Query psy15323
Match_columns 139
No_of_seqs 157 out of 826
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:04:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15323.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15323hhsearch_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 99.6 2.5E-16 5.4E-21 99.8 3.2 41 64-104 1-42 (54)
2 cd00202 ZnF_GATA Zinc finger D 99.5 2.7E-15 5.8E-20 95.0 1.3 43 10-52 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 1.1E-14 2.4E-19 91.5 3.3 43 62-104 3-47 (52)
4 smart00401 ZnF_GATA zinc finge 99.5 9.3E-15 2E-19 91.9 2.7 45 7-51 2-48 (52)
5 PF00320 GATA: GATA zinc finge 99.4 2.6E-14 5.5E-19 83.5 1.6 35 65-99 1-36 (36)
6 PF00320 GATA: GATA zinc finge 99.4 3.7E-14 8E-19 82.8 -0.4 34 11-44 1-35 (36)
7 COG5641 GAT1 GATA Zn-finger-co 99.3 2.2E-12 4.7E-17 112.4 4.3 97 8-104 158-341 (498)
8 KOG1601|consensus 99.1 1.2E-10 2.5E-15 90.3 5.8 95 9-103 143-241 (340)
9 COG5641 GAT1 GATA Zn-finger-co 98.8 3.7E-09 8E-14 92.4 2.4 53 62-124 158-216 (498)
10 KOG1601|consensus 98.3 2.8E-07 6E-12 71.3 2.9 42 8-49 199-241 (340)
11 TIGR01384 TFS_arch transcripti 91.0 0.23 5E-06 34.5 2.7 80 10-94 2-101 (104)
12 PF08271 TF_Zn_Ribbon: TFIIB z 89.7 0.22 4.8E-06 29.4 1.5 27 10-38 2-28 (43)
13 PF06677 Auto_anti-p27: Sjogre 89.3 0.31 6.7E-06 29.0 1.9 25 8-36 17-41 (41)
14 KOG3554|consensus 88.2 0.32 7E-06 43.1 2.1 37 61-97 385-424 (693)
15 PF11781 RRN7: RNA polymerase 85.9 0.65 1.4E-05 26.8 1.9 32 2-37 2-33 (36)
16 KOG3554|consensus 84.8 0.35 7.5E-06 42.9 0.5 40 4-43 382-424 (693)
17 PF14803 Nudix_N_2: Nudix N-te 81.0 0.88 1.9E-05 26.0 1.1 26 9-37 1-30 (34)
18 smart00105 ArfGap Putative GTP 81.0 0.85 1.8E-05 32.3 1.2 39 7-46 2-40 (112)
19 PRK14559 putative protein seri 80.8 1.6 3.5E-05 40.0 3.2 23 9-38 2-24 (645)
20 COG5347 GTPase-activating prot 79.0 1.4 3E-05 37.1 2.1 39 6-45 18-56 (319)
21 COG1645 Uncharacterized Zn-fin 78.1 1.3 2.9E-05 32.8 1.5 26 8-38 28-53 (131)
22 PRK12286 rpmF 50S ribosomal pr 77.9 1.8 4E-05 27.4 1.9 28 4-39 23-50 (57)
23 PF01412 ArfGap: Putative GTPa 77.1 1.5 3.2E-05 31.2 1.5 39 5-44 10-48 (116)
24 PF12773 DZR: Double zinc ribb 75.3 3 6.4E-05 24.9 2.3 10 62-71 29-38 (50)
25 PRK03564 formate dehydrogenase 74.9 3.2 7E-05 34.8 3.1 70 8-96 187-265 (309)
26 KOG0703|consensus 74.8 1.8 4E-05 35.9 1.6 31 6-37 23-53 (287)
27 PF04216 FdhE: Protein involve 74.7 0.78 1.7E-05 37.5 -0.6 71 8-97 172-252 (290)
28 PF13248 zf-ribbon_3: zinc-rib 73.3 2 4.4E-05 22.7 1.1 22 9-37 3-24 (26)
29 PRK00420 hypothetical protein; 72.5 3 6.5E-05 30.0 2.1 29 8-40 23-51 (112)
30 TIGR01562 FdhE formate dehydro 72.2 3.5 7.7E-05 34.5 2.8 70 8-96 184-265 (305)
31 PRK00423 tfb transcription ini 70.7 3.4 7.3E-05 34.2 2.3 34 3-38 6-39 (310)
32 PLN03114 ADP-ribosylation fact 67.9 4 8.6E-05 35.2 2.2 40 6-46 20-59 (395)
33 KOG0706|consensus 67.6 3.1 6.8E-05 36.5 1.6 40 6-46 21-60 (454)
34 PF12760 Zn_Tnp_IS1595: Transp 67.0 5.9 0.00013 23.5 2.3 30 6-37 16-45 (46)
35 PF02318 FYVE_2: FYVE-type zin 66.9 2.9 6.4E-05 29.8 1.1 50 7-91 53-102 (118)
36 PRK03988 translation initiatio 66.9 2.3 5.1E-05 31.6 0.6 30 62-91 102-131 (138)
37 smart00653 eIF2B_5 domain pres 65.7 3.1 6.7E-05 29.7 1.0 28 10-37 82-109 (110)
38 smart00653 eIF2B_5 domain pres 65.5 2.7 5.8E-05 30.1 0.6 30 62-91 80-109 (110)
39 TIGR00311 aIF-2beta translatio 64.5 2.9 6.2E-05 30.9 0.6 30 62-91 97-126 (133)
40 PF09723 Zn-ribbon_8: Zinc rib 64.1 3.6 7.7E-05 24.2 0.9 15 29-43 5-20 (42)
41 smart00778 Prim_Zn_Ribbon Zinc 63.5 6.4 0.00014 22.8 1.9 29 9-37 4-33 (37)
42 PRK14892 putative transcriptio 61.5 5.2 0.00011 28.1 1.5 35 61-95 20-54 (99)
43 smart00105 ArfGap Putative GTP 60.2 4.4 9.6E-05 28.6 0.9 43 62-105 3-49 (112)
44 smart00661 RPOL9 RNA polymeras 60.0 8.6 0.00019 22.9 2.1 30 9-41 1-32 (52)
45 PF01873 eIF-5_eIF-2B: Domain 57.2 5.9 0.00013 28.9 1.2 29 63-91 94-122 (125)
46 PF01783 Ribosomal_L32p: Ribos 56.1 6.8 0.00015 24.5 1.2 27 5-39 23-49 (56)
47 PRK12336 translation initiatio 55.8 5.4 0.00012 31.2 0.9 30 10-39 100-129 (201)
48 PF09297 zf-NADH-PPase: NADH p 55.3 9.7 0.00021 20.8 1.6 28 8-38 3-30 (32)
49 PF07754 DUF1610: Domain of un 55.2 8.9 0.00019 20.2 1.4 24 11-37 1-24 (24)
50 PF07282 OrfB_Zn_ribbon: Putat 54.8 9.2 0.0002 24.2 1.7 29 7-38 27-55 (69)
51 PLN03119 putative ADP-ribosyla 54.0 8.9 0.00019 35.0 2.0 34 5-39 20-53 (648)
52 PRK14559 putative protein seri 53.9 12 0.00025 34.5 2.8 46 5-78 12-57 (645)
53 COG3529 Predicted nucleic-acid 53.2 4.2 9.1E-05 26.4 -0.1 33 61-93 9-42 (66)
54 PRK12336 translation initiatio 52.6 5.7 0.00012 31.1 0.5 30 62-91 98-127 (201)
55 KOG3740|consensus 52.3 5.4 0.00012 36.6 0.4 34 6-39 460-497 (706)
56 PLN03131 hypothetical protein; 51.4 10 0.00022 34.9 2.0 33 5-38 20-52 (705)
57 PF01412 ArfGap: Putative GTPa 51.3 15 0.00032 26.0 2.5 37 60-97 11-47 (116)
58 smart00659 RPOLCX RNA polymera 51.2 9.9 0.00021 22.7 1.3 24 10-37 4-27 (44)
59 PRK11827 hypothetical protein; 50.8 16 0.00034 23.5 2.2 33 10-45 10-43 (60)
60 PF01363 FYVE: FYVE zinc finge 50.2 6.2 0.00013 25.0 0.3 56 7-92 8-66 (69)
61 KOG2907|consensus 50.1 7.8 0.00017 28.1 0.8 82 7-91 6-110 (116)
62 PRK08351 DNA-directed RNA poly 49.2 11 0.00025 24.2 1.4 16 8-23 15-31 (61)
63 TIGR02605 CxxC_CxxC_SSSS putat 48.5 10 0.00022 22.7 1.1 27 10-37 7-34 (52)
64 PRK14890 putative Zn-ribbon RN 48.2 15 0.00033 23.6 1.9 31 5-38 4-34 (59)
65 COG2888 Predicted Zn-ribbon RN 48.1 11 0.00023 24.4 1.1 27 8-37 9-35 (61)
66 TIGR01031 rpmF_bact ribosomal 47.6 14 0.00031 23.0 1.7 28 4-39 22-49 (55)
67 PF01096 TFIIS_C: Transcriptio 47.3 9 0.00019 22.1 0.7 30 10-39 2-38 (39)
68 smart00834 CxxC_CXXC_SSSS Puta 47.0 11 0.00023 21.3 0.9 8 30-37 6-13 (41)
69 PF10058 DUF2296: Predicted in 46.9 13 0.00029 23.1 1.5 30 8-37 22-52 (54)
70 smart00440 ZnF_C2C2 C2C2 Zinc 46.5 13 0.00028 21.6 1.3 30 10-39 2-38 (40)
71 PHA00626 hypothetical protein 45.2 9.9 0.00021 24.3 0.7 32 64-95 2-35 (59)
72 PF13240 zinc_ribbon_2: zinc-r 45.0 13 0.00028 19.1 1.0 6 11-16 2-7 (23)
73 PF09526 DUF2387: Probable met 44.4 15 0.00032 24.3 1.4 37 8-44 8-45 (71)
