Query 040960
Match_columns 117
No_of_seqs 126 out of 1053
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 02:28:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03030 cationic peroxidase; 100.0 1.3E-48 2.7E-53 319.9 7.9 113 2-117 6-120 (324)
2 cd00693 secretory_peroxidase H 100.0 2.2E-43 4.9E-48 285.6 6.7 100 18-117 1-100 (298)
3 PF00141 peroxidase: Peroxidas 100.0 1.6E-30 3.5E-35 203.4 3.9 78 35-117 1-80 (230)
4 cd00691 ascorbate_peroxidase A 99.9 1.7E-23 3.8E-28 166.4 4.5 80 30-117 11-94 (253)
5 PLN02608 L-ascorbate peroxidas 99.9 5.8E-23 1.3E-27 166.6 4.6 74 31-117 14-95 (289)
6 PLN02364 L-ascorbate peroxidas 99.9 2.5E-22 5.4E-27 159.8 5.0 85 21-117 3-97 (250)
7 cd00314 plant_peroxidase_like 99.9 3.1E-22 6.8E-27 157.0 3.9 76 34-117 2-86 (255)
8 cd00692 ligninase Ligninase an 99.8 7.3E-20 1.6E-24 150.6 4.8 78 31-117 16-108 (328)
9 cd08201 plant_peroxidase_like_ 99.7 6.2E-19 1.3E-23 141.7 -3.3 63 42-117 34-104 (264)
10 PLN02879 L-ascorbate peroxidas 99.6 2.9E-15 6.2E-20 119.6 5.0 71 35-117 20-98 (251)
11 TIGR00198 cat_per_HPI catalase 98.0 3.8E-06 8.2E-11 75.7 2.7 73 35-117 57-146 (716)
12 cd00649 catalase_peroxidase_1 97.3 0.00014 3E-09 62.2 2.6 75 33-117 45-136 (409)
13 cd08200 catalase_peroxidase_2 96.7 0.0023 5E-08 52.8 4.1 75 37-117 17-104 (297)
14 PRK15061 catalase/hydroperoxid 96.3 0.0031 6.8E-08 57.3 2.9 74 34-117 58-148 (726)
15 TIGR00198 cat_per_HPI catalase 94.8 0.028 6E-07 51.2 3.5 70 39-117 437-517 (716)
16 PRK15061 catalase/hydroperoxid 94.0 0.065 1.4E-06 48.9 4.0 75 37-117 442-529 (726)
17 KOG0427 Ubiquitin conjugating 54.0 8.2 0.00018 29.1 1.5 40 4-60 117-158 (161)
18 PF08782 c-SKI_SMAD_bind: c-SK 49.1 4.5 9.7E-05 28.5 -0.5 16 57-73 4-19 (96)
19 PF01816 LRV: Leucine rich rep 45.9 18 0.00039 19.5 1.7 23 38-60 2-24 (26)
20 COG3763 Uncharacterized protei 43.0 31 0.00066 23.1 2.8 26 34-59 24-49 (71)
21 KOG3803 Transcription factor c 40.7 18 0.00038 33.7 1.8 70 26-108 670-741 (968)
22 PF06764 DUF1223: Protein of u 29.9 24 0.00053 27.4 0.8 25 26-59 11-35 (202)
23 PF15240 Pro-rich: Proline-ric 28.6 49 0.0011 25.7 2.3 20 1-20 1-20 (179)
24 TIGR00412 redox_disulf_2 small 27.9 53 0.0011 20.8 2.0 14 21-34 3-16 (76)
25 PF01530 zf-C2HC: Zinc finger, 27.3 35 0.00077 19.3 1.0 15 60-74 3-17 (31)
26 PHA03163 hypothetical protein; 24.0 1E+02 0.0022 21.5 3.0 13 17-29 34-46 (92)
27 COG2250 Uncharacterized conser 23.7 43 0.00092 24.1 1.1 31 18-48 23-53 (132)
28 COG3262 HycE Ni,Fe-hydrogenase 23.2 47 0.001 25.6 1.3 31 35-65 113-143 (165)
29 PRK00523 hypothetical protein; 22.8 1.1E+02 0.0024 20.5 2.8 26 34-59 25-50 (72)
30 PF03076 GP3: Equine arteritis 22.7 39 0.00085 25.2 0.8 22 48-69 6-27 (160)
31 PRK01844 hypothetical protein; 22.6 1.1E+02 0.0025 20.4 2.9 26 34-59 24-49 (72)
32 PF07983 X8: X8 domain; Inter 22.1 83 0.0018 20.8 2.2 20 97-116 12-32 (78)
33 COG1766 fliF Flagellar basal b 21.3 68 0.0015 28.7 2.1 27 34-60 518-544 (545)
34 COG0376 KatG Catalase (peroxid 20.9 67 0.0014 29.5 1.9 59 49-117 94-161 (730)
No 1
>PLN03030 cationic peroxidase; Provisional
Probab=100.00 E-value=1.3e-48 Score=319.93 Aligned_cols=113 Identities=36% Similarity=0.654 Sum_probs=102.8
Q ss_pred hHHHHHHHHHhh--ccCCCCCcCcccCCCccHHHHHHHHHHHHHHhCcCchhhhhhhhhccccccCCCCcccccCCCCCC
Q 040960 2 VLILWGSCCLFA--GGNGELVLHFYKKSCPSAEMLVKEEMKRKMLSDISSAATILRLAFHDCQVDGCDGSILLGNSNGIT 79 (117)
Q Consensus 2 ~~~~~~~~~l~~--~~~~~L~~~fY~~sCP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FHDCfV~GCDaSiLL~~~~~~~ 79 (117)
|+++.|+++.+. .+.++|+++||++|||++|+||+++|++++++||+++|++||||||||||+||||||||+++ .
