Query 033376
Match_columns 120
No_of_seqs 134 out of 616
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 13:08:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4742 Predicted chitinase [G 100.0 2E-32 4.3E-37 219.0 5.7 108 13-120 36-159 (286)
2 PF00182 Glyco_hydro_19: Chiti 100.0 4.8E-30 1E-34 201.1 4.7 73 41-113 1-74 (232)
3 cd00325 chitinase_glyco_hydro_ 100.0 2.3E-29 5.1E-34 197.1 5.6 72 42-113 1-73 (230)
4 PF00187 Chitin_bind_1: Chitin 99.1 1.8E-11 3.9E-16 72.6 0.4 25 2-27 16-40 (40)
5 smart00270 ChtBD1 Chitin bindi 99.0 2.5E-10 5.4E-15 67.0 1.6 24 2-25 14-37 (38)
6 cd00035 ChtBD1 Chitin binding 98.6 1.7E-08 3.7E-13 59.7 1.2 26 2-28 14-39 (40)
7 cd06918 ChtBD1_like Domain obs 96.4 0.0014 3E-08 40.7 1.1 21 2-22 27-48 (51)
8 COG3179 Predicted chitinase [G 95.6 0.0047 1E-07 47.9 0.8 58 41-111 3-61 (206)
9 PF15182 OTOS: Otospiralin 56.9 5.6 0.00012 25.9 0.9 34 61-104 25-59 (69)
10 PF01830 Peptidase_C7: Peptida 49.0 27 0.00059 27.6 3.7 37 65-104 92-128 (243)
11 PRK15321 putative type III sec 47.7 22 0.00047 25.3 2.7 35 62-96 15-50 (120)
12 cd00491 4Oxalocrotonate_Tautom 38.2 30 0.00065 20.2 2.1 32 83-114 10-47 (58)
13 PF04651 Pox_A12: Poxvirus A12 34.9 30 0.00066 26.7 2.0 29 64-104 9-37 (189)
14 cd08327 CARD_RAIDD Caspase act 34.1 14 0.00031 25.2 0.1 39 41-79 35-82 (94)
15 PF01361 Tautomerase: Tautomer 32.8 33 0.00071 20.5 1.6 33 82-114 9-47 (60)
16 PF06744 DUF1215: Protein of u 30.4 65 0.0014 22.4 3.0 31 66-97 44-75 (125)
17 PRK02220 4-oxalocrotonate taut 29.7 49 0.0011 19.7 2.0 32 82-113 10-47 (61)
18 PF14659 Phage_int_SAM_3: Phag 28.6 31 0.00067 19.9 1.0 39 61-99 17-57 (58)
19 PF01616 Orbi_NS3: Orbivirus N 27.4 42 0.00091 26.1 1.7 17 81-97 37-53 (195)
20 PF06796 NapE: Periplasmic nit 27.2 47 0.001 20.9 1.6 13 84-96 10-22 (56)
21 COG1942 Uncharacterized protei 26.8 49 0.0011 21.4 1.7 31 84-114 13-49 (69)
22 PF09447 Cnl2_NKP2: Cnl2/NKP2 23.3 42 0.00092 21.7 0.9 21 35-55 13-33 (67)
23 PF08837 DUF1810: Protein of u 22.9 1.2E+02 0.0027 22.3 3.4 23 76-98 38-67 (139)
24 PRK02289 4-oxalocrotonate taut 20.8 74 0.0016 19.2 1.6 33 82-114 10-48 (60)
No 1
>KOG4742 consensus Predicted chitinase [General function prediction only]
