Query psy12567
Match_columns 142
No_of_seqs 202 out of 914
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 22:39:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12567.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12567hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.7 1.6E-17 3.5E-22 108.5 3.6 43 80-122 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.6 1.4E-16 3.1E-21 103.1 3.8 48 77-124 2-51 (52)
3 PF00320 GATA: GATA zinc finge 99.5 2.2E-15 4.8E-20 90.8 1.1 35 81-115 1-36 (36)
4 KOG1601|consensus 99.3 3.7E-12 8.1E-17 98.6 5.8 104 21-127 143-249 (340)
5 cd00202 ZnF_GATA Zinc finger D 99.0 8.6E-11 1.9E-15 76.7 0.5 34 22-55 1-35 (54)
6 smart00401 ZnF_GATA zinc finge 99.0 1.7E-10 3.8E-15 74.6 1.8 38 19-56 2-40 (52)
7 PF00320 GATA: GATA zinc finge 99.0 4.8E-11 1E-15 71.8 -1.2 33 23-55 1-34 (36)
8 COG5641 GAT1 GATA Zn-finger-co 99.0 9.4E-10 2E-14 98.6 5.8 61 77-137 296-360 (498)
9 COG5641 GAT1 GATA Zn-finger-co 98.9 4.5E-10 9.7E-15 100.7 2.0 50 78-127 158-213 (498)
10 KOG1601|consensus 97.7 1.8E-05 3.9E-10 61.2 2.3 36 20-55 199-235 (340)
11 TIGR01384 TFS_arch transcripti 91.1 0.21 4.7E-06 35.4 2.8 83 22-110 2-101 (104)
12 KOG3554|consensus 88.5 0.26 5.7E-06 45.2 1.8 37 77-113 385-424 (693)
13 PF12773 DZR: Double zinc ribb 86.4 0.84 1.8E-05 28.1 2.8 13 78-90 29-41 (50)
14 PF08271 TF_Zn_Ribbon: TFIIB z 85.5 0.4 8.6E-06 29.2 0.9 26 22-49 2-27 (43)
15 COG5347 GTPase-activating prot 81.7 0.79 1.7E-05 39.6 1.5 29 18-47 18-46 (319)
16 PRK12286 rpmF 50S ribosomal pr 80.8 0.99 2.1E-05 29.7 1.4 25 19-51 26-50 (57)
17 PF01412 ArfGap: Putative GTPa 80.6 1 2.2E-05 32.8 1.6 39 75-114 10-48 (116)
18 smart00105 ArfGap Putative GTP 79.1 1.8 3.8E-05 31.4 2.4 38 77-115 2-39 (112)
19 PF01783 Ribosomal_L32p: Ribos 78.1 1.2 2.6E-05 28.9 1.2 25 19-51 25-49 (56)
20 PRK14892 putative transcriptio 75.9 1.6 3.5E-05 31.7 1.4 37 75-111 18-54 (99)
21 COG3529 Predicted nucleic-acid 75.3 0.73 1.6E-05 31.2 -0.5 34 76-109 8-42 (66)
22 smart00105 ArfGap Putative GTP 74.5 1.6 3.5E-05 31.6 1.1 28 20-48 3-30 (112)
23 KOG0703|consensus 73.2 1.8 3.9E-05 37.1 1.2 29 18-47 23-51 (287)
24 PF01412 ArfGap: Putative GTPa 72.9 1.8 3.9E-05 31.5 1.1 30 18-48 11-40 (116)
25 COG5347 GTPase-activating prot 72.2 2.3 5.1E-05 36.7 1.7 40 73-113 15-54 (319)
26 PF06677 Auto_anti-p27: Sjogre 70.5 2.8 6.1E-05 25.9 1.4 25 20-48 17-41 (41)
27 COG1594 RPB9 DNA-directed RNA 69.6 3.5 7.6E-05 30.4 2.0 88 21-110 3-111 (113)
28 TIGR01031 rpmF_bact ribosomal 69.4 2.7 5.8E-05 27.4 1.1 24 20-51 26-49 (55)
29 PRK03564 formate dehydrogenase 68.7 6.1 0.00013 34.1 3.5 72 18-112 185-265 (309)
30 PRK00423 tfb transcription ini 68.4 3.5 7.7E-05 34.8 2.0 32 16-49 7-38 (310)
31 PF11781 RRN7: RNA polymerase 68.3 2.2 4.8E-05 25.5 0.6 25 79-107 9-33 (36)
32 PLN03114 ADP-ribosylation fact 67.3 3.8 8.3E-05 36.4 2.0 42 73-115 17-58 (395)
33 smart00778 Prim_Zn_Ribbon Zinc 66.3 4.9 0.00011 24.3 1.8 29 21-49 4-33 (37)
34 PF09526 DUF2387: Probable met 66.0 3 6.4E-05 28.6 0.9 35 20-54 8-43 (71)
35 KOG3740|consensus 65.6 2.5 5.4E-05 39.9 0.6 32 76-107 460-495 (706)
36 PLN03114 ADP-ribosylation fact 65.6 3.6 7.9E-05 36.6 1.6 30 18-48 20-49 (395)
37 PF12760 Zn_Tnp_IS1595: Transp 65.3 4.6 9.9E-05 24.8 1.6 29 18-48 16-44 (46)
38 TIGR02443 conserved hypothetic 65.0 3.3 7.1E-05 27.7 0.9 34 20-53 9-43 (59)
39 TIGR02443 conserved hypothetic 64.9 2.5 5.5E-05 28.2 0.4 34 76-109 7-41 (59)
40 PF09526 DUF2387: Probable met 64.2 2.6 5.7E-05 28.9 0.4 35 76-110 6-41 (71)
41 PRK03988 translation initiatio 63.8 2.6 5.6E-05 32.3 0.3 30 78-107 102-131 (138)
42 PF07282 OrfB_Zn_ribbon: Putat 63.6 4.5 9.7E-05 26.3 1.4 37 11-50 19-55 (69)
43 PRK14559 putative protein seri 63.6 8.3 0.00018 36.3 3.6 18 76-93 39-56 (645)
44 TIGR01562 FdhE formate dehydro 63.3 8.8 0.00019 33.0 3.5 72 18-112 182-265 (305)
45 smart00653 eIF2B_5 domain pres 62.1 2.9 6.3E-05 30.8 0.3 30 78-107 80-109 (110)
46 TIGR00311 aIF-2beta translatio 62.1 2.9 6.4E-05 31.8 0.3 30 78-107 97-126 (133)
47 PRK14892 putative transcriptio 61.3 6.9 0.00015 28.4 2.1 39 14-52 15-53 (99)
48 PRK03988 translation initiatio 59.8 4.1 8.9E-05 31.2 0.8 33 19-51 101-133 (138)
49 TIGR00311 aIF-2beta translatio 57.7 4.8 0.0001 30.6 0.8 33 19-51 96-128 (133)
50 KOG0706|consensus 56.9 5.6 0.00012 36.1 1.2 44 72-116 17-60 (454)
51 COG3529 Predicted nucleic-acid 56.8 2.7 5.8E-05 28.5 -0.6 31 20-50 10-41 (66)
52 KOG1598|consensus 55.7 7.5 0.00016 35.9 1.8 27 21-49 1-27 (521)
53 PRK08351 DNA-directed RNA poly 55.4 8.1 0.00018 25.9 1.5 15 20-34 15-30 (61)
54 smart00653 eIF2B_5 domain pres 55.1 4.9 0.00011 29.6 0.5 30 20-49 80-109 (110)
55 PRK00423 tfb transcription ini 54.5 7.1 0.00015 33.0 1.5 20 76-95 28-54 (310)
56 PRK06393 rpoE DNA-directed RNA 53.5 9.2 0.0002 25.9 1.6 15 20-34 17-32 (64)
57 PRK01110 rpmF 50S ribosomal pr 52.2 7.4 0.00016 25.7 0.9 23 20-51 27-49 (60)
58 PRK12336 translation initiatio 52.2 5.1 0.00011 32.1 0.2 30 78-107 98-127 (201)
59 KOG0706|consensus 52.1 7.7 0.00017 35.2 1.3 29 18-47 21-49 (454)
60 PRK14714 DNA polymerase II lar 51.3 14 0.00031 37.6 3.1 22 20-50 667-688 (1337)
61 PLN03119 putative ADP-ribosyla 50.6 9.9 0.00022 35.8 1.8 29 18-47 21-49 (648)
62 PF01873 eIF-5_eIF-2B: Domain 50.6 6.2 0.00013 29.6 0.4 29 79-107 94-122 (125)
63 PRK12336 translation initiatio 50.2 7 0.00015 31.4 0.7 34 19-52 97-130 (201)
64 PLN03131 hypothetical protein; 47.9 11 0.00025 35.7 1.7 29 18-47 21-49 (705)
65 PF13248 zf-ribbon_3: zinc-rib 47.6 12 0.00026 20.4 1.2 22 79-107 3-24 (26)
66 smart00661 RPOL9 RNA polymeras 47.5 13 0.00029 22.6 1.5 28 22-51 2-30 (52)
67 PRK00420 hypothetical protein; 47.0 14 0.0003 27.5 1.8 27 20-50 23-49 (112)
68 PLN03119 putative ADP-ribosyla 46.9 11 0.00023 35.5 1.4 35 73-108 18-52 (648)
69 PF04216 FdhE: Protein involve 46.8 3.1 6.7E-05 34.6 -1.9 71 19-112 171-251 (290)
70 KOG1598|consensus 46.4 11 0.00024 34.8 1.4 27 79-107 1-27 (521)
71 KOG2907|consensus 46.4 13 0.00028 28.0 1.5 87 19-108 6-111 (116)
72 PF14803 Nudix_N_2: Nudix N-te 45.9 6.2 0.00013 23.3 -0.2 25 80-107 2-30 (34)
73 COG1499 NMD3 NMD protein affec 42.7 13 0.00029 32.6 1.3 67 18-105 4-71 (355)
74 PF01873 eIF-5_eIF-2B: Domain 42.1 11 0.00023 28.3 0.6 29 21-49 94-122 (125)
75 smart00659 RPOLCX RNA polymera 41.7 12 0.00026 23.2 0.7 25 79-107 3-27 (44)
76 PRK00222 methionine sulfoxide 41.4 29 0.00064 26.8 2.9 65 31-96 33-110 (142)
77 PLN03131 hypothetical protein; 41.0 16 0.00036 34.7 1.7 34 74-108 19-52 (705)
78 PF08273 Prim_Zn_Ribbon: Zinc- 40.5 12 0.00026 22.9 0.5 26 22-47 5-32 (40)
79 PHA02942 putative transposase; 40.5 18 0.00039 31.7 1.8 34 14-51 319-352 (383)
80 COG0333 RpmF Ribosomal protein 40.3 18 0.00038 24.0 1.3 24 20-51 27-50 (57)
81 PHA00626 hypothetical protein 40.2 18 0.00039 24.2 1.3 31 22-52 2-34 (59)
82 PF01286 XPA_N: XPA protein N- 40.1 15 0.00033 21.8 0.9 29 19-47 2-30 (34)
83 PF09723 Zn-ribbon_8: Zinc rib 39.8 11 0.00024 22.8 0.2 9 78-86 26-34 (42)
84 KOG0703|consensus 39.5 13 0.00029 31.8 0.8 38 75-113 22-59 (287)
85 TIGR00357 methionine-R-sulfoxi 39.4 17 0.00038 27.8 1.3 66 30-96 29-107 (134)
86 PRK00432 30S ribosomal protein 38.4 21 0.00046 22.6 1.4 27 19-49 19-45 (50)
87 PF06689 zf-C4_ClpX: ClpX C4-t 38.2 11 0.00025 22.8 0.1 28 79-107 2-32 (41)
88 COG1405 SUA7 Transcription ini 37.9 16 0.00035 31.0 1.0 26 80-107 3-28 (285)
89 TIGR00595 priA primosomal prot 34.7 32 0.0007 31.1 2.5 23 77-107 239-261 (505)
90 PF04161 Arv1: Arv1-like famil 34.5 20 0.00044 28.6 1.1 28 80-107 2-32 (208)
91 PF04810 zf-Sec23_Sec24: Sec23 33.6 26 0.00056 20.9 1.2 32 20-51 2-34 (40)
92 COG0675 Transposase and inacti 33.1 24 0.00051 28.3 1.3 28 15-50 304-331 (364)
93 cd07169 NR_DBD_GCNF_like DNA-b 32.9 34 0.00075 24.0 1.9 33 77-113 5-37 (90)
94 PF04981 NMD3: NMD3 family ; 32.8 35 0.00076 27.6 2.2 52 23-95 1-53 (236)
95 PF03604 DNA_RNApol_7kD: DNA d 31.9 40 0.00087 19.6 1.8 24 22-49 2-25 (32)
96 PF02148 zf-UBP: Zn-finger in 31.1 18 0.0004 23.3 0.3 20 23-50 1-20 (63)
97 KOG1597|consensus 31.0 28 0.0006 30.2 1.4 30 80-109 2-31 (308)
98 smart00834 CxxC_CXXC_SSSS Puta 30.7 20 0.00043 20.7 0.3 8 100-107 27-34 (41)
99 PF02701 zf-Dof: Dof domain, z 30.5 94 0.002 21.0 3.6 44 76-119 3-50 (63)
100 smart00290 ZnF_UBP Ubiquitin C 30.0 30 0.00064 20.9 1.1 20 22-50 1-20 (50)
101 PF09538 FYDLN_acid: Protein o 29.9 30 0.00064 25.4 1.2 32 76-111 7-38 (108)
102 TIGR02605 CxxC_CxxC_SSSS putat 29.4 23 0.0005 21.7 0.5 8 100-107 27-34 (52)
103 cd06968 NR_DBD_ROR DNA-binding 29.1 42 0.00092 23.8 1.9 33 77-113 4-36 (95)
104 PRK00085 recO DNA repair prote 28.9 33 0.00071 27.3 1.4 31 18-48 147-177 (247)
105 PRK05580 primosome assembly pr 28.8 45 0.00098 31.3 2.5 23 77-107 407-429 (679)
106 smart00440 ZnF_C2C2 C2C2 Zinc 28.2 18 0.00038 21.8 -0.2 30 80-109 2-38 (40)
107 PRK14873 primosome assembly pr 27.5 44 0.00096 31.5 2.2 22 77-107 409-430 (665)
108 COG5082 AIR1 Arginine methyltr 27.3 78 0.0017 25.7 3.3 33 12-47 52-84 (190)
109 KOG0704|consensus 26.9 33 0.00071 30.6 1.2 28 19-47 18-45 (386)
110 cd07173 NR_DBD_AR DNA-binding 26.9 47 0.001 23.0 1.7 31 79-113 4-34 (82)
111 PF09297 zf-NADH-PPase: NADH p 26.1 15 0.00032 20.8 -0.8 26 78-107 3-29 (32)
112 PF01096 TFIIS_C: Transcriptio 25.9 13 0.00029 22.2 -1.0 30 80-109 2-38 (39)