T Consensus 6 ~~~~~~~~~~~~~~~~~~~L~~~fY~~sCP~aE~iV~~~v~~~~~~d~~~aa~llRL~FHDCfv~GCDaSvLl~~~---~ 82 (324)
T PLN03030 6 VILFFLLAMMATTLVQGQGTRVGFYSTTCPQAESIVRKTVQSHFQSNPAIAPGLLRMHFHDCFVRGCDASILIDGS---N 82 (324)
T ss_pred hHHHHHHHHHhcccchhccCccchhhCcCCCHHHHHHHHHHHHHhhCcccchhhhhhhhhhheecCCceEEeeCCC---c
Confidence 455666665554 33467999999999999999999999999999999999999999999999999999999975 3
Q ss_pred cccccccCCCCcchHHHHHHHHHhhhhCCCcccccccC
Q 040960 80 TETLSDKNFGIRKVDIINEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 80 ~E~~a~~n~~l~gfd~Id~iK~~lE~~CPgvVSCADIl 117 (117)
+||++++|.++||||+||+||++||++|||+||||||+
T Consensus 83 ~Ek~a~~N~~l~Gf~~i~~iK~~~e~~CPg~VSCADil 120 (324)
T PLN03030 83 TEKTALPNLLLRGYDVIDDAKTQLEAACPGVVSCADIL 120 (324)
T ss_pred ccccCCCCcCcchHHHHHHHHHHHHhhCCCcccHHHHH
Confidence 79999999999999999999999999999999999996
No 2
>cd00693 secretory_peroxidase Horseradish peroxidase and related secretory plant peroxidases. Secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants where they have been implicated in hydrogen peroxide detoxification, auxin catabolism and lignin biosynthesis, and stress response. Class III peroxidases contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=100.00 E-value=2.2e-43 Score=285.62 Aligned_cols=100 Identities=45% Similarity=0.815 Sum_probs=97.2
Q ss_pred CCCcCcccCCCccHHHHHHHHHHHHHHhCcCchhhhhhhhhccccccCCCCcccccCCCCCCcccccccCCCCcchHHHH
Q 040960 18 ELVLHFYKKSCPSAEMLVKEEMKRKMLSDISSAATILRLAFHDCQVDGCDGSILLGNSNGITTETLSDKNFGIRKVDIIN 97 (117)
Q Consensus 18 ~L~~~fY~~sCP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FHDCfV~GCDaSiLL~~~~~~~~E~~a~~n~~l~gfd~Id 97 (117)
||+++||++|||++|+||+++|++.+.+|++++|++|||+||||||+||||||||+++.+...|+++++|.+++||++||
T Consensus 1 ~L~~~~Y~~sCP~~e~iV~~~v~~~~~~~~~~a~~~lRl~FHDc~v~GcDaSill~~~~~~~~E~~~~~N~~l~g~~~i~ 80 (298)
T cd00693 1 QLSVGFYSKSCPNAESIVRSVVRAAVKADPRLAAALLRLHFHDCFVRGCDASVLLDSTANNTSEKDAPPNLSLRGFDVID 80 (298)
T ss_pred CCCcccccCCCCChHHHHHHHHHHHHHhCCCcCchhhhhhhHhhhccCcceeEEecCCCCCchhccCCCCCCcchhHHHH
Confidence 69999999999999999999999999999999999999999999999999999999987777899999999999999999
Q ss_pred HHHHHhhhhCCCcccccccC
Q 040960 98 EIKGSLEKICPETVSCADII 117 (117)
Q Consensus 98 ~iK~~lE~~CPgvVSCADIl 117 (117)
.||+++|+.||++|||||||
T Consensus 81 ~iK~~~e~~cp~~VScADii 100 (298)
T cd00693 81 DIKAALEAACPGVVSCADIL 100 (298)
T ss_pred HHHHHHHhhCCCcccHHHHH
Confidence 99999999999999999985
No 3
>PF00141 peroxidase: Peroxidase; InterPro: IPR002016 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme: Fe3+ + H2O2 --> [Fe4+=O]R' (Compound I) + H2O [Fe4+=O]R' + substrate --> [Fe4+=O]R (Compound II) + oxidised substrate [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidised substrate In this mechanism, the enzyme reacts with one equivalent of H2O2 to give [Fe4+=O]R' (compound I). This is a two-electron oxidation/reduction reaction where H2O2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl [] intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical []. Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes []. Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress []. Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+ serves as the reducing substrate []. Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites. Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes. The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded. ; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1QPA_B 2DV2_A 2B2R_B 1MWV_B 2FXJ_A 2FXG_A 2B2O_B 1X7U_B 2B2Q_A 2FXH_A ....
Probab=99.96 E-value=1.6e-30 Score=203.41 Aligned_cols=78 Identities=50% Similarity=0.859 Sum_probs=73.7
Q ss_pred HHHHHHHHHHhCcCchhhhhhhhhccccc-cCCCCcccccCCCCCCcccccccCCCCc-chHHHHHHHHHhhhhCCCccc
Q 040960 35 VKEEMKRKMLSDISSAATILRLAFHDCQV-DGCDGSILLGNSNGITTETLSDKNFGIR-KVDIINEIKGSLEKICPETVS 112 (117)
Q Consensus 35 V~~~v~~~~~~d~~~aa~lLRL~FHDCfV-~GCDaSiLL~~~~~~~~E~~a~~n~~l~-gfd~Id~iK~~lE~~CPgvVS 112 (117)
||+.|++++++|++++|++|||+|||||| +|||||||+ ...|+++++|.+|+ ||++|+.||+++|++||++||
T Consensus 1 Vr~~v~~~~~~~~~~~~~~lRl~FHDc~~~~GcDgSil~-----~~~e~~~~~N~gl~~~~~~i~~ik~~~~~~cp~~VS 75 (230)
T PF00141_consen 1 VRSDVRAAFKKDPTLAPGLLRLAFHDCFVYGGCDGSILL-----FSAEKDAPPNRGLRDGFDVIDPIKAKLEAACPGVVS 75 (230)
T ss_dssp HHHHHHHHHHHHTTSHHHHHHHHHHHHTTHTSSSSGGGG-----STTGGGSGGGTTHHHHHHHHHHHHHHHCHHSTTTS-
T ss_pred CHHHHHHHHHHCcCccHHHHHHHccccccccccccceec-----cccccccccccCcceeeechhhHHhhhcccccCCCC
Confidence 78999999999999999999999999999 999999998 25899999999998 999999999999999999999
Q ss_pred ccccC
Q 040960 113 CADII 117 (117)
Q Consensus 113 CADIl 117 (117)
|||||
T Consensus 76 ~ADii 80 (230)
T PF00141_consen 76 CADII 80 (230)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99985
No 4
>cd00691 ascorbate_peroxidase Ascorbate peroxidases and cytochrome C peroxidases. Ascorbate peroxidases are a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Along with related catalase-peroxidases, ascorbate peroxidases belong to class I of the plant superfamily. Ascorbate peroxidases are found in the chloroplasts and/or cytosol of algae and plants, where they have been shown to control the concentration of lethal hydrogen peroxide molecules. The yeast cytochrome c peroxidase is a divergent member of the family; it forms a complex with cytochrome c to catalyze the reduction of hydrogen peroxide to water.