Probab=99.97 E-value=2e-32 Score=219.04 Aligned_cols=108 Identities=39% Similarity=0.668 Sum_probs=100.5
Q ss_pred CChhhhcCCCCccccCCCC-CCCCccccccccchhhhccccc-CCCcCcCCcccchHHHHHHhcCCCcccCCCChhhHHH
Q 033376 13 TSDEYCGAGSQQGPYDAPP-ATNDVSVVDIVTPKFFNGILNQ-ADASCVGKNFYSRSAFLDALGSFSQFGRTGAEEDTMR 90 (120)
Q Consensus 13 ~t~~yCg~gCQsg~C~~~~-~~~~~~vssiiTea~Fd~lf~~-~~~~c~~~~fYty~~fi~Aa~~fp~F~~~G~~~~~kr 90 (120)
++++||+.+|++++|.++. +.+..+|+++||+.+||+||++ ++..|++++||||++||.|++.||+|+++|+..+.||
T Consensus 36 ~~~~~~~~~c~~g~c~~~~~~~p~~~i~~~~T~~~F~~i~~~~~~g~c~~~gfyty~aFi~Aa~sfp~fg~t~~~~~~kr 115 (286)
T KOG4742|consen 36 TTPPYCKFGCGPGPCSGPGPPNPASKIESSVTPELFEDIFSKVGSGWCPAKGFYTYDAFIIAARSFPEFGGTGNKNTAKR 115 (286)
T ss_pred cccccccCCCCCCCCCCCCCCCCcccccccccHHHHHHHhccccCCCCCCCCCccccHHHHHHHhcccccccCcccccch
Confidence 8999999999999998863 4467899999999999999999 5455999999999999999999999999999999999
Q ss_pred HHHHHhhhhcCCC---------C----CeEEeeccCC-CCCCCC
Q 033376 91 EIAAFFAHVTHET---------G----HMADKHDNCG-PAKMND 120 (120)
Q Consensus 91 ElAAf~a~~shET---------~----g~c~~~E~~~-~~~~~~ 120 (120)
||||||||++||| + +|||+||+.+ ...|||
T Consensus 116 eiAaf~ah~~~ETs~g~~~~~~G~~~~~fc~~~e~s~~~~~YC~ 159 (286)
T KOG4742|consen 116 EIAAFFAHVTHETSGGSNCAPRGPFYWGFCYKEEISPSSGRYCD 159 (286)
T ss_pred hhhhhhhhheecccCcccccCCCccccCcccccccChhhhccCC
Confidence 9999999999999 5 8999999999 889997
No 2
>PF00182 Glyco_hydro_19: Chitinase class I; InterPro: IPR000726 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. Glycoside hydrolase family 19 GH19 from CAZY comprises enzymes with only one known activity; chitinase (3.2.1.14 from EC). Chitinases [] are enzymes that catalyse the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19 []. Chitinases of family 19 (also known as classes IA or I and IB or II) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Class IA/I and IB/II enzymes differ in the presence (IA/I) or absence (IB/II) of a N-terminal chitin-binding domain. The catalytic domain of these enzymes consist of about 220 to 230 amino acid residues.; GO: 0004568 chitinase activity, 0006032 chitin catabolic process, 0016998 cell wall macromolecule catabolic process; PDB: 3IWR_A 2DKV_A 3CQL_A 2Z38_A 2Z37_D 2Z39_B 1DXJ_A 1WVU_B 1WVV_B 2DBT_C ....
