-terminus of esterase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=97.02 E-value=0.0011 Score=46.02 Aligned_cols=35 Identities=34% Similarity=0.585 Sum_probs=27.3
Q ss_pred ccCCeeEEEEEEeCCEEEEcCCCCeeeCCCCCccc
Q 031974 3 VLPSGVYQYRFLVDGLWKYAPDLPSTQDDDGNVYN 37 (150)
Q Consensus 3 ~Lp~G~~~yKFiVDG~W~~d~~~p~~~d~~G~~nN 37 (150)
.|.+|.|+|+|+|||.|..||..+...=..+..-+
T Consensus 48 ~l~~g~Y~Y~~~vdg~~~~DP~s~~~~~~~~~~~~ 82 (85)
T cd02858 48 PLAPGIYTYSFLVDGVRVIDPSNPTTKPGRQVDTS 82 (85)
T ss_pred CCCCcEEEEEEEECCeEecCCCCCceeecccccce
Confidence 47789999999999999999999876533443333
No 6
>cd02688 E_set E or "early" set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=94.95 E-value=0.019 Score=37.67 Aligned_cols=27 Identities=26% Similarity=0.529 Sum_probs=21.8
Q ss_pred eeEEEEEEeCCEEEEcCCCCeeeCCCC
Q 031974 7 GVYQYRFLVDGLWKYAPDLPSTQDDDG 33 (150)
Q Consensus 7 G~~~yKFiVDG~W~~d~~~p~~~d~~G 33 (150)
|.+.|+|.|||.|..++..+...+...
T Consensus 51 ~~~~Y~~~v~~~~~~~~~~~~~~~~~~ 77 (83)
T cd02688 51 GKYQYKYVLDGGKGPDEGEPKADEGGS 77 (83)
T ss_pred CCeEEEEEEeCCCCCCCCChhhhcCCc
Confidence 889999999999999998865544333
No 7
>KOG0045 consensus Cytosolic Ca2+-dependent cysteine protease (calpain), large subunit (EF-Hand protein superfamily) [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=79.03 E-value=2.2 Score=39.86 Aligned_cols=26 Identities=27% Similarity=0.776 Sum_probs=21.7
Q ss_pred CCeeEEEEEEeCCEEE---EcCCCCeeeC
Q 031974 5 PSGVYQYRFLVDGLWK---YAPDLPSTQD 30 (150)
Q Consensus 5 p~G~~~yKFiVDG~W~---~d~~~p~~~d 30 (150)
..|.|+|||.++|+|+ .|+-+|+..+
T Consensus 115 yaGif~f~~w~~G~W~~VvIDD~LP~~~~ 143 (612)
T KOG0045|consen 115 YAGIFHFRFWQNGEWVEVVIDDRLPTSNG 143 (612)
T ss_pred cceEEEEEEEeCCeEEEEEeeeecceEcC
Confidence 5799999999999997 4777888654
No 8
>PF01378 IgG_binding_B: B domain; InterPro: IPR000724 This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding proteins G and MIG. These proteins are type I membrane proteins that bind to the constant Fc region of IgG with high affinity. The N terminus of MIG mediates binding to plasma proteinase inhibitor alpha 2-macroglobulin after complex formation with proteases.; GO: 0005618 cell wall; PDB: 1IGC_A 2IGH_A 2NMQ_A 1IGD_A 1PGX_A 2IGD_A 1QKZ_A 1GB4_A 1FCC_D 1FCL_A ....
Probab=64.47 E-value=5.2 Score=26.05 Aligned_cols=13 Identities=38% Similarity=0.828 Sum_probs=11.1
Q ss_pred eCCEEEEcCCCCe
Q 031974 15 VDGLWKYAPDLPS 27 (150)
Q Consensus 15 VDG~W~~d~~~p~ 27 (150)
|||+|.+|+.-.+
T Consensus 38 v~gew~yd~at~t 50 (55)
T PF01378_consen 38 VDGEWSYDDATKT 50 (55)
T ss_dssp TTSEEEEETTTTE
T ss_pred CCCccccccchhh
Confidence 7999999988764
No 9
>cd00044 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
Probab=62.36 E-value=10 Score=31.92 Aligned_cols=25 Identities=32% Similarity=0.763 Sum_probs=20.9
Q ss_pred cCCeeEEEEEEeCCEEEE---cCCCCee
Q 031974 4 LPSGVYQYRFLVDGLWKY---APDLPST 28 (150)
Q Consensus 4 Lp~G~~~yKFiVDG~W~~---d~~~p~~ 28 (150)
-+-|.|..||..+|+|+. |+..|+.
T Consensus 106 ~~~G~y~v~l~~~G~w~~V~VDD~lP~~ 133 (315)
T cd00044 106 NYAGIYHFRFWKNGEWVEVVIDDRLPTS 133 (315)
T ss_pred CcCcEEEEEEEECCEEEEEEecCCCeec
Confidence 357999999999999986 6777764
No 10
>PF02922 CBM_48: Carbohydrate-binding module 48 (Isoamylase N-terminal domain); InterPro: IPR004193 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Enzymes containing this domain belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. This domain is found in a range of enzymes that act on branched substrates ie. isoamylase, pullulanase and branching enzyme. Isoamylase hydrolyses 1,6-alpha-D-glucosidic branch linkages in glycogen, amylopectin and dextrin; 1,4-alpha-glucan branching enzyme functions in the formation of 1,6-glucosidic linkages of glycogen; and pullulanase is a starch-debranching enzyme.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 2BHZ_A 2BY2_A 2BY3_A 2BXY_A 2BY1_A 2BHY_A 2BHU_A 2BXZ_A 2BY0_A 2FHB_A ....