Probab=99.88 E-value=1.7e-23 Score=166.40 Aligned_cols=80 Identities=26% Similarity=0.383 Sum_probs=71.4
Q ss_pred cHHHHHHHHHHHHHHhCcCchhhhhhhhhccccccCCCCcccccCCCCC---CcccccccCCCC-cchHHHHHHHHHhhh
Q 040960 30 SAEMLVKEEMKRKMLSDISSAATILRLAFHDCQVDGCDGSILLGNSNGI---TTETLSDKNFGI-RKVDIINEIKGSLEK 105 (117)
Q Consensus 30 ~aE~IV~~~v~~~~~~d~~~aa~lLRL~FHDCfV~GCDaSiLL~~~~~~---~~E~~a~~n~~l-~gfd~Id~iK~~lE~ 105 (117)
+.++||++.|++.++ |++++|++|||+||||| +||+|+++++.++. .+|+++++|.+| +||++||.||+++
T Consensus 11 ~~~~~V~~~v~~~~~-~~~~~~~llRl~FHDc~--~~d~s~~~~G~d~s~~~~~E~~~~~N~~L~~~~~~i~~iK~~~-- 85 (253)
T cd00691 11 KDLEAARNDIAKLID-DKNCAPILVRLAWHDSG--TYDKETKTGGSNGTIRFDPELNHGANAGLDIARKLLEPIKKKY-- 85 (253)
T ss_pred HHHHHHHHHHHHHHH-cCCcHHHHHHHHHHHHh--ccccccCCCCCCccccchhhcCCccccchHHHHHHHHHHHHHc--
Confidence 478899999999999 99999999999999999 59999988765432 369999999999 8999999999987
Q ss_pred hCCCcccccccC
Q 040960 106 ICPETVSCADII 117 (117)
Q Consensus 106 ~CPgvVSCADIl 117 (117)
| +|||||||
T Consensus 86 --~-~VScADil 94 (253)
T cd00691 86 --P-DISYADLW 94 (253)
T ss_pred --C-CCCHHHHH
Confidence 4 89999986
No 5
>PLN02608 L-ascorbate peroxidase
Probab=99.87 E-value=5.8e-23 Score=166.56 Aligned_cols=74 Identities=27% Similarity=0.413 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHHHhCcCchhhhhhhhhcccc-------ccCCCCcccccCCCCCCcccccccCCCC-cchHHHHHHHHH
Q 040960 31 AEMLVKEEMKRKMLSDISSAATILRLAFHDCQ-------VDGCDGSILLGNSNGITTETLSDKNFGI-RKVDIINEIKGS 102 (117)
Q Consensus 31 aE~IV~~~v~~~~~~d~~~aa~lLRL~FHDCf-------V~GCDaSiLL~~~~~~~~E~~a~~n~~l-~gfd~Id~iK~~ 102 (117)
++.+.++. ..+.+||+.+|++|||+||||| ++||||||++. .|+++++|.+| +||++||.||++
T Consensus 14 ~~~~~~~~--~~~~~d~~~a~~llRLaFHDc~t~d~~~~~gGcDgSIll~------~E~~~~~N~gL~~g~~vid~iK~~ 85 (289)
T PLN02608 14 IEKARRDL--RALIASKNCAPIMLRLAWHDAGTYDAKTKTGGPNGSIRNE------EEYSHGANNGLKIAIDLCEPVKAK 85 (289)
T ss_pred HHHHHHHH--HHHHHCCCcHHHHHHHhhhhcCCcCCCCCCCCCCeeeecc------cccCCccccchHHHHHHHHHHHHH
Confidence 56655555 4477899999999999999999 99999999973 69999999999 699999999999
Q ss_pred hhhhCCCcccccccC
Q 040960 103 LEKICPETVSCADII 117 (117)
Q Consensus 103 lE~~CPgvVSCADIl 117 (117)
+ ++|||||||
T Consensus 86 ~-----~~VScADil 95 (289)
T PLN02608 86 H-----PKITYADLY 95 (289)
T ss_pred c-----CCcCHHHHH
Confidence 7 589999986
No 6
>PLN02364 L-ascorbate peroxidase 1
Probab=99.86 E-value=2.5e-22 Score=159.79 Aligned_cols=85 Identities=25% Similarity=0.404 Sum_probs=75.4
Q ss_pred cCcccCC--CccHHHHHHHHHHHHHHhCcCchhhhhhhhhc-----ccccc--CCCCcccccCCCCCCcccccccCCCC-
Q 040960 21 LHFYKKS--CPSAEMLVKEEMKRKMLSDISSAATILRLAFH-----DCQVD--GCDGSILLGNSNGITTETLSDKNFGI- 90 (117)
Q Consensus 21 ~~fY~~s--CP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FH-----DCfV~--GCDaSiLL~~~~~~~~E~~a~~n~~l- 90 (117)
.+||..+ ||++++-+++.+++.+ .||+.+|++|||+|| |||++ ||||||. .+.|+++++|.+|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~lRl~FHd~~t~dc~~~~GG~dgSi~------~~~E~~~~~N~gl~ 75 (250)
T PLN02364 3 KNYPTVSEDYKKAVEKCRRKLRGLI-AEKNCAPIMVRLAWHSAGTFDCQSRTGGPFGTMR------FDAEQAHGANSGIH 75 (250)
T ss_pred CCCCCccHHHHHHHHHHHHHHHHHH-hCCCcHHHHHHHHHccccCcCcCCCCCCCCcccc------ccccccCCCccCHH
Confidence 3677654 8899999999999977 789999999999999 99998 9999983 2469999999999
Q ss_pred cchHHHHHHHHHhhhhCCCcccccccC
Q 040960 91 RKVDIINEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 91 ~gfd~Id~iK~~lE~~CPgvVSCADIl 117 (117)
+||++|+.||+++ ++|||||||
T Consensus 76 ~~~~~i~~ik~~~-----~~VScADil 97 (250)
T PLN02364 76 IALRLLDPIREQF-----PTISFADFH 97 (250)
T ss_pred HHHHHHHHHHHHc-----CCcCHHHHH
Confidence 8999999999998 689999996
No 7
>cd00314 plant_peroxidase_like Heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX), which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions. Several sub-families can be identified. Class I includes intracellular peroxidases present in fungi, plants, archaea and bacteria, called catalase-peroxidases, that can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. Catalase-peroxidases are typically comprised of two homologous domains that probably arose via a single gene duplication event. Class II includes ligninase and other extracellular fungal peroxidases, while class III is comprised
Probab=99.85 E-value=3.1e-22 Score=157.02 Aligned_cols=76 Identities=32% Similarity=0.434 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHhCcCchhhhhhhhhcccccc--------CCCCcccccCCCCCCcccccccCCCC-cchHHHHHHHHHhh
Q 040960 34 LVKEEMKRKMLSDISSAATILRLAFHDCQVD--------GCDGSILLGNSNGITTETLSDKNFGI-RKVDIINEIKGSLE 104 (117)
Q Consensus 34 IV~~~v~~~~~~d~~~aa~lLRL~FHDCfV~--------GCDaSiLL~~~~~~~~E~~a~~n~~l-~gfd~Id~iK~~lE 104 (117)
.|++.|++.+.++++.++++|||+|||||+. ||||||++++ |++.++|.++ +++++|+.||.++|
T Consensus 2 ~v~~~l~~~~~~~~~~~~~llRl~fHD~~~~~~~~~~~gg~dgsi~~~~------e~~~~~N~~l~~~~~~l~~ik~~~~ 75 (255)
T cd00314 2 AIKAILEDLITQAGALAGSLLRLAFHDAGTYDIADGKGGGADGSIRFEP------ELDRPENGGLDKALRALEPIKSAYD 75 (255)