Probab=99.96 E-value=4.8e-30 Score=201.12 Aligned_cols=73 Identities=47% Similarity=0.758 Sum_probs=65.5
Q ss_pred cccchhhhccccc-CCCcCcCCcccchHHHHHHhcCCCcccCCCChhhHHHHHHHHhhhhcCCCCCeEEeeccC
Q 033376 41 IVTPKFFNGILNQ-ADASCVGKNFYSRSAFLDALGSFSQFGRTGAEEDTMREIAAFFAHVTHETGHMADKHDNC 113 (120)
Q Consensus 41 iiTea~Fd~lf~~-~~~~c~~~~fYty~~fi~Aa~~fp~F~~~G~~~~~krElAAf~a~~shET~g~c~~~E~~ 113 (120)
|||+++||+|||| +++.||+++||||++||+|+++||+|++||+++++||||||||||++|||+|+++++|++
T Consensus 1 ivt~~~F~~~~~~~n~~~c~~~~FYTY~~Fi~Aa~~fp~F~~tG~~~~~krElAAFLA~~~hET~g~~~~~e~~ 74 (232)
T PF00182_consen 1 IVTESFFNQMFPHRNDNGCPGKGFYTYDAFIAAAKSFPAFGNTGDDEDRKRELAAFLAQVSHETGGFWYIEEIG 74 (232)
T ss_dssp TS-HHHHHHHTTTTTSTTSTTTTTS-HHHHHHHHTTSTTTTTSSSHHHHHHHHHHHHHHHHHHTTTTTTTBTTS
T ss_pred CCCHHHHHHHHhcCCccCCCCCCcccHHHHHHHhhcCchhccCccHHHHHHHHHhhhcccchhccccccccccc
Confidence 7999999999999 679999999999999999999999999999999999999999999999998665555543
No 3
>cd00325 chitinase_glyco_hydro_19 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but some are found in bacteria. Class I and II chitinases are similar in their catalytic domains. Class I chitinases have an N-terminal cysteine-rich, chitin-binding domain which is separated from the catalytic domain by a proline and glycine-rich hinge region. Class II chitinases lack both the chitin-binding domain and the hinge region. Class IV chitinases are similar to class I chitinases but they are smaller in size due to certain deletions. Despite any significant sequence homology with lysozymes, structural analysis reveals that family 19 chitinases, together with family 46 chitosanases, are similar to several lysozymes including those from T4-phage and from goose. The structures reveal that the different en
Probab=99.95 E-value=2.3e-29 Score=197.09 Aligned_cols=72 Identities=44% Similarity=0.751 Sum_probs=67.0
Q ss_pred ccchhhhccccc-CCCcCcCCcccchHHHHHHhcCCCcccCCCChhhHHHHHHHHhhhhcCCCCCeEEeeccC
Q 033376 42 VTPKFFNGILNQ-ADASCVGKNFYSRSAFLDALGSFSQFGRTGAEEDTMREIAAFFAHVTHETGHMADKHDNC 113 (120)
Q Consensus 42 iTea~Fd~lf~~-~~~~c~~~~fYty~~fi~Aa~~fp~F~~~G~~~~~krElAAf~a~~shET~g~c~~~E~~ 113 (120)
||+++||+||+| ++..||+++||||++||+||++||+|+++|+++++||||||||||++|||+|+++++|+.
T Consensus 1 ~t~~~f~~~~~~~~~~~c~~~~fYTy~~fi~Aa~~fp~f~~~g~~~~~krElAaFlAq~~hETgg~~~~~e~~ 73 (230)
T cd00325 1 VTESLFEGIFSHRNDSGCPAKGFYTYDAFITAANSFPGFGTTGDDDTRKREIAAFFAHTSHETGGGCYIAPDG 73 (230)
T ss_pred CCHHHHHHHhhcCCCCCCCCCCCCcHHHHHHHHHhccccccCCCchhhHHHHHHHHhhhcccCCCCccccccc
Confidence 689999999999 688999999999999999999999999999999999999999999999999776666654
No 4
>PF00187 Chitin_bind_1: Chitin recognition protein; InterPro: IPR001002 A number of plant and fungal proteins that bind N-acetylglucosamine (e.g. solanaceous lectins of tomato and potato, plant endochitinases, the wound-induced proteins: hevein, win1 and win2, and the Kluyveromyces lactis killer toxin alpha subunit) contain this domain []. The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits [, ]. In chitinases, as well as in the potato wound-induced proteins, the 43-residue domain directly follows the signal sequence and is therefore at the N terminus of the mature protein; in the killer toxin alpha subunit it is located in the central section of the protein. ; GO: 0008061 chitin binding; PDB: 9WGA_B 2WGC_B 1ULK_B 2UVO_B 1WGC_B 2CWG_A 2X3T_C 4AML_B 7WGA_B 1ZWU_A ....