Probab=59.43 E-value=4.2 Score=27.04 Aligned_cols=17 Identities=41% Similarity=0.728 Sum_probs=13.1
Q ss_pred ccCCeeEEEEEEeCCEE
Q 031974 3 VLPSGVYQYRFLVDGLW 19 (150)
Q Consensus 3 ~Lp~G~~~yKFiVDG~W 19 (150)
.+++|.+.|+|.|||.+
T Consensus 58 ~~~~g~~~Y~y~i~~~~ 74 (85)
T PF02922_consen 58 DLPPGGYYYKYRIDGDD 74 (85)
T ss_dssp CGTTTT-EEEEEEEETT
T ss_pred CcCCCCEEEEEEEEeCC
Confidence 47788899999999876
No 11
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
Probab=58.13 E-value=12 Score=27.11 Aligned_cols=18 Identities=33% Similarity=0.780 Sum_probs=15.7
Q ss_pred CeeEEEEEEeCCEEEEcCC
Q 031974 6 SGVYQYRFLVDGLWKYAPD 24 (150)
Q Consensus 6 ~G~~~yKFiVDG~W~~d~~ 24 (150)
.|-++|.|. +|+|++.-+
T Consensus 69 sG~~hf~~~-~~~W~~~r~ 86 (109)
T PF01491_consen 69 SGPFHFDYD-DGKWIDTRD 86 (109)
T ss_dssp TEEEEEEEE-SSSEEETTT
T ss_pred CCceEEEEc-CCEEEECCC
Confidence 799999999 999998764
No 12
>cd00503 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet.
Probab=56.96 E-value=7.3 Score=28.26 Aligned_cols=19 Identities=21% Similarity=0.649 Sum_probs=15.3
Q ss_pred CCeeEEEEEEeCCEEEEcCC
Q 031974 5 PSGVYQYRFLVDGLWKYAPD 24 (150)
Q Consensus 5 p~G~~~yKFiVDG~W~~d~~ 24 (150)
|-|-|+|.|. ||.|++.-+
T Consensus 65 p~G~~hf~~~-~~~W~~~r~ 83 (105)
T cd00503 65 KVGGYHFDYK-NGKWICTRS 83 (105)
T ss_pred CCCCccceec-CCEEEECCC
Confidence 4588999995 999998754
No 13
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=56.46 E-value=8.8 Score=27.56 Aligned_cols=18 Identities=44% Similarity=0.942 Sum_probs=14.9
Q ss_pred CeeEEEEEEeCCEEEEcCC
Q 031974 6 SGVYQYRFLVDGLWKYAPD 24 (150)
Q Consensus 6 ~G~~~yKFiVDG~W~~d~~ 24 (150)
.|-|+|.| +||.|++.-+
T Consensus 66 sGp~hfd~-~~~~Wi~~r~ 83 (97)
T TIGR03422 66 SGPKRYDY-VNGEWIYLRD 83 (97)
T ss_pred CCCcceee-cCCEEEECCC
Confidence 58899999 5999998754
No 14
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=56.18 E-value=8.1 Score=28.13 Aligned_cols=19 Identities=26% Similarity=0.674 Sum_probs=15.5
Q ss_pred CCeeEEEEEEeCCEEEEcCC
Q 031974 5 PSGVYQYRFLVDGLWKYAPD 24 (150)
Q Consensus 5 p~G~~~yKFiVDG~W~~d~~ 24 (150)
|.|-++|.|. ||.|++.-+
T Consensus 64 ~sG~~hf~~~-~~~W~~~r~ 82 (105)
T PRK00446 64 KSGGFHFDYK-DGEWICDRS 82 (105)
T ss_pred CCCCccceec-CCeEEECCC
Confidence 5688999995 999998744
No 15
>PF00648 Peptidase_C2: Calpain family cysteine protease This is family C2 in the peptidase classification. ; InterPro: IPR001300 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. Calpains are a family of cytosolic cysteine proteinases (see PDOC00126 from PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [, ]. The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs []. The crystal structure of calpain has been solved [, ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [][]. The profile covers the whole catalytic domain.; GO: 0004198 calcium-dependent cysteine-type endopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 2NQA_A 1KFU_L 1KFX_L 1QXP_B 2R9C_A 1TL9_A 2G8E_A 1KXR_B 2G8J_A 2NQG_A ....
Probab=55.54 E-value=11 Score=31.06 Aligned_cols=22 Identities=32% Similarity=0.856 Sum_probs=18.3
Q ss_pred CeeEEEEEEeCCEEE---EcCCCCe
Q 031974 6 SGVYQYRFLVDGLWK---YAPDLPS 27 (150)
Q Consensus 6 ~G~~~yKFiVDG~W~---~d~~~p~ 27 (150)
-|.|.+||..||+|+ .|+..|+
T Consensus 87 ~G~y~v~l~~~G~w~~V~VDd~lP~ 111 (298)
T PF00648_consen 87 NGIYTVRLFKNGEWREVTVDDRLPC 111 (298)
T ss_dssp SSEEEEEEEETTEEEEEEEES-EEE
T ss_pred CceeeEeeccCCeeeeeccchhhhc
Confidence 399999999999998 4777777
No 16
>smart00230 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
Probab=54.53 E-value=13 Score=31.63 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=20.7
Q ss_pred CCeeEEEEEEeCCEEE---EcCCCCee
Q 031974 5 PSGVYQYRFLVDGLWK---YAPDLPST 28 (150)
Q Consensus 5 p~G~~~yKFiVDG~W~---~d~~~p~~ 28 (150)
+.|.|.+||..+|+|+ .|+..|+.