74 KOG3740|consensus 44.0 8.8 0.00019 35.3 0.4 32 60-91 460-495 (706)
75 PF03604 DNA_RNApol_7kD: DNA d 43.6 20 0.00044 20.0 1.7 24 10-37 2-25 (32)
76 PRK06393 rpoE DNA-directed RNA 43.5 16 0.00035 23.8 1.5 16 8-23 17-33 (64)
77 PF04810 zf-Sec23_Sec24: Sec23 43.2 17 0.00037 21.0 1.5 32 8-39 2-34 (40)
78 COG1405 SUA7 Transcription ini 43.1 16 0.00034 30.3 1.7 29 9-39 2-30 (285)
79 PF06689 zf-C4_ClpX: ClpX C4-t 43.0 8.4 0.00018 22.5 0.1 29 9-37 2-32 (41)
80 PF09538 FYDLN_acid: Protein o 42.8 18 0.00038 25.8 1.7 31 5-39 6-36 (108)
81 KOG1598|consensus 42.1 16 0.00035 32.8 1.7 28 9-38 1-28 (521)
82 PRK14714 DNA polymerase II lar 42.1 23 0.0005 35.2 2.9 21 9-38 668-688 (1337)
83 PF09526 DUF2387: Probable met 41.2 15 0.00033 24.2 1.1 35 61-95 7-42 (71)
84 PRK00432 30S ribosomal protein 40.6 21 0.00045 21.9 1.6 26 8-37 20-45 (50)
85 PRK11823 DNA repair protein Ra 39.7 17 0.00038 31.6 1.6 29 8-43 7-35 (446)
86 TIGR02443 conserved hypothetic 38.6 20 0.00043 23.0 1.3 34 8-41 9-43 (59)
87 cd01121 Sms Sms (bacterial rad 37.9 21 0.00045 30.5 1.7 27 10-43 2-28 (372)
88 PRK00423 tfb transcription ini 37.9 17 0.00038 30.0 1.3 17 62-78 30-53 (310)
89 PRK01110 rpmF 50S ribosomal pr 37.0 21 0.00046 22.7 1.3 26 5-39 24-49 (60)
90 PF08273 Prim_Zn_Ribbon: Zinc- 36.9 30 0.00065 20.3 1.8 26 10-35 5-32 (40)
91 smart00064 FYVE Protein presen 35.7 47 0.001 20.7 2.8 28 64-91 36-64 (68)
92 TIGR00416 sms DNA repair prote 34.6 23 0.00051 30.9 1.6 29 8-43 7-35 (454)
93 COG5347 GTPase-activating prot 33.6 28 0.0006 29.4 1.8 35 59-94 17-51 (319)
94 COG1405 SUA7 Transcription ini 33.4 20 0.00042 29.7 0.8 26 64-91 3-28 (285)
95 PRK04023 DNA polymerase II lar 33.1 37 0.00079 33.2 2.6 42 28-90 625-670 (1121)
96 COG2835 Uncharacterized conser 32.9 33 0.00072 22.1 1.7 32 14-45 11-43 (60)
97 KOG1729|consensus 32.2 19 0.00041 29.9 0.6 26 7-37 167-193 (288)
98 KOG1598|consensus 32.1 26 0.00056 31.5 1.4 26 64-91 2-27 (521)
99 KOG0706|consensus 30.1 28 0.00061 30.7 1.3 41 58-99 19-59 (454)
100 PRK00085 recO DNA repair prote 29.7 40 0.00087 26.3 2.1 31 6-36 147-177 (247)
101 COG2816 NPY1 NTP pyrophosphohy 29.6 33 0.00071 28.5 1.6 28 8-38 111-138 (279)
102 PF08792 A2L_zn_ribbon: A2L zi 29.5 56 0.0012 18.3 2.1 28 8-38 3-30 (33)
103 PF15396 FAM60A: Protein Famil 29.2 27 0.00059 27.9 1.0 16 84-99 50-65 (213)
104 cd06955 NR_DBD_VDR DNA-binding 28.9 50 0.0011 23.4 2.2 33 7-43 5-37 (107)
105 COG1594 RPB9 DNA-directed RNA 28.8 26 0.00056 25.0 0.8 32 63-94 73-111 (113)
106 COG5525 Bacteriophage tail ass 28.6 39 0.00085 31.0 2.0 60 30-102 228-289 (611)
107 PF08274 PhnA_Zn_Ribbon: PhnA 28.3 26 0.00056 19.4 0.5 25 9-37 3-27 (30)
108 TIGR02300 FYDLN_acid conserved 27.8 43 0.00094 24.7 1.8 32 4-39 5-36 (129)
109 PF02701 zf-Dof: Dof domain, z 27.6 70 0.0015 20.8 2.5 41 62-102 5-49 (63)
110 PF04981 NMD3: NMD3 family ; 27.3 51 0.0011 26.1 2.3 52 11-79 1-53 (236)
111 PRK11788 tetratricopeptide rep 27.0 54 0.0012 26.5 2.4 20 63-82 369-388 (389)
112 PHA02942 putative transposase; 26.4 50 0.0011 28.2 2.2 28 7-38 324-351 (383)
113 PF01258 zf-dskA_traR: Prokary 26.3 8.1 0.00018 21.7 -1.8 28 9-36 4-31 (36)
114 PRK00398 rpoP DNA-directed RNA 25.9 52 0.0011 19.2 1.6 26 10-38 5-30 (46)
115 TIGR00613 reco DNA repair prot 25.8 56 0.0012 25.3 2.2 32 6-37 145-176 (241)
116 PF04161 Arv1: Arv1-like famil 25.8 34 0.00075 26.6 1.0 29 10-38 2-33 (208)
117 cd02337 ZZ_CBP Zinc finger, ZZ 25.5 41 0.00089 19.6 1.1 29 10-38 2-31 (41)
118 COG3183 Predicted restriction 25.4 21 0.00046 29.4 -0.2 41 30-70 196-249 (272)
119 KOG0703|consensus 25.3 36 0.00079 28.4 1.1 29 61-90 24-52 (287)
120 PF10571 UPF0547: Uncharacteri 25.1 58 0.0013 17.2 1.5 8 30-37 15-22 (26)
121 PRK12495 hypothetical protein; 24.6 40 0.00087 27.2 1.2 31 5-40 39-69 (226)
122 cd07169 NR_DBD_GCNF_like DNA-b 24.2 39 0.00085 23.0 0.9 34 5-42 3-36 (90)
123 TIGR03573 WbuX N-acetyl sugar 23.8 48 0.001 27.7 1.6 32 9-41 2-33 (343)
124 COG4888 Uncharacterized Zn rib 23.6 36 0.00077 24.2 0.6 30 64-93 24-56 (104)
125 PF03811 Zn_Tnp_IS1: InsA N-te 23.5 55 0.0012 18.7 1.3 28 61-89 4-35 (36)
126 smart00531 TFIIE Transcription 23.4 36 0.00078 25.0 0.7 8 30-37 100-107 (147)
127 cd06966 NR_DBD_CAR DNA-binding 23.3 52 0.0011 22.6 1.4 31 9-43 1-31 (94)
128 cd06964 NR_DBD_RAR DNA-binding 23.2 67 0.0015 21.6 1.9 32 7-42 3-34 (85)
129 PF13695 zf-3CxxC: Zinc-bindin 23.0 34 0.00074 23.5 0.4 18 60-77 36-53 (98)
130 TIGR00100 hypA hydrogenase nic 22.9 40 0.00086 23.9 0.8 8 30-37 71-78 (115)
131 COG1499 NMD3 NMD protein affec 22.9 50 0.0011 28.3 1.5 62 5-83 3-65 (355)
132 PF07191 zinc-ribbons_6: zinc- 22.9 42 0.00092 22.2 0.9 55 10-90 3-57 (70)
133 cd07168 NR_DBD_DHR4_like DNA-b 21.6 60 0.0013 22.0 1.5 32 62-97 6-37 (90)
134 COG0675 Transposase and inacti 21.5 63 0.0014 25.5 1.8 25 6-38 307-331 (364)
135 COG0333 RpmF Ribosomal protein 21.2 69 0.0015 20.3 1.5 26 6-39 25-50 (57)
136 PF01286 XPA_N: XPA protein N- 20.5 47 0.001 18.9 0.6 29 8-36 3-31 (34)
137 PF00569 ZZ: Zinc finger, ZZ t 20.3 77 0.0017 18.6 1.6 31 62-92 4-37 (46)
138 PLN03114 ADP-ribosylation fact 20.3 65 0.0014 27.9 1.7 38 60-98 20-57 (395)
139 cd07173 NR_DBD_AR DNA-binding 20.1 49 0.0011 22.2 0.8 32 7-42 2-33 (82)
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=99.62 E-value=2.5e-16 Score=99.81 Aligned_cols=41 Identities=59% Similarity=1.237 Sum_probs=37.7
Q ss_pred ccccCCCCCCcceecCCCC-CcccchhhhhHHhhCCCCCchh
Q psy15323 64 CCTNCGTRMTTLWRRNNDG-EPVCNACGLYYKLHNVNRPLAM 104 (139)
Q Consensus 64 ~C~~C~t~~t~~Wr~~~~g-~~lCnaCgly~~~~~~~Rp~~~ 104 (139)
+|+||++++||+||+++++ .+|||||||||++++..||++.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCccc
Confidence 5999999999999999955 5999999999999999999953
No 2
>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=99.52 E-value=2.7e-15 Score=95.05 Aligned_cols=43 Identities=58% Similarity=1.189 Sum_probs=39.6
Q ss_pred ccccCCCCCCCceeecCC-CCcccccccccccccCCCCCCCCCc
Q psy15323 10 ECVNCGAISTPLWRRDGT-GHYLCNACGLYHKMNGMNRPLVKPS 52 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~-g~~lCnaCgly~k~hg~nRP~~kps 52 (139)
+|+||++++||+||++++ +.+||||||||+++++..||.....