113 TIGR00613 reco DNA repair prot 25.9 49 0.0011 26.1 1.9 32 18-49 145-176 (241)
114 KOG3740|consensus 25.8 27 0.00059 33.3 0.5 33 18-50 460-496 (706)
115 cd07166 NR_DBD_REV_ERB DNA-bin 25.7 30 0.00065 24.2 0.6 31 78-112 3-33 (89)
116 cd07168 NR_DBD_DHR4_like DNA-b 25.5 53 0.0011 23.0 1.8 32 78-113 6-37 (90)
117 cd07172 NR_DBD_GR_PR DNA-bindi 25.0 51 0.0011 22.5 1.7 31 79-113 3-33 (78)
118 cd07171 NR_DBD_ER DNA-binding 24.8 55 0.0012 22.6 1.8 31 79-113 4-34 (82)
119 KOG0909|consensus 24.2 54 0.0012 30.1 2.0 38 19-56 160-209 (500)
120 cd07160 NR_DBD_LXR DNA-binding 24.0 49 0.0011 23.9 1.4 32 78-113 18-49 (101)
121 PF07295 DUF1451: Protein of u 23.5 50 0.0011 25.4 1.5 12 39-50 110-121 (146)
122 PF10005 DUF2248: Uncharacteri 23.4 1.1E+02 0.0025 26.9 3.9 31 76-107 51-82 (343)
123 PRK00398 rpoP DNA-directed RNA 23.4 33 0.00072 20.8 0.4 26 79-107 4-29 (46)
124 PRK05508 methionine sulfoxide 23.3 53 0.0012 24.7 1.6 19 31-49 23-41 (119)
125 PF13240 zinc_ribbon_2: zinc-r 23.0 50 0.0011 17.6 1.0 6 23-28 2-7 (23)
126 KOG0818|consensus 23.0 38 0.00082 31.8 0.8 28 19-47 7-34 (669)
127 COG2816 NPY1 NTP pyrophosphohy 22.7 39 0.00084 28.9 0.8 31 76-110 109-140 (279)
128 PF07754 DUF1610: Domain of un 22.5 69 0.0015 17.6 1.5 23 23-48 1-23 (24)
129 cd06965 NR_DBD_Ppar DNA-bindin 22.1 36 0.00079 23.5 0.5 29 81-113 2-30 (84)
130 PRK00085 recO DNA repair prote 22.1 50 0.0011 26.2 1.3 31 76-106 147-177 (247)
131 TIGR01385 TFSII transcription 21.6 40 0.00088 28.8 0.7 36 75-110 255-297 (299)
132 smart00531 TFIIE Transcription 21.3 39 0.00085 25.4 0.5 31 18-48 97-130 (147)
133 PF15396 FAM60A: Protein Famil 20.7 50 0.0011 27.3 1.0 11 101-111 51-61 (213)
134 cd07158 NR_DBD_Ppar_like The D 20.6 60 0.0013 21.6 1.3 28 81-112 1-28 (73)
135 COG3952 Predicted membrane pro 20.6 24 0.00051 26.4 -0.8 20 91-111 76-95 (113)
136 cd07165 NR_DBD_DmE78_like DNA- 20.6 59 0.0013 22.2 1.2 29 81-113 1-29 (81)
137 PF02591 DUF164: Putative zinc 20.3 36 0.00079 21.4 0.1 31 76-107 20-54 (56)
138 cd07155 NR_DBD_ER_like DNA-bin 20.1 61 0.0013 21.8 1.2 28 81-112 1-28 (75)
139 PRK14714 DNA polymerase II lar 20.0 94 0.002 32.0 2.9 49 20-96 679-728 (1337)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.69 E-value=1.6e-17 Score=108.48 Aligned_cols=43 Identities=58% Similarity=1.202 Sum_probs=40.7
Q ss_pred cccccCCCCCCccccCCCC-CcccchhhhhHHhcCCCCCCCCCC
Q psy12567 80 ECVNCGAISTPLWRRDGTG-HYLCNACGLYHKMNGMNRPLVKQP 122 (142)
Q Consensus 80 ~C~nC~tt~Tp~WRr~~~G-~~lCNaCGly~k~~~~~RP~~~~k 122 (142)
+|+||++++||+||++++| ..|||||||||++++..||+.+++
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 5999999999999999965 799999999999999999999988
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.64 E-value=1.4e-16 Score=103.09 Aligned_cols=48 Identities=54% Similarity=1.056 Sum_probs=43.8
Q ss_pred CCccccccCCCCCCccccCCCCC-cccchhhhhHHhcCCC-CCCCCCCCC
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGH-YLCNACGLYHKMNGMN-RPLVKQPRR 124 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~-~lCNaCGly~k~~~~~-RP~~~~k~~ 124 (142)
....|+||++++||+||+++.|. .|||||||||++++.. ||+.+.+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~~ 51 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKDV 51 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCcccccccC
Confidence 36789999999999999999996 9999999999999998 999887754
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. 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, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.52 E-value=2.2e-15 Score=90.83 Aligned_cols=35 Identities=57% Similarity=1.165 Sum_probs=28.2
Q ss_pred ccccCCCCCCccccCCCCCc-ccchhhhhHHhcCCC
Q psy12567 81 CVNCGAISTPLWRRDGTGHY-LCNACGLYHKMNGMN 115 (142)
Q Consensus 81 C~nC~tt~Tp~WRr~~~G~~-lCNaCGly~k~~~~~ 115 (142)
|+||+|++||+||++++|.. |||||||||++++++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 89999999999999999975 999999999998863
No 4
>KOG1601|consensus
Probab=99.30 E-value=3.7e-12 Score=98.57 Aligned_cols=104 Identities=36% Similarity=0.544 Sum_probs=74.2
Q ss_pred cccccCCCCCCCCcccCCCCcccccccccccccccccccccc--cccCCCccccccCCCCccccccCCCCCCccccCCCC
Q psy12567 21 RECVNCGAISTPLWRRDGTGHYLCNARLFSTSFTGYFIMSRF--LFASLPVEDIEYFTEGRECVNCGAISTPLWRRDGTG 98 (142)
Q Consensus 21 ~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k~~G~~~~~R~--~~~~~~~~~~~~~~~~~~C~nC~tt~Tp~WRr~~~G 98 (142)
.+|.+++...||.|+.+..+++.+..+..+....+ ..+. .........+........|.+|+++.||+||+++.|
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~t~~~r~~~~g 219 (340)
T KOG1601|consen 143 GESVSSLLFPTPLQRRDSSGHYNSINKELKKKSNG---ESSSDLESKPKKSSSASSEQNLRQCSNCGTTKTPLWRRGPEG 219 (340)
T ss_pred cccccccccccceeccCCCCccccccccccccccc---cccCCccccchhhhhccccccCcccCCCCCCCCcceecCCCC
Confidence 38999999999999999888888888862222222 1111 111111111122122589999999999999999999
Q ss_pred -CcccchhhhhHHhcCCCCCCCCCCCCccc
Q psy12567 99 -HYLCNACGLYHKMNGMNRPLVKQPRRLRF 127 (142)
Q Consensus 99 -~~lCNaCGly~k~~~~~RP~~~~k~~~~~ 127 (142)
+.+|||||+|++++++.|++.+.+..+..
T Consensus 220 ~~~~cnacgl~~k~~~~~r~~~~~~~~~~~ 249 (340)
T KOG1601|consen 220 PKSLCNACGLRYKKGGVRRPLPEKRPASSP 249 (340)
T ss_pred CccccccchhhhhhcCccccccccCccccc
Confidence 89999999999999988888776655443
No 5
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=98.99 E-value=8.6e-11 Score=76.70 Aligned_cols=34 Identities=47% Similarity=0.891 Sum_probs=30.2
Q ss_pred ccccCCCCCCCCcccCCC-Cccccccccccccccc
Q psy12567 22 ECVNCGAISTPLWRRDGT-GHYLCNARLFSTSFTG 55 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~-g~~lCnacg~~~k~~G 55 (142)
+|+||+++.||+||+++. +..||||||+|.+..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 599999999999999995 5899999999876665
No 6
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=98.99 E-value=1.7e-10 Score=74.59 Aligned_cols=38 Identities=47% Similarity=0.879 Sum_probs=33.2
Q ss_pred CCcccccCCCCCCCCcccCCCCc-ccccccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGH-YLCNARLFSTSFTGY 56 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~-~lCnacg~~~k~~G~ 56 (142)
..+.|+||+++.||+||+++.|. .||||||++.+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 46799999999999999999996 999999988765553
No 7
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. 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, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=98.97 E-value=4.8e-11 Score=71.85 Aligned_cols=33 Identities=45% Similarity=0.853 Sum_probs=25.1
Q ss_pred cccCCCCCCCCcccCCCCcc-ccccccccccccc
Q psy12567 23 CVNCGAISTPLWRRDGTGHY-LCNARLFSTSFTG 55 (142)
Q Consensus 23 C~nCgt~~TplWr~~~~g~~-lCnacg~~~k~~G 55 (142)
|++|+++.||+||+++.|.. ||||||++.+..+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 89999999999999999976 9999998765443
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.95 E-value=9.4e-10 Score=98.64 Aligned_cols=61 Identities=30% Similarity=0.532 Sum_probs=43.7
Q ss_pred CCccccccCC-CCCCccccCCC-CCcccchhhhhHHhcCCCCCCCCCCCCccc-cc-CCCCCCcc
Q psy12567 77 EGRECVNCGA-ISTPLWRRDGT-GHYLCNACGLYHKMNGMNRPLVKQPRRLRF-DR-GNFNCYER 137 (142)
Q Consensus 77 ~~~~C~nC~t-t~Tp~WRr~~~-G~~lCNaCGly~k~~~~~RP~~~~k~~~~~-~R-~~~n~~~~ 137 (142)
....+.+|.+ +.||+||+... +-++||||+++-+.++..||+..+-+.... .+ -.|||++-
T Consensus 296 s~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~~~~~~~~N~s~~ 360 (498)
T COG5641 296 SDKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSKRSNATCMNCSST 360 (498)
T ss_pred hhcCcccccccccCcccccccccccccccccccccCCcccccccCCCCChhhhhhhheecccccc
Confidence 3567888887 77888888765 579999999999999999999764332111 00 34777654
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.91 E-value=4.5e-10 Score=100.69 Aligned_cols=50 Identities=46% Similarity=0.979 Sum_probs=44.9
Q ss_pred CccccccCCCCCCccccCCC-----CCcccchhhhhHHhcCCCC-CCCCCCCCccc
Q psy12567 78 GRECVNCGAISTPLWRRDGT-----GHYLCNACGLYHKMNGMNR-PLVKQPRRLRF 127 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~-----G~~lCNaCGly~k~~~~~R-P~~~~k~~~~~ 127 (142)
..+|.||.|+.||+|||+.. |.+||||||||+++||++| |+.++..-+.+
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks 213 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKS 213 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCcccccccccc
Confidence 34999999999999999999 8999999999999999999 99887665543
No 10
>KOG1601|consensus
Probab=97.73 E-value=1.8e-05 Score=61.19 Aligned_cols=36 Identities=47% Similarity=0.863 Sum_probs=33.0
Q ss_pred CcccccCCCCCCCCcccCCCC-ccccccccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTG-HYLCNARLFSTSFTG 55 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g-~~lCnacg~~~k~~G 55 (142)
...|.+|++..||+||+++.| +.+|||||++.+..+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 589999999999999999999 999999999877664
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=91.12 E-value=0.21 Score=35.39 Aligned_cols=83 Identities=28% Similarity=0.637 Sum_probs=47.3
Q ss_pred ccccCCCCCCCCcccCCCCcccccccccccccc---cccccccccccCC--C--c--ccc-ccCCCCccccccCCCCCCc
Q psy12567 22 ECVNCGAISTPLWRRDGTGHYLCNARLFSTSFT---GYFIMSRFLFASL--P--V--EDI-EYFTEGRECVNCGAISTPL 91 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~g~~lCnacg~~~k~~---G~~~~~R~~~~~~--~--~--~~~-~~~~~~~~C~nC~tt~Tp~ 91 (142)
-|.+||+.-.|. .+.+.|..|++..... .+....+ +..+. . . ... ........|.+||...--.