T Consensus 99 ~~G~y~vrl~~~G~w~~V~VDd~lP~~ 125 (318)
T smart00230 99 YAGIFHFRFWRFGKWVDVVIDDRLPTY 125 (318)
T ss_pred cCCEEEEEEEECCEEEEEEecCCCeee
Confidence 5799999999999997 47778874
No 17
>cd02856 Glycogen_debranching_enzyme_N_term Glycogen_debranching_enzyme N-terminal domain. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or another 1,4-alpha-D-glucan. As a glucosidase it catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. The N-terminus of the glycogen debranching enzyme may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=53.03 E-value=15 Score=25.72 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=10.6
Q ss_pred cCCeeEEEEEEeCCE
Q 031974 4 LPSGVYQYRFLVDGL 18 (150)
Q Consensus 4 Lp~G~~~yKFiVDG~ 18 (150)
+.+|. .|+|.|||.
T Consensus 54 ~~~g~-~Y~y~i~g~ 67 (103)
T cd02856 54 IKAGQ-RYGFRVHGP 67 (103)
T ss_pred CCCCC-EEEEEECCc
Confidence 44555 799999995
No 18
>cd05814 CBM20_Prei4 Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 contains a C-terminal glycerophosphoryl diester phosphodiesterase (GDPD) domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch.
Probab=51.79 E-value=18 Score=26.28 Aligned_cols=15 Identities=47% Similarity=0.924 Sum_probs=12.1
Q ss_pred cccCCe-eEEEEEEeC
Q 031974 2 KVLPSG-VYQYRFLVD 16 (150)
Q Consensus 2 ~~Lp~G-~~~yKFiVD 16 (150)
+.||.| .++|||++.
T Consensus 52 v~lp~~~~veYkY~~~ 67 (120)
T cd05814 52 IELPRGVDFQYRYFVA 67 (120)
T ss_pred EEECCCCeEEEEEEEE
Confidence 357777 799999994
No 19
>PF13954 PapC_N: PapC N-terminal domain; PDB: 2VQI_B 3FIP_A 3RFZ_E 3OHN_A 1ZDV_A 1ZE3_D 3BWU_D 1ZDX_A.
Probab=47.71 E-value=20 Score=26.80 Aligned_cols=38 Identities=26% Similarity=0.454 Sum_probs=28.5
Q ss_pred ccCCeeEEEEEEeCCEEEEcCCCCeeeCCCCCccceee
Q 031974 3 VLPSGVYQYRFLVDGLWKYAPDLPSTQDDDGNVYNILD 40 (150)
Q Consensus 3 ~Lp~G~~~yKFiVDG~W~~d~~~p~~~d~~G~~nN~i~ 40 (150)
.++||+|....+|+|+|.-..+.....++.+.+.=.|.
T Consensus 26 ~~~pG~Y~vdv~vN~~~~~~~~i~f~~~~~~~~~pClt 63 (146)
T PF13954_consen 26 AIPPGEYSVDVYVNGKFIGRYDIEFINNDDGKLQPCLT 63 (146)
T ss_dssp SS-SEEEEEEEEETTEEEEEEEEEEEESSSTSEEEE-B
T ss_pred CCCCeEEEEEEEECCeeeeeEEEEEEeCCCcceeEEeC
Confidence 47899999999999999998887777776663444443
No 20
>PF14645 Chibby: Chibby family
Probab=45.49 E-value=17 Score=26.97 Aligned_cols=16 Identities=38% Similarity=0.627 Sum_probs=13.2
Q ss_pred cCCeeEEEEEEeCCEEE
Q 031974 4 LPSGVYQYRFLVDGLWK 20 (150)
Q Consensus 4 Lp~G~~~yKFiVDG~W~ 20 (150)
|.-|.-+|+| .||+|.
T Consensus 45 l~Lg~~~l~F-~dG~W~ 60 (116)
T PF14645_consen 45 LNLGDQTLVF-EDGQWT 60 (116)
T ss_pred EeECCeEEEE-ECCEEe
Confidence 3447788999 999999
No 21
>cd05818 CBM20_water_dikinase Phosphoglucan water dikinase (also known as alpha-glucan water dikinase), N-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in the chloroplast-encoded phosphoglucan water dikinase, one of two enzymes involved in the phosphorylation of plant starches. In addition to the CBM20 domain, phosphoglucan water dikinase contains a C-terminal pyruvate binding domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognitio
Probab=45.09 E-value=34 Score=23.67 Aligned_cols=22 Identities=32% Similarity=0.916 Sum_probs=14.3
Q ss_pred ccCCe-eEEEEEEe---CC--EEEEcCC
Q 031974 3 VLPSG-VYQYRFLV---DG--LWKYAPD 24 (150)
Q Consensus 3 ~Lp~G-~~~yKFiV---DG--~W~~d~~ 24 (150)
+||.| .++|||++ || .|...++
T Consensus 48 ~l~~~~~ieyKy~~~~~~~~v~WE~g~N 75 (92)
T cd05818 48 ELDGGELVEYKFVIVKRDGSVIWEGGNN 75 (92)
T ss_pred EeCCCCcEEEEEEEEcCCCCEEEEeCCC
Confidence 46666 59999998 33 4554444
No 22
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=43.90 E-value=16 Score=26.38 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=15.6
Q ss_pred CCeeEEEEEEeCCEEEEcCCC
Q 031974 5 PSGVYQYRFLVDGLWKYAPDL 25 (150)
Q Consensus 5 p~G~~~yKFiVDG~W~~d~~~ 25 (150)
|.|-|+|.|. ||.|++.-+.