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 599999999999999995 4899999999999999999998765
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.51 E-value=1.1e-14 Score=91.52 Aligned_cols=43 Identities=58% Similarity=1.208 Sum_probs=39.6
Q ss_pred CcccccCCCCCCcceecCCCCC-cccchhhhhHHhhCCC-CCchh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGE-PVCNACGLYYKLHNVN-RPLAM 104 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~-~lCnaCgly~~~~~~~-Rp~~~ 104 (139)
...|+||++++||+||+++.|. .|||||||||++++.. ||.++
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~ 47 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSL 47 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCcccc
Confidence 4689999999999999999997 9999999999999998 99853
No 4
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=9.3e-15 Score=91.85 Aligned_cols=45 Identities=58% Similarity=1.132 Sum_probs=40.2
Q ss_pred CCCccccCCCCCCCceeecCCCC-cccccccccccccCCC-CCCCCC
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGH-YLCNACGLYHKMNGMN-RPLVKP 51 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~-~lCnaCgly~k~hg~n-RP~~kp 51 (139)
....|+||++++||+||+++.|. +||||||||++.++.. +|....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 46799999999999999999995 9999999999999887 777654
No 5
>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=99.45 E-value=2.6e-14 Score=83.50 Aligned_cols=35 Identities=54% Similarity=1.158 Sum_probs=27.7
Q ss_pred cccCCCCCCcceecCCCCC-cccchhhhhHHhhCCC
Q psy15323 65 CTNCGTRMTTLWRRNNDGE-PVCNACGLYYKLHNVN 99 (139)
Q Consensus 65 C~~C~t~~t~~Wr~~~~g~-~lCnaCgly~~~~~~~ 99 (139)
|++|+|++||+||++++|. +|||+|||||++|+++
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 8999999999999999998 5999999999998863
No 6
>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=99.39 E-value=3.7e-14 Score=82.82 Aligned_cols=34 Identities=59% Similarity=1.221 Sum_probs=27.4
Q ss_pred cccCCCCCCCceeecCCCCc-ccccccccccccCC
Q psy15323 11 CVNCGAISTPLWRRDGTGHY-LCNACGLYHKMNGM 44 (139)
Q Consensus 11 C~nC~~~~tp~WRr~~~g~~-lCnaCgly~k~hg~ 44 (139)
|+||++++||+||++++|.. ||||||+|+++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999965 99999999988764
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=99.29 E-value=2.2e-12 Score=112.42 Aligned_cols=97 Identities=42% Similarity=0.718 Sum_probs=75.4
Q ss_pred CCccccCCCCCCCceeecCC-----CCcccccccccccccCCCC-CCCCCcc----chh-----------h---c-----
Q psy15323 8 GRECVNCGAISTPLWRRDGT-----GHYLCNACGLYHKMNGMNR-PLVKPSK----RLT-----------A---T----- 58 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~-----g~~lCnaCgly~k~hg~nR-P~~kpsK----R~~-----------a---t----- 58 (139)
+.+|.||.++.||+|||+.. |.+||||||||+++|+..| |...+.. +.. . .
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~~~~~~~~n~~~~~~~n~~S~~~ 237 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRSSRSSHNNNDSNGENANTESIGN 237 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCcccccccccccccccccccccccccccccccccc
Confidence 45999999999999999998 8899999999999999999 8643221 000 0 0
Q ss_pred --------------c------------------------------------------ccCcccccCCC-CCCcceecCCC
Q psy15323 59 --------------R------------------------------------------RLGLCCTNCGT-RMTTLWRRNND 81 (139)
Q Consensus 59 --------------k------------------------------------------~~~~~C~~C~t-~~t~~Wr~~~~ 81 (139)
+ .....+++|.+ +.||+||+...
T Consensus 238 ~~~~~~~~s~~~~~~~~~~~~~~~~~~~~s~~~k~~~le~l~gs~~~~~~~tp~~~~ps~~~~s~~~~~~~tp~~~r~~~ 317 (498)
T COG5641 238 SSASKLTKSWEERPQGRQLLSDAGSLSPRSNNPKSPLLEGLMGSTSLQPVSTPKLVLPSDKKRSTLTTSTATPLWRRTSD 317 (498)
T ss_pred cccccccchhhhccccccccccccccccccCCCcchhhhhcccCccccccCCccccchhhcCcccccccccCcccccccc
Confidence 0 12345778876 67888887765
Q ss_pred -CCcccchhhhhHHhhCCCCCchh
Q psy15323 82 -GEPVCNACGLYYKLHNVNRPLAM 104 (139)
Q Consensus 82 -g~~lCnaCgly~~~~~~~Rp~~~ 104 (139)
..++||+|+++.+.++.+||+.+
T Consensus 318 ~~s~~~n~~~~~~~~~~~~~p~~p 341 (498)
T COG5641 318 KSSFSCNASGSALKPPGSKRPLLP 341 (498)
T ss_pred cccccccccccccCCcccccccCC
Confidence 45999999999999999999854
No 8
>KOG1601|consensus
Probab=99.11 E-value=1.2e-10 Score=90.28 Aligned_cols=95 Identities=44% Similarity=0.701 Sum_probs=70.1
Q ss_pred CccccCCCCCCCceeecCCCCcccccccccccccCCCC--CCCCCccchhhcccc-CcccccCCCCCCcceecCCCC-Cc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNR--PLVKPSKRLTATRRL-GLCCTNCGTRMTTLWRRNNDG-EP 84 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nR--P~~kpsKR~~atk~~-~~~C~~C~t~~t~~Wr~~~~g-~~ 84 (139)
..|.+++.+.+++|+.+..+.+++..+.++.......+ +.....+........ ...|++|+++.|++||+++.| ..
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~t~~~r~~~~g~~~ 222 (340)
T KOG1601|consen 143 GESVSSLLFPTPLQRRDSSGHYNSINKELKKKSNGESSSDLESKPKKSSSASSEQNLRQCSNCGTTKTPLWRRGPEGPKS 222 (340)
T ss_pred cccccccccccceeccCCCCccccccccccccccccccCCccccchhhhhccccccCcccCCCCCCCCcceecCCCCCcc
Confidence 37899999999999987666778888875544444444 222222222111112 579999999999999999999 69
Q ss_pred ccchhhhhHHhhCCCCCch
Q psy15323 85 VCNACGLYYKLHNVNRPLA 103 (139)
Q Consensus 85 lCnaCgly~~~~~~~Rp~~ 103 (139)
+|||||+||+.+...|++.
T Consensus 223 ~cnacgl~~k~~~~~r~~~ 241 (340)
T KOG1601|consen 223 LCNACGLRYKKGGVRRPLP 241 (340)
T ss_pred ccccchhhhhhcCcccccc
Confidence 9999999999999777773
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.75 E-value=3.7e-09 Score=92.40 Aligned_cols=53 Identities=47% Similarity=1.019 Sum_probs=46.3
Q ss_pred CcccccCCCCCCcceecCCC-----CCcccchhhhhHHhhCCCC-CchhhhcccCcccccccccccccC
Q psy15323 62 GLCCTNCGTRMTTLWRRNND-----GEPVCNACGLYYKLHNVNR-PLAMRHLAMRPLAMRKDGIQTRKR 124 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~-----g~~lCnaCgly~~~~~~~R-p~~~~~~~~~~~~~~~~~i~~~~r 124 (139)
..+|.||.|+.||+|||+.. |.+||||||||++.|+++| |+ .++.+.|+++.+
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~----------t~ks~~~ks~~~ 216 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPI----------SLKSDSIKSRSS 216 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCCCc----------cccccccccccc
Confidence 33899999999999999998 7799999999999999999 98 466677776664
No 10
>KOG1601|consensus
Probab=98.35 E-value=2.8e-07 Score=71.33 Aligned_cols=42 Identities=57% Similarity=1.117 Sum_probs=36.9
Q ss_pred CCccccCCCCCCCceeecCCC-CcccccccccccccCCCCCCC
Q psy15323 8 GRECVNCGAISTPLWRRDGTG-HYLCNACGLYHKMNGMNRPLV 49 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g-~~lCnaCgly~k~hg~nRP~~ 49 (139)
...|.+|+++.||+||++++| ..+|||||+|++++...++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~ 241 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLP 241 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCcccccc
Confidence 479999999999999999999 899999999999998444443
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=90.96 E-value=0.23 Score=34.45 Aligned_cols=80 Identities=25% Similarity=0.666 Sum_probs=44.8
Q ss_pred ccccCCCCCCCceeecCCCCccccccccccccc-CCC---C-CCCCC--c------cchhhccccCcccccCCCCCCcce
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN-GMN---R-PLVKP--S------KRLTATRRLGLCCTNCGTRMTTLW 76 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~h-g~n---R-P~~kp--s------KR~~atk~~~~~C~~C~t~~t~~W 76 (139)
.|.+||..-.+. .+.+.|..|+...... ..+ + .+... . ............|..|+-.+.--|
T Consensus 2 fC~~Cg~~l~~~-----~~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 2 FCPKCGSLMTPK-----NGVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYW 76 (104)
T ss_pred CCcccCcccccC-----CCeEECcCCCCccccccccccEEEEEeccccccceeeccccccCCCcccCCCCCCCCCeeEEE
Confidence 699999655432 3578999999754331 100 0 00000 0 000111234678999998775554
Q ss_pred ----ecCCCCC---cccchhhhhHH
Q psy15323 77 ----RRNNDGE---PVCNACGLYYK 94 (139)
Q Consensus 77 ----r~~~~g~---~lCnaCgly~~ 94 (139)
|..+++. ++|-.|+..|+
T Consensus 77 ~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 77 LLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred EeccCCCCCCcEEEEEeCCCCCeeE
Confidence 3344443 78999998775
No 12
>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=89.66 E-value=0.22 Score=29.40 Aligned_cols=27 Identities=33% Similarity=0.899 Sum_probs=19.4
Q ss_pred ccccCCCCCCCceeecCCCCccccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.|.+|+++. -.+. ...|+++|..||+-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEc-CCCCeEECCCCCCE
Confidence 699999866 2333 55789999999984
No 13
>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=89.25 E-value=0.31 Score=29.05 Aligned_cols=25 Identities=48% Similarity=1.163 Sum_probs=20.6
Q ss_pred CCccccCCCCCCCceeecCCCCccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACG 36 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCg 36 (139)
+..|..|+ +|+.| +.+|+.+|.+|+
T Consensus 17 ~~~Cp~C~---~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCG---TPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCC---CeeEE-ecCCCEECCCCC
Confidence 45788996 99999 557789999985
No 14
>KOG3554|consensus
Probab=88.22 E-value=0.32 Score=43.13 Aligned_cols=37 Identities=24% Similarity=0.604 Sum_probs=31.5
Q ss_pred cCcccccCCCCCCccee-cCCCC-C-cccchhhhhHHhhC
Q psy15323 61 LGLCCTNCGTRMTTLWR-RNNDG-E-PVCNACGLYYKLHN 97 (139)
Q Consensus 61 ~~~~C~~C~t~~t~~Wr-~~~~g-~-~lCnaCgly~~~~~ 97 (139)
.+.-|.+|+|+.+-.|- .|+.+ + .||-.|-+||++.+
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 36689999999999998 46665 3 89999999998877
No 15
>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=85.86 E-value=0.65 Score=26.77 Aligned_cols=32 Identities=31% Similarity=0.897 Sum_probs=23.4
Q ss_pred CCCCCCCCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 2 DFQFGEGRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 2 ~~~~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
+.--+....|..|++. |-...+|.+.|..||-
T Consensus 2 e~~~~~~~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 2 EWMRGPNEPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cccccCCCcCCCCCCe----EeEccCCEEEhhhCce
Confidence 3344445569999976 5556789999999985
No 16
>KOG3554|consensus
Probab=84.76 E-value=0.35 Score=42.94 Aligned_cols=40 Identities=30% Similarity=0.643 Sum_probs=31.7
Q ss_pred CCCCCCccccCCCCCCCceee-cCCC--CcccccccccccccC
Q psy15323 4 QFGEGRECVNCGAISTPLWRR-DGTG--HYLCNACGLYHKMNG 43 (139)
Q Consensus 4 ~~~~~~~C~nC~~~~tp~WRr-~~~g--~~lCnaCgly~k~hg 43 (139)
++..++-|.+|+|+..-.|-. |+.+ ..||-.|-+|+++.|
T Consensus 382 ~~~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 382 QNQDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred cCCCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 344578999999999999996 4433 579999999998763
No 17
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.02 E-value=0.88 Score=25.98 Aligned_cols=26 Identities=42% Similarity=0.935 Sum_probs=13.8
Q ss_pred CccccCCCCCCCceeecCC--C--Ccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGT--G--HYLCNACGL 37 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~--g--~~lCnaCgl 37 (139)
+.|.+|| +|+=++-++ + +.+|.+||.