T ss_pred hHHHHHHHHHHhCcchHHHHHHHHHHHhccccccCCCCCCCCceEeccc------cccCcccccHHHHHHHHHHHHHHcC
Confidence 4788889999999999999999999999997 9999999974 9999999986 99999999999999
Q ss_pred hhCCCcccccccC
Q 040960 105 KICPETVSCADII 117 (117)
Q Consensus 105 ~~CPgvVSCADIl 117 (117)
. |++||||||+
T Consensus 76 ~--~~~vS~ADli 86 (255)
T cd00314 76 G--GNPVSRADLI 86 (255)
T ss_pred C--CCcccHHHHH
Confidence 9 9999999985
No 8
>cd00692 ligninase Ligninase and other manganese-dependent fungal peroxidases. Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of lignin, the main cell wall component of woody plants. They contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=99.79 E-value=7.3e-20 Score=150.64 Aligned_cols=78 Identities=31% Similarity=0.438 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHHHhCcC---chhhhhhhhhccccc------------cCCCCcccccCCCCCCcccccccCCCCcchHH
Q 040960 31 AEMLVKEEMKRKMLSDIS---SAATILRLAFHDCQV------------DGCDGSILLGNSNGITTETLSDKNFGIRKVDI 95 (117)
Q Consensus 31 aE~IV~~~v~~~~~~d~~---~aa~lLRL~FHDCfV------------~GCDaSiLL~~~~~~~~E~~a~~n~~l~gfd~ 95 (117)
++.-|++.+++.+..+.. .|+.+|||+|||||+ +|||||||++++ .|+++++|.+|+ ++
T Consensus 16 ~~~~v~~dl~~~~~~~~~c~~~a~~~lRL~FHD~~~~~~~~~~~~~~~gGcDgSill~~~----~E~~~~~N~gL~--~v 89 (328)
T cd00692 16 VWFDILDDIQGNLFNGGECGEEAHESLRLTFHDAIGFSPALAAGQFGGGGADGSIVLFDD----IETAFHANIGLD--EI 89 (328)
T ss_pred chHHHHHHHHHHHhcCCCCchHHHHhHHHhhhcccccccccccCCCCCCCcCceeecCCc----ccccCCCCCCHH--HH
Confidence 677889999999875544 677799999999997 799999999853 699999999998 99
Q ss_pred HHHHHHHhhhhCCCcccccccC
Q 040960 96 INEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 96 Id~iK~~lE~~CPgvVSCADIl 117 (117)
|+.+|..+|+.| |||||||
T Consensus 90 vd~lk~~~e~~c---VScADii 108 (328)
T cd00692 90 VEALRPFHQKHN---VSMADFI 108 (328)
T ss_pred HHHHHHHHHhcC---cCHHHHH
Confidence 999999999999 9999985
No 9
>cd08201 plant_peroxidase_like_1 Uncharacterized family of plant peroxidase-like proteins. This is a subgroup of heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX) which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions.
Probab=99.69 E-value=6.2e-19 Score=141.67 Aligned_cols=63 Identities=30% Similarity=0.239 Sum_probs=53.2
Q ss_pred HHHhCcCchhhhhhhhhcccc-------ccCCCCcccccCCCCCCcccc-cccCCCCcchHHHHHHHHHhhhhCCCcccc
Q 040960 42 KMLSDISSAATILRLAFHDCQ-------VDGCDGSILLGNSNGITTETL-SDKNFGIRKVDIINEIKGSLEKICPETVSC 113 (117)
Q Consensus 42 ~~~~d~~~aa~lLRL~FHDCf-------V~GCDaSiLL~~~~~~~~E~~-a~~n~~l~gfd~Id~iK~~lE~~CPgvVSC 113 (117)
....+++++|.+|||+||||| ++||||||+++.. .+|+. ..+|.++++|+.|+.+ +|||
T Consensus 34 ~~~~~~~~aa~~LRL~FHDc~t~~~~~g~gGcDgSIlle~~---~~En~G~~~n~~l~~~~~i~~~----------~VSc 100 (264)
T cd08201 34 APGPGRQAAAEWLRTAFHDMATHNVDDGTGGLDASIQYELD---RPENIGSGFNTTLNFFVNFYSP----------RSSM 100 (264)
T ss_pred CcCCCccHHHHHHHHHHHhhcCcccCCCCCCCCcceeecCC---ChhhccCchhhccccceeeccC----------ccCH
Confidence 345789999999999999999 9999999999843 46877 5566789999998765 4999
Q ss_pred cccC
Q 040960 114 ADII 117 (117)
Q Consensus 114 ADIl 117 (117)
|||+
T Consensus 101 ADii 104 (264)
T cd08201 101 ADLI 104 (264)
T ss_pred HHHH
Confidence 9985
No 10
>PLN02879 L-ascorbate peroxidase
Probab=99.56 E-value=2.9e-15 Score=119.63 Aligned_cols=71 Identities=28% Similarity=0.413 Sum_probs=60.2
Q ss_pred HHHHHHHHHHhCcCchhhhhhhhhcccc-------ccCCCCcccccCCCCCCcccccccCCCCc-chHHHHHHHHHhhhh
Q 040960 35 VKEEMKRKMLSDISSAATILRLAFHDCQ-------VDGCDGSILLGNSNGITTETLSDKNFGIR-KVDIINEIKGSLEKI 106 (117)
Q Consensus 35 V~~~v~~~~~~d~~~aa~lLRL~FHDCf-------V~GCDaSiLL~~~~~~~~E~~a~~n~~l~-gfd~Id~iK~~lE~~ 106 (117)
+++.+.+.+ ++...+|.+|||.|||+. .+||||||... .|++.++|.+|+ ++++|+.||+++
T Consensus 20 ~~~~~~~~~-~~~~~~p~~vRla~Hdagt~~~~~~~GG~~Gsirf~------~E~~~~~N~gL~~~~~~i~~iK~~~--- 89 (251)
T PLN02879 20 CKRKLRGLI-AEKHCAPIVLRLAWHSAGTFDVKTKTGGPFGTIRHP------QELAHDANNGLDIAVRLLDPIKELF--- 89 (251)
T ss_pred HHHHHHHHH-hCCCchhHhHHHHHhhhccccCCCCCCCCCeeecCh------hhccCCCcCChHHHHHHHHHHHHHc---
Confidence 455566655 467899999999999994 37999999852 599999999997 999999999998
Q ss_pred CCCcccccccC
Q 040960 107 CPETVSCADII 117 (117)
Q Consensus 107 CPgvVSCADIl 117 (117)
++||||||+
T Consensus 90 --~~VScADil 98 (251)
T PLN02879 90 --PILSYADFY 98 (251)
T ss_pred --CCcCHHHHH
Confidence 689999985
No 11
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=97.98 E-value=3.8e-06 Score=75.69 Aligned_cols=73 Identities=22% Similarity=0.316 Sum_probs=53.7
Q ss_pred HHHHHHHHHHhC--------cCchhhhhhhhhccccc-------cCC-CCcccccCCCCCCcccccccCCCC-cchHHHH
Q 040960 35 VKEEMKRKMLSD--------ISSAATILRLAFHDCQV-------DGC-DGSILLGNSNGITTETLSDKNFGI-RKVDIIN 97 (117)
Q Consensus 35 V~~~v~~~~~~d--------~~~aa~lLRL~FHDCfV-------~GC-DaSiLL~~~~~~~~E~~a~~n~~l-~gfd~Id 97 (117)
|++-+++.+... ..-+|-+|||.+|+.-. +|+ .|+|.+. .|++-+.|.+| ++.++++
T Consensus 57 ~~~dl~~l~~~s~~wwpad~g~ygp~~vRlAWHsAgTYr~~d~rGGa~gg~iRf~------P~~sw~~N~~Ldka~~lL~ 130 (716)
T TIGR00198 57 VKQDLKHLMTDSQSWWPADWGHYGGLFIRMAWHAAGTYRIADGRGGAATGNQRFA------PLNSWPDNVNLDKARRLLW 130 (716)