T Consensus 62 psG~~hF~~~-~~~Wi~~r~g 81 (102)
T TIGR03421 62 KSGGFHFDYD-GGAWIDTRDG 81 (102)
T ss_pred CCCCccceec-CCEEEECCCC
Confidence 5688899984 8999986553
No 23
>cd05809 CBM20_beta_amylase Beta-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Beta-amylase has, in addition to its C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 14, which hydrolyzes the alpha-1,4-glucosidic bonds of starch, yielding beta-maltose from the nonreducing end of the substrate. Beta-amylase is found in both plants and microorganisms, however the plant members lack a C-terminal CBM20 domain and are not included in this group. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1
Probab=40.37 E-value=26 Score=24.46 Aligned_cols=14 Identities=21% Similarity=0.505 Sum_probs=11.3
Q ss_pred cccCCee-EEEEEEe
Q 031974 2 KVLPSGV-YQYRFLV 15 (150)
Q Consensus 2 ~~Lp~G~-~~yKFiV 15 (150)
+.||.|. ++|||++
T Consensus 54 ~~lp~~~~veyKyv~ 68 (99)
T cd05809 54 VHLPAGRNIEFKAIK 68 (99)
T ss_pred EEecCCCcEEEEEEE
Confidence 4577774 9999998
No 24
>PF14347 DUF4399: Domain of unknown function (DUF4399)
Probab=38.97 E-value=25 Score=24.68 Aligned_cols=26 Identities=23% Similarity=0.280 Sum_probs=20.6
Q ss_pred cccCCeeEEEEEEeCCEEEEcCCCCee
Q 031974 2 KVLPSGVYQYRFLVDGLWKYAPDLPST 28 (150)
Q Consensus 2 ~~Lp~G~~~yKFiVDG~W~~d~~~p~~ 28 (150)
++|+||+|...-+. |.+.+-+..|.+
T Consensus 57 I~L~PG~htLtl~~-~d~~h~~~~~~v 82 (87)
T PF14347_consen 57 IELPPGKHTLTLQL-GDGDHVPHDPPV 82 (87)
T ss_pred EEeCCCCEEEEEEe-CCCCcccCCCce
Confidence 57999999999887 777777776653
No 25
>cd05807 CBM20_CGTase CGTase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. CGTase, also known as cyclodextrin glycosyltransferase and cyclodextrin glucanotransferase, catalyzes the formation of various cyclodextrins (alpha-1,4-glucans) from starch. CGTase has, in addition to its C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13 and an IPT domain of unknown function. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific
Probab=38.23 E-value=49 Score=23.04 Aligned_cols=14 Identities=21% Similarity=0.745 Sum_probs=11.0
Q ss_pred cccCCe-eEEEEEEe
Q 031974 2 KVLPSG-VYQYRFLV 15 (150)
Q Consensus 2 ~~Lp~G-~~~yKFiV 15 (150)
++||.| .++|||++
T Consensus 56 ~~lp~~~~~eyK~~~ 70 (101)
T cd05807 56 VSVPAGTTIEFKFIK 70 (101)
T ss_pred EEcCCCCcEEEEEEE
Confidence 457777 49999998
No 26
>cd02852 Isoamylase_N_term Isoamylase N-terminus domain. Isoamylase (aka glycogen 6-glucanohydrolase) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes. The N-terminus of isoamylase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=37.11 E-value=32 Score=24.52 Aligned_cols=16 Identities=38% Similarity=0.713 Sum_probs=11.0
Q ss_pred cCCeeEEEEEEeCCEEE
Q 031974 4 LPSGVYQYRFLVDGLWK 20 (150)
Q Consensus 4 Lp~G~~~yKFiVDG~W~ 20 (150)
+.+|. .|+|.|||.|.
T Consensus 58 ~~~g~-~Y~y~v~g~~~ 73 (119)
T cd02852 58 LKPGQ-LYGYRVDGPFE 73 (119)
T ss_pred CCCCC-EEEEEECCCCC
Confidence 44564 68888888754
No 27
>cd05820 CBM20_novamyl Novamyl (also known as acarviose transferase, ATase, maltogenic alpha-amylase, glucan 1,4-alpha-maltohydrolase, and AcbD), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Novamyl has a five-domain structure similar to that of cyclodextrin glucanotransferase (CGTase). Novamyl has a substrate-binding surface with an open groove which can accommodate both cyclodextrins and linear substrates. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific reco
Probab=36.38 E-value=57 Score=22.99 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=11.1
Q ss_pred cccCCe-eEEEEEEe
Q 031974 2 KVLPSG-VYQYRFLV 15 (150)
Q Consensus 2 ~~Lp~G-~~~yKFiV 15 (150)
+.||.| .++|||++
T Consensus 56 ~~lp~~~~veyK~v~ 70 (103)
T cd05820 56 ASVPAGTYIEFKFLK 70 (103)
T ss_pred EEcCCCCcEEEEEEE
Confidence 457777 49999998
No 28
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=35.80 E-value=20 Score=26.12 Aligned_cols=14 Identities=43% Similarity=1.023 Sum_probs=12.0
Q ss_pred CeeEEEEEEeCCEEE
Q 031974 6 SGVYQYRFLVDGLWK 20 (150)
Q Consensus 6 ~G~~~yKFiVDG~W~ 20 (150)
.|-|+|.|. ||.|+
T Consensus 66 sG~~hF~y~-~g~W~ 79 (103)
T PRK01379 66 SGPYHFFYE-QGKWK 79 (103)
T ss_pred CCCcceecC-CCeeE
Confidence 588999994 89999
No 29
>cd02860 Pullulanase_N_term Pullulanase domain N-terminus. Pullulanase (AKA dextrinase; alpha-dextrin endo-1,6-alpha glucosidase) is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. The N-terminus of pullulanase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=35.73 E-value=38 Score=23.38 Aligned_cols=24 Identities=17% Similarity=0.083 Sum_probs=15.2
Q ss_pred CCeeEEEEEEeCCE-----EEEcCCCCeee
Q 031974 5 PSGVYQYRFLVDGL-----WKYAPDLPSTQ 29 (150)
Q Consensus 5 p~G~~~yKFiVDG~-----W~~d~~~p~~~ 29 (150)
.+|. .|+|.|||. .+.||-....+
T Consensus 57 ~~g~-~Y~y~i~~~~~~~~~~~DPyA~~~~ 85 (100)
T cd02860 57 LEGY-YYLYEVKVYKGETNEVVDPYAKALS 85 (100)
T ss_pred cCCc-EEEEEEEEeceEEEEEcCcccEeEe
Confidence 3455 388888876 56666665443
No 30
>TIGR00481 Raf kinase inhibitor-like protein, YbhB/YbcL family.