T Consensus 1 kfC~~CG---~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCG---GPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT-----B-EEE--TT-SS-EEEETTTTE
T ss_pred Ccccccc---ChhhhhcCCCCCccceECCCCCC
Confidence 4699999 455554443 2 479999987
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=81.01 E-value=0.85 Score=32.29 Aligned_cols=39 Identities=31% Similarity=0.813 Sum_probs=31.3
Q ss_pred CCCccccCCCCCCCceeecCCCCcccccccccccccCCCC
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNR 46 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nR 46 (139)
..+.|++|++ .-|.|=.-.-|.+||-.|.-..+..|.+.
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~hi 40 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGVHI 40 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCCCc
Confidence 4579999998 56999988889999999988666556543
No 19
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=80.85 E-value=1.6 Score=40.00 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=14.2
Q ss_pred CccccCCCCCCCceeecCCCCccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
..|.+||+. .+++.-.|..||..
T Consensus 2 ~~Cp~Cg~~-------n~~~akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFE-------NPNNNRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCc-------CCCCCccccccCCC
Confidence 367777755 23444577777763
No 20
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=78.99 E-value=1.4 Score=37.10 Aligned_cols=39 Identities=31% Similarity=0.818 Sum_probs=31.9
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccccccccCCC
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMN 45 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~n 45 (139)
++.+.|..|++.. |.|-.-.-|.|||-.|.--.|--|.+
T Consensus 18 ~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHRsLGvh 56 (319)
T COG5347 18 SSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHRSLGVH 56 (319)
T ss_pred cccCccccCCCCC-CceEecccCeEEEeecchhhhccccc
Confidence 4578999999999 99998888999999997755444544
No 21
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=78.05 E-value=1.3 Score=32.75 Aligned_cols=26 Identities=42% Similarity=1.132 Sum_probs=22.1
Q ss_pred CCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
+.-|..|| |||++ -+|..+|..|+..
T Consensus 28 ~~hCp~Cg---~PLF~--KdG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCG---TPLFR--KDGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccC---Cccee--eCCeEECCCCCce
Confidence 45788888 99999 6789999999953
No 22
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=77.92 E-value=1.8 Score=27.41 Aligned_cols=28 Identities=39% Similarity=0.876 Sum_probs=19.7
Q ss_pred CCCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 4 QFGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 4 ~~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
..+..-.|.+||...-| +.+|..||.|.
T Consensus 23 ~~~~l~~C~~CG~~~~~--------H~vC~~CG~Y~ 50 (57)
T PRK12286 23 KAPGLVECPNCGEPKLP--------HRVCPSCGYYK 50 (57)
T ss_pred cCCcceECCCCCCccCC--------eEECCCCCcCC
Confidence 34555679999954433 56999999875
No 23
>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=77.10 E-value=1.5 Score=31.22 Aligned_cols=39 Identities=31% Similarity=0.715 Sum_probs=25.9
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccccccCC
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGM 44 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~ 44 (139)
.+.-+.|++|++.. |.|-.-.-|-+||-.|.-..+..|.
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 35568999999554 5999888899999999876555554
No 24
>PF12773 DZR: Double zinc ribbon
Probab=75.35 E-value=3 Score=24.88 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=6.2
Q ss_pred CcccccCCCC
Q psy15323 62 GLCCTNCGTR 71 (139)
Q Consensus 62 ~~~C~~C~t~ 71 (139)
...|.+|++.
T Consensus 29 ~~~C~~Cg~~ 38 (50)
T PF12773_consen 29 KKICPNCGAE 38 (50)
T ss_pred CCCCcCCcCC
Confidence 4467777763
No 25
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=74.88 E-value=3.2 Score=34.79 Aligned_cols=70 Identities=23% Similarity=0.544 Sum_probs=45.0
Q ss_pred CCccccCCCCCCCce-ee-cCCC--CcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCc-ceecCC--
Q psy15323 8 GRECVNCGAISTPLW-RR-DGTG--HYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTT-LWRRNN-- 80 (139)
Q Consensus 8 ~~~C~nC~~~~tp~W-Rr-~~~g--~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~-~Wr~~~-- 80 (139)
...|-.||+...--. +. +.+| ...|.-|+-.|.... ..|++|+.++.- .|--..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R-------------------~~C~~Cg~~~~l~y~~~~~~~ 247 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVR-------------------VKCSNCEQSGKLHYWSLDSEQ 247 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccC-------------------ccCCCCCCCCceeeeeecCCC
Confidence 568999998765443 32 3345 358999998664432 259999976543 343222
Q ss_pred CCC--cccchhhhhHHhh
Q psy15323 81 DGE--PVCNACGLYYKLH 96 (139)
Q Consensus 81 ~g~--~lCnaCgly~~~~ 96 (139)
.+. .+|..|+.|.|.-
T Consensus 248 ~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 248 AAVKAESCGDCGTYLKIL 265 (309)
T ss_pred cceEeeecccccccceec
Confidence 222 6899999998763
No 26
>KOG0703|consensus
Probab=74.83 E-value=1.8 Score=35.94 Aligned_cols=31 Identities=29% Similarity=0.797 Sum_probs=26.6
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
++.+.|+.|++. .|.|-.---|.|+|--|-=
T Consensus 23 ~~N~~CADC~a~-~P~WaSwnlGvFiC~~C~g 53 (287)
T KOG0703|consen 23 PDNKVCADCGAK-GPRWASWNLGVFICLRCAG 53 (287)
T ss_pred cccCcccccCCC-CCCeEEeecCeEEEeeccc
Confidence 347899999998 9999987789999988754
No 27
>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=74.72 E-value=0.78 Score=37.48 Aligned_cols=71 Identities=27% Similarity=0.520 Sum_probs=32.9
Q ss_pred CCccccCCCCCCCceeecCC--C--CcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCc-ceec---C
Q psy15323 8 GRECVNCGAISTPLWRRDGT--G--HYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTT-LWRR---N 79 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~--g--~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~-~Wr~---~ 79 (139)
...|-.||+...--+-++.. | ...|--|+-.|.... ..|++|+.+... +|-= +
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R-------------------~~Cp~Cg~~~~~~l~~~~~e~ 232 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVR-------------------IKCPYCGNTDHEKLEYFTVEG 232 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--T-------------------TS-TTT---SS-EEE------
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecC-------------------CCCcCCCCCCCcceeeEecCC
Confidence 35788888766665555554 5 357888888664422 249999988754 4442 2
Q ss_pred CCCC--cccchhhhhHHhhC
Q psy15323 80 NDGE--PVCNACGLYYKLHN 97 (139)
Q Consensus 80 ~~g~--~lCnaCgly~~~~~ 97 (139)
.++. .+|..|+.|.+.--
T Consensus 233 ~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 233 EPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp --SEEEEEETTTTEEEEEEE
T ss_pred CCcEEEEECCcccchHHHHh
Confidence 3332 69999999986543
No 28
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.27 E-value=2 Score=22.66 Aligned_cols=22 Identities=41% Similarity=0.815 Sum_probs=12.5
Q ss_pred CccccCCCCCCCceeecCCCCcccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
..|.+||+...+- ...|..||.
T Consensus 3 ~~Cp~Cg~~~~~~-------~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPD-------AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcc-------cccChhhCC
Confidence 4677777644332 236666664
No 29
>PRK00420 hypothetical protein; Validated
Probab=72.51 E-value=3 Score=30.03 Aligned_cols=29 Identities=28% Similarity=0.647 Sum_probs=23.4
Q ss_pred CCccccCCCCCCCceeecCCCCccccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHK 40 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k 40 (139)
+..|..|| +|+.+- .+|+.+|.+||....
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCCceECCCCCCeee
Confidence 46899999 899984 567899999999543
No 30
>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=72.20 E-value=3.5 Score=34.46 Aligned_cols=70 Identities=20% Similarity=0.434 Sum_probs=45.4
Q ss_pred CCccccCCCCCCCce-eec--CCC--CcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCc-ceecCC-
Q psy15323 8 GRECVNCGAISTPLW-RRD--GTG--HYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTT-LWRRNN- 80 (139)
Q Consensus 8 ~~~C~nC~~~~tp~W-Rr~--~~g--~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~-~Wr~~~- 80 (139)
...|-.||+...--. +.+ .+| ...|.-|+-.|.... ..|++|+.+..- .|.-..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R-------------------~~C~~Cg~~~~l~y~~~e~~ 244 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVR-------------------VKCSHCEESKHLAYLSLEHD 244 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccC-------------------ccCCCCCCCCceeeEeecCC
Confidence 348999998766533 332 355 358999998664432 259999987643 354322
Q ss_pred ---CCC--cccchhhhhHHhh
Q psy15323 81 ---DGE--PVCNACGLYYKLH 96 (139)
Q Consensus 81 ---~g~--~lCnaCgly~~~~ 96 (139)
.+. .+|..|+.|.|.-
T Consensus 245 ~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 245 AEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred CCCcceEEeeccccccchhhh
Confidence 222 5899999998764
No 31
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=70.70 E-value=3.4 Score=34.22 Aligned_cols=34 Identities=29% Similarity=0.617 Sum_probs=24.4
Q ss_pred CCCCCCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 3 FQFGEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 3 ~~~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.+......|.+|+. +.+=-....|+++|..||+-
T Consensus 6 ~~~~~~~~Cp~Cg~--~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 6 LEEEEKLVCPECGS--DKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred hhcccCCcCcCCCC--CCeeEECCCCeEeecccCCc
Confidence 34456778999996 34433346789999999994
No 32
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=67.93 E-value=4 Score=35.19 Aligned_cols=40 Identities=28% Similarity=0.725 Sum_probs=32.3
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccccccccCCCC
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNR 46 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nR 46 (139)
+..+.|+.|++.. |.|=.-.-|.|||..|.-..+..|.+.