Probab=99.09 E-value=1.8e-11 Score=72.58 Aligned_cols=25 Identities=60% Similarity=1.375 Sum_probs=22.0
Q ss_pred cccccccccccCChhhhcCCCCcccc
Q 033376 2 WQCCSQWGYCGTSDEYCGAGSQQGPY 27 (120)
Q Consensus 2 ~~CCS~~G~CG~t~~yCg~gCQsg~C 27 (120)
++|||+|||||+|++||+.+||+ +|
T Consensus 16 ~~CCS~~G~CG~t~~yCg~gCQ~-~C 40 (40)
T PF00187_consen 16 GLCCSQYGYCGTTSDYCGAGCQS-QC 40 (40)
T ss_dssp G-EEETTSBEESSHHHHSTTEES-ST
T ss_pred CCccCCCCcccCChhhhhccccc-CC
Confidence 68999999999999999999995 45
No 5
>smart00270 ChtBD1 Chitin binding domain.
Probab=98.96 E-value=2.5e-10 Score=67.02 Aligned_cols=24 Identities=63% Similarity=1.430 Sum_probs=22.5
Q ss_pred cccccccccccCChhhhcCCCCcc
Q 033376 2 WQCCSQWGYCGTSDEYCGAGSQQG 25 (120)
Q Consensus 2 ~~CCS~~G~CG~t~~yCg~gCQsg 25 (120)
++|||+|||||++.+||+.|||++
T Consensus 14 ~~CCS~~G~CG~t~~yCg~gCqs~ 37 (38)
T smart00270 14 NLCCSQFGYCGSGDEYCGKGCQSQ 37 (38)
T ss_pred CCccCCCcCccCCHHHHhccccCC
Confidence 589999999999999999999984
No 6
>cd00035 ChtBD1 Chitin binding domain, involved in recognition or binding of chitin subunits; fold analogous to hevein; occurs in plant and fungal proteins that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins, and K.lactis killer toxin alpha subunit, occurs singly or multiply
Probab=98.59 E-value=1.7e-08 Score=59.69 Aligned_cols=26 Identities=62% Similarity=1.352 Sum_probs=24.0
Q ss_pred cccccccccccCChhhhcCCCCccccC
Q 033376 2 WQCCSQWGYCGTSDEYCGAGSQQGPYD 28 (120)
Q Consensus 2 ~~CCS~~G~CG~t~~yCg~gCQsg~C~ 28 (120)
++|||++||||++.+||+.+||++ |.
T Consensus 14 ~~CCS~~G~CG~t~~~Cg~gcq~~-c~ 39 (40)
T cd00035 14 GLCCSQFGYCGTTDDYCGRGCQSG-CW 39 (40)
T ss_pred CccccccccccCCccccccccccc-cC
Confidence 579999999999999999999997 64
No 7
>cd06918 ChtBD1_like Domain observed in several metazoan proteins. The pattern of conserved cysteine residues resembles that of chitin binding domains found in plants and fungi.