Probab=32.29 E-value=30 Score=26.10 Aligned_cols=11 Identities=45% Similarity=0.769 Sum_probs=9.0
Q ss_pred CCeeEEEEEEe
Q 031974 5 PSGVYQYRFLV 15 (150)
Q Consensus 5 p~G~~~yKFiV 15 (150)
|+|.|+|.|.|
T Consensus 94 P~g~HrY~f~v 104 (141)
T TIGR00481 94 PKGDHRYLFTV 104 (141)
T ss_pred cCCCEEEEEEE
Confidence 46789999986
No 31
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=32.01 E-value=32 Score=25.54 Aligned_cols=14 Identities=21% Similarity=0.304 Sum_probs=11.2
Q ss_pred eeEEEEEEeCCEEE
Q 031974 7 GVYQYRFLVDGLWK 20 (150)
Q Consensus 7 G~~~yKFiVDG~W~ 20 (150)
-+|+|+|-|+|++.
T Consensus 69 A~HEYtF~V~~~yQ 82 (112)
T PF06573_consen 69 ARHEYTFSVVDDYQ 82 (112)
T ss_dssp EEEEEEEEEETTEE
T ss_pred EeeeEEEEEeccch
Confidence 36999999987664
No 32
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=31.61 E-value=54 Score=26.04 Aligned_cols=21 Identities=33% Similarity=0.422 Sum_probs=18.5
Q ss_pred CCcEEEEeeeeeeCceeeEEE
Q 031974 123 GPSVVALGSTHRFLAKYVTVV 143 (150)
Q Consensus 123 ~~~vl~l~~T~Ryk~KyvTtv 143 (150)
..+.+.+....|=++|+||+|
T Consensus 87 ~~~~V~I~~~~R~krK~VT~V 107 (173)
T TIGR01159 87 LPQKVTIKREPRTKRKFVTVI 107 (173)
T ss_pred CCCeEEEEEEecCCCceEEEE
Confidence 457789999999999999998
No 33
>smart00155 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not be
Probab=30.50 E-value=60 Score=17.43 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=11.4
Q ss_pred CeeEEEE-EEeCCEEEEc
Q 031974 6 SGVYQYR-FLVDGLWKYA 22 (150)
Q Consensus 6 ~G~~~yK-FiVDG~W~~d 22 (150)
.|..+=| ++|||+|.+-
T Consensus 2 ~~~~H~K~~v~D~~~~~i 19 (28)
T smart00155 2 DGVLHTKLMIVDDEIAYI 19 (28)
T ss_pred CCcEEeEEEEEcCCEEEE
Confidence 3566778 4579987653
No 34
>smart00107 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Probab=29.95 E-value=19 Score=21.47 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=13.9
Q ss_pred eEEEEEEeCCEEEEcCCCC
Q 031974 8 VYQYRFLVDGLWKYAPDLP 26 (150)
Q Consensus 8 ~~~yKFiVDG~W~~d~~~p 26 (150)
.|+=.|++||.|.+--...
T Consensus 7 ~yHP~~~~~G~W~CC~q~~ 25 (36)
T smart00107 7 KYHPSFWVDGKWLCCQQSE 25 (36)
T ss_pred ccCCCceeCCeEccCCCcC
Confidence 3555789999999865543
No 35
>TIGR03769 P_ac_wall_RPT actinobacterial surface-anchored protein domain. This model describes a repeat domain that one to three times in Actinobacterial proteins, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. Where it occurs with duplication in an LPXTG-anchored protein, it tends to be adjacent to the substrate-binding protein of the gene trio of an ABC transporter system, where that substrate-binding protein has a single copy of this same domain. This arrangement suggests a substrate-binding relay system, with the LPXTG protein acting as a substrate receptor.
Probab=29.27 E-value=79 Score=19.07 Aligned_cols=11 Identities=18% Similarity=0.383 Sum_probs=9.7
Q ss_pred CCeeEEEEEEe
Q 031974 5 PSGVYQYRFLV 15 (150)
Q Consensus 5 p~G~~~yKFiV 15 (150)
.||.|+..|-.
T Consensus 11 ~PG~Y~l~~~a 21 (41)
T TIGR03769 11 KPGTYTLTVQA 21 (41)
T ss_pred CCeEEEEEEEE
Confidence 58999999987
No 36
>PF08308 PEGA: PEGA domain; InterPro: IPR013229 This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands.