T Consensus 2 fC~~Cg~~l~~~-----~~~~~C~~C~~~~~~~~~~~~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f 75 (104)
T TIGR01384 2 FCPKCGSLMTPK-----NGVYVCPSCGYEKEKKPEDDYKVTEK-VKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYY 75 (104)
T ss_pred CCcccCcccccC-----CCeEECcCCCCccccccccccEEEEE-eccccccceeeccccccCCCcccCCCCCCCCCeeEE
Confidence 589999987652 3578999999754321 1111111 11100 0 0 000 1123468999999776433
Q ss_pred c----ccCCCCC---cccchhhhhHH
Q psy12567 92 W----RRDGTGH---YLCNACGLYHK 110 (142)
Q Consensus 92 W----Rr~~~G~---~lCNaCGly~k 110 (142)
| |..++|. ++|-.||..|+
T Consensus 76 ~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 76 WLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred EEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 3 4455563 79999998775
No 12
>KOG3554|consensus
Probab=88.53 E-value=0.26 Score=45.16 Aligned_cols=37 Identities=30% Similarity=0.695 Sum_probs=31.2
Q ss_pred CCccccccCCCCCCccc-cCCCC--CcccchhhhhHHhcC
Q psy12567 77 EGRECVNCGAISTPLWR-RDGTG--HYLCNACGLYHKMNG 113 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WR-r~~~G--~~lCNaCGly~k~~~ 113 (142)
.++.|.+|+|++.-.|= .||.| ..||-.|-+|||+.|
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 37899999999999873 47776 479999999999975
No 13
>PF12773 DZR: Double zinc ribbon
Probab=86.44 E-value=0.84 Score=28.12 Aligned_cols=13 Identities=46% Similarity=0.994 Sum_probs=7.3
Q ss_pred CccccccCCCCCC
Q psy12567 78 GRECVNCGAISTP 90 (142)
Q Consensus 78 ~~~C~nC~tt~Tp 90 (142)
...|.+|++...+
T Consensus 29 ~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 29 KKICPNCGAENPP 41 (50)
T ss_pred CCCCcCCcCCCcC
Confidence 4566666665433
No 14
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=85.45 E-value=0.4 Score=29.20 Aligned_cols=26 Identities=23% Similarity=0.533 Sum_probs=19.1
Q ss_pred ccccCCCCCCCCcccCCCCccccccccc
Q psy12567 22 ECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
.|.+||+.. +--...+|.++|..||+
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCCC
Confidence 599999966 33345678999999974
No 15
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=81.74 E-value=0.79 Score=39.60 Aligned_cols=29 Identities=31% Similarity=0.855 Sum_probs=26.7
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
.+-..|.+||+.. |.|-.-.=|-+||..|
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlGvfiCi~C 46 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLGVFLCIDC 46 (319)
T ss_pred cccCccccCCCCC-CceEecccCeEEEeec
Confidence 5567999999999 9998888899999999
No 16
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=80.80 E-value=0.99 Score=29.67 Aligned_cols=25 Identities=32% Similarity=0.616 Sum_probs=20.4
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
.--+|.+||...-| |.+|..||+|.
T Consensus 26 ~l~~C~~CG~~~~~--------H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEPKLP--------HRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCccCC--------eEECCCCCcCC
Confidence 34579999987776 77999999885
No 17
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=80.62 E-value=1 Score=32.84 Aligned_cols=39 Identities=31% Similarity=0.730 Sum_probs=28.0
Q ss_pred CCCCccccccCCCCCCccccCCCCCcccchhhhhHHhcCC
Q psy12567 75 FTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGM 114 (142)
Q Consensus 75 ~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~~ 114 (142)
......|++|+... |.|-.-.-|-.||-.|.-..+..|+
T Consensus 10 ~~~N~~CaDCg~~~-p~w~s~~~GiflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 10 KPGNKVCADCGAPN-PTWASLNYGIFLCLECAGIHRSLGV 48 (116)
T ss_dssp STTCTB-TTT-SBS---EEETTTTEEE-HHHHHHHHHHTT
T ss_pred CcCcCcCCCCCCCC-CCEEEeecChhhhHHHHHHHHHhcc
Confidence 46789999999665 5999999999999999887776664
No 18
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=79.12 E-value=1.8 Score=31.44 Aligned_cols=38 Identities=32% Similarity=0.829 Sum_probs=31.9
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhhhHHhcCCC
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMN 115 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~~~ 115 (142)
....|++|+.. -|.|-.-.-|-.||-.|.-..+..|++
T Consensus 2 ~N~~CaDC~~~-~p~w~s~~~GifvC~~CsgiHR~lg~h 39 (112)
T smart00105 2 GNKKCFDCGAP-NPTWASVNLGVFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCCcccCCCCC-CCCcEEeccceeEhHHhHHHHHhcCCC
Confidence 46789999984 599999999999999998887777653
No 19
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=78.13 E-value=1.2 Score=28.87 Aligned_cols=25 Identities=28% Similarity=0.607 Sum_probs=19.3
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
..-.|.+||...-| |.+|.+||+|.
T Consensus 25 ~l~~c~~cg~~~~~--------H~vc~~cG~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP--------HRVCPSCGYYK 49 (56)
T ss_dssp SEEESSSSSSEEST--------TSBCTTTBBSS
T ss_pred ceeeeccCCCEecc--------cEeeCCCCeEC
Confidence 44689999975544 67999999875
No 20
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=75.86 E-value=1.6 Score=31.75 Aligned_cols=37 Identities=27% Similarity=0.642 Sum_probs=23.7
Q ss_pred CCCCccccccCCCCCCccccCCCCCcccchhhhhHHh
Q psy12567 75 FTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKM 111 (142)
Q Consensus 75 ~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~ 111 (142)
....-.|.+|+...-++=....-++.+|-.||+|+-.
T Consensus 18 lpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 3456889999953322211123457899999998554
No 21
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=75.31 E-value=0.73 Score=31.23 Aligned_cols=34 Identities=29% Similarity=0.628 Sum_probs=28.3
Q ss_pred CCCccccccCCCCCC-ccccCCCCCcccchhhhhH
Q psy12567 76 TEGRECVNCGAISTP-LWRRDGTGHYLCNACGLYH 109 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp-~WRr~~~G~~lCNaCGly~ 109 (142)
..+..|..|.+.+|- +||.+.-...-|-+||.-.
T Consensus 8 IAGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 8 IAGAVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred hccCCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 457899999999998 7887777788999999843
No 22
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=74.48 E-value=1.6 Score=31.64 Aligned_cols=28 Identities=32% Similarity=0.875 Sum_probs=24.2
Q ss_pred CcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
-..|.+||+ .-|.|-.-.-|-+||..|-
T Consensus 3 N~~CaDC~~-~~p~w~s~~~GifvC~~Cs 30 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLGVFLCIECS 30 (112)
T ss_pred CCcccCCCC-CCCCcEEeccceeEhHHhH
Confidence 468999998 4599988888999999994
No 23
>KOG0703|consensus
Probab=73.20 E-value=1.8 Score=37.08 Aligned_cols=29 Identities=28% Similarity=0.759 Sum_probs=26.4
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
.+.+.|.+||+. .|-|-...-|-++|.-|
T Consensus 23 ~~N~~CADC~a~-~P~WaSwnlGvFiC~~C 51 (287)
T KOG0703|consen 23 PDNKVCADCGAK-GPRWASWNLGVFICLRC 51 (287)
T ss_pred cccCcccccCCC-CCCeEEeecCeEEEeec
Confidence 447899999998 99999989999999998
No 24
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=72.94 E-value=1.8 Score=31.51 Aligned_cols=30 Identities=30% Similarity=0.732 Sum_probs=20.6
Q ss_pred CCCcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
.+-+.|.+||+.. |.|..-.-|-+||..|.
T Consensus 11 ~~N~~CaDCg~~~-p~w~s~~~GiflC~~Ca 40 (116)
T PF01412_consen 11 PGNKVCADCGAPN-PTWASLNYGIFLCLECA 40 (116)
T ss_dssp TTCTB-TTT-SBS---EEETTTTEEE-HHHH
T ss_pred cCcCcCCCCCCCC-CCEEEeecChhhhHHHH
Confidence 4557999999655 48988888999999994
No 25
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=72.19 E-value=2.3 Score=36.74 Aligned_cols=40 Identities=30% Similarity=0.740 Sum_probs=32.7
Q ss_pred ccCCCCccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 73 EYFTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 73 ~~~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
........|+.|++.. |.|-.=.-|-.||-.|.=..|.-|
T Consensus 15 ~~~~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRsLG 54 (319)
T COG5347 15 KSDSSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRSLG 54 (319)
T ss_pred hhccccCccccCCCCC-CceEecccCeEEEeecchhhhccc
Confidence 3456789999999999 999999999999999965444433
No 26
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=70.49 E-value=2.8 Score=25.86 Aligned_cols=25 Identities=36% Similarity=0.752 Sum_probs=19.7
Q ss_pred CcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
+..|.+| .+|+.+ +-+|...|.+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCCCEECCCCC
Confidence 4578888 489997 667888999884
No 27
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=69.55 E-value=3.5 Score=30.37 Aligned_cols=88 Identities=18% Similarity=0.443 Sum_probs=49.0
Q ss_pred cccccCCCCCCCCcccCC-CCcccccccccccccccccccccccccCCCc------------cccccCCC-CccccccCC
Q psy12567 21 RECVNCGAISTPLWRRDG-TGHYLCNARLFSTSFTGYFIMSRFLFASLPV------------EDIEYFTE-GRECVNCGA 86 (142)
Q Consensus 21 ~~C~nCgt~~TplWr~~~-~g~~lCnacg~~~k~~G~~~~~R~~~~~~~~------------~~~~~~~~-~~~C~nC~t 86 (142)
.-|.+||+.--| +.+. .+.+.|-.||+........+.........+. ........ ...|..||.
T Consensus 3 ~FCp~Cgsll~p--~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~ 80 (113)
T COG1594 3 RFCPKCGSLLYP--KKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGN 80 (113)
T ss_pred cccCCccCeeEE--eEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCCC
Confidence 468999998877 4443 3478899999865443211001100110010 00001111 356999998
Q ss_pred CCCC----ccccCCCCC---cccchhhhhHH
Q psy12567 87 ISTP----LWRRDGTGH---YLCNACGLYHK 110 (142)
Q Consensus 87 t~Tp----~WRr~~~G~---~lCNaCGly~k 110 (142)
.+=- +=|.++++. +.|-.||-.|+
T Consensus 81 ~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 81 KEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 7633 336666663 68999998776
No 28
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=69.37 E-value=2.7 Score=27.36 Aligned_cols=24 Identities=29% Similarity=0.627 Sum_probs=18.8
Q ss_pred CcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
--+|.+||...-| |.+|..||+|.