T Consensus 20 PgNk~CaDCga~n-PtWASvn~GIFLCl~CSGVHRsLGvHI 59 (395)
T PLN03114 20 SDNKICFDCNAKN-PTWASVTYGIFLCIDCSAVHRSLGVHI 59 (395)
T ss_pred cCCCcCccCCCCC-CCceeeccceeehhhhhHhhccCCCCC
Confidence 4578999999865 999988889999999987666556543
No 33
>KOG0706|consensus
Probab=67.58 E-value=3.1 Score=36.51 Aligned_cols=40 Identities=33% Similarity=0.799 Sum_probs=33.2
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccccccccCCCC
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNR 46 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nR 46 (139)
++-++|..|++ +-|.|-.-+.|-|||-.|.-..+--|++.
T Consensus 21 ~~NKvCFDCgA-knPtWaSVTYGIFLCiDCSAvHRnLGVHi 60 (454)
T KOG0706|consen 21 SENKVCFDCGA-KNPTWASVTYGIFLCIDCSAVHRNLGVHI 60 (454)
T ss_pred CCCceecccCC-CCCCceeecceEEEEEecchhhhccccce
Confidence 46789999996 46999999999999999998766556553
No 34
>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=66.96 E-value=5.9 Score=23.53 Aligned_cols=30 Identities=30% Similarity=0.718 Sum_probs=18.7
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
+++.+|-.||.+ ...|-+ ..+.+.|++|.-
T Consensus 16 ~~g~~CP~Cg~~-~~~~~~-~~~~~~C~~C~~ 45 (46)
T PF12760_consen 16 PDGFVCPHCGST-KHYRLK-TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCCe-eeEEeC-CCCeEECCCCCC
Confidence 345678888877 333333 356778888863
No 35
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=66.94 E-value=2.9 Score=29.77 Aligned_cols=50 Identities=26% Similarity=0.649 Sum_probs=29.7
Q ss_pred CCCccccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCcceecCCCCCccc
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVC 86 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~Wr~~~~g~~lC 86 (139)
....|..|+..-+-++.++ .+|..|..+ +|..|++. .......||
T Consensus 53 ~~~~C~~C~~~fg~l~~~~----~~C~~C~~~-------------------------VC~~C~~~------~~~~~~WlC 97 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG----RVCVDCKHR-------------------------VCKKCGVY------SKKEPIWLC 97 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC----EEETTTTEE-------------------------EETTSEEE------TSSSCCEEE
T ss_pred CCcchhhhCCcccccCCCC----CcCCcCCcc-------------------------ccCccCCc------CCCCCCEEC
Confidence 3567888886655554433 467777663 68888875 122334789
Q ss_pred chhhh
Q psy15323 87 NACGL 91 (139)
Q Consensus 87 naCgl 91 (139)
+.|.-
T Consensus 98 ~vC~k 102 (118)
T PF02318_consen 98 KVCQK 102 (118)
T ss_dssp HHHHH
T ss_pred hhhHH
Confidence 99964
No 36
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.89 E-value=2.3 Score=31.55 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=22.8
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
=..|..|+..+|.+-+.+.--...|+|||-
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 467999999999997643322467999983
No 37
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=65.71 E-value=3.1 Score=29.73 Aligned_cols=28 Identities=32% Similarity=0.672 Sum_probs=21.1
Q ss_pred ccccCCCCCCCceeecCCCCcccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
.|..|+..+|-+=..+..-...|+|||.
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 6999999999888763222457999985
No 38
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=65.53 E-value=2.7 Score=30.06 Aligned_cols=30 Identities=33% Similarity=0.566 Sum_probs=22.5
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
=..|..|+..+|.+-..+..-...|+|||-
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 468999999999997762222356999983
No 39
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=64.54 E-value=2.9 Score=30.90 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=22.3
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
-..|..|+..+|.+-..+.--...|+|||-
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 467999999999987643222357999983
No 40
>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=64.12 E-value=3.6 Score=24.17 Aligned_cols=15 Identities=27% Similarity=0.919 Sum_probs=8.0
Q ss_pred Cccccccc-ccccccC
Q psy15323 29 HYLCNACG-LYHKMNG 43 (139)
Q Consensus 29 ~~lCnaCg-ly~k~hg 43 (139)
+|.|.+|| .+..+..
T Consensus 5 ey~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS 20 (42)
T ss_pred EEEeCCCCCEEEEEEE
Confidence 35677777 3444433
No 41
>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=63.47 E-value=6.4 Score=22.83 Aligned_cols=29 Identities=34% Similarity=0.907 Sum_probs=20.3
Q ss_pred CccccCCCCCCCceee-cCCCCcccccccc
Q psy15323 9 RECVNCGAISTPLWRR-DGTGHYLCNACGL 37 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr-~~~g~~lCnaCgl 37 (139)
--|.+|+.+..=.|.. ...|..+|+.|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4588999866555543 3357899999974
No 42
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.49 E-value=5.2 Score=28.14 Aligned_cols=35 Identities=26% Similarity=0.547 Sum_probs=20.9
Q ss_pred cCcccccCCCCCCcceecCCCCCcccchhhhhHHh
Q psy15323 61 LGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKL 95 (139)
Q Consensus 61 ~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~ 95 (139)
.-..|.+|+...-++-....-+..+|..||+|+-.
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 45579999943222111112235899999998744
No 43
>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=60.18 E-value=4.4 Score=28.58 Aligned_cols=43 Identities=26% Similarity=0.482 Sum_probs=33.3
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhhhHHhhCC----CCCchhh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNV----NRPLAMR 105 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~~----~Rp~~~~ 105 (139)
...|+.|+. ..|.|=.-+-|-.||-.|.-..+..+. .|++++-
T Consensus 3 N~~CaDC~~-~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md 49 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLD 49 (112)
T ss_pred CCcccCCCC-CCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccC
Confidence 457999998 668998888898999999887777664 3455443
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.97 E-value=8.6 Score=22.86 Aligned_cols=30 Identities=27% Similarity=0.873 Sum_probs=19.1
Q ss_pred CccccCCCCCCCceeecCC--CCcccccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGT--GHYLCNACGLYHKM 41 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~--g~~lCnaCgly~k~ 41 (139)
+.|..||.. +-..... ..++|..||.....
T Consensus 1 ~FCp~Cg~~---l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNM---LIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCc---cccccCCCCCEEECCcCCCeEEC
Confidence 368999963 3333332 26899999975433
No 45
>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=57.17 E-value=5.9 Score=28.88 Aligned_cols=29 Identities=31% Similarity=0.599 Sum_probs=22.9
Q ss_pred cccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 63 LCCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 63 ~~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
..|..|+..+|-+-..+.--..-|+|||-
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 57999999999987774333467999983
No 46
>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=56.15 E-value=6.8 Score=24.47 Aligned_cols=27 Identities=33% Similarity=0.759 Sum_probs=17.8
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
+.+.-.|.+||. +.. .+.+|.+||.|.
T Consensus 23 ~~~l~~c~~cg~-----~~~---~H~vc~~cG~y~ 49 (56)
T PF01783_consen 23 APNLVKCPNCGE-----PKL---PHRVCPSCGYYK 49 (56)
T ss_dssp TTSEEESSSSSS-----EES---TTSBCTTTBBSS
T ss_pred ccceeeeccCCC-----Eec---ccEeeCCCCeEC
Confidence 345567888984 222 246999999664
No 47
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=55.76 E-value=5.4 Score=31.19 Aligned_cols=30 Identities=33% Similarity=0.631 Sum_probs=23.1
Q ss_pred ccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
.|..|+..+|-+=..+..-...|+|||...
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 699999999999765322246899999954
No 48
>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=55.34 E-value=9.7 Score=20.83 Aligned_cols=28 Identities=36% Similarity=0.606 Sum_probs=13.4
Q ss_pred CCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.+.|..||+ |+-.....-..+|.+|+..
T Consensus 3 ~rfC~~CG~---~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGA---PTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT-----BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCc---cccCCCCcCEeECCCCcCE
Confidence 467889994 3333222225689999873
No 49
>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=55.17 E-value=8.9 Score=20.25 Aligned_cols=24 Identities=29% Similarity=0.807 Sum_probs=15.2
Q ss_pred cccCCCCCCCceeecCCCCcccccccc
Q psy15323 11 CVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 11 C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
|..|+....|.=+ .-.|.|..||.
T Consensus 1 C~sC~~~i~~r~~---~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQ---AVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCccc---CceEeCCCCCC
Confidence 5667766665432 23688888873
No 50
>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=54.76 E-value=9.2 Score=24.18 Aligned_cols=29 Identities=24% Similarity=0.681 Sum_probs=19.7
Q ss_pred CCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
....|+.||..... ......+.|..||+.
T Consensus 27 TSq~C~~CG~~~~~---~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK---RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc---ccccceEEcCCCCCE
Confidence 56789999975554 122235789999885
No 51
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=54.05 E-value=8.9 Score=35.00 Aligned_cols=34 Identities=26% Similarity=0.683 Sum_probs=27.8
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
.+..+.|++|+... |.|=.-.-|-|||-.|.=-.
T Consensus 20 lPgNk~CADCgs~~-P~WASiNlGIFICi~CSGIH 53 (648)
T PLN03119 20 LPPNRRCINCNSLG-PQYVCTTFWTFVCMACSGIH 53 (648)
T ss_pred CcCCCccccCCCCC-CCceeeccceEEeccchhhh
Confidence 45568999999865 99998888999999997643
No 52
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=53.91 E-value=12 Score=34.47 Aligned_cols=46 Identities=35% Similarity=0.720 Sum_probs=32.7
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCcceec
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRR 78 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~Wr~ 78 (139)
+..++.|.+||+.-+ ...|..||-- -| .....|.+||+...+.|..
T Consensus 12 ~~~akFC~~CG~~l~---------~~~Cp~CG~~-------~~------------~~~~fC~~CG~~~~~~~~~ 57 (645)
T PRK14559 12 PNNNRFCQKCGTSLT---------HKPCPQCGTE-------VP------------VDEAHCPNCGAETGTIWWA 57 (645)
T ss_pred CCCCccccccCCCCC---------CCcCCCCCCC-------CC------------cccccccccCCcccchhhh
Confidence 456899999996543 1369999873 11 1234799999999888874
No 53
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=53.18 E-value=4.2 Score=26.41 Aligned_cols=33 Identities=33% Similarity=0.693 Sum_probs=25.5
Q ss_pred cCcccccCCCCCCc-ceecCCCCCcccchhhhhH
Q psy15323 61 LGLCCTNCGTRMTT-LWRRNNDGEPVCNACGLYY 93 (139)
Q Consensus 61 ~~~~C~~C~t~~t~-~Wr~~~~g~~lCnaCgly~ 93 (139)
.+..|..|.+..|- +|+.+.-...-|-+||.-.