Probab=29.24 E-value=48 Score=21.30 Aligned_cols=17 Identities=24% Similarity=0.149 Sum_probs=14.8
Q ss_pred ccCCeeEEEEEEeCCEE
Q 031974 3 VLPSGVYQYRFLVDGLW 19 (150)
Q Consensus 3 ~Lp~G~~~yKFiVDG~W 19 (150)
.|++|.|++++.-+|-.
T Consensus 31 ~l~~G~~~v~v~~~Gy~ 47 (71)
T PF08308_consen 31 DLPPGEHTVTVEKPGYE 47 (71)
T ss_pred ecCCccEEEEEEECCCe
Confidence 48999999999999943
No 37
>PF00686 CBM_20: Starch binding domain; InterPro: IPR002044 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain binds to starch, and is found often at the C terminus of a variety of glycosyl hydrolases acting on polysaccharides more rapidly than on oligosaccharides. Reations include: the hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose, the degradation of starch to cyclodextrins by formation of a 1,4-alpha-D-glucosidic bond, and hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides to remove successive maltose units from the non-reducing ends of the chains.; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1KUL_A 1ACZ_A 1AC0_A 1KUM_A 2Z0B_C 9CGT_A 3CGT_A 6CGT_A 4CGT_A 1CGT_A ....
Probab=29.06 E-value=26 Score=24.07 Aligned_cols=13 Identities=31% Similarity=1.073 Sum_probs=10.6
Q ss_pred ccCCe-eEEEEEEe
Q 031974 3 VLPSG-VYQYRFLV 15 (150)
Q Consensus 3 ~Lp~G-~~~yKFiV 15 (150)
.||.| .++|||++
T Consensus 55 ~lp~~~~~eYKy~i 68 (96)
T PF00686_consen 55 DLPAGTPFEYKYVI 68 (96)
T ss_dssp EEETTSEEEEEEEE
T ss_pred ECcCCCEEEEEEEE
Confidence 56667 59999998
No 38
>PF05738 Cna_B: Cna protein B-type domain; InterPro: IPR008454 This entry represents a repeated B region domain found in the collagen-binding surface protein Cna in Staphylococcus aureus, as well as other related domains. The B region domain of Cna has a prealbumin-like beta-sandwich fold of seven strands in two sheets with a Greek key topology []. However, this domain does not mediate collagen binding, the IPR008456 from INTERPRO region carries out that function; instead it appears to form a stalk that presents the ligand binding domain away from the bacterial cell surface. Cna is a collagen-binding MSCRAMM (Microbial Surface Component Recognizing Adhesive Matrix Molecules), and is necessary and sufficient for S. aureus cells to adhere to cartilage.; PDB: 2X5P_A 3RKP_A 3KPT_A 1VLF_T 1TI2_F 1TI6_D 1TI4_J 1VLE_V 1VLD_X 3PF2_A ....
Probab=28.65 E-value=70 Score=20.20 Aligned_cols=31 Identities=29% Similarity=0.368 Sum_probs=20.2
Q ss_pred ccCCeeEEEEEEe--CCEEEEcCCCCeeeCCCC
Q 031974 3 VLPSGVYQYRFLV--DGLWKYAPDLPSTQDDDG 33 (150)
Q Consensus 3 ~Lp~G~~~yKFiV--DG~W~~d~~~p~~~d~~G 33 (150)
.|++|.|..+++. +|--...........+++
T Consensus 33 ~L~~G~Y~l~E~~aP~GY~~~~~~~~~~i~~~~ 65 (70)
T PF05738_consen 33 NLPPGTYTLKETKAPDGYQLDDTPYEFTITEDG 65 (70)
T ss_dssp EEESEEEEEEEEETTTTEEEEECEEEEEECTTS
T ss_pred ecCCeEEEEEEEECCCCCEECCCceEEEEecCC
Confidence 5889999999987 675554444444444444
No 39
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=27.43 E-value=45 Score=20.84 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=15.1
Q ss_pred CeeEEEEEEe---CCEEEEcCCCC
Q 031974 6 SGVYQYRFLV---DGLWKYAPDLP 26 (150)
Q Consensus 6 ~G~~~yKFiV---DG~W~~d~~~p 26 (150)
++..+|+|.+ |++|....+.-
T Consensus 5 ~~~~~Y~Y~l~g~d~~W~~~~~~~ 28 (66)
T PF07495_consen 5 PENIRYRYRLEGFDDEWITLGSYS 28 (66)
T ss_dssp CTTEEEEEEEETTESSEEEESSTS
T ss_pred CCceEEEEEEECCCCeEEECCCCc
Confidence 5667888855 68998876654
No 40
>cd05808 CBM20_alpha_amylase Alpha-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in several bacterial and fungal alpha-amylases including the maltopentaose-forming amylases (G5-amylases). Most alpha-amylases have, in addition to the C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13, which hydrolyzes internal alpha-1,4-glucosidic bonds in starch and related saccharides, yielding maltotriose and maltose. Two types of soluble substrates are used by alpha-amylases including long substrates (e.g. amylose) and short substrates (e.g. maltodextrins or maltooligosaccharides). The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. lafo
Probab=26.74 E-value=69 Score=21.60 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=10.7
Q ss_pred cccCCe-eEEEEEEe
Q 031974 2 KVLPSG-VYQYRFLV 15 (150)
Q Consensus 2 ~~Lp~G-~~~yKFiV 15 (150)
+.||.| .++|||++
T Consensus 49 v~l~~~~~~eYKy~~ 63 (95)
T cd05808 49 VDLPAGTAIEYKYIK 63 (95)
T ss_pred EEeCCCCeEEEEEEE
Confidence 356766 59999996
No 41
>PF09829 DUF2057: Uncharacterized protein conserved in bacteria (DUF2057); InterPro: IPR018635 The proteins in this entry are functionally uncharacterised.