T ss_pred HHHHHHHHHhcCcccCccccCCcceeeeeeeccccccccCCCCCCCCCCCceecc------cccCchhhhhHHHHHHHHH
Confidence 666677776653 35799999999999976 465 4666654 36666777766 4666777
Q ss_pred HHHHHhhhhCCCcccccccC
Q 040960 98 EIKGSLEKICPETVSCADII 117 (117)
Q Consensus 98 ~iK~~lE~~CPgvVSCADIl 117 (117)
.||+ .||++||||||+
T Consensus 131 pIk~----kyp~~VS~ADLi 146 (716)
T TIGR00198 131 PIKK----KYGNKLSWADLI 146 (716)
T ss_pred HHHH----HCCCceeHHHHH
Confidence 6665 699999999985
No 12
>cd00649 catalase_peroxidase_1 N-terminal catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms, where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to class I of the plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C
Probab=97.32 E-value=0.00014 Score=62.16 Aligned_cols=75 Identities=20% Similarity=0.301 Sum_probs=57.8
Q ss_pred HHHHHHHHHHHHhC--------cCchhhhhhhhhccccc-------cCCC-CcccccCCCCCCcccccccCCCC-cchHH
Q 040960 33 MLVKEEMKRKMLSD--------ISSAATILRLAFHDCQV-------DGCD-GSILLGNSNGITTETLSDKNFGI-RKVDI 95 (117)
Q Consensus 33 ~IV~~~v~~~~~~d--------~~~aa~lLRL~FHDCfV-------~GCD-aSiLL~~~~~~~~E~~a~~n~~l-~gfd~ 95 (117)
+.|++-+++.+... ..-+|-++||.|||... +|+. |+|.+. .|++.+.|.+| ++.++
T Consensus 45 ~~~~~di~~ll~~s~~~wp~D~g~~gp~lvRlAWh~AgTy~~~d~~GG~ngg~iRf~------pe~~~~~N~gL~~a~~~ 118 (409)
T cd00649 45 EALKEDLKALMTDSQDWWPADYGHYGPLFIRMAWHSAGTYRIADGRGGAGTGQQRFA------PLNSWPDNVNLDKARRL 118 (409)
T ss_pred HHHHHHHHHHHhcccccCccccCCcccceeeeeccccccccCcCCCCCCCCCccccc------cccCcHhhhhHHHHHHH
Confidence 45677777777653 35899999999999986 4775 777764 47778888888 57889
Q ss_pred HHHHHHHhhhhCCCcccccccC
Q 040960 96 INEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 96 Id~iK~~lE~~CPgvVSCADIl 117 (117)
++.||++. |..||.||++
T Consensus 119 L~pik~k~----~~~iS~ADL~ 136 (409)
T cd00649 119 LWPIKQKY----GNKISWADLM 136 (409)
T ss_pred HHHHHHHc----CCCccHHHHH
Confidence 99999877 4579999964
No 13
>cd08200 catalase_peroxidase_2 C-terminal non-catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal do
Probab=96.66 E-value=0.0023 Score=52.78 Aligned_cols=75 Identities=20% Similarity=0.323 Sum_probs=56.6
Q ss_pred HHHHHHHHhCcCchhhhhhhhhccccc-------cCCCCc-ccccCCCCCCcccccccCCC--C-cchHHHHHHHHHhh-
Q 040960 37 EEMKRKMLSDISSAATILRLAFHDCQV-------DGCDGS-ILLGNSNGITTETLSDKNFG--I-RKVDIINEIKGSLE- 104 (117)
Q Consensus 37 ~~v~~~~~~d~~~aa~lLRL~FHDCfV-------~GCDaS-iLL~~~~~~~~E~~a~~n~~--l-~gfd~Id~iK~~lE- 104 (117)
+.+++.+......++-|+|+.||+.-. +|+.|+ |-+. .|++-+.|.+ | +..++++.||++.-
T Consensus 17 ~~lk~~i~~~gl~~~~lvrlAWhsAgTyr~sd~rGGaNGariRl~------pe~~w~~N~~~~L~~~~~~Le~ik~~~~~ 90 (297)
T cd08200 17 AALKAKILASGLTVSELVSTAWASASTFRNSDKRGGANGARIRLA------PQKDWEVNEPEELAKVLAVLEGIQKEFNE 90 (297)
T ss_pred HHHHHHHHhcCCcHHHHHHHhhhccccccCCCCCCCCCcccccCc------cccCcCccCcHHHHHHHHHHHHHHHHhcc
Confidence 456777777777899999999999976 588877 5554 4777778877 7 57889999998873
Q ss_pred hhCCC-cccccccC
Q 040960 105 KICPE-TVSCADII 117 (117)
Q Consensus 105 ~~CPg-vVSCADIl 117 (117)
..-+| .||.||++
T Consensus 91 ~~~~~~~vS~ADLi 104 (297)
T cd08200 91 SQSGGKKVSLADLI 104 (297)
T ss_pred cccCCccccHHHHH
Confidence 22233 69999964
No 14
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=96.26 E-value=0.0031 Score=57.27 Aligned_cols=74 Identities=19% Similarity=0.303 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHhC--------cCchhhhhhhhhccccc-------cCCC-CcccccCCCCCCcccccccCCCC-cchHHH
Q 040960 34 LVKEEMKRKMLSD--------ISSAATILRLAFHDCQV-------DGCD-GSILLGNSNGITTETLSDKNFGI-RKVDII 96 (117)
Q Consensus 34 IV~~~v~~~~~~d--------~~~aa~lLRL~FHDCfV-------~GCD-aSiLL~~~~~~~~E~~a~~n~~l-~gfd~I 96 (117)
.|++-+.+.+... ..-+|-+|||.||+.-. +|+. |+|.+. .|.+-+.|.+| ++.+++
T Consensus 58 a~k~di~~l~~~sqdwwpaD~g~ygp~~vRlAWH~AgTYr~~d~rGGangg~iRf~------pe~~w~~N~gL~ka~~~L 131 (726)
T PRK15061 58 ALKKDLKALMTDSQDWWPADYGHYGPLFIRMAWHSAGTYRIGDGRGGAGGGQQRFA------PLNSWPDNVNLDKARRLL 131 (726)
T ss_pred HHHHHHHHHHhcccccccccCCCccceeeeeeecccccccCcCCCCCCCCCcccCc------ccccchhhhhHHHHHHHH
Confidence 3666666666543 35789999999999976 4765 677654 36777888888 688899
Q ss_pred HHHHHHhhhhCCCcccccccC
Q 040960 97 NEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 97 d~iK~~lE~~CPgvVSCADIl 117 (117)
+.||++. |..||.||++
T Consensus 132 ~pik~ky----~~~iS~ADLi 148 (726)
T PRK15061 132 WPIKQKY----GNKISWADLM 148 (726)
T ss_pred HHHHHHh----CCCccHHHHH
Confidence 9999887 4579999964
No 15
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=94.83 E-value=0.028 Score=51.25 Aligned_cols=70 Identities=23% Similarity=0.378 Sum_probs=51.9
Q ss_pred HHHHHHhCcCchhhhhhhhhccccc-------cCCCCc-ccccCCCCCCcccccccC--CCC-cchHHHHHHHHHhhhhC
Q 040960 39 MKRKMLSDISSAATILRLAFHDCQV-------DGCDGS-ILLGNSNGITTETLSDKN--FGI-RKVDIINEIKGSLEKIC 107 (117)
Q Consensus 39 v~~~~~~d~~~aa~lLRL~FHDCfV-------~GCDaS-iLL~~~~~~~~E~~a~~n--~~l-~gfd~Id~iK~~lE~~C 107 (117)
+++.+....-..+-|+|+.||+.-. +|+.|+ |.+. .|++-+.| .+| +..++++.||++.-.