Probab=96.42 E-value=0.0014 Score=40.71 Aligned_cols=21 Identities=48% Similarity=1.159 Sum_probs=18.2
Q ss_pred cccccccccccCChhhhc-CCC
Q 033376 2 WQCCSQWGYCGTSDEYCG-AGS 22 (120)
Q Consensus 2 ~~CCS~~G~CG~t~~yCg-~gC 22 (120)
..|||.+||||+|.+||. .+|
T Consensus 27 ~pCCS~~gwCG~t~~hC~C~~C 48 (51)
T cd06918 27 KPCCSNGGYCGSGSEHCDCPGC 48 (51)
T ss_pred CcccCCCceeCCCcccccCCCC
Confidence 469999999999999996 555
No 8
>COG3179 Predicted chitinase [General function prediction only]
Probab=95.57 E-value=0.0047 Score=47.91 Aligned_cols=58 Identities=28% Similarity=0.361 Sum_probs=39.6
Q ss_pred cccchhhhcccccCCCcCcCCcccchHHHHHHhc-CCCcccCCCChhhHHHHHHHHhhhhcCCCCCeEEeec
Q 033376 41 IVTPKFFNGILNQADASCVGKNFYSRSAFLDALG-SFSQFGRTGAEEDTMREIAAFFAHVTHETGHMADKHD 111 (120)
Q Consensus 41 iiTea~Fd~lf~~~~~~c~~~~fYty~~fi~Aa~-~fp~F~~~G~~~~~krElAAf~a~~shET~g~c~~~E 111 (120)
.|++..|.+|+|++ .+.| ..++.|+. ....||- +.+-.+|.||||+.||++||-=+.|
T Consensus 3 ~i~e~~~~ki~p~a-----~k~~---~~v~~al~~~l~~~gi-----~~p~r~AmFlAQ~~HESggf~rl~E 61 (206)
T COG3179 3 TITEVDLRKIFPKA-----RKEF---VDVIVALQPALDEAGI-----TTPLRQAMFLAQVMHESGGFTRLDE 61 (206)
T ss_pred chhHHHHHHhcchh-----hhhh---HHHHHHHHHHHHHhcC-----CCHHHHHHHHHHHhhhcCCceeehh
Confidence 57888999999984 2333 23444444 2335542 3477899999999999999765555
No 9
>PF15182 OTOS: Otospiralin
Probab=56.86 E-value=5.6 Score=25.93 Aligned_cols=34 Identities=26% Similarity=0.663 Sum_probs=24.8
Q ss_pred CcccchHHHHHHhcCCCcccCCCChhhHHHHHH-HHhhhhcCCCC
Q 033376 61 KNFYSRSAFLDALGSFSQFGRTGAEEDTMREIA-AFFAHVTHETG 104 (120)
Q Consensus 61 ~~fYty~~fi~Aa~~fp~F~~~G~~~~~krElA-Af~a~~shET~ 104 (120)
.+|+.|..+.+++.+|+.. .||| +||||..--++
T Consensus 25 sDFW~YveyFrtlGAY~~i----------ndmARtfFAh~plG~t 59 (69)
T PF15182_consen 25 SDFWNYVEYFRTLGAYNQI----------NDMARTFFAHFPLGDT 59 (69)
T ss_pred hHHHHHHHHHHHhccHHHH----------HHHHHHHHhhCccccc
Confidence 4688999988888888764 3555 69999865443
No 10
>PF01830 Peptidase_C7: Peptidase C7 family; InterPro: IPR002704 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 MEROPS peptidase family C7 (clan CA). These are found in fungi and viruses (Hypoviridae). They are involved in transmissible hypovirulence and may indicate the possible origins of hypovirulence-associated dsRNAs [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=48.96 E-value=27 Score=27.59 Aligned_cols=37 Identities=24% Similarity=0.226 Sum_probs=30.4
Q ss_pred chHHHHHHhcCCCcccCCCChhhHHHHHHHHhhhhcCCCC
Q 033376 65 SRSAFLDALGSFSQFGRTGAEEDTMREIAAFFAHVTHETG 104 (120)
Q Consensus 65 ty~~fi~Aa~~fp~F~~~G~~~~~krElAAf~a~~shET~ 104 (120)