Probab=26.71 E-value=60 Score=25.25 Aligned_cols=24 Identities=25% Similarity=0.289 Sum_probs=19.6
Q ss_pred cccCCeeEEEEEEeCCEEEEcCCC
Q 031974 2 KVLPSGVYQYRFLVDGLWKYAPDL 25 (150)
Q Consensus 2 ~~Lp~G~~~yKFiVDG~W~~d~~~ 25 (150)
+.|++|.||.-|.+++.|..+.+.
T Consensus 30 l~L~~G~~Qiv~ry~~~~~~~~~~ 53 (189)
T PF09829_consen 30 LELPPGENQIVFRYSKIFSSGGDH 53 (189)
T ss_pred EEeCCCcEEEEEEEeEeeccCCCe
Confidence 579999999999999999444444
No 42
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=26.50 E-value=77 Score=20.39 Aligned_cols=21 Identities=24% Similarity=0.510 Sum_probs=15.4
Q ss_pred EEEEEEeCCEEEEcCCCCeeeC
Q 031974 9 YQYRFLVDGLWKYAPDLPSTQD 30 (150)
Q Consensus 9 ~~yKFiVDG~W~~d~~~p~~~d 30 (150)
+.||| +|+.|+.-=.......
T Consensus 13 ~tYrf-cDnVWTFi~kn~~fk~ 33 (52)
T PF02751_consen 13 DTYRF-CDNVWTFILKNVEFKM 33 (52)
T ss_dssp EEEEE-ETTEEEEEEEEEEEEE
T ss_pred eEEEe-eCcEEEEEEcCEEEEE
Confidence 77887 5999998766665443
No 43
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=26.33 E-value=75 Score=23.41 Aligned_cols=20 Identities=20% Similarity=0.157 Sum_probs=16.7
Q ss_pred CcEEEEeeeeeeCceeeEEE
Q 031974 124 PSVVALGSTHRFLAKYVTVV 143 (150)
Q Consensus 124 ~~vl~l~~T~Ryk~KyvTtv 143 (150)
.+++.+-...|=.+|+||+|
T Consensus 25 ~~~I~Iri~qR~grK~VTiI 44 (110)
T TIGR01160 25 SNYIHIRIQQRNGRKTLTTV 44 (110)
T ss_pred cceEEEEEEEccCCccEEEE
Confidence 46788888888888999997
No 44
>cd05815 CBM20_DPE2_repeat1 Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 1. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on the pathway from starch to sucrose and DPE2 is thought to metabolize the maltose that is exported from the chloroplast. DPE2 has two N-terminal CBM20 starch binding domains as well as a C-terminal amylomaltase (4-alpha-glucanotransferase) catalytic domain. DPE1, the plastid version of this enzyme, has a transglucosidase domain that is similar to that of DPE2 but lacks the N-terminal carbohydrate-binding domains. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabol
Probab=25.46 E-value=1e+02 Score=21.25 Aligned_cols=13 Identities=31% Similarity=0.789 Sum_probs=9.7
Q ss_pred ccCCe-eEEEEEEe
Q 031974 3 VLPSG-VYQYRFLV 15 (150)
Q Consensus 3 ~Lp~G-~~~yKFiV 15 (150)
.+|.| .++|||+|
T Consensus 52 ~~~~~~~veYky~v 65 (101)
T cd05815 52 SVPPGFSSEYNYYV 65 (101)
T ss_pred EeCCCCcEEEEEEE
Confidence 35555 49999998
No 45
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=25.16 E-value=70 Score=23.25 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=18.1
Q ss_pred EEEEEEeCCEEEEcCCCCeeeCCCC
Q 031974 9 YQYRFLVDGLWKYAPDLPSTQDDDG 33 (150)
Q Consensus 9 ~~yKFiVDG~W~~d~~~p~~~d~~G 33 (150)
-.+||++||+-.--+.-|-.-|..|
T Consensus 63 ~slRfL~dG~rI~~dqTP~dldmEd 87 (103)
T COG5227 63 SSLRFLFDGKRIDLDQTPGDLDMED 87 (103)
T ss_pred ceeEEEEcceecCCCCChhhcCCcc
Confidence 4689999998766666676666555
No 46
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=24.29 E-value=88 Score=21.21 Aligned_cols=21 Identities=29% Similarity=0.398 Sum_probs=16.4
Q ss_pred CcEEEEeeeeeeCceeeEEEE
Q 031974 124 PSVVALGSTHRFLAKYVTVVL 144 (150)
Q Consensus 124 ~~vl~l~~T~Ryk~KyvTtvl 144 (150)
...+.+.+..|=++|+||.|-
T Consensus 4 ~~~I~I~~e~r~~~K~vT~V~ 24 (83)
T PF01253_consen 4 PPKIHIRVEKRRGRKFVTIVS 24 (83)
T ss_dssp TTCEEEEEEESSSSEEEEEEE
T ss_pred CCEEEEEEEeCcCCeEEEEEE
Confidence 345677777898899999983
No 47
>PHA02639 EEV host range protein; Provisional
Probab=23.48 E-value=85 Score=26.77 Aligned_cols=33 Identities=24% Similarity=0.585 Sum_probs=24.1
Q ss_pred eCCEEEEcCCCCeeeCCCCCccceeecc--cCCCCccc
Q 031974 15 VDGLWKYAPDLPSTQDDDGNVYNILDLQ--EYVPDDLE 50 (150)
Q Consensus 15 VDG~W~~d~~~p~~~d~~G~~nN~i~v~--~~~p~~~~ 50 (150)
.||+| ++..|+..-.. .+++++.++ +..+++++
T Consensus 194 ~nG~W--s~~~P~C~~~~-~~~~~~~~~~~~~~~~~~~ 228 (295)
T PHA02639 194 INATW--FPSIPTCVRNK-PIDDIIYLKPVDDNFDDLD 228 (295)
T ss_pred CCCeE--CCCCCeEeccC-CccceEEeccCcCCchhcc
Confidence 68999 67889876444 688999877 55666665
No 48
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.85 E-value=20 Score=29.49 Aligned_cols=32 Identities=16% Similarity=0.194 Sum_probs=22.5
Q ss_pred EEEEeCCEEEEcCCCC-----eeeCCCCCccceeecc
Q 031974 11 YRFLVDGLWKYAPDLP-----STQDDDGNVYNILDLQ 42 (150)
Q Consensus 11 yKFiVDG~W~~d~~~p-----~~~d~~G~~nN~i~v~ 42 (150)
++|++||-|-+..... .+.-..|.+||+++=.