T Consensus 26 l~~C~~cG~~~~~--------H~vc~~cG~Y~ 49 (55)
T TIGR01031 26 LVVCPNCGEFKLP--------HRVCPSCGYYK 49 (55)
T ss_pred ceECCCCCCcccC--------eeECCccCeEC
Confidence 3479999986555 67999999885
No 29
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.69 E-value=6.1 Score=34.09 Aligned_cols=72 Identities=22% Similarity=0.434 Sum_probs=46.4
Q ss_pred CCCcccccCCCCCCCCccc--CCCC--cccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-cc
Q psy12567 18 TEGRECVNCGAISTPLWRR--DGTG--HYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-LW 92 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~--~~~g--~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~W 92 (142)
.....|.-||+...-.+.+ +..| ...|.-|+..=. .....|.+||.+..- .|
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~-----------------------~~R~~C~~Cg~~~~l~y~ 241 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH-----------------------VVRVKCSNCEQSGKLHYW 241 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc-----------------------ccCccCCCCCCCCceeee
Confidence 3467999999987665433 2345 567999953211 113679999986544 35
Q ss_pred ccCCC--C--CcccchhhhhHHhc
Q psy12567 93 RRDGT--G--HYLCNACGLYHKMN 112 (142)
Q Consensus 93 Rr~~~--G--~~lCNaCGly~k~~ 112 (142)
--+++ + -.+|..|+-|.|.-
T Consensus 242 ~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 242 SLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred eecCCCcceEeeecccccccceec
Confidence 43332 3 26999999998863
No 30
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=68.35 E-value=3.5 Score=34.84 Aligned_cols=32 Identities=22% Similarity=0.331 Sum_probs=24.1
Q ss_pred cCCCCcccccCCCCCCCCcccCCCCccccccccc
Q psy12567 16 YFTEGRECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 16 ~~~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
+......|.+||. ++.-.....|.++|..||+
T Consensus 7 ~~~~~~~Cp~Cg~--~~iv~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 7 EEEEKLVCPECGS--DKLIYDYERGEIVCADCGL 38 (310)
T ss_pred hcccCCcCcCCCC--CCeeEECCCCeEeecccCC
Confidence 3455678999996 4554456789999999985
No 31
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=68.29 E-value=2.2 Score=25.48 Aligned_cols=25 Identities=36% Similarity=1.034 Sum_probs=20.8
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
..|..|+.. |-...+|.+.|..||-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 459999987 6668899999999985
No 32
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=67.28 E-value=3.8 Score=36.43 Aligned_cols=42 Identities=26% Similarity=0.684 Sum_probs=34.1
Q ss_pred ccCCCCccccccCCCCCCccccCCCCCcccchhhhhHHhcCCC
Q psy12567 73 EYFTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMN 115 (142)
Q Consensus 73 ~~~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~~~ 115 (142)
........|+.|+... |.|-.-.-|-.||..|.=..|..|++
T Consensus 17 ~~kPgNk~CaDCga~n-PtWASvn~GIFLCl~CSGVHRsLGvH 58 (395)
T PLN03114 17 KAKSDNKICFDCNAKN-PTWASVTYGIFLCIDCSAVHRSLGVH 58 (395)
T ss_pred HhCcCCCcCccCCCCC-CCceeeccceeehhhhhHhhccCCCC
Confidence 3446789999999875 99999999999999997766665543
No 33
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=66.32 E-value=4.9 Score=24.28 Aligned_cols=29 Identities=28% Similarity=0.612 Sum_probs=21.4
Q ss_pred cccccCCCCCCCCccc-CCCCccccccccc
Q psy12567 21 RECVNCGAISTPLWRR-DGTGHYLCNARLF 49 (142)
Q Consensus 21 ~~C~nCgt~~TplWr~-~~~g~~lCnacg~ 49 (142)
..|.+||....=.|.. +..|.++|+.|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4689999877766533 3568999999963
No 34
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=66.05 E-value=3 Score=28.59 Aligned_cols=35 Identities=26% Similarity=0.581 Sum_probs=26.6
Q ss_pred CcccccCCCCCCC-CcccCCCCcccccccccccccc
Q psy12567 20 GRECVNCGAISTP-LWRRDGTGHYLCNARLFSTSFT 54 (142)
Q Consensus 20 ~~~C~nCgt~~Tp-lWr~~~~g~~lCnacg~~~k~~ 54 (142)
+-.|..|++..|= +|+.++....-|.+|||....+
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQP 43 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeeccC
Confidence 4589999998887 5555555577899999876544
No 35
>KOG3740|consensus
Probab=65.62 E-value=2.5 Score=39.91 Aligned_cols=32 Identities=28% Similarity=0.721 Sum_probs=28.7
Q ss_pred CCCccccccCCCCCCccccCCCC----Ccccchhhh
Q psy12567 76 TEGRECVNCGAISTPLWRRDGTG----HYLCNACGL 107 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WRr~~~G----~~lCNaCGl 107 (142)
.+.-.|..|.|..||.|+.-+.| +++|.+|--
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvt 495 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVT 495 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhh
Confidence 44789999999999999999998 789999965
No 36
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=65.56 E-value=3.6 Score=36.56 Aligned_cols=30 Identities=27% Similarity=0.699 Sum_probs=26.0
Q ss_pred CCCcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
..-+.|.+||+.. |.|-.-.-|-+||..|-
T Consensus 20 PgNk~CaDCga~n-PtWASvn~GIFLCl~CS 49 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYGIFLCIDCS 49 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccceeehhhhh
Confidence 4567999999875 99988888999999993
No 37
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=65.26 E-value=4.6 Score=24.81 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=19.5
Q ss_pred CCCcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
.++.+|..||.+ ..-+.. ..+.+-|.+|+
T Consensus 16 ~~g~~CP~Cg~~-~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 16 PDGFVCPHCGST-KHYRLK-TRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCCCe-eeEEeC-CCCeEECCCCC
Confidence 345679999887 443333 36778888885
No 38
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=65.02 E-value=3.3 Score=27.70 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=25.9
Q ss_pred CcccccCCCCCCC-CcccCCCCccccccccccccc
Q psy12567 20 GRECVNCGAISTP-LWRRDGTGHYLCNARLFSTSF 53 (142)
Q Consensus 20 ~~~C~nCgt~~Tp-lWr~~~~g~~lCnacg~~~k~ 53 (142)
+-.|..|++..|= +|+.++....-|.+|||....
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQEQQ 43 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCcccc
Confidence 4589999998887 565555567789999887543
No 39
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=64.87 E-value=2.5 Score=28.23 Aligned_cols=34 Identities=26% Similarity=0.663 Sum_probs=26.3
Q ss_pred CCCccccccCCCCCC-ccccCCCCCcccchhhhhH
Q psy12567 76 TEGRECVNCGAISTP-LWRRDGTGHYLCNACGLYH 109 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp-~WRr~~~G~~lCNaCGly~ 109 (142)
..+..|-.|++.+|- +|+.++....-|-+||...
T Consensus 7 IAGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 7 IAGAVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred eccccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 447899999999998 5655555568999999854
No 40
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=64.22 E-value=2.6 Score=28.86 Aligned_cols=35 Identities=31% Similarity=0.785 Sum_probs=26.7
Q ss_pred CCCccccccCCCCCCc-cccCCCCCcccchhhhhHH
Q psy12567 76 TEGRECVNCGAISTPL-WRRDGTGHYLCNACGLYHK 110 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~-WRr~~~G~~lCNaCGly~k 110 (142)
..+-.|-.|++.+|.+ |+-+..-..-|-+||....
T Consensus 6 IAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 6 IAGAVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ecCccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 3478999999999995 5544444679999998544
No 41
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=63.81 E-value=2.6 Score=32.29 Aligned_cols=30 Identities=30% Similarity=0.537 Sum_probs=23.1
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
=..|..|+..+|-+=+.+..=...|+|||-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 478999999999996642222468999996
No 42
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=63.57 E-value=4.5 Score=26.35 Aligned_cols=37 Identities=19% Similarity=0.411 Sum_probs=24.9
Q ss_pred CCccccCCCCcccccCCCCCCCCcccCCCCcccccccccc
Q psy12567 11 VEDIEYFTEGRECVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 11 ~~~~~~~~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
.-.++....+..|+.||...-. ......+.|..||+.
T Consensus 19 v~~v~~~~TSq~C~~CG~~~~~---~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 19 VVEVDEAYTSQTCPRCGHRNKK---RRSGRVFTCPNCGFE 55 (69)
T ss_pred EEEECCCCCccCccCccccccc---ccccceEEcCCCCCE
Confidence 3344444578899999997665 222236899999875
No 43
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=63.56 E-value=8.3 Score=36.31 Aligned_cols=18 Identities=33% Similarity=0.905 Sum_probs=10.9
Q ss_pred CCCccccccCCCCCCccc
Q psy12567 76 TEGRECVNCGAISTPLWR 93 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WR 93 (142)
.....|.+||+...+.|.
T Consensus 39 ~~~~fC~~CG~~~~~~~~ 56 (645)
T PRK14559 39 VDEAHCPNCGAETGTIWW 56 (645)
T ss_pred cccccccccCCcccchhh
Confidence 345667777766655554
No 44
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=63.34 E-value=8.8 Score=32.99 Aligned_cols=72 Identities=18% Similarity=0.289 Sum_probs=47.3
Q ss_pred CCCcccccCCCCCCCCcccC---CCC--cccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-c
Q psy12567 18 TEGRECVNCGAISTPLWRRD---GTG--HYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-L 91 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~---~~g--~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~ 91 (142)
.....|.-||+...-...+. ..| ...|.-|+..-. .....|.+||.++.- .
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~-----------------------~~R~~C~~Cg~~~~l~y 238 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH-----------------------YVRVKCSHCEESKHLAY 238 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc-----------------------ccCccCCCCCCCCceee
Confidence 34568999999887655544 345 567999943211 113689999987644 3
Q ss_pred cccCC----CC--CcccchhhhhHHhc
Q psy12567 92 WRRDG----TG--HYLCNACGLYHKMN 112 (142)
Q Consensus 92 WRr~~----~G--~~lCNaCGly~k~~ 112 (142)
|--.. .+ -.+|..|+-|.|.-
T Consensus 239 ~~~e~~~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 239 LSLEHDAEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred EeecCCCCCcceEEeeccccccchhhh
Confidence 65332 23 25999999998874
No 45
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=62.10 E-value=2.9 Score=30.78 Aligned_cols=30 Identities=30% Similarity=0.561 Sum_probs=22.6
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
=..|..|+..+|-+=+.+..=...|+|||-
T Consensus 80 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 378999999999997652221357999994
No 46
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=62.06 E-value=2.9 Score=31.77 Aligned_cols=30 Identities=23% Similarity=0.488 Sum_probs=22.7
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
=..|..|+..+|-+=+.+..=...|+|||-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 478999999999987642221358999996
No 47
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.28 E-value=6.9 Score=28.45 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=25.2
Q ss_pred cccCCCCcccccCCCCCCCCcccCCCCcccccccccccc
Q psy12567 14 IEYFTEGRECVNCGAISTPLWRRDGTGHYLCNARLFSTS 52 (142)
Q Consensus 14 ~~~~~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k 52 (142)
.......-.|.+||...-+.=.....+|..|..||+|..
T Consensus 15 k~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 15 KPKLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred ccCCCcEeECCCCCCeEeeeecCCCcceEECCCCCCccC
Confidence 333345668999995333322223567999999998854
No 48
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.82 E-value=4.1 Score=31.16 Aligned_cols=33 Identities=27% Similarity=0.292 Sum_probs=24.3
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
+--.|..|+...|-+-..+..-...|+|||...
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 345799999999999764333356799997543
No 49
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.65 E-value=4.8 Score=30.60 Aligned_cols=33 Identities=15% Similarity=0.203 Sum_probs=23.8
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
+--.|..|+...|-+-..+-.-...|+|||...
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 345799999999998864332245799997543
No 50
>KOG0706|consensus
Probab=56.88 E-value=5.6 Score=36.07 Aligned_cols=44 Identities=30% Similarity=0.711 Sum_probs=36.3
Q ss_pred cccCCCCccccccCCCCCCccccCCCCCcccchhhhhHHhcCCCC
Q psy12567 72 IEYFTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNR 116 (142)
Q Consensus 72 ~~~~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~~~R 116 (142)
+....+..+|+.|+... |-|-.-..|-.||-.|.-..|--||+-
T Consensus 17 LRs~~~NKvCFDCgAkn-PtWaSVTYGIFLCiDCSAvHRnLGVHi 60 (454)
T KOG0706|consen 17 LRSQSENKVCFDCGAKN-PTWASVTYGIFLCIDCSAVHRNLGVHI 60 (454)
T ss_pred HhcCCCCceecccCCCC-CCceeecceEEEEEecchhhhccccce
Confidence 44557789999999865 899999999999999988777666654
No 51
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.84 E-value=2.7 Score=28.52 Aligned_cols=31 Identities=26% Similarity=0.485 Sum_probs=25.7
Q ss_pred CcccccCCCCCCC-CcccCCCCcccccccccc
Q psy12567 20 GRECVNCGAISTP-LWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 20 ~~~C~nCgt~~Tp-lWr~~~~g~~lCnacg~~ 50 (142)
+-.|.-|.+.+|= +|+.+.-.+.-|.+||+-
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHH 41 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchH
Confidence 4589999998886 777788889999999864
No 52
>KOG1598|consensus
Probab=55.67 E-value=7.5 Score=35.90 Aligned_cols=27 Identities=33% Similarity=0.599 Sum_probs=21.7
Q ss_pred cccccCCCCCCCCcccCCCCccccccccc
Q psy12567 21 RECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 21 ~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
..|.|||.+.-- ++.++|...|.+||.
T Consensus 1 ~~C~~C~~s~fe--~d~a~g~~~C~~CG~ 27 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATGNLYCTACGT 27 (521)
T ss_pred CcCCCCCCCCcc--cccccCCceeccccc
Confidence 369999987654 566789999999985
No 53
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=55.41 E-value=8.1 Score=25.87 Aligned_cols=15 Identities=27% Similarity=0.806 Sum_probs=9.3
Q ss_pred CcccccCCCCC-CCCc
Q psy12567 20 GRECVNCGAIS-TPLW 34 (142)
Q Consensus 20 ~~~C~nCgt~~-TplW 34 (142)
...|.+||+++ |..|
T Consensus 15 ~~~CP~Cgs~~~T~~W 30 (61)
T PRK08351 15 EDRCPVCGSRDLSDEW 30 (61)
T ss_pred CCcCCCCcCCcccccc
Confidence 33567776665 6666
No 54
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.08 E-value=4.9 Score=29.56 Aligned_cols=30 Identities=23% Similarity=0.275 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCCcccCCCCccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
--.|..|+..+|-+-..+..-..-|+|||.