..-+-++|...-|.++ +.+.+-|||-+-|-|..|.+-
T Consensus 92 eHPavlaA~~grprrC---s~eq~treLD~~Fl~lV~~~~ 128 (243)
T PF01830_consen 92 EHPAVLAAYLGRPRRC---SLEQRTRELDSQFLHLVHSGL 128 (243)
T ss_pred CCHHHHHHHcCCCccc---cHHHHHHHHHHHHHHHHHcCC
Confidence 3456677777888887 678899999999999999983
No 11
>PRK15321 putative type III secretion system effector protein OrgC; Provisional
Probab=47.68 E-value=22 Score=25.26 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=23.1
Q ss_pred cccchHHHHHHhcCCCcccCCC-ChhhHHHHHHHHh
Q 033376 62 NFYSRSAFLDALGSFSQFGRTG-AEEDTMREIAAFF 96 (120)
Q Consensus 62 ~fYty~~fi~Aa~~fp~F~~~G-~~~~~krElAAf~ 96 (120)
..=-|++|..++...|.....- -.+.--||+-||=
T Consensus 15 ~vdlydAF~Q~l~~LP~la~S~~~KD~I~q~m~~F~ 50 (120)
T PRK15321 15 DVDLYDAFYQRLLALPESASSETLKDSIYQEMNAFK 50 (120)
T ss_pred cchHHHHHHHHHHhCCcccCcHHHHHHHHHHHHHhC
Confidence 3446999999999999865322 2334556666663
No 12
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=38.23 E-value=30 Score=20.24 Aligned_cols=32 Identities=13% Similarity=0.083 Sum_probs=23.7
Q ss_pred CChhhHHHHHHHHhhhhcCCCCC------eEEeeccCC
Q 033376 83 GAEEDTMREIAAFFAHVTHETGH------MADKHDNCG 114 (120)
Q Consensus 83 G~~~~~krElAAf~a~~shET~g------~c~~~E~~~ 114 (120)
|.+..+||+|++=+.+...+.-| +..++|+.+
T Consensus 10 grt~eqk~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 10 GRTDEQKRELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 55688999999999888877654 555666543
No 13
>PF04651 Pox_A12: Poxvirus A12 protein; InterPro: IPR006744 This family contains vaccinia virus protein A12 and its homologues. VVA12 is a virion protein though its function is unknown.
Probab=34.89 E-value=30 Score=26.75 Aligned_cols=29 Identities=17% Similarity=0.490 Sum_probs=22.0
Q ss_pred cchHHHHHHhcCCCcccCCCChhhHHHHHHHHhhhhcCCCC
Q 033376 64 YSRSAFLDALGSFSQFGRTGAEEDTMREIAAFFAHVTHETG 104 (120)
Q Consensus 64 Yty~~fi~Aa~~fp~F~~~G~~~~~krElAAf~a~~shET~ 104 (120)
=+||.||+++++.-+ |.|. .|||++-|+.
T Consensus 9 SSYDDYIeTinKitP---------QLrt---lLahI~geq~ 37 (189)
T PF04651_consen 9 SSYDDYIETINKITP---------QLRT---LLAHISGEQA 37 (189)
T ss_pred ccHHHHHHHHHHhCH---------HHHH---HHHHhccccc
Confidence 479999999996532 4454 4899998885
No 14
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=34.15 E-value=14 Score=25.24 Aligned_cols=39 Identities=26% Similarity=0.276 Sum_probs=28.7
Q ss_pred cccchhhhcccccCCC---------cCcCCcccchHHHHHHhcCCCcc
Q 033376 41 IVTPKFFNGILNQADA---------SCVGKNFYSRSAFLDALGSFSQF 79 (120)
Q Consensus 41 iiTea~Fd~lf~~~~~---------~c~~~~fYty~~fi~Aa~~fp~F 79 (120)
|+|..+.+.+-..... .-|.+|..-|+.|++|++.||-.