T Consensus 437 lk~~i~~sgl~~~~lVr~AWhsA~Tyr~sd~rGGaNGariRl~------pe~~w~~N~p~gL~~vl~~Le~Ik~~f~~-- 508 (716)
T TIGR00198 437 LKQQILASGLSVSELVCTAWASASTFRSSDYRGGANGARIRLE------PQKNWPVNEPTRLAKVLAVLEKIQAEFAK-- 508 (716)
T ss_pred HHHHHHhcCCcHHHHHHHhhhhcccccCCCCCCCCCcceeecc------hhcCcccCCHHHHHHHHHHHHHHHHHcCC--
Confidence 4444555666789999999999976 577777 6654 47777888 567 678899999988731
Q ss_pred CCcccccccC
Q 040960 108 PETVSCADII 117 (117)
Q Consensus 108 PgvVSCADIl 117 (117)
+.||-||++
T Consensus 509 -~~vS~ADLi 517 (716)
T TIGR00198 509 -GPVSLADLI 517 (716)
T ss_pred -CcccHHHHH
Confidence 269999964
No 16
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=94.01 E-value=0.065 Score=48.94 Aligned_cols=75 Identities=21% Similarity=0.347 Sum_probs=55.9
Q ss_pred HHHHHHHHhCcCchhhhhhhhhccccc-------cCCCCc-ccccCCCCCCcccccccCC--CC-cchHHHHHHHHHhhh
Q 040960 37 EEMKRKMLSDISSAATILRLAFHDCQV-------DGCDGS-ILLGNSNGITTETLSDKNF--GI-RKVDIINEIKGSLEK 105 (117)
Q Consensus 37 ~~v~~~~~~d~~~aa~lLRL~FHDCfV-------~GCDaS-iLL~~~~~~~~E~~a~~n~--~l-~gfd~Id~iK~~lE~ 105 (117)
..+++.+....-..+-|+|+.+|+.-. +|..|+ |.+. .|++-..|. +| +..++++.||++...
T Consensus 442 ~~lk~~i~~~gl~~~~LVr~AWhsA~Tyr~sd~rGGaNGarIRl~------Pq~~w~~N~p~~L~~vl~~LE~Ik~~f~~ 515 (726)
T PRK15061 442 AALKAKILASGLSVSELVSTAWASASTFRGSDKRGGANGARIRLA------PQKDWEVNEPAQLAKVLAVLEGIQAEFNA 515 (726)
T ss_pred HHHHHHHHhcCCcHHHHHHHHHhhcccccCCCCCCCCCccceecc------cccCccccCHHHHHHHHHHHHHHHHHHhh
Confidence 356666666667899999999999975 477777 6654 377777887 66 578999999998843
Q ss_pred h-CC-CcccccccC
Q 040960 106 I-CP-ETVSCADII 117 (117)
Q Consensus 106 ~-CP-gvVSCADIl 117 (117)
. -. ..||-||++
T Consensus 516 ~~~~~~~vS~ADLi 529 (726)
T PRK15061 516 AQSGGKKVSLADLI 529 (726)
T ss_pred ccCCCCceeHHHHH
Confidence 3 22 259999964
No 17
>KOG0427 consensus Ubiquitin conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=54.02 E-value=8.2 Score=29.06 Aligned_cols=40 Identities=23% Similarity=0.194 Sum_probs=26.7
Q ss_pred HHHHHHHHhhccCCC--CCcCcccCCCccHHHHHHHHHHHHHHhCcCchhhhhhhhhcc
Q 040960 4 ILWGSCCLFAGGNGE--LVLHFYKKSCPSAEMLVKEEMKRKMLSDISSAATILRLAFHD 60 (117)
Q Consensus 4 ~~~~~~~l~~~~~~~--L~~~fY~~sCP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FHD 60 (117)
++.++-+|.++..-| -..++|-++|-+ +..|.=-|-||||
T Consensus 117 ClSIlSMLSSs~eKqrP~Dn~~Yvk~C~~-----------------grsPk~TrWwfHD 158 (161)
T KOG0427|consen 117 CLSILSMLSSSKEKQRPTDNDRYVKNCKN-----------------GRSPKETRWWFHD 158 (161)
T ss_pred HHHHHHHHccCccccCCCccchhhhhccC-----------------CCCcccceeeecc
Confidence 455566666544433 668899999954 2345667899998
No 18
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=49.15 E-value=4.5 Score=28.46 Aligned_cols=16 Identities=38% Similarity=1.045 Sum_probs=10.8
Q ss_pred hhccccccCCCCccccc
Q 040960 57 AFHDCQVDGCDGSILLG 73 (117)
Q Consensus 57 ~FHDCfV~GCDaSiLL~ 73 (117)
.+|+|| .||.|+....
T Consensus 4 V~HeC~-g~c~G~f~P~ 19 (96)
T PF08782_consen 4 VYHECF-GGCRGSFIPE 19 (96)
T ss_dssp EEE-ST-T-EEEEE-GG
T ss_pred eEEeec-CccceEechh
Confidence 379999 8999998755
No 19
>PF01816 LRV: Leucine rich repeat variant; InterPro: IPR004830 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This signature describes a leucine-rich repeat variant (LRV), which has a novel repetitive structural motif consisting of alternating alpha- and 3(10)-helices arranged in a right-handed superhelix, with the absence of the beta-sheets present in other LRRs [].; PDB: 1LRV_A.