T Consensus 80 yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 357999999999988763333456999974
No 55
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=54.54 E-value=7.1 Score=33.00 Aligned_cols=20 Identities=30% Similarity=0.757 Sum_probs=10.9
Q ss_pred CCCccccccCCC-------CCCccccC
Q psy12567 76 TEGRECVNCGAI-------STPLWRRD 95 (142)
Q Consensus 76 ~~~~~C~nC~tt-------~Tp~WRr~ 95 (142)
....+|.+||+- ..|.||.-
T Consensus 28 ~Ge~vC~~CG~Vl~e~~iD~g~EWR~f 54 (310)
T PRK00423 28 RGEIVCADCGLVIEENIIDQGPEWRAF 54 (310)
T ss_pred CCeEeecccCCcccccccccCCCccCC
Confidence 345666666662 35566644
No 56
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=53.51 E-value=9.2 Score=25.90 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=8.0
Q ss_pred CcccccCCCCC-CCCc
Q psy12567 20 GRECVNCGAIS-TPLW 34 (142)
Q Consensus 20 ~~~C~nCgt~~-TplW 34 (142)
...|.+||+++ |+.|
T Consensus 17 ~~~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 17 EKTCPVHGDEKTTTEW 32 (64)
T ss_pred CCcCCCCCCCcCCcCc
Confidence 34566666554 4455
No 57
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=52.24 E-value=7.4 Score=25.73 Aligned_cols=23 Identities=13% Similarity=0.103 Sum_probs=18.2
Q ss_pred CcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
..+|.+||...-| |.+|. ||+|.
T Consensus 27 ~~~c~~cg~~~~p--------H~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEYHLP--------HHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCceecc--------ceecC-CcccC
Confidence 4589999987766 56899 99885
No 58
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=52.19 E-value=5.1 Score=32.14 Aligned_cols=30 Identities=33% Similarity=0.583 Sum_probs=22.9
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
=..|..|+..+|-+=+.+..=..-|+|||-
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVLMLRCDACGA 127 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 478999999999996543221458999996
No 59
>KOG0706|consensus
Probab=52.15 E-value=7.7 Score=35.20 Aligned_cols=29 Identities=34% Similarity=0.833 Sum_probs=25.4
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
.+-++|.+||+. -|.|-.=.=|-+||..|
T Consensus 21 ~~NKvCFDCgAk-nPtWaSVTYGIFLCiDC 49 (454)
T KOG0706|consen 21 SENKVCFDCGAK-NPTWASVTYGIFLCIDC 49 (454)
T ss_pred CCCceecccCCC-CCCceeecceEEEEEec
Confidence 567899999985 58898888899999999
No 60
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=51.27 E-value=14 Score=37.56 Aligned_cols=22 Identities=27% Similarity=0.347 Sum_probs=14.7
Q ss_pred CcccccCCCCCCCCcccCCCCcccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
.+.|.+||+. |+.. .|..||-.
T Consensus 667 ~rkCPkCG~~-t~~~--------fCP~CGs~ 688 (1337)
T PRK14714 667 RRRCPSCGTE-TYEN--------RCPDCGTH 688 (1337)
T ss_pred EEECCCCCCc-cccc--------cCcccCCc
Confidence 4789999985 4432 77777543
No 61
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=50.61 E-value=9.9 Score=35.77 Aligned_cols=29 Identities=24% Similarity=0.626 Sum_probs=25.7
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
.+-+.|.+||+.. |.|-.-.-|-++|.+|
T Consensus 21 PgNk~CADCgs~~-P~WASiNlGIFICi~C 49 (648)
T PLN03119 21 PPNRRCINCNSLG-PQYVCTTFWTFVCMAC 49 (648)
T ss_pred cCCCccccCCCCC-CCceeeccceEEeccc
Confidence 4567999999976 9998888899999999
No 62
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=50.61 E-value=6.2 Score=29.62 Aligned_cols=29 Identities=31% Similarity=0.609 Sum_probs=23.4
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
..|..|+..+|-+=..+..=...|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 68999999999997764443578999994
No 63
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=50.19 E-value=7 Score=31.37 Aligned_cols=34 Identities=26% Similarity=0.298 Sum_probs=25.4
Q ss_pred CCcccccCCCCCCCCcccCCCCcccccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFSTS 52 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k 52 (142)
+--.|..|+...|-+-..+..-..-|+|||....
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 3457999999999997654333668999986543
No 64
>PLN03131 hypothetical protein; Provisional
Probab=47.87 E-value=11 Score=35.71 Aligned_cols=29 Identities=21% Similarity=0.628 Sum_probs=25.2
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
.+-+.|.+||+.. |.|-.-.-|-+||.+|
T Consensus 21 PgNk~CADCga~~-P~WASiNlGIFICi~C 49 (705)
T PLN03131 21 PPNRRCINCNSLG-PQFVCTNFWTFICMTC 49 (705)
T ss_pred cCCCccccCCCCC-CCeeEeccceEEchhc
Confidence 4567999999865 9998888899999999
No 65
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.58 E-value=12 Score=20.38 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=12.8
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
..|.+||+.. +.+...|-.||-
T Consensus 3 ~~Cp~Cg~~~-------~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI-------DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC-------CcccccChhhCC
Confidence 4677777743 233446777763
No 66
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=47.52 E-value=13 Score=22.61 Aligned_cols=28 Identities=18% Similarity=0.542 Sum_probs=18.5
Q ss_pred ccccCCCCCCCCcccCCC-Cccccccccccc
Q psy12567 22 ECVNCGAISTPLWRRDGT-GHYLCNARLFST 51 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~-g~~lCnacg~~~ 51 (142)
-|.+||..-.+. .+.. ..+.|..|++..
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeE
Confidence 588999865553 1222 278999998654
No 67
>PRK00420 hypothetical protein; Validated
Probab=47.02 E-value=14 Score=27.50 Aligned_cols=27 Identities=26% Similarity=0.623 Sum_probs=21.0
Q ss_pred CcccccCCCCCCCCcccCCCCcccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
+..|..|| +|+.+- ..|...|.+||-.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCC---Ccceec-CCCceECCCCCCe
Confidence 46899998 788753 6788999999753
No 68
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=46.91 E-value=11 Score=35.54 Aligned_cols=35 Identities=23% Similarity=0.584 Sum_probs=29.4
Q ss_pred ccCCCCccccccCCCCCCccccCCCCCcccchhhhh
Q psy12567 73 EYFTEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 108 (142)
Q Consensus 73 ~~~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly 108 (142)
........|++|+... |.|---..|-.||-+|.=.
T Consensus 18 lklPgNk~CADCgs~~-P~WASiNlGIFICi~CSGI 52 (648)
T PLN03119 18 MKLPPNRRCINCNSLG-PQYVCTTFWTFVCMACSGI 52 (648)
T ss_pred hhCcCCCccccCCCCC-CCceeeccceEEeccchhh
Confidence 3457789999999876 9999999999999999553
No 69
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=46.83 E-value=3.1 Score=34.65 Aligned_cols=71 Identities=23% Similarity=0.337 Sum_probs=34.1
Q ss_pred CCcccccCCCCCCCCcccCCC--C--cccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-ccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGT--G--HYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-LWR 93 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~--g--~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~WR 93 (142)
....|.-||+...-.+.++.. | +..|.-|+..=. .....|.+||.++-- +|-
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~-----------------------~~R~~Cp~Cg~~~~~~l~~ 227 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR-----------------------FVRIKCPYCGNTDHEKLEY 227 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE-------------------------TTS-TTT---SS-EEE-
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee-----------------------ecCCCCcCCCCCCCcceee
Confidence 356899999987777777766 6 557888853211 113579999998754 443
Q ss_pred c---CCCC--CcccchhhhhHHhc
Q psy12567 94 R---DGTG--HYLCNACGLYHKMN 112 (142)
Q Consensus 94 r---~~~G--~~lCNaCGly~k~~ 112 (142)
= +..+ -.+|..|+-|.|.-
T Consensus 228 ~~~e~~~~~rve~C~~C~~YlK~v 251 (290)
T PF04216_consen 228 FTVEGEPAYRVEVCESCGSYLKTV 251 (290)
T ss_dssp -------SEEEEEETTTTEEEEEE
T ss_pred EecCCCCcEEEEECCcccchHHHH
Confidence 2 2333 26999999998753
No 70
>KOG1598|consensus
Probab=46.41 E-value=11 Score=34.84 Aligned_cols=27 Identities=37% Similarity=0.829 Sum_probs=20.7
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
+.|.||+.++--. +-..|...|++||.
T Consensus 1 ~~C~~C~~s~fe~--d~a~g~~~C~~CG~ 27 (521)
T KOG1598|consen 1 MVCKNCGGSNFER--DEATGNLYCTACGT 27 (521)
T ss_pred CcCCCCCCCCccc--ccccCCceeccccc
Confidence 4699999887433 34568899999997
No 71
>KOG2907|consensus
Probab=46.40 E-value=13 Score=27.98 Aligned_cols=87 Identities=22% Similarity=0.399 Sum_probs=48.3
Q ss_pred CCcccccCCCCCCCCcccCCCCcccccccccccc---cccccc---cccccccCC---Cc---cccccCCCCccccccCC
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLFSTS---FTGYFI---MSRFLFASL---PV---EDIEYFTEGRECVNCGA 86 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k---~~G~~~---~~R~~~~~~---~~---~~~~~~~~~~~C~nC~t 86 (142)
+..-|..||++-- -....+..+|..|..... +.+... .....+... .+ ...........|..||.
T Consensus 6 ~~~FC~~CG~ll~---~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCpkCgh 82 (116)
T KOG2907|consen 6 DLDFCSDCGSLLE---EPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCPKCGH 82 (116)
T ss_pred Ccchhhhhhhhcc---cccccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCcccCC
Confidence 4567999998532 233344567999964321 111100 000000000 00 01123456789999998
Q ss_pred CC----CCccccCCCCC---cccchhhhh
Q psy12567 87 IS----TPLWRRDGTGH---YLCNACGLY 108 (142)
Q Consensus 87 t~----Tp~WRr~~~G~---~lCNaCGly 108 (142)
.. |-+-|..++|+ +-|-.|+..
T Consensus 83 e~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 83 EEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred chhhhhhhhcccccCCceEEEEcCcccee
Confidence 75 77889999997 468888763
No 72
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.93 E-value=6.2 Score=23.35 Aligned_cols=25 Identities=40% Similarity=0.884 Sum_probs=12.4
Q ss_pred cccccCCCCCCccccCCCC----Ccccchhhh
Q psy12567 80 ECVNCGAISTPLWRRDGTG----HYLCNACGL 107 (142)
Q Consensus 80 ~C~nC~tt~Tp~WRr~~~G----~~lCNaCGl 107 (142)
-|.+||+.-+ .+-++| ..+|.+||.
T Consensus 2 fC~~CG~~l~---~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLE---RRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-E---EE--TT-SS-EEEETTTTE
T ss_pred ccccccChhh---hhcCCCCCccceECCCCCC
Confidence 4788887642 233333 378999986
No 73
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=42.74 E-value=13 Score=32.60 Aligned_cols=67 Identities=24% Similarity=0.392 Sum_probs=41.2
Q ss_pred CCCcccccCCCCCCCCcccCCCCcccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-ccccCC
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-LWRRDG 96 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~WRr~~ 96 (142)
.....|+.||...-| ..+-||..|.+-.. . ...+.....-..|.+||...++ .|=+.+
T Consensus 4 ~~~~~C~~CGr~~~~------~~~~lC~dC~~~~~-~--------------~~~ip~~~~v~~C~~Cga~~~~~~W~~~~ 62 (355)
T COG1499 4 ASTILCVRCGRSVDP------LIDGLCGDCYVETT-P--------------LIEIPDEVNVEVCRHCGAYRIRGRWVDEE 62 (355)
T ss_pred CcccEeccCCCcCch------hhccccHHHHhccC-c--------------cccCCCceEEEECCcCCCccCCCcceecc
Confidence 345689999987653 34569999965421 1 0111111346899999988888 688755
Q ss_pred CCCcccchh
Q psy12567 97 TGHYLCNAC 105 (142)
Q Consensus 97 ~G~~lCNaC 105 (142)
.+.-+=.++
T Consensus 63 ~~~~~l~~~ 71 (355)
T COG1499 63 GANRLLEAL 71 (355)
T ss_pred ccchHHHHH
Confidence 443333443
No 74
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=42.07 E-value=11 Score=28.34 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=23.1
Q ss_pred cccccCCCCCCCCcccCCCCccccccccc
Q psy12567 21 RECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 21 ~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
-.|..|+..+|-+-..+..-...|+|||.