T Consensus 35 IlT~~~~e~I~a~~T~~~k~~~LLdiLp~RG~~AF~~F~~aL~e~~~l 82 (94)
T cd08327 35 ILTESHVEEIESQTTSRRKTMKLLDILPSRGPKAFHAFLDSLEEFPWV 82 (94)
T ss_pred CCCHHHHHHHHccCChHHHHHHHHHHHHhhChhHHHHHHHHHHHHHHH
Confidence 7777777777654221 25678899999999999988753
No 15
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=32.82 E-value=33 Score=20.51 Aligned_cols=33 Identities=15% Similarity=0.064 Sum_probs=23.1
Q ss_pred CCChhhHHHHHHHHhhhhcCCCCC------eEEeeccCC
Q 033376 82 TGAEEDTMREIAAFFAHVTHETGH------MADKHDNCG 114 (120)
Q Consensus 82 ~G~~~~~krElAAf~a~~shET~g------~c~~~E~~~ 114 (120)
.|.++.+|++|++=+.++..|..| .-.++|+.+
T Consensus 9 ~g~~~e~K~~l~~~it~~~~~~lg~~~~~i~V~i~E~~~ 47 (60)
T PF01361_consen 9 EGRTAEQKRELAEAITDAVVEVLGIPPERISVVIEEVPP 47 (60)
T ss_dssp STS-HHHHHHHHHHHHHHHHHHHTS-GGGEEEEEEEE-C
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcCCCeEEEEEEEECh
Confidence 456788999999988888877654 555666643
No 16
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=30.37 E-value=65 Score=22.43 Aligned_cols=31 Identities=16% Similarity=0.397 Sum_probs=20.5
Q ss_pred hHHHHHHhc-CCCcccCCCChhhHHHHHHHHhh
Q 033376 66 RSAFLDALG-SFSQFGRTGAEEDTMREIAAFFA 97 (120)
Q Consensus 66 y~~fi~Aa~-~fp~F~~~G~~~~~krElAAf~a 97 (120)
|..+.++++ +|| |....+.|+...++++||+
T Consensus 44 ~~~~~~~i~gRYP-F~~~s~~dv~l~Df~~fF~ 75 (125)
T PF06744_consen 44 YPFCRQAIAGRYP-FDPDSSRDVSLADFARFFG 75 (125)
T ss_pred HHHHHHHhcCCCC-CCCCCcccCCHHHHHHHhc
Confidence 444556665 677 5555566777788888876
No 17
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=29.73 E-value=49 Score=19.66 Aligned_cols=32 Identities=6% Similarity=0.099 Sum_probs=24.3
Q ss_pred CCChhhHHHHHHHHhhhhcCCCCC------eEEeeccC
Q 033376 82 TGAEEDTMREIAAFFAHVTHETGH------MADKHDNC 113 (120)
Q Consensus 82 ~G~~~~~krElAAf~a~~shET~g------~c~~~E~~ 113 (120)
.|-++.+||+|++=+.+...|.-| +..++|+.
T Consensus 10 ~Grs~eqk~~l~~~it~~l~~~~~~p~~~v~V~i~e~~ 47 (61)
T PRK02220 10 EGRTEEQLKALVKDVTAAVSKNTGAPAEHIHVIINEMS 47 (61)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcChhhEEEEEEEeC
Confidence 366788999999999888877764 46667754
No 18
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=28.60 E-value=31 Score=19.91 Aligned_cols=39 Identities=15% Similarity=0.272 Sum_probs=28.4
Q ss_pred CcccchHHHHHHhcC--CCcccCCCChhhHHHHHHHHhhhh
Q 033376 61 KNFYSRSAFLDALGS--FSQFGRTGAEEDTMREIAAFFAHV 99 (120)
Q Consensus 61 ~~fYty~~fi~Aa~~--fp~F~~~G~~~~~krElAAf~a~~ 99 (120)
..-=|+..+....+. .|.||+.-=.+.+.++|..|+...
T Consensus 17 ~~~~T~~~y~~~~~~~i~p~~g~~~i~~It~~~i~~~~~~l 57 (58)
T PF14659_consen 17 LKPSTYKNYKSIIKNHILPYFGNKKIKDITPRDIQNFINEL 57 (58)
T ss_dssp SSHHHHHHHHHHHHHHHHHHTTSSBGGG--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCcCcHHHCCHHHHHHHHHHc
Confidence 344578888888876 689987766788999999998764
No 19
>PF01616 Orbi_NS3: Orbivirus NS3; InterPro: IPR002565 This is a family of Orbivirus non structural protein of unknown function, but which may play a role in release of the virus from infected cells [].