Probab=45.91 E-value=18 Score=19.50 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=15.6
Q ss_pred HHHHHHHhCcCchhhhhhhhhcc
Q 040960 38 EMKRKMLSDISSAATILRLAFHD 60 (117)
Q Consensus 38 ~v~~~~~~d~~~aa~lLRL~FHD 60 (117)
.|+..+.++|.+++.+|+-.-||
T Consensus 2 ~VR~avA~~P~~P~~~L~~La~D 24 (26)
T PF01816_consen 2 EVRAAVARRPNLPPEVLEQLAHD 24 (26)
T ss_dssp HHHHHHHHH--S-GGGGGGGTT-
T ss_pred HHHHHHHHccCCCHHHHHHhccC
Confidence 46778888899999999887776
No 20
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.99 E-value=31 Score=23.11 Aligned_cols=26 Identities=12% Similarity=0.413 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhCcCchhhhhhhhhc
Q 040960 34 LVKEEMKRKMLSDISSAATILRLAFH 59 (117)
Q Consensus 34 IV~~~v~~~~~~d~~~aa~lLRL~FH 59 (117)
|.|+.+++.+++||.+-+-.+|+.+-
T Consensus 24 iark~~~k~lk~NPpine~~iR~M~~ 49 (71)
T COG3763 24 IARKQMKKQLKDNPPINEEMIRMMMA 49 (71)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHH
Confidence 67999999999999999999998774
No 21
>KOG3803 consensus Transcription factor containing C2HC type Zn finger [Transcription]
Probab=40.67 E-value=18 Score=33.74 Aligned_cols=70 Identities=21% Similarity=0.303 Sum_probs=40.1
Q ss_pred CCCccHHHHHHHHHHHHHHhCcCchhhhhhhhhccccccCCCCcccccCCCCCCcccccccCCCCcchHHHHH--HHHHh
Q 040960 26 KSCPSAEMLVKEEMKRKMLSDISSAATILRLAFHDCQVDGCDGSILLGNSNGITTETLSDKNFGIRKVDIINE--IKGSL 103 (117)
Q Consensus 26 ~sCP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FHDCfV~GCDaSiLL~~~~~~~~E~~a~~n~~l~gfd~Id~--iK~~l 103 (117)
+-||-+++++|+.+...-++ --|-.-|||||--+.+..+.......=|...=.|..++.. .|..=
T Consensus 670 sgcpladks~Rslma~~sqe-------------LkCPTPGCDGSGHiTGnYasHRSLSGCPRa~k~gvkv~qtke~keD~ 736 (968)
T KOG3803|consen 670 SGCPLADKSLRSLMAAGSQE-------------LKCPTPGCDGSGHITGNYASHRSLSGCPRAKKSGVKVAQTKEDKEDP 736 (968)
T ss_pred cCCchhHHHHHHHHhccccc-------------ccCCCCCCCCCCcccccccccccccCCCCCCCCCceeccchhhccCc
Confidence 35999999999877655332 1377789999998876432211122112212235555543 23444
Q ss_pred hhhCC
Q 040960 104 EKICP 108 (117)
Q Consensus 104 E~~CP 108 (117)
|-.||
T Consensus 737 elrCp 741 (968)
T KOG3803|consen 737 ELRCP 741 (968)
T ss_pred eeecC
Confidence 55786
No 22
>PF06764 DUF1223: Protein of unknown function (DUF1223); InterPro: IPR010634 This family consists of several hypothetical proteins of around 250 residues in length, which are found in both plants and bacteria. The function of this family is unknown.; PDB: 2AXO_A.
Probab=29.89 E-value=24 Score=27.44 Aligned_cols=25 Identities=44% Similarity=0.806 Sum_probs=19.0
Q ss_pred CCCccHHHHHHHHHHHHHHhCcCchhhhhhhhhc
Q 040960 26 KSCPSAEMLVKEEMKRKMLSDISSAATILRLAFH 59 (117)
Q Consensus 26 ~sCP~aE~IV~~~v~~~~~~d~~~aa~lLRL~FH 59 (117)
+|||.|+..+.+...+ +.+|=|-||
T Consensus 11 sSCPpAD~~L~~l~~~---------~~Vi~LafH 35 (202)
T PF06764_consen 11 SSCPPADRLLSELAAR---------PDVIALAFH 35 (202)
T ss_dssp TT-HHHHHHHHHHHHH---------TSSEEEEEE
T ss_pred CCCcHHHHHHHHhhcC---------CCEEEEEec
Confidence 5899999988887666 366778899
No 23
>PF15240 Pro-rich: Proline-rich
Probab=28.59 E-value=49 Score=25.69 Aligned_cols=20 Identities=20% Similarity=0.184 Sum_probs=14.2
Q ss_pred ChHHHHHHHHHhhccCCCCC
Q 040960 1 MVLILWGSCCLFAGGNGELV 20 (117)
Q Consensus 1 ~~~~~~~~~~l~~~~~~~L~ 20 (117)
|+|+|+-..+||++++..+.
T Consensus 1 MLlVLLSvALLALSSAQ~~d 20 (179)
T PF15240_consen 1 MLLVLLSVALLALSSAQSTD 20 (179)
T ss_pred ChhHHHHHHHHHhhhccccc
Confidence 77788778888876654454
No 24
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=27.94 E-value=53 Score=20.78 Aligned_cols=14 Identities=21% Similarity=0.717 Sum_probs=10.8
Q ss_pred cCcccCCCccHHHH
Q 040960 21 LHFYKKSCPSAEML 34 (117)
Q Consensus 21 ~~fY~~sCP~aE~I 34 (117)
..||..+||.-..+
T Consensus 3 i~~~a~~C~~C~~~ 16 (76)
T TIGR00412 3 IQIYGTGCANCQMT 16 (76)
T ss_pred EEEECCCCcCHHHH
Confidence 56999999976654
No 25
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=27.33 E-value=35 Score=19.32 Aligned_cols=15 Identities=40% Similarity=0.853 Sum_probs=10.5
Q ss_pred cccccCCCCcccccC
Q 040960 60 DCQVDGCDGSILLGN 74 (117)
Q Consensus 60 DCfV~GCDaSiLL~~ 74 (117)
-|-+.||||+--+++
T Consensus 3 ~CPtpGCdg~GHi~G 17 (31)
T PF01530_consen 3 KCPTPGCDGSGHITG 17 (31)
T ss_dssp SSSSTT--SCSTTTS
T ss_pred cCCCCCCCccccccC
Confidence 377899999988876
No 26
>PHA03163 hypothetical protein; Provisional
Probab=24.00 E-value=1e+02 Score=21.53 Aligned_cols=13 Identities=15% Similarity=0.127 Sum_probs=9.8
Q ss_pred CCCCcCcccCCCc
Q 040960 17 GELVLHFYKKSCP 29 (117)
Q Consensus 17 ~~L~~~fY~~sCP 29 (117)
.+-..+||+.+|-
T Consensus 34 p~~~~~FYs~~C~ 46 (92)
T PHA03163 34 PHDFDMFHQYDCN 46 (92)
T ss_pred CCCCcccccCCCC
Confidence 3455789999994
No 27
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=23.72 E-value=43 Score=24.10 Aligned_cols=31 Identities=23% Similarity=0.238 Sum_probs=26.7
Q ss_pred CCCcCcccCCCccHHHHHHHHHHHHHHhCcC
Q 040960 18 ELVLHFYKKSCPSAEMLVKEEMKRKMLSDIS 48 (117)
Q Consensus 18 ~L~~~fY~~sCP~aE~IV~~~v~~~~~~d~~ 48 (117)
.|..|+|+.+|=.+++.|+..++..+...+.