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 47999999999988775555677999975
No 75
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.69 E-value=12 Score=23.18 Aligned_cols=25 Identities=24% Similarity=0.543 Sum_probs=17.9
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
-.|.+||...+.. ..+..-|..||-
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCc
Confidence 3689999977654 234568999985
No 76
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=41.42 E-value=29 Score=26.84 Aligned_cols=65 Identities=12% Similarity=0.201 Sum_probs=35.8
Q ss_pred CCCcccCCCCccccccccc--cc------ccccccccccccccCCCccccc-----cCCCCccccccCCCCCCccccCC
Q psy12567 31 TPLWRRDGTGHYLCNARLF--ST------SFTGYFIMSRFLFASLPVEDIE-----YFTEGRECVNCGAISTPLWRRDG 96 (142)
Q Consensus 31 TplWr~~~~g~~lCnacg~--~~------k~~G~~~~~R~~~~~~~~~~~~-----~~~~~~~C~nC~tt~Tp~WRr~~ 96 (142)
.++|.....|.|+|-+|+. +. +.+|..-..++... ..+.... -.+....|.+|+..--=+...||
T Consensus 33 g~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~-~~V~~~~D~s~gm~RtEv~C~~Cg~HLGHVF~DGP 110 (142)
T PRK00222 33 GEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDE-EAIRELRDTSHGMVRTEVRCANCDSHLGHVFPDGP 110 (142)
T ss_pred CCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCC-CceEEeeccCCCceEEEEEeCCCCCccCcccCCCC
Confidence 3688888899999999973 22 22343211222111 1121111 12345789999887766665553
No 77
>PLN03131 hypothetical protein; Provisional
Probab=40.99 E-value=16 Score=34.68 Aligned_cols=34 Identities=21% Similarity=0.623 Sum_probs=28.6
Q ss_pred cCCCCccccccCCCCCCccccCCCCCcccchhhhh
Q psy12567 74 YFTEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 108 (142)
Q Consensus 74 ~~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly 108 (142)
.......|++|+... |.|---..|-.||-.|.=.
T Consensus 19 k~PgNk~CADCga~~-P~WASiNlGIFICi~CSGI 52 (705)
T PLN03131 19 KLPPNRRCINCNSLG-PQFVCTNFWTFICMTCSGI 52 (705)
T ss_pred hCcCCCccccCCCCC-CCeeEeccceEEchhchhh
Confidence 457789999999865 8999989999999999653
No 78
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=40.54 E-value=12 Score=22.91 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=14.2
Q ss_pred ccccCCCCCCCC-ccc-CCCCccccccc
Q psy12567 22 ECVNCGAISTPL-WRR-DGTGHYLCNAR 47 (142)
Q Consensus 22 ~C~nCgt~~Tpl-Wr~-~~~g~~lCnac 47 (142)
.|..||.+.-=. |.. +..|+++|+.|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 588898865554 543 34589999999
No 79
>PHA02942 putative transposase; Provisional
Probab=40.52 E-value=18 Score=31.68 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=23.4
Q ss_pred cccCCCCcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 14 IEYFTEGRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 14 ~~~~~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
++....+..|+.||....++ ....+.|..||+..
T Consensus 319 V~p~yTSq~Cs~CG~~~~~l----~~r~f~C~~CG~~~ 352 (383)
T PHA02942 319 VNPSYSSVSCPKCGHKMVEI----AHRYFHCPSCGYEN 352 (383)
T ss_pred ECCCCCCccCCCCCCccCcC----CCCEEECCCCCCEe
Confidence 33334678999999876543 12368999998753
No 80
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=40.31 E-value=18 Score=23.96 Aligned_cols=24 Identities=29% Similarity=0.578 Sum_probs=18.7
Q ss_pred CcccccCCCCCCCCcccCCCCccccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFST 51 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~ 51 (142)
..+|.+||...=| |.+|..||+|.
T Consensus 27 ~~~c~~cG~~~l~--------Hrvc~~cg~Y~ 50 (57)
T COG0333 27 LSVCPNCGEYKLP--------HRVCLKCGYYK 50 (57)
T ss_pred ceeccCCCCcccC--------ceEcCCCCCcc
Confidence 5689999876655 56999999875
No 81
>PHA00626 hypothetical protein
Probab=40.24 E-value=18 Score=24.16 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=19.9
Q ss_pred ccccCCCCCCC--CcccCCCCcccccccccccc
Q psy12567 22 ECVNCGAISTP--LWRRDGTGHYLCNARLFSTS 52 (142)
Q Consensus 22 ~C~nCgt~~Tp--lWr~~~~g~~lCnacg~~~k 52 (142)
.|.+||+.+-- ---+.+...|.|..|||..+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence 58889884332 11234456799999998643
No 82
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=40.09 E-value=15 Score=21.84 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=15.9
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
+..+|..||..-...|-...=+..+|+.|
T Consensus 2 ~~~~C~eC~~~f~dSyL~~~F~~~VCD~C 30 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLNNFDLPVCDKC 30 (34)
T ss_dssp S-EE-TTT--EES-SSCCCCTS-S--TTT
T ss_pred CCchHhHhCCHHHHHHHHHhCCccccccc
Confidence 35678899887777776677777888888
No 83
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=39.81 E-value=11 Score=22.83 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=5.5
Q ss_pred CccccccCC
Q psy12567 78 GRECVNCGA 86 (142)
Q Consensus 78 ~~~C~nC~t 86 (142)
...|..||.
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 456666665
No 84
>KOG0703|consensus
Probab=39.51 E-value=13 Score=31.82 Aligned_cols=38 Identities=29% Similarity=0.720 Sum_probs=30.7
Q ss_pred CCCCccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 75 FTEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 75 ~~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
..+...|+.|++. .|.|-.-..|--+|--|.=..|.-|
T Consensus 22 ~~~N~~CADC~a~-~P~WaSwnlGvFiC~~C~giHR~lg 59 (287)
T KOG0703|consen 22 EPDNKVCADCGAK-GPRWASWNLGVFICLRCAGIHRSLG 59 (287)
T ss_pred CcccCcccccCCC-CCCeEEeecCeEEEeeccccccccc
Confidence 3558999999999 9999999999999999965444433
No 85
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=39.39 E-value=17 Score=27.82 Aligned_cols=66 Identities=15% Similarity=0.144 Sum_probs=36.8
Q ss_pred CCCCcccCCCCccccccccc--cc------ccccccccccccccCCCccccc-----cCCCCccccccCCCCCCccccCC
Q psy12567 30 STPLWRRDGTGHYLCNARLF--ST------SFTGYFIMSRFLFASLPVEDIE-----YFTEGRECVNCGAISTPLWRRDG 96 (142)
Q Consensus 30 ~TplWr~~~~g~~lCnacg~--~~------k~~G~~~~~R~~~~~~~~~~~~-----~~~~~~~C~nC~tt~Tp~WRr~~ 96 (142)
+.+.|.....|.|+|-+|+. +. +.+|..-..++..+ ..+.... -.+....|.+|+.---=+...||
T Consensus 29 tg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~-~~V~~~~D~s~gm~RtEv~C~~Cg~HLGHVF~DGP 107 (134)
T TIGR00357 29 TNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISE-EVVAYERDESHGMIRTEVRCRNCDAHLGHVFDDGP 107 (134)
T ss_pred CCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCC-CceEEeecCCCCcEEEEEEecCCCCccCcccCCCC
Confidence 34678888899999999973 32 22343212222211 1122111 12345789999987666665554
No 86
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=38.40 E-value=21 Score=22.64 Aligned_cols=27 Identities=15% Similarity=0.413 Sum_probs=18.9
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
..+.|.+||+. -+. ...+.+.|..||+
T Consensus 19 ~~~fCP~Cg~~--~m~--~~~~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG--FMA--EHLDRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc--hhe--ccCCcEECCCcCC
Confidence 45699999974 322 2236789999986
No 87
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=38.17 E-value=11 Score=22.78 Aligned_cols=28 Identities=29% Similarity=0.751 Sum_probs=17.6
Q ss_pred ccccccCCCCCC---ccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTP---LWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp---~WRr~~~G~~lCNaCGl 107 (142)
..|+-||.+.+. |- .|+.|..+|+.|..
T Consensus 2 ~~CSFCgr~~~~v~~li-~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLI-SGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEE-EES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhcee-cCCCCcEECHHHHH
Confidence 468999988864 33 56767889999976
No 88
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=37.90 E-value=16 Score=31.04 Aligned_cols=26 Identities=31% Similarity=0.873 Sum_probs=13.1
Q ss_pred cccccCCCCCCccccCCCCCcccchhhh
Q psy12567 80 ECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 80 ~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
.|.+|+.+. +=..-..|..+|-.||+
T Consensus 3 ~CpeCg~~~--~~~d~~~ge~VC~~CG~ 28 (285)
T COG1405 3 SCPECGSTN--IITDYERGEIVCADCGL 28 (285)
T ss_pred CCCCCCCcc--ceeeccCCeEEeccCCE
Confidence 466666651 11112345666666665
No 89
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.68 E-value=32 Score=31.09 Aligned_cols=23 Identities=26% Similarity=0.514 Sum_probs=17.5
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
....|..||.+...-| .|-.||-
T Consensus 239 ~~l~Ch~Cg~~~~~~~--------~Cp~C~s 261 (505)
T TIGR00595 239 GKLRCHYCGYQEPIPK--------TCPQCGS 261 (505)
T ss_pred CeEEcCCCcCcCCCCC--------CCCCCCC
Confidence 3578999998887665 5888864
No 90
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=34.48 E-value=20 Score=28.62 Aligned_cols=28 Identities=32% Similarity=0.822 Sum_probs=23.5
Q ss_pred cccccCCCCCCccccCCCCC---cccchhhh
Q psy12567 80 ECVNCGAISTPLWRRDGTGH---YLCNACGL 107 (142)
Q Consensus 80 ~C~nC~tt~Tp~WRr~~~G~---~lCNaCGl 107 (142)
.|.+||.....++++-.+|. +.|..||-
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 69999999988999887773 78999974
No 91
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=33.57 E-value=26 Score=20.93 Aligned_cols=32 Identities=25% Similarity=0.478 Sum_probs=19.9
Q ss_pred CcccccCCCCCCCCcccCCCC-ccccccccccc
Q psy12567 20 GRECVNCGAISTPLWRRDGTG-HYLCNARLFST 51 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g-~~lCnacg~~~ 51 (142)
...|..|++.--|.-.-+..| ...|+-|+...
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EE
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcC
Confidence 457999999999987777765 78999997543
No 92
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.14 E-value=24 Score=28.28 Aligned_cols=28 Identities=18% Similarity=0.388 Sum_probs=20.7
Q ss_pred ccCCCCcccccCCCCCCCCcccCCCCcccccccccc
Q psy12567 15 EYFTEGRECVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 15 ~~~~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
+...++..|+.||. -..+.+.|..||+.
T Consensus 304 ~~~~tS~~C~~cg~--------~~~r~~~C~~cg~~ 331 (364)
T COG0675 304 PPYYTSKTCPCCGH--------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCCCCcccccccCC--------ccceeEECCCCCCe
Confidence 34567789999999 11346799999874
No 93
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=32.87 E-value=34 Score=24.02 Aligned_cols=33 Identities=33% Similarity=0.604 Sum_probs=23.7
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
+...|.-|+...+-.+ -|...|+||..|++..-
T Consensus 5 ~~~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~v 37 (90)
T cd07169 5 EQRTCLICGDRATGLH----YGIISCEGCKGFFKRSI 37 (90)
T ss_pred cCCCCeecCCcCcceE----ECcceehhhHHHHHHHh
Confidence 4567899987655432 45678999999988753
No 94
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=32.84 E-value=35 Score=27.63 Aligned_cols=52 Identities=25% Similarity=0.465 Sum_probs=34.6
Q ss_pred cccCCCCCCCCcccCCCCcccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-ccccC
Q psy12567 23 CVNCGAISTPLWRRDGTGHYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-LWRRD 95 (142)
Q Consensus 23 C~nCgt~~TplWr~~~~g~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~WRr~ 95 (142)
|..||....|+- .-||..|.+... . ... +.....-..|..||....+ .|...
T Consensus 1 C~~CG~~~~~~~------~~lC~~C~~~~~--~-------i~e------i~~~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 1 CPRCGREIEPLI------DGLCPDCYLKRF--D-------IIE------IPDRIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CCCCCCCCCCcc------cccChHHhcccC--C-------eee------cCCccCceECCCCCCEECCCEeeec
Confidence 889998665543 239999965431 1 011 1122456899999999887 89887
No 95
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=31.85 E-value=40 Score=19.60 Aligned_cols=24 Identities=21% Similarity=0.224 Sum_probs=11.8
Q ss_pred ccccCCCCCCCCcccCCCCccccccccc
Q psy12567 22 ECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
.|.+||+...-. +.+..-|..||+
T Consensus 2 ~C~~Cg~~~~~~----~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELK----PGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BS----TSSTSSBSSSS-
T ss_pred CCCcCCCeeEcC----CCCcEECCcCCC
Confidence 477777765511 122345776753
No 96
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=31.11 E-value=18 Score=23.35 Aligned_cols=20 Identities=35% Similarity=0.953 Sum_probs=13.9
Q ss_pred cccCCCCCCCCcccCCCCcccccccccc
Q psy12567 23 CVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 23 C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
|..|++....+| +|..|+..
T Consensus 1 C~~C~~~~~~lw--------~CL~Cg~~ 20 (63)
T PF02148_consen 1 CSVCGSTNSNLW--------LCLTCGYV 20 (63)
T ss_dssp -SSSHTCSSSEE--------EETTTS-E
T ss_pred CCCCCCcCCceE--------EeCCCCcc
Confidence 677876666777 89999754
No 97
>KOG1597|consensus
Probab=30.95 E-value=28 Score=30.21 Aligned_cols=30 Identities=27% Similarity=0.668 Sum_probs=21.3
Q ss_pred cccccCCCCCCccccCCCCCcccchhhhhH
Q psy12567 80 ECVNCGAISTPLWRRDGTGHYLCNACGLYH 109 (142)
Q Consensus 80 ~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~ 109 (142)
.|..|....-.+--....|.++|-.|||..