T Consensus 128 ~v~vtDka~s~~~A~~~l~~~~ehr~~~ylnN~iE~d 164 (215)
T COG3316 128 RVFVTDKAPSYTAALRKLGSEVEHRTSKYLNNRIEQD 164 (215)
T ss_pred ceEEecCccchHHHHHhcCcchheecccccccchhhc
Confidence 6899998777665553 3333678889998753
No 49
>PF14321 DUF4382: Domain of unknown function (DUF4382)
Probab=22.19 E-value=65 Score=23.81 Aligned_cols=16 Identities=44% Similarity=0.872 Sum_probs=14.0
Q ss_pred cccCCeeE-EEEEEeCC
Q 031974 2 KVLPSGVY-QYRFLVDG 17 (150)
Q Consensus 2 ~~Lp~G~~-~yKFiVDG 17 (150)
.+||+|.| +.||.|++
T Consensus 63 ~~lpaG~Y~~irl~l~~ 79 (139)
T PF14321_consen 63 AELPAGTYNQIRLVLDD 79 (139)
T ss_pred cccCCCcEEEEEEEEeC
Confidence 47899998 99999985
No 50
>cd05810 CBM20_alpha_MTH Glucan 1,4-alpha-maltotetraohydrolase (alpha-MTH), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Alpha-MTH, also known as maltotetraose-forming exo-amylase or G4-amylase, is an exo-amylase found in bacteria that degrades starch from its non-reducing end. Most alpha-MTHs have, in addition to the C-terminal CBM20 domain, an N-terminal glycosyl hydrolase family 13 catalytic domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognitio
Probab=21.93 E-value=1.3e+02 Score=20.87 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=10.6
Q ss_pred cccCCe-eEEEEEEe
Q 031974 2 KVLPSG-VYQYRFLV 15 (150)
Q Consensus 2 ~~Lp~G-~~~yKFiV 15 (150)
+.||.| ..+|||++
T Consensus 50 v~lp~~~~veyKyv~ 64 (97)
T cd05810 50 ISLPASTNVEWKCLK 64 (97)
T ss_pred EEcCCCCeEEEEEEE
Confidence 356776 49999987
No 51
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=20.38 E-value=74 Score=23.46 Aligned_cols=18 Identities=28% Similarity=0.431 Sum_probs=12.9
Q ss_pred CeeEEEEEEeCCEEEEcCC
Q 031974 6 SGVYQYRFLVDGLWKYAPD 24 (150)
Q Consensus 6 ~G~~~yKFiVDG~W~~d~~ 24 (150)
-|--+++|. ||+|.....
T Consensus 47 Lg~~~l~F~-dG~W~~e~~ 64 (108)
T cd07429 47 LGGQELVFE-DGRWISESG 64 (108)
T ss_pred eCCceEEee-CCEEecCCC
Confidence 355667776 999987654
No 52
>PF14416 PMR5N: PMR5 N terminal Domain
Probab=20.31 E-value=80 Score=20.44 Aligned_cols=17 Identities=29% Similarity=0.642 Sum_probs=13.0
Q ss_pred eCCEEEEcCCCCeeeCC
Q 031974 15 VDGLWKYAPDLPSTQDD 31 (150)
Q Consensus 15 VDG~W~~d~~~p~~~d~ 31 (150)
-+|+|+.|+..|.-++.
T Consensus 7 ~~G~WV~D~~~PlY~~~ 23 (55)
T PF14416_consen 7 FDGRWVPDPSYPLYTNS 23 (55)
T ss_pred ccCEEEeCCCCCccCCC
Confidence 47999999999864433
No 53
>PF03072 DUF237: MG032/MG096/MG288 family 1; InterPro: IPR004306 This domain is found entirely in Mycoplasma pneumoniae proteins of unknown function. Another related domain (IPR004319 from INTERPRO) is found entirely in mycoplasmal proteins of the MG032/MG096/MG288 family and both domains often occur together.
Probab=20.24 E-value=1.1e+02 Score=23.62 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=14.9
Q ss_pred CeeEEEEEEeCC---EEEEcCC
Q 031974 6 SGVYQYRFLVDG---LWKYAPD 24 (150)
Q Consensus 6 ~G~~~yKFiVDG---~W~~d~~ 24 (150)
.|+..-||+||| .|.++.-
T Consensus 87 kGkm~vk~~~DG~vp~w~~~k~ 108 (137)
T PF03072_consen 87 KGKMNVKFIFDGDVPSWIVGKP 108 (137)
T ss_pred cceEEEEEEEcccccceeecCC
Confidence 488999999999 5777543
Done!