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 46789999998886 7776555557899999754
No 54
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=52.59 E-value=5.7 Score=31.07 Aligned_cols=30 Identities=30% Similarity=0.581 Sum_probs=22.4
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
-..|..|+..+|.+-..+.--..-|+|||-
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 468999999999996653222357999984
No 55
>KOG3740|consensus
Probab=52.27 E-value=5.4 Score=36.62 Aligned_cols=34 Identities=24% Similarity=0.637 Sum_probs=29.1
Q ss_pred CCCCccccCCCCCCCceeecCCC----Ccccccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTG----HYLCNACGLYH 39 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g----~~lCnaCgly~ 39 (139)
.++-.|.-|.+..||.|.....+ .++|.+|.-..
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSn 497 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSN 497 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhhhc
Confidence 35678999999999999987776 68999998854
No 56
>PLN03131 hypothetical protein; Provisional
Probab=51.43 E-value=10 Score=34.89 Aligned_cols=33 Identities=21% Similarity=0.631 Sum_probs=27.2
Q ss_pred CCCCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.+..+.|++|++. -|.|=.-.-|.|||..|.--
T Consensus 20 ~PgNk~CADCga~-~P~WASiNlGIFICi~CSGI 52 (705)
T PLN03131 20 LPPNRRCINCNSL-GPQFVCTNFWTFICMTCSGI 52 (705)
T ss_pred CcCCCccccCCCC-CCCeeEeccceEEchhchhh
Confidence 4567899999975 59999877899999999753
No 57
>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=51.27 E-value=15 Score=25.96 Aligned_cols=37 Identities=22% Similarity=0.438 Sum_probs=25.5
Q ss_pred ccCcccccCCCCCCcceecCCCCCcccchhhhhHHhhC
Q psy15323 60 RLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHN 97 (139)
Q Consensus 60 ~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~ 97 (139)
.....|+.|+. .-|.|-.-+-|-.||-.|.--.+..+
T Consensus 11 ~~N~~CaDCg~-~~p~w~s~~~GiflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGA-PNPTWASLNYGIFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-S-BS--EEETTTTEEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCC-CCCCEEEeecChhhhHHHHHHHHHhc
Confidence 45678999996 55699888888899999987777666
No 58
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.18 E-value=9.9 Score=22.74 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=17.3
Q ss_pred ccccCCCCCCCceeecCCCCcccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
.|.+||++.+.. ..+..-|..||.
T Consensus 4 ~C~~Cg~~~~~~----~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK----SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC----CCCceECCCCCc
Confidence 689999866544 334578999987
No 59
>PRK11827 hypothetical protein; Provisional
Probab=50.83 E-value=16 Score=23.50 Aligned_cols=33 Identities=21% Similarity=0.603 Sum_probs=21.6
Q ss_pred ccccCCCCCCCceeecCCCCcccccccc-cccccCCC
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGL-YHKMNGMN 45 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgl-y~k~hg~n 45 (139)
.|-.|. +++.-.....+.+|.+|++ |....|..
T Consensus 10 aCP~ck---g~L~~~~~~~~Lic~~~~laYPI~dgIP 43 (60)
T PRK11827 10 ACPVCN---GKLWYNQEKQELICKLDNLAFPLRDGIP 43 (60)
T ss_pred ECCCCC---CcCeEcCCCCeEECCccCeeccccCCcc
Confidence 455554 7776544455799999999 55555543
No 60
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=50.22 E-value=6.2 Score=24.96 Aligned_cols=56 Identities=27% Similarity=0.634 Sum_probs=24.2
Q ss_pred CCCccccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCcce--ecCCCC-C
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLW--RRNNDG-E 83 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~W--r~~~~g-~ 83 (139)
+...|..|+..-+-+-|+ ..|-.||. .+|..|......+. ..+... .
T Consensus 8 ~~~~C~~C~~~F~~~~rr-----hhCr~CG~-------------------------~vC~~Cs~~~~~~~~~~~~~~~~~ 57 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRR-----HHCRNCGR-------------------------VVCSSCSSQRIPLPTPSSGSGEPV 57 (69)
T ss_dssp G-SB-TTT--B-BSSS-E-----EE-TTT---------------------------EEECCCS-EEEEET--GGTESEEE
T ss_pred CCCcCcCcCCcCCCceee-----EccCCCCC-------------------------EECCchhCCEEcccccccCCCCcC
Confidence 466788888766444333 45666665 35666666665554 111111 2
Q ss_pred cccchhhhh
Q psy15323 84 PVCNACGLY 92 (139)
Q Consensus 84 ~lCnaCgly 92 (139)
.+|+.|...
T Consensus 58 RvC~~C~~~ 66 (69)
T PF01363_consen 58 RVCDSCYSK 66 (69)
T ss_dssp EE-HHHHHH
T ss_pred EECHHHHHH
Confidence 678888643
No 61
>KOG2907|consensus
Probab=50.11 E-value=7.8 Score=28.08 Aligned_cols=82 Identities=20% Similarity=0.374 Sum_probs=47.2
Q ss_pred CCCccccCCCCCCCceeecCCCCccccccccccccc-CCC-----------CCCCCCccch----hhccccCcccccCCC
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN-GMN-----------RPLVKPSKRL----TATRRLGLCCTNCGT 70 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~h-g~n-----------RP~~kpsKR~----~atk~~~~~C~~C~t 70 (139)
....|+.||+. |--.+....++|-.|..-+-.. -.+ .+.....+.. .....+...|..|+-
T Consensus 6 ~~~FC~~CG~l---l~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCpkCgh 82 (116)
T KOG2907|consen 6 DLDFCSDCGSL---LEEPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCPKCGH 82 (116)
T ss_pred Ccchhhhhhhh---cccccccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCcccCC
Confidence 67789999963 2222333446799999844221 111 1111111110 112345678999998
Q ss_pred CC----CcceecCCCCC---cccchhhh
Q psy15323 71 RM----TTLWRRNNDGE---PVCNACGL 91 (139)
Q Consensus 71 ~~----t~~Wr~~~~g~---~lCnaCgl 91 (139)
.+ |-.-|..++|+ +.|-.|+.
T Consensus 83 e~m~Y~T~QlRSADEGQTVFYTC~kC~~ 110 (116)
T KOG2907|consen 83 EEMSYHTLQLRSADEGQTVFYTCPKCKY 110 (116)
T ss_pred chhhhhhhhcccccCCceEEEEcCccce
Confidence 77 55677788887 56888875
No 62
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=49.22 E-value=11 Score=24.24 Aligned_cols=16 Identities=25% Similarity=0.690 Sum_probs=12.2
Q ss_pred CCccccCCCCC-CCcee
Q psy15323 8 GRECVNCGAIS-TPLWR 23 (139)
Q Consensus 8 ~~~C~nC~~~~-tp~WR 23 (139)
...|.|||.+. |.-|.
T Consensus 15 ~~~CP~Cgs~~~T~~W~ 31 (61)
T PRK08351 15 EDRCPVCGSRDLSDEWF 31 (61)
T ss_pred CCcCCCCcCCccccccc
Confidence 44788888877 77887
No 63
>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=48.53 E-value=10 Score=22.72 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=11.2
Q ss_pred ccccCCCCCCCceeecC-CCCcccccccc
Q psy15323 10 ECVNCGAISTPLWRRDG-TGHYLCNACGL 37 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~-~g~~lCnaCgl 37 (139)
.|.+|+.+-+ .|+... +....|..||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 3555554333 333322 12334555554
No 64
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.24 E-value=15 Score=23.57 Aligned_cols=31 Identities=29% Similarity=0.662 Sum_probs=21.1
Q ss_pred CCCCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.....+|.-|+...+|.=+ .-.|.|..||-.
T Consensus 4 ~~~~~~CtSCg~~i~~~~~---~~~F~CPnCG~~ 34 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPREK---AVKFLCPNCGEV 34 (59)
T ss_pred cccCccccCCCCcccCCCc---cCEeeCCCCCCe
Confidence 3456689999977665422 236899999864
No 65
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.07 E-value=11 Score=24.39 Aligned_cols=27 Identities=26% Similarity=0.576 Sum_probs=19.4
Q ss_pred CCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
..+|..||...+|.=+ ...|+|..||-
T Consensus 9 ~~~CtSCg~~i~p~e~---~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGET---AVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCCc---eeEeeCCCCCc
Confidence 6799999977665322 23689999994
No 66
>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=47.63 E-value=14 Score=23.05 Aligned_cols=28 Identities=32% Similarity=0.724 Sum_probs=18.0
Q ss_pred CCCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 4 QFGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 4 ~~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
.++..-.|.+||... . -+.+|..||.|.
T Consensus 22 ~~p~l~~C~~cG~~~-----~---~H~vc~~cG~Y~ 49 (55)
T TIGR01031 22 TAPTLVVCPNCGEFK-----L---PHRVCPSCGYYK 49 (55)
T ss_pred cCCcceECCCCCCcc-----c---CeeECCccCeEC
Confidence 345556788888422 1 246899999764
No 67
>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=47.29 E-value=9 Score=22.14 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=17.4
Q ss_pred ccccCCCCCCCceee----cCCC---Ccccccccccc
Q psy15323 10 ECVNCGAISTPLWRR----DGTG---HYLCNACGLYH 39 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr----~~~g---~~lCnaCgly~ 39 (139)
.|.+|+..++-.|.. ++++ -+.|..|+-.+
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 588899888777642 2233 25888888644
No 68
>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=47.03 E-value=11 Score=21.27 Aligned_cols=8 Identities=50% Similarity=1.410 Sum_probs=3.7
Q ss_pred cccccccc
Q psy15323 30 YLCNACGL 37 (139)
Q Consensus 30 ~lCnaCgl 37 (139)
|.|..||.
T Consensus 6 y~C~~Cg~ 13 (41)
T smart00834 6 YRCEDCGH 13 (41)
T ss_pred EEcCCCCC
Confidence 34444444
No 69
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=46.90 E-value=13 Score=23.14 Aligned_cols=30 Identities=20% Similarity=0.392 Sum_probs=17.5
Q ss_pred CCccccCCCCCCCceeecCCC-Ccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTG-HYLCNACGL 37 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g-~~lCnaCgl 37 (139)
+.+|.+|..-..-.-...... .|.|-.||.