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeee
Confidence 477777665556666777888888888843
No 98
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.71 E-value=20 Score=20.70 Aligned_cols=8 Identities=38% Similarity=0.866 Sum_probs=3.9
Q ss_pred cccchhhh
Q psy12567 100 YLCNACGL 107 (142)
Q Consensus 100 ~lCNaCGl 107 (142)
..|-.||-
T Consensus 27 ~~CP~Cg~ 34 (41)
T smart00834 27 ATCPECGG 34 (41)
T ss_pred CCCCCCCC
Confidence 34555554
No 99
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=30.53 E-value=94 Score=21.02 Aligned_cols=44 Identities=20% Similarity=0.536 Sum_probs=32.4
Q ss_pred CCCccccccCCCCCCc--cccCCCC--CcccchhhhhHHhcCCCCCCC
Q psy12567 76 TEGRECVNCGAISTPL--WRRDGTG--HYLCNACGLYHKMNGMNRPLV 119 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~--WRr~~~G--~~lCNaCGly~k~~~~~RP~~ 119 (142)
.+...|..|..+.|-. .-..... .+.|-+|--||-..|..|-+.
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVP 50 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVP 50 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCc
Confidence 3467899999988863 2223333 479999999999999877663
No 100
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=29.95 E-value=30 Score=20.88 Aligned_cols=20 Identities=40% Similarity=0.863 Sum_probs=14.8
Q ss_pred ccccCCCCCCCCcccCCCCcccccccccc
Q psy12567 22 ECVNCGAISTPLWRRDGTGHYLCNARLFS 50 (142)
Q Consensus 22 ~C~nCgt~~TplWr~~~~g~~lCnacg~~ 50 (142)
.|.+|++.. .+| +|..|+..
T Consensus 1 ~C~~C~~~~-~l~--------~CL~C~~~ 20 (50)
T smart00290 1 RCSVCGTIE-NLW--------LCLTCGQV 20 (50)
T ss_pred CcccCCCcC-CeE--------EecCCCCc
Confidence 488999766 377 89988653
No 101
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=29.93 E-value=30 Score=25.41 Aligned_cols=32 Identities=31% Similarity=0.567 Sum_probs=19.0
Q ss_pred CCCccccccCCCCCCccccCCCCCcccchhhhhHHh
Q psy12567 76 TEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKM 111 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~ 111 (142)
...+.|.+||+..==|=| .| .+|-.||--|-.
T Consensus 7 GtKR~Cp~CG~kFYDLnk-~P---ivCP~CG~~~~~ 38 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNK-DP---IVCPKCGTEFPP 38 (108)
T ss_pred CCcccCCCCcchhccCCC-CC---ccCCCCCCccCc
Confidence 345778888887644421 22 368888874443
No 102
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=29.35 E-value=23 Score=21.72 Aligned_cols=8 Identities=38% Similarity=0.866 Sum_probs=3.7
Q ss_pred cccchhhh
Q psy12567 100 YLCNACGL 107 (142)
Q Consensus 100 ~lCNaCGl 107 (142)
..|-.||-
T Consensus 27 ~~CP~Cg~ 34 (52)
T TIGR02605 27 ATCPECGG 34 (52)
T ss_pred CCCCCCCC
Confidence 34555543
No 103
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=29.12 E-value=42 Score=23.83 Aligned_cols=33 Identities=24% Similarity=0.503 Sum_probs=23.5
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
+...|.-||...+-.+ -|...|+||..|++..-
T Consensus 4 ~~~~C~VCg~~~~g~h----yGv~sC~aC~~FFRR~v 36 (95)
T cd06968 4 EVIPCKICGDKSSGIH----YGVITCEGCKGFFRRSQ 36 (95)
T ss_pred cccCCcccCCcCcceE----ECceeehhhHHhhHHhe
Confidence 3457899987655432 45668999999988743
No 104
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=28.93 E-value=33 Score=27.26 Aligned_cols=31 Identities=19% Similarity=0.334 Sum_probs=25.2
Q ss_pred CCCcccccCCCCCCCCcccCCCCcccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
.+-..|..||......+-....|..+|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 4456899999887767777778899999996
No 105
>PRK05580 primosome assembly protein PriA; Validated
Probab=28.79 E-value=45 Score=31.28 Aligned_cols=23 Identities=26% Similarity=0.575 Sum_probs=16.7
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
....|..||.+...-| .|..||-
T Consensus 407 ~~l~Ch~Cg~~~~~~~--------~Cp~Cg~ 429 (679)
T PRK05580 407 RRLRCHHCGYQEPIPK--------ACPECGS 429 (679)
T ss_pred CeEECCCCcCCCCCCC--------CCCCCcC
Confidence 4578999998876666 4888853
No 106
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=28.23 E-value=18 Score=21.81 Aligned_cols=30 Identities=27% Similarity=0.769 Sum_probs=14.2
Q ss_pred cccccCCCCCCcc----ccCCCC---CcccchhhhhH
Q psy12567 80 ECVNCGAISTPLW----RRDGTG---HYLCNACGLYH 109 (142)
Q Consensus 80 ~C~nC~tt~Tp~W----Rr~~~G---~~lCNaCGly~ 109 (142)
.|.+|+-.+.-.| |..+++ -+.|..||-.|
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 3555554443322 333444 25666666543
No 107
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.54 E-value=44 Score=31.54 Aligned_cols=22 Identities=36% Similarity=0.952 Sum_probs=16.3
Q ss_pred CCccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 77 EGRECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 77 ~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
....|.+||... +-| .|-.||-
T Consensus 409 ~~l~Ch~CG~~~-~p~--------~Cp~Cgs 430 (665)
T PRK14873 409 GTPRCRWCGRAA-PDW--------RCPRCGS 430 (665)
T ss_pred CeeECCCCcCCC-cCc--------cCCCCcC
Confidence 358899999876 344 5899975
No 108
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=27.30 E-value=78 Score=25.68 Aligned_cols=33 Identities=30% Similarity=0.524 Sum_probs=21.3
Q ss_pred CccccCCCCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 12 EDIEYFTEGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 12 ~~~~~~~~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
+......+.+.|.|||...= -++|-. +.||-.|
T Consensus 52 d~~~~~~~~~~C~nCg~~GH--~~~DCP-~~iC~~C 84 (190)
T COG5082 52 DVSAIREENPVCFNCGQNGH--LRRDCP-HSICYNC 84 (190)
T ss_pred ccccccccccccchhcccCc--ccccCC-hhHhhhc
Confidence 33355678999999987543 245555 5666666
No 109
>KOG0704|consensus
Probab=26.89 E-value=33 Score=30.56 Aligned_cols=28 Identities=32% Similarity=0.845 Sum_probs=23.9
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
+-..|+.|++. -|+|..---|-++|..|
T Consensus 18 eNk~CfeC~a~-NPQWvSvsyGIfICLEC 45 (386)
T KOG0704|consen 18 ENKKCFECGAP-NPQWVSVSYGIFICLEC 45 (386)
T ss_pred cCCceeecCCC-CCCeEeecccEEEEEec
Confidence 45689999876 49998877799999999
No 110
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=26.88 E-value=47 Score=22.97 Aligned_cols=31 Identities=23% Similarity=0.654 Sum_probs=22.0
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
..|.-|+...+-. --|..-|+||..+++..-
T Consensus 4 ~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 34 (82)
T cd07173 4 KTCLICGDEASGC----HYGALTCGSCKVFFKRAA 34 (82)
T ss_pred CCCeecCCcCcce----EECcchhhhHHHHHHHHh
Confidence 4588888655432 235668999999998753
No 111
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=26.05 E-value=15 Score=20.81 Aligned_cols=26 Identities=38% Similarity=0.779 Sum_probs=13.8
Q ss_pred CccccccCCCCCCccccCCCC-Ccccchhhh
Q psy12567 78 GRECVNCGAISTPLWRRDGTG-HYLCNACGL 107 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G-~~lCNaCGl 107 (142)
.+.|..||+...+. +.| ..+|.+||.
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcC
Confidence 46788888876543 334 568888887
No 112
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=25.88 E-value=13 Score=22.20 Aligned_cols=30 Identities=27% Similarity=0.719 Sum_probs=13.7
Q ss_pred cccccCCCCCCcc----ccCCCCC---cccchhhhhH
Q psy12567 80 ECVNCGAISTPLW----RRDGTGH---YLCNACGLYH 109 (142)
Q Consensus 80 ~C~nC~tt~Tp~W----Rr~~~G~---~lCNaCGly~ 109 (142)
.|.+|+..+.-.| |..+++. +.|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 3566666554332 3344442 5677776543
No 113
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=25.86 E-value=49 Score=26.15 Aligned_cols=32 Identities=19% Similarity=0.292 Sum_probs=23.1
Q ss_pred CCCcccccCCCCCCCCcccCCCCccccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g~~lCnacg~ 49 (142)
.+-..|+.||......+-.-..|..+|..|..
T Consensus 145 p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 145 LDLDKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred cccCccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 45568999998544455555578899999954
No 114
>KOG3740|consensus
Probab=25.77 E-value=27 Score=33.26 Aligned_cols=33 Identities=27% Similarity=0.626 Sum_probs=29.3
Q ss_pred CCCcccccCCCCCCCCcccCCCC----cccccccccc
Q psy12567 18 TEGRECVNCGAISTPLWRRDGTG----HYLCNARLFS 50 (142)
Q Consensus 18 ~~~~~C~nCgt~~TplWr~~~~g----~~lCnacg~~ 50 (142)
++..+|.-|.+.-||.|..-..+ +.+|-+|..+
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtS 496 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTS 496 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhhh
Confidence 56889999999999999998887 8999999765
No 115
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=25.73 E-value=30 Score=24.23 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=21.9
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhhhHHhc
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 112 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~ 112 (142)
...|.-|+...+-.+ -|...|+||..|++..
T Consensus 3 ~~~C~VCg~~a~g~h----yGv~sC~aCk~FFRR~ 33 (89)
T cd07166 3 VVLCKVCGDKASGFH----YGVHACEGCKGFFRRS 33 (89)
T ss_pred CCCCcccCccCcceE----EChhhhhhHhhEecce
Confidence 346888887655432 4567899999988864
No 116
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=25.54 E-value=53 Score=23.03 Aligned_cols=32 Identities=25% Similarity=0.438 Sum_probs=22.6
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
...|.-|+...+-. --|...|+||..+++..-
T Consensus 6 ~~~C~VCg~~~~g~----hyGv~sC~aCk~FFRR~v 37 (90)
T cd07168 6 PKLCSICEDKATGL----HYGIITCEGCKGFFKRTV 37 (90)
T ss_pred CCCCcccCCcCcce----EECceehhhhhHhhhhhh
Confidence 45688898755432 235678999999988743
No 117
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=25.03 E-value=51 Score=22.47 Aligned_cols=31 Identities=19% Similarity=0.513 Sum_probs=21.4
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
..|.-|+...+-. .-|..-|+||..+++..-
T Consensus 3 ~~C~VCg~~a~g~----hyGv~sC~aC~~FFRR~v 33 (78)
T cd07172 3 KICLVCSDEASGC----HYGVLTCGSCKVFFKRAV 33 (78)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHe
Confidence 4588888654432 235668999999988754
No 118
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=24.85 E-value=55 Score=22.58 Aligned_cols=31 Identities=19% Similarity=0.499 Sum_probs=21.8
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
..|.-|+...+-. --|...|+||..|++..-
T Consensus 4 ~~C~VCg~~~~g~----hyGv~sC~aC~~FFRR~v 34 (82)
T cd07171 4 HFCAVCSDYASGY----HYGVWSCEGCKAFFKRSI 34 (82)
T ss_pred CCCeecCCcCcce----EECceeehhhHHhHHHHe
Confidence 4688888655432 235668999999998754
No 119
>KOG0909|consensus
Probab=24.20 E-value=54 Score=30.14 Aligned_cols=38 Identities=29% Similarity=0.524 Sum_probs=26.6
Q ss_pred CCcccccCCCCC-CCCcccCCC------C-----cccccccccccccccc
Q psy12567 19 EGRECVNCGAIS-TPLWRRDGT------G-----HYLCNARLFSTSFTGY 56 (142)
Q Consensus 19 ~~~~C~nCgt~~-TplWr~~~~------g-----~~lCnacg~~~k~~G~ 56 (142)
..+.|..||... +++=...|+ | -|.||+||....++-|
T Consensus 160 N~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRY 209 (500)
T KOG0909|consen 160 NNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRY 209 (500)
T ss_pred CCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCccc
Confidence 456899999966 555443333 2 4789999988777665
No 120
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=24.00 E-value=49 Score=23.89 Aligned_cols=32 Identities=16% Similarity=0.432 Sum_probs=23.0
Q ss_pred CccccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 78 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 78 ~~~C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
...|.-|+...+-. --|...|+||..|++..-
T Consensus 18 ~~~C~VCg~~a~g~----hyGv~sC~aCk~FFRR~v 49 (101)
T cd07160 18 NEVCSVCGDKASGF----HYNVLSCEGCKGFFRRSV 49 (101)
T ss_pred CCCCeecCCcCcce----EECcceehhhhhhhhhcc
Confidence 45799999755432 235678999999988653
No 121
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=23.47 E-value=50 Score=25.43 Aligned_cols=12 Identities=17% Similarity=0.384 Sum_probs=8.3
Q ss_pred CCcccccccccc
Q psy12567 39 TGHYLCNARLFS 50 (142)
Q Consensus 39 ~g~~lCnacg~~ 50 (142)
.|.+.|..||..