T Consensus 23 ~le~G~y~~a~f~aqQAvel~lKalL~~~~~ 53 (132)
T COG2250 23 DLELGDYDLACFHAQQAVELALKALLIRLGG 53 (132)
T ss_pred HHHCCChHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3788999999999999999999988877554
No 28
>COG3262 HycE Ni,Fe-hydrogenase III component G [Energy production and conversion]
Probab=23.25 E-value=47 Score=25.55 Aligned_cols=31 Identities=23% Similarity=0.190 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCcCchhhhhhhhhccccccC
Q 040960 35 VKEEMKRKMLSDISSAATILRLAFHDCQVDG 65 (117)
Q Consensus 35 V~~~v~~~~~~d~~~aa~lLRL~FHDCfV~G 65 (117)
..++++..+.-|+.-+|.=-||+.||||-.|
T Consensus 113 fEREi~Dm~Gl~~vg~PD~RRLvLpddwPeg 143 (165)
T COG3262 113 FEREIRDMYGLDPVGAPDPRRLVLPDDWPEG 143 (165)
T ss_pred HHHHHHHhhCcccCCCCCcceeeccccCCcc
Confidence 4567888888899999999999999999644
No 29
>PRK00523 hypothetical protein; Provisional
Probab=22.84 E-value=1.1e+02 Score=20.48 Aligned_cols=26 Identities=12% Similarity=0.308 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhCcCchhhhhhhhhc
Q 040960 34 LVKEEMKRKMLSDISSAATILRLAFH 59 (117)
Q Consensus 34 IV~~~v~~~~~~d~~~aa~lLRL~FH 59 (117)
+-|+.+++.+++||.+-...||..|-
T Consensus 25 iark~~~k~l~~NPpine~mir~M~~ 50 (72)
T PRK00523 25 VSKKMFKKQIRENPPITENMIRAMYM 50 (72)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHH
Confidence 45889999999999999999998764
No 30
>PF03076 GP3: Equine arteritis virus GP3; InterPro: IPR004310 This entry contains proteins encoded by ORF3 of Equine arteritis virus. They are possible envelope glcoproteins.
Probab=22.73 E-value=39 Score=25.23 Aligned_cols=22 Identities=23% Similarity=0.197 Sum_probs=19.4
Q ss_pred CchhhhhhhhhccccccCCCCc
Q 040960 48 SSAATILRLAFHDCQVDGCDGS 69 (117)
Q Consensus 48 ~~aa~lLRL~FHDCfV~GCDaS 69 (117)
..+.++|-++||=+|+.|-.||
T Consensus 6 ~~pva~lcfff~~lfi~g~~gs 27 (160)
T PF03076_consen 6 NRPVAFLCFFFYFLFICGSVGS 27 (160)
T ss_pred cccHHHHHHHHHHHheecccCC
Confidence 3578899999999999998887
No 31
>PRK01844 hypothetical protein; Provisional
Probab=22.56 E-value=1.1e+02 Score=20.42 Aligned_cols=26 Identities=8% Similarity=0.207 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhCcCchhhhhhhhhc
Q 040960 34 LVKEEMKRKMLSDISSAATILRLAFH 59 (117)
Q Consensus 34 IV~~~v~~~~~~d~~~aa~lLRL~FH 59 (117)
+-|+.+++.+++||.+-...||..|-
T Consensus 24 ~ark~~~k~lk~NPpine~mir~Mm~ 49 (72)
T PRK01844 24 IARKYMMNYLQKNPPINEQMLKMMMM 49 (72)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 45899999999999999999998764
No 32
>PF07983 X8: X8 domain; InterPro: IPR012946 The X8 domain [] contains 6 conserved cysteine residues that presumably form three disulphide bridges. The domain is found in an Olive pollen allergen [] as well as at the C terminus of family 17 glycosyl hydrolases []. This domain may be involved in carbohydrate binding.; PDB: 2JON_A 2W61_A 2W62_A 2W63_A.
Probab=22.14 E-value=83 Score=20.78 Aligned_cols=20 Identities=30% Similarity=0.639 Sum_probs=15.6
Q ss_pred HHHHHHhhhhCC-Cccccccc
Q 040960 97 NEIKGSLEKICP-ETVSCADI 116 (117)
Q Consensus 97 d~iK~~lE~~CP-gvVSCADI 116 (117)
+.+++.++-+|- +.|.|++|
T Consensus 12 ~~l~~~l~~aC~~~~~dC~~I 32 (78)
T PF07983_consen 12 KELQDLLDYACGQGGVDCSPI 32 (78)
T ss_dssp HHHHHHHHHHTTT-SSSCCCC
T ss_pred HHHHHHHHHHHcCCCCChhhh
Confidence 456788899995 47999988
No 33
>COG1766 fliF Flagellar basal body M-ring protein [Cell motility and secretion]
Probab=21.32 E-value=68 Score=28.75 Aligned_cols=27 Identities=15% Similarity=0.290 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhCcCchhhhhhhhhcc
Q 040960 34 LVKEEMKRKMLSDISSAATILRLAFHD 60 (117)
Q Consensus 34 IV~~~v~~~~~~d~~~aa~lLRL~FHD 60 (117)
...+.+++.++.+|...|.+||-|+++
T Consensus 518 ~~~~~l~~ma~~~Pe~vA~vir~Wl~e 544 (545)
T COG1766 518 VLLERLREMAKEDPERVAKVIRQWLNE 544 (545)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHhhc
Confidence 467788999999999999999999875
No 34
>COG0376 KatG Catalase (peroxidase I) [Inorganic ion transport and metabolism]
Probab=20.95 E-value=67 Score=29.52 Aligned_cols=59 Identities=20% Similarity=0.327 Sum_probs=37.8
Q ss_pred chhhhhhhhhccccccCCCCcccccC-CCCC--Cc-----ccccccCCCC-cchHHHHHHHHHhhhhCCCcccccccC
Q 040960 49 SAATILRLAFHDCQVDGCDGSILLGN-SNGI--TT-----ETLSDKNFGI-RKVDIINEIKGSLEKICPETVSCADII 117 (117)
Q Consensus 49 ~aa~lLRL~FHDCfV~GCDaSiLL~~-~~~~--~~-----E~~a~~n~~l-~gfd~Id~iK~~lE~~CPgvVSCADIl 117 (117)
-.+-+|||.+|-.. +--+-. .++. .. +.+=|-|.+| +++.++--||.+- +..+|+||.+
T Consensus 94 YGplfIRmAWHsAG------TYRi~DGRGGa~~G~qRFaPlnSWPDN~nLDKarRLLWPIKkKY----G~kiSWaDL~ 161 (730)
T COG0376 94 YGPLFIRMAWHSAG------TYRIGDGRGGAGGGQQRFAPLNSWPDNANLDKARRLLWPIKKKY----GRKISWADLI 161 (730)
T ss_pred cccceeeeeecccC------ceecccCCCCCCCCceecccccCCCcccchHHHHHHhhhHhHhh----cccccHhHhh
Confidence 57889999999763 333322 2221 11 2222444566 6888998898876 6789999964
Done!