T Consensus 22 aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred eEECcccchhhcccccccCCceEEEcCCCCC
Confidence 667777776544433333322 567777765
No 70
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=46.52 E-value=13 Score=21.58 Aligned_cols=30 Identities=23% Similarity=0.733 Sum_probs=19.1
Q ss_pred ccccCCCCCCCcee----ecCCC---Ccccccccccc
Q psy15323 10 ECVNCGAISTPLWR----RDGTG---HYLCNACGLYH 39 (139)
Q Consensus 10 ~C~nC~~~~tp~WR----r~~~g---~~lCnaCgly~ 39 (139)
.|.+|+-.+.-.|. .++++ -+.|..|+..+
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 58888877766664 23333 25888888654
No 71
>PHA00626 hypothetical protein
Probab=45.18 E-value=9.9 Score=24.31 Aligned_cols=32 Identities=25% Similarity=0.538 Sum_probs=20.1
Q ss_pred ccccCCCCCCccee--cCCCCCcccchhhhhHHh
Q psy15323 64 CCTNCGTRMTTLWR--RNNDGEPVCNACGLYYKL 95 (139)
Q Consensus 64 ~C~~C~t~~t~~Wr--~~~~g~~lCnaCgly~~~ 95 (139)
.|++|+..+-.+-- +.+...++|..||.++.+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 58888885322111 234456999999987743
No 72
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.00 E-value=13 Score=19.13 Aligned_cols=6 Identities=83% Similarity=1.885 Sum_probs=2.8
Q ss_pred cccCCC
Q psy15323 11 CVNCGA 16 (139)
Q Consensus 11 C~nC~~ 16 (139)
|.+||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 445553
No 73
>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=44.38 E-value=15 Score=24.28 Aligned_cols=37 Identities=24% Similarity=0.485 Sum_probs=27.1
Q ss_pred CCccccCCCCCCCceeecCCC-CcccccccccccccCC
Q psy15323 8 GRECVNCGAISTPLWRRDGTG-HYLCNACGLYHKMNGM 44 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g-~~lCnaCgly~k~hg~ 44 (139)
+-+|-.|++..|=.|.+..+. ..-|.+||....+...
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 558999999888755544434 5689999997766544
No 74
>KOG3740|consensus
Probab=43.98 E-value=8.8 Score=35.30 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=27.0
Q ss_pred ccCcccccCCCCCCcceecCCCC----Ccccchhhh
Q psy15323 60 RLGLCCTNCGTRMTTLWRRNNDG----EPVCNACGL 91 (139)
Q Consensus 60 ~~~~~C~~C~t~~t~~Wr~~~~g----~~lCnaCgl 91 (139)
...-.|..|.|..||.|+.-..+ .++|..|.-
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 34668999999999999987776 589999963
No 75
>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=43.57 E-value=20 Score=20.02 Aligned_cols=24 Identities=29% Similarity=0.578 Sum_probs=12.1
Q ss_pred ccccCCCCCCCceeecCCCCcccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
.|.+|+++.. -......-|..||.
T Consensus 2 ~C~~Cg~~~~----~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVE----LKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-----BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeE----cCCCCcEECCcCCC
Confidence 4677776555 11222456777765
No 76
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=43.54 E-value=16 Score=23.79 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=12.1
Q ss_pred CCccccCCCCC-CCcee
Q psy15323 8 GRECVNCGAIS-TPLWR 23 (139)
Q Consensus 8 ~~~C~nC~~~~-tp~WR 23 (139)
...|.+||.+. |+.|.
T Consensus 17 ~~~Cp~Cgs~~~S~~w~ 33 (64)
T PRK06393 17 EKTCPVHGDEKTTTEWF 33 (64)
T ss_pred CCcCCCCCCCcCCcCcc
Confidence 45788888877 66776
No 77
>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=43.22 E-value=17 Score=20.96 Aligned_cols=32 Identities=31% Similarity=0.728 Sum_probs=19.6
Q ss_pred CCccccCCCCCCCceeecCCC-Ccccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTG-HYLCNACGLYH 39 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g-~~lCnaCgly~ 39 (139)
+..|.+|++-.-|.=.-+..+ ...||-|+...
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 457999999999988877765 57999998743
No 78
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=43.10 E-value=16 Score=30.31 Aligned_cols=29 Identities=28% Similarity=0.708 Sum_probs=20.1
Q ss_pred CccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
..|.+|+.+ -+=..-..|+.+|-.||+--
T Consensus 2 ~~CpeCg~~--~~~~d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGST--NIITDYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCc--cceeeccCCeEEeccCCEEe
Confidence 479999987 22222236899999999953
No 79
>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=43.04 E-value=8.4 Score=22.54 Aligned_cols=29 Identities=28% Similarity=0.729 Sum_probs=17.7
Q ss_pred CccccCCCCCCCcee--ecCCCCcccccccc
Q psy15323 9 RECVNCGAISTPLWR--RDGTGHYLCNACGL 37 (139)
Q Consensus 9 ~~C~nC~~~~tp~WR--r~~~g~~lCnaCgl 37 (139)
+.|+=||.+.+..=+ .++++.++|+.|-.
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 478999998875433 56667889999865
No 80
>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=42.77 E-value=18 Score=25.77 Aligned_cols=31 Identities=35% Similarity=0.722 Sum_probs=17.0
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
.|..++|.+||+...-|=+ .| .+|.-||--+
T Consensus 6 lGtKR~Cp~CG~kFYDLnk-~P---ivCP~CG~~~ 36 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNK-DP---IVCPKCGTEF 36 (108)
T ss_pred cCCcccCCCCcchhccCCC-CC---ccCCCCCCcc
Confidence 4556666666655554444 22 4566666643
No 81
>KOG1598|consensus
Probab=42.15 E-value=16 Score=32.84 Aligned_cols=28 Identities=39% Similarity=0.873 Sum_probs=20.4
Q ss_pred CccccCCCCCCCceeecCCCCccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
..|.||+.+. +=++..+|...|.+||.-
T Consensus 1 ~~C~~C~~s~--fe~d~a~g~~~C~~CG~v 28 (521)
T KOG1598|consen 1 MVCKNCGGSN--FERDEATGNLYCTACGTV 28 (521)
T ss_pred CcCCCCCCCC--cccccccCCceeccccce
Confidence 3699999543 233445789999999984
No 82
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.11 E-value=23 Score=35.20 Aligned_cols=21 Identities=38% Similarity=0.787 Sum_probs=13.9
Q ss_pred CccccCCCCCCCceeecCCCCccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
+.|-+||+. |+. ..|..||-.
T Consensus 668 rkCPkCG~~-t~~--------~fCP~CGs~ 688 (1337)
T PRK14714 668 RRCPSCGTE-TYE--------NRCPDCGTH 688 (1337)
T ss_pred EECCCCCCc-ccc--------ccCcccCCc
Confidence 688899874 222 267778764
No 83
>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=41.17 E-value=15 Score=24.22 Aligned_cols=35 Identities=29% Similarity=0.526 Sum_probs=25.9
Q ss_pred cCcccccCCCCCCcceecCCCCC-cccchhhhhHHh
Q psy15323 61 LGLCCTNCGTRMTTLWRRNNDGE-PVCNACGLYYKL 95 (139)
Q Consensus 61 ~~~~C~~C~t~~t~~Wr~~~~g~-~lCnaCgly~~~ 95 (139)
.+..|..|....+..|-+.++-+ .-|=+||.....
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 47789999999998655544454 679999965443
No 84
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.63 E-value=21 Score=21.88 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=17.2
Q ss_pred CCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
.+.|.+||.+ =+.. ..+.+.|..||.
T Consensus 20 ~~fCP~Cg~~--~m~~--~~~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG--FMAE--HLDRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc--hhec--cCCcEECCCcCC
Confidence 4588888863 2222 236788888887
No 85
>PRK11823 DNA repair protein RadA; Provisional
Probab=39.66 E-value=17 Score=31.59 Aligned_cols=29 Identities=31% Similarity=0.850 Sum_probs=21.6
Q ss_pred CCccccCCCCCCCceeecCCCCcccccccccccccC
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 43 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg 43 (139)
.-+|.+||.+ ++.|.- .|++|+-|..+..
T Consensus 7 ~y~C~~Cg~~-~~~~~g------~Cp~C~~w~t~~e 35 (446)
T PRK11823 7 AYVCQECGAE-SPKWLG------RCPECGAWNTLVE 35 (446)
T ss_pred eEECCcCCCC-CcccCe------eCcCCCCccceee
Confidence 4589999965 566653 6999999876654
No 86
>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=38.64 E-value=20 Score=23.03 Aligned_cols=34 Identities=26% Similarity=0.674 Sum_probs=24.4
Q ss_pred CCccccCCCCCCC-ceeecCCCCcccccccccccc
Q psy15323 8 GRECVNCGAISTP-LWRRDGTGHYLCNACGLYHKM 41 (139)
Q Consensus 8 ~~~C~nC~~~~tp-~WRr~~~g~~lCnaCgly~k~ 41 (139)
+-+|-.|++-.|= +|+.+.....-|.+||....+
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQEQQ 43 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCcccc
Confidence 4589999997776 555444445789999996543
No 87
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=37.93 E-value=21 Score=30.48 Aligned_cols=27 Identities=30% Similarity=0.931 Sum_probs=20.7
Q ss_pred ccccCCCCCCCceeecCCCCcccccccccccccC
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 43 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg 43 (139)
+|.+||.+ ++.|.- -|.+|+-|..+..
T Consensus 2 ~c~~cg~~-~~~~~g------~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYV-SPKWLG------KCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCC-CCCccE------ECcCCCCceeeee
Confidence 69999965 566663 6999999876654
No 88
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=37.90 E-value=17 Score=29.98 Aligned_cols=17 Identities=29% Similarity=0.907 Sum_probs=10.1
Q ss_pred CcccccCCC-------CCCcceec
Q psy15323 62 GLCCTNCGT-------RMTTLWRR 78 (139)
Q Consensus 62 ~~~C~~C~t-------~~t~~Wr~ 78 (139)
..+|.+||+ .+.|.||.
T Consensus 30 e~vC~~CG~Vl~e~~iD~g~EWR~ 53 (310)
T PRK00423 30 EIVCADCGLVIEENIIDQGPEWRA 53 (310)
T ss_pred eEeecccCCcccccccccCCCccC
Confidence 456777766 23566664
No 89
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=36.96 E-value=21 Score=22.70 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=16.2
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
++..-+|.+||...-| +.+|. ||+|.