T Consensus 110 ~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 110 PGTLVCENCGHE 121 (146)
T ss_pred CceEecccCCCE
Confidence 367788888644
No 122
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=23.43 E-value=1.1e+02 Score=26.87 Aligned_cols=31 Identities=29% Similarity=0.547 Sum_probs=21.9
Q ss_pred CCCccccccCCCCCCccccCCCC-Ccccchhhh
Q psy12567 76 TEGRECVNCGAISTPLWRRDGTG-HYLCNACGL 107 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WRr~~~G-~~lCNaCGl 107 (142)
..-+.|.| .....--|=-..++ ..+|-||-+
T Consensus 51 ~~~~~C~N-~~~~~CNWlvp~~~~~~~C~aCrl 82 (343)
T PF10005_consen 51 RRYRRCAN-AEHAVCNWLVPADDPDALCRACRL 82 (343)
T ss_pred ceeeeCCC-CCccccceeecCCCCCCcchhhhc
Confidence 45688999 66666678765554 689999943
No 123
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.42 E-value=33 Score=20.78 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=13.8
Q ss_pred ccccccCCCCCCccccCCCCCcccchhhh
Q psy12567 79 RECVNCGAISTPLWRRDGTGHYLCNACGL 107 (142)
Q Consensus 79 ~~C~nC~tt~Tp~WRr~~~G~~lCNaCGl 107 (142)
-.|.+||+..+-. ...+...|..||-
T Consensus 4 y~C~~CG~~~~~~---~~~~~~~Cp~CG~ 29 (46)
T PRK00398 4 YKCARCGREVELD---EYGTGVRCPYCGY 29 (46)
T ss_pred EECCCCCCEEEEC---CCCCceECCCCCC
Confidence 3577777755321 1111456777775
No 124
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=23.30 E-value=53 Score=24.73 Aligned_cols=19 Identities=16% Similarity=0.093 Sum_probs=16.1
Q ss_pred CCCcccCCCCccccccccc
Q psy12567 31 TPLWRRDGTGHYLCNARLF 49 (142)
Q Consensus 31 TplWr~~~~g~~lCnacg~ 49 (142)
.+.|.....|.|+|-.|+.
T Consensus 23 g~y~~~~~~G~Y~C~~Cg~ 41 (119)
T PRK05508 23 GEYNDFFEKGTYVCKQCGA 41 (119)
T ss_pred CCCcCcCCCeEEEecCCCC
Confidence 4688888899999999983
No 125
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.99 E-value=50 Score=17.64 Aligned_cols=6 Identities=83% Similarity=1.885 Sum_probs=2.5
Q ss_pred cccCCC
Q psy12567 23 CVNCGA 28 (142)
Q Consensus 23 C~nCgt 28 (142)
|.+||+
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 344443
No 126
>KOG0818|consensus
Probab=22.98 E-value=38 Score=31.78 Aligned_cols=28 Identities=25% Similarity=0.789 Sum_probs=0.0
Q ss_pred CCcccccCCCCCCCCcccCCCCccccccc
Q psy12567 19 EGRECVNCGAISTPLWRRDGTGHYLCNAR 47 (142)
Q Consensus 19 ~~~~C~nCgt~~TplWr~~~~g~~lCnac 47 (142)
+..+|.+||+.. |.|-.=.-|-+||..|
T Consensus 7 ~~evC~DC~~~d-p~WASvnrGt~lC~eC 34 (669)
T KOG0818|consen 7 SSEVCADCSGPD-PSWASVNRGTFLCDEC 34 (669)
T ss_pred hhhhhcccCCCC-CcceeecCceEehHhh
No 127
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.68 E-value=39 Score=28.92 Aligned_cols=31 Identities=32% Similarity=0.643 Sum_probs=23.9
Q ss_pred CCCccccccCCCCCCccccCCCC-CcccchhhhhHH
Q psy12567 76 TEGRECVNCGAISTPLWRRDGTG-HYLCNACGLYHK 110 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WRr~~~G-~~lCNaCGly~k 110 (142)
...+.|..||+...+. ..| ..+|+.||.+++
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 4579999999998764 233 689999998544
No 128
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.48 E-value=69 Score=17.61 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=11.1
Q ss_pred cccCCCCCCCCcccCCCCcccccccc
Q psy12567 23 CVNCGAISTPLWRRDGTGHYLCNARL 48 (142)
Q Consensus 23 C~nCgt~~TplWr~~~~g~~lCnacg 48 (142)
|+.||..-.|. .-.-.|.|..||
T Consensus 1 C~sC~~~i~~r---~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPR---EQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCc---ccCceEeCCCCC
Confidence 45555554441 111246676665
No 129
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=22.13 E-value=36 Score=23.51 Aligned_cols=29 Identities=21% Similarity=0.523 Sum_probs=19.2
Q ss_pred ccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 81 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 81 C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
|.-|+...+-.+ -|...|+||..+++..-
T Consensus 2 C~VCg~~~~g~h----yGv~sC~aCk~FFRR~v 30 (84)
T cd06965 2 CRVCGDKASGFH----YGVHACEGCKGFFRRTI 30 (84)
T ss_pred CcccCccCcceE----EChhhhhhhhhheeeee
Confidence 666775444332 35568999999888643
No 130
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=22.07 E-value=50 Score=26.22 Aligned_cols=31 Identities=26% Similarity=0.598 Sum_probs=25.4
Q ss_pred CCCccccccCCCCCCccccCCCCCcccchhh
Q psy12567 76 TEGRECVNCGAISTPLWRRDGTGHYLCNACG 106 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~WRr~~~G~~lCNaCG 106 (142)
..-..|..||+.....+-.-.+|..+|..|+
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3456899999887767777788899999996
No 131
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.62 E-value=40 Score=28.81 Aligned_cols=36 Identities=22% Similarity=0.433 Sum_probs=25.7
Q ss_pred CCCCccccccCCCCCCcc----ccCCCC---CcccchhhhhHH
Q psy12567 75 FTEGRECVNCGAISTPLW----RRDGTG---HYLCNACGLYHK 110 (142)
Q Consensus 75 ~~~~~~C~nC~tt~Tp~W----Rr~~~G---~~lCNaCGly~k 110 (142)
......|..|+-.....| |..+++ -++|..||-.|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 345689999998887544 333444 369999998776
No 132
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.28 E-value=39 Score=25.43 Aligned_cols=31 Identities=26% Similarity=0.285 Sum_probs=19.7
Q ss_pred CCCcccccCCCCCCCC--c-ccCCCCcccccccc
Q psy12567 18 TEGRECVNCGAISTPL--W-RRDGTGHYLCNARL 48 (142)
Q Consensus 18 ~~~~~C~nCgt~~Tpl--W-r~~~~g~~lCnacg 48 (142)
.....|.+||..-|.+ - -.+++|.+.|..||
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg 130 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCG 130 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCC
Confidence 4466788888766541 1 11456678888885
No 133
>PF15396 FAM60A: Protein Family FAM60A
Probab=20.66 E-value=50 Score=27.27 Aligned_cols=11 Identities=55% Similarity=0.975 Sum_probs=8.9
Q ss_pred ccchhhhhHHh
Q psy12567 101 LCNACGLYHKM 111 (142)
Q Consensus 101 lCNaCGly~k~ 111 (142)
+||||-|..++
T Consensus 51 ICNACVLLVKR 61 (213)
T PF15396_consen 51 ICNACVLLVKR 61 (213)
T ss_pred hhHHHHHHHHH
Confidence 89999995555
No 134
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=20.60 E-value=60 Score=21.59 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=17.8
Q ss_pred ccccCCCCCCccccCCCCCcccchhhhhHHhc
Q psy12567 81 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 112 (142)
Q Consensus 81 C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~ 112 (142)
|.-|+...+-. .-|...|+||..++++.
T Consensus 1 C~VCg~~~~g~----hyGv~~C~aC~~FFRR~ 28 (73)
T cd07158 1 CKVCGDKASGF----HYGVHSCEGCKGFFRRT 28 (73)
T ss_pred CcccCccCcce----EECcchhhHHHHHHhhh
Confidence 44565544422 23556899999998864
No 135
>COG3952 Predicted membrane protein [Function unknown]
Probab=20.59 E-value=24 Score=26.41 Aligned_cols=20 Identities=35% Similarity=0.669 Sum_probs=13.6
Q ss_pred ccccCCCCCcccchhhhhHHh
Q psy12567 91 LWRRDGTGHYLCNACGLYHKM 111 (142)
Q Consensus 91 ~WRr~~~G~~lCNaCGly~k~ 111 (142)
+||.||- ..+|++||++-.+
T Consensus 76 i~~~DpV-~Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPV-FVLGQACGLFIYL 95 (113)
T ss_pred HHhcchH-HHHHHhhhHHHHH
Confidence 4555555 4699999996544
No 136
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=20.57 E-value=59 Score=22.21 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=18.4
Q ss_pred ccccCCCCCCccccCCCCCcccchhhhhHHhcC
Q psy12567 81 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 113 (142)
Q Consensus 81 C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~~ 113 (142)
|.-|+...+-. --|...|+||..+++..-
T Consensus 1 C~VCg~~~~g~----hyG~~sC~aC~~FFRR~~ 29 (81)
T cd07165 1 CKVCGDKASGY----HYGVTSCEGCKGFFRRSI 29 (81)
T ss_pred CCccCccCcce----EECchhhhhHHHHHHhHh
Confidence 44566544322 235668999999888743
No 137
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.28 E-value=36 Score=21.45 Aligned_cols=31 Identities=29% Similarity=0.651 Sum_probs=21.6
Q ss_pred CCCccccccCCCCCCc----cccCCCCCcccchhhh
Q psy12567 76 TEGRECVNCGAISTPL----WRRDGTGHYLCNACGL 107 (142)
Q Consensus 76 ~~~~~C~nC~tt~Tp~----WRr~~~G~~lCNaCGl 107 (142)
-.+..|..|+..-+|. ++++ ++-..|..||-
T Consensus 20 v~~~~C~gC~~~l~~~~~~~i~~~-~~i~~Cp~CgR 54 (56)
T PF02591_consen 20 VEGGTCSGCHMELPPQELNEIRKG-DEIVFCPNCGR 54 (56)
T ss_pred eeCCccCCCCEEcCHHHHHHHHcC-CCeEECcCCCc
Confidence 3456899999988885 3333 44578888874
No 138
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=20.07 E-value=61 Score=21.77 Aligned_cols=28 Identities=32% Similarity=0.737 Sum_probs=17.7
Q ss_pred ccccCCCCCCccccCCCCCcccchhhhhHHhc
Q psy12567 81 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 112 (142)
Q Consensus 81 C~nC~tt~Tp~WRr~~~G~~lCNaCGly~k~~ 112 (142)
|.-|+...+-. .-|...|+||..+++..
T Consensus 1 C~VC~~~~~g~----hygv~sC~aCk~FFRR~ 28 (75)
T cd07155 1 CLVCGDIASGY----HYGVASCEACKAFFKRT 28 (75)
T ss_pred CcccCccCcce----EEChhhhhhhHHHHHHH
Confidence 44555443322 23556899999998874
No 139
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.04 E-value=94 Score=32.05 Aligned_cols=49 Identities=27% Similarity=0.516 Sum_probs=30.5
Q ss_pred CcccccCCCCCCCCcccCCCCcccccccccccccccccccccccccCCCccccccCCCCccccccCCCCCC-ccccCC
Q psy12567 20 GRECVNCGAISTPLWRRDGTGHYLCNARLFSTSFTGYFIMSRFLFASLPVEDIEYFTEGRECVNCGAISTP-LWRRDG 96 (142)
Q Consensus 20 ~~~C~nCgt~~TplWr~~~~g~~lCnacg~~~k~~G~~~~~R~~~~~~~~~~~~~~~~~~~C~nC~tt~Tp-~WRr~~ 96 (142)
...|.+||+..+|. +.|..||..... . ++ . ...|.+|++..++ .+++-+
T Consensus 679 ~~fCP~CGs~te~v--------y~CPsCGaev~~----------------d--es-~-a~~CP~CGtplv~~~~~~i~ 728 (1337)
T PRK14714 679 ENRCPDCGTHTEPV--------YVCPDCGAEVPP----------------D--ES-G-RVECPRCDVELTPYQRRTIN 728 (1337)
T ss_pred cccCcccCCcCCCc--------eeCccCCCccCC----------------C--cc-c-cccCCCCCCcccccceEEec
Confidence 34899999987664 489999642110 0 01 1 4579999988766 344433
Done!