Probab=27.41 E-value=42 Score=26.11 Aligned_cols=17 Identities=47% Similarity=0.432 Sum_probs=15.0
Q ss_pred CCCChhhHHHHHHHHhh
Q 033376 81 RTGAEEDTMREIAAFFA 97 (120)
Q Consensus 81 ~~G~~~~~krElAAf~a 97 (120)
+||.++..|+|=|||=|
T Consensus 37 tTGA~~~~K~EKaAyga 53 (195)
T PF01616_consen 37 TTGATEAQKNEKAAYGA 53 (195)
T ss_pred CccCchhhhHHHHHHHH
Confidence 56999999999999865
No 20
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=27.15 E-value=47 Score=20.88 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=10.8
Q ss_pred ChhhHHHHHHHHh
Q 033376 84 AEEDTMREIAAFF 96 (120)
Q Consensus 84 ~~~~~krElAAf~ 96 (120)
+...+|+|+-+|+
T Consensus 10 ~~~~k~~E~~~fl 22 (56)
T PF06796_consen 10 DKSTKRSELKAFL 22 (56)
T ss_pred ccchhHHHHHHHH
Confidence 3567999999997
No 21
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=26.80 E-value=49 Score=21.38 Aligned_cols=31 Identities=26% Similarity=0.083 Sum_probs=24.0
Q ss_pred ChhhHHHHHHHHhhhhcCCCCC------eEEeeccCC
Q 033376 84 AEEDTMREIAAFFAHVTHETGH------MADKHDNCG 114 (120)
Q Consensus 84 ~~~~~krElAAf~a~~shET~g------~c~~~E~~~ 114 (120)
.++.+|||||+=+..+.+|+-| .-.++|+.+
T Consensus 13 ~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 13 LDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 4556799999999999998865 566677654
No 22
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=23.27 E-value=42 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=18.1
Q ss_pred CccccccccchhhhcccccCC
Q 033376 35 DVSVVDIVTPKFFNGILNQAD 55 (120)
Q Consensus 35 ~~~vssiiTea~Fd~lf~~~~ 55 (120)
...+.+|||-..|-.|||++.
T Consensus 13 ~s~L~~iisl~qF~~LFPr~~ 33 (67)
T PF09447_consen 13 PSSLPDIISLEQFRKLFPRRL 33 (67)
T ss_pred cCccccccCHHHHHHHccccC
Confidence 468899999999999999843
No 23
>PF08837 DUF1810: Protein of unknown function (DUF1810); InterPro: IPR014937 This is a family of uncharacterised proteins. The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure. ; PDB: 2JEK_A.
Probab=22.93 E-value=1.2e+02 Score=22.34 Aligned_cols=23 Identities=30% Similarity=0.559 Sum_probs=12.1
Q ss_pred CCcccCCCChhh-------HHHHHHHHhhh
Q 033376 76 FSQFGRTGAEED-------TMREIAAFFAH 98 (120)
Q Consensus 76 fp~F~~~G~~~~-------~krElAAf~a~ 98 (120)
||.+..-|..++ .+-|-.|||+|
T Consensus 38 FPQl~gLG~S~~a~~Y~I~sl~EA~AYL~H 67 (139)
T PF08837_consen 38 FPQLKGLGRSPTARRYAIASLDEARAYLAH 67 (139)
T ss_dssp S--BTTS--SHHHHHTSB-SHHHHHHHHHS
T ss_pred hhhhcccCCChHHHHhccCCHHHHHHHHcC
Confidence 787776665543 34477777776
No 24
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=20.81 E-value=74 Score=19.21 Aligned_cols=33 Identities=12% Similarity=0.076 Sum_probs=25.6
Q ss_pred CCChhhHHHHHHHHhhhhcCCCCC------eEEeeccCC
Q 033376 82 TGAEEDTMREIAAFFAHVTHETGH------MADKHDNCG 114 (120)
Q Consensus 82 ~G~~~~~krElAAf~a~~shET~g------~c~~~E~~~ 114 (120)
.|-++.+|++|++=+.+..+|+-| ...++|+.+
T Consensus 10 ~Grs~EqK~~L~~~it~a~~~~~~~p~~~v~V~i~ev~~ 48 (60)
T PRK02289 10 EGRSQEQKNALAREVTEVVSRIAKAPKEAIHVFINDMPE 48 (60)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcCcceEEEEEEEeCh
Confidence 366788999999999988888865 366777643
Done!