T Consensus 24 ~~~~~~c~~cg~~~~p--------H~vc~-cG~Y~ 49 (60)
T PRK01110 24 APTLSVDKTTGEYHLP--------HHVSP-KGYYK 49 (60)
T ss_pred CCceeEcCCCCceecc--------ceecC-CcccC
Confidence 3445678888843322 35788 88875
No 90
>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=36.87 E-value=30 Score=20.32 Aligned_cols=26 Identities=31% Similarity=0.866 Sum_probs=12.7
Q ss_pred ccccCCCCCCCc-eee-cCCCCcccccc
Q psy15323 10 ECVNCGAISTPL-WRR-DGTGHYLCNAC 35 (139)
Q Consensus 10 ~C~nC~~~~tp~-WRr-~~~g~~lCnaC 35 (139)
.|-.|+.+.-=. |.. ...|..+|+.|
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 488888744332 332 23478999999
No 91
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=34.59 E-value=23 Score=30.93 Aligned_cols=29 Identities=31% Similarity=0.814 Sum_probs=21.9
Q ss_pred CCccccCCCCCCCceeecCCCCcccccccccccccC
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 43 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg 43 (139)
.-+|.+||.+ ++.|.- .|.+|+-|..+..
T Consensus 7 ~y~C~~Cg~~-~~~~~g------~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQG------KCPACHAWNTITE 35 (454)
T ss_pred eEECCcCCCC-CccccE------ECcCCCCccccch
Confidence 4689999965 566663 6999999976654
No 93
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=33.56 E-value=28 Score=29.37 Aligned_cols=35 Identities=23% Similarity=0.484 Sum_probs=29.2
Q ss_pred cccCcccccCCCCCCcceecCCCCCcccchhhhhHH
Q psy15323 59 RRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYK 94 (139)
Q Consensus 59 k~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~ 94 (139)
......|..|++.. |.|=.-+-|..||-.|.--.|
T Consensus 17 ~~~Nk~CaDCga~~-P~W~S~nlGvfiCi~CagvHR 51 (319)
T COG5347 17 DSSNKKCADCGAPN-PTWASVNLGVFLCIDCAGVHR 51 (319)
T ss_pred ccccCccccCCCCC-CceEecccCeEEEeecchhhh
Confidence 35677899999988 999998889999999974333
No 94
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=33.39 E-value=20 Score=29.74 Aligned_cols=26 Identities=38% Similarity=0.949 Sum_probs=15.4
Q ss_pred ccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 64 CCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 64 ~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
.|++|+.+ .-.++ -..|+++|-.||+
T Consensus 3 ~CpeCg~~-~~~~d-~~~ge~VC~~CG~ 28 (285)
T COG1405 3 SCPECGST-NIITD-YERGEIVCADCGL 28 (285)
T ss_pred CCCCCCCc-cceee-ccCCeEEeccCCE
Confidence 57777776 22221 2356777888875
No 95
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.12 E-value=37 Score=33.17 Aligned_cols=42 Identities=31% Similarity=0.681 Sum_probs=0.0
Q ss_pred CCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCccee----cCCCCCcccchhh
Q psy15323 28 GHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWR----RNNDGEPVCNACG 90 (139)
Q Consensus 28 g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~Wr----~~~~g~~lCnaCg 90 (139)
+...|+.||... ....|.+||+...+.|+ ....+.+.|..||
T Consensus 625 g~RfCpsCG~~t---------------------~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG 670 (1121)
T PRK04023 625 GRRKCPSCGKET---------------------FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCG 670 (1121)
T ss_pred cCccCCCCCCcC---------------------CcccCCCCCCCCCcceeCccccCcCCCCcCCCCC
No 96
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=32.95 E-value=33 Score=22.06 Aligned_cols=32 Identities=22% Similarity=0.515 Sum_probs=24.3
Q ss_pred CCCCCCCceeecCCCCccccccccccccc-CCC
Q psy15323 14 CGAISTPLWRRDGTGHYLCNACGLYHKMN-GMN 45 (139)
Q Consensus 14 C~~~~tp~WRr~~~g~~lCnaCgly~k~h-g~n 45 (139)
|-.++.|++-....+..+|..|++.|... |..
T Consensus 11 CP~~kg~L~~~~~~~~L~c~~~~~aYpI~dGIP 43 (60)
T COG2835 11 CPVCKGPLVYDEEKQELICPRCKLAYPIRDGIP 43 (60)
T ss_pred ccCcCCcceEeccCCEEEecccCceeecccCcc
Confidence 66677889987777789999999966443 443
No 97
>KOG1729|consensus
Probab=32.16 E-value=19 Score=29.93 Aligned_cols=26 Identities=42% Similarity=0.754 Sum_probs=18.2
Q ss_pred CCCccccCCC-CCCCceeecCCCCcccccccc
Q psy15323 7 EGRECVNCGA-ISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 7 ~~~~C~nC~~-~~tp~WRr~~~g~~lCnaCgl 37 (139)
++.+|..|+. ..|-.|||- .|-+||.
T Consensus 167 ea~~C~~C~~~~Ftl~~RRH-----HCR~CG~ 193 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRH-----HCRNCGD 193 (288)
T ss_pred cceecccCCCccccHHHHHH-----HHHhcch
Confidence 4778999998 666677764 3666655
No 98
>KOG1598|consensus
Probab=32.06 E-value=26 Score=31.54 Aligned_cols=26 Identities=35% Similarity=0.783 Sum_probs=19.2
Q ss_pred ccccCCCCCCcceecCCCCCcccchhhh
Q psy15323 64 CCTNCGTRMTTLWRRNNDGEPVCNACGL 91 (139)
Q Consensus 64 ~C~~C~t~~t~~Wr~~~~g~~lCnaCgl 91 (139)
.|.||+-+..-. ....|...|++||.
T Consensus 2 ~C~~C~~s~fe~--d~a~g~~~C~~CG~ 27 (521)
T KOG1598|consen 2 VCKNCGGSNFER--DEATGNLYCTACGT 27 (521)
T ss_pred cCCCCCCCCccc--ccccCCceeccccc
Confidence 699999876544 22457789999995
No 99
>KOG0706|consensus
Probab=30.10 E-value=28 Score=30.72 Aligned_cols=41 Identities=20% Similarity=0.455 Sum_probs=32.8
Q ss_pred ccccCcccccCCCCCCcceecCCCCCcccchhhhhHHhhCCC
Q psy15323 58 TRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVN 99 (139)
Q Consensus 58 tk~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~~~ 99 (139)
......+|..|+. ..|.|-.-+-|..||-.|.--.|--|++
T Consensus 19 s~~~NKvCFDCgA-knPtWaSVTYGIFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 19 SQSENKVCFDCGA-KNPTWASVTYGIFLCIDCSAVHRNLGVH 59 (454)
T ss_pred cCCCCceecccCC-CCCCceeecceEEEEEecchhhhccccc
Confidence 3456779999998 8899999999999999998655544443
No 100
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=29.70 E-value=40 Score=26.25 Aligned_cols=31 Identities=26% Similarity=0.565 Sum_probs=24.7
Q ss_pred CCCCccccCCCCCCCceeecCCCCccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACG 36 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCg 36 (139)
+.-..|..||......+-.-.+|.++|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3456899999877766666678899999997
No 101
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.58 E-value=33 Score=28.49 Aligned_cols=28 Identities=36% Similarity=0.756 Sum_probs=19.8
Q ss_pred CCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
-+.|..||+...+ +...-..+|+.|+..
T Consensus 111 ~RFCg~CG~~~~~---~~~g~~~~C~~cg~~ 138 (279)
T COG2816 111 HRFCGRCGTKTYP---REGGWARVCPKCGHE 138 (279)
T ss_pred CcCCCCCCCcCcc---ccCceeeeCCCCCCc
Confidence 5789999954443 333336799999984
No 102
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=29.48 E-value=56 Score=18.26 Aligned_cols=28 Identities=21% Similarity=0.451 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.+.|..|+. +.--...++.++|.-|+.-
T Consensus 3 ~~~C~~C~~---~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGG---NGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCC---CeEEEecCCeEEcccCCcE
Confidence 456777773 3222234556788888763
No 103
>PF15396 FAM60A: Protein Family FAM60A
Probab=29.22 E-value=27 Score=27.89 Aligned_cols=16 Identities=38% Similarity=0.578 Sum_probs=12.4
Q ss_pred cccchhhhhHHhhCCC
Q psy15323 84 PVCNACGLYYKLHNVN 99 (139)
Q Consensus 84 ~lCnaCgly~~~~~~~ 99 (139)
-+||||.|..++-++.
T Consensus 50 eICNACVLLVKRwKKL 65 (213)
T PF15396_consen 50 EICNACVLLVKRWKKL 65 (213)
T ss_pred hhhHHHHHHHHHHhhC
Confidence 5899999988765543
No 104
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=28.90 E-value=50 Score=23.37 Aligned_cols=33 Identities=21% Similarity=0.408 Sum_probs=23.8
Q ss_pred CCCccccCCCCCCCceeecCCCCcccccccccccccC
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 43 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg 43 (139)
.+..|..|+...+-.+- |.+-|+||..+++..-
T Consensus 5 ~~~~C~VCg~~a~g~hy----Gv~sC~aCk~FFRR~v 37 (107)
T cd06955 5 VPRICGVCGDRATGFHF----NAMTCEGCKGFFRRSM 37 (107)
T ss_pred CCCCCeecCCcCcccEE----Ccceeeeecceeccee
Confidence 45779999975554433 4568999999887643
No 105
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=28.82 E-value=26 Score=24.98 Aligned_cols=32 Identities=22% Similarity=0.699 Sum_probs=23.7
Q ss_pred cccccCCCCCCcceec----CCCC---CcccchhhhhHH
Q psy15323 63 LCCTNCGTRMTTLWRR----NNDG---EPVCNACGLYYK 94 (139)
Q Consensus 63 ~~C~~C~t~~t~~Wr~----~~~g---~~lCnaCgly~~ 94 (139)
..|..|+-.+-..|-. ++++ ++.|-.||..|+
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 4699999999777753 3333 378999998765
No 106
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=28.61 E-value=39 Score=30.96 Aligned_cols=60 Identities=18% Similarity=0.265 Sum_probs=36.5
Q ss_pred cccccccccccccC--CCCCCCCCccchhhccccCcccccCCCCCCcceecCCCCCcccchhhhhHHhhCCCCCc
Q psy15323 30 YLCNACGLYHKMNG--MNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPL 102 (139)
Q Consensus 30 ~lCnaCgly~k~hg--~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~~~Rp~ 102 (139)
.+|+.||-++.+.- +.-|.-.+.- .. ...-.+|.||+...-+ ++|++++.++.+...|+.
T Consensus 228 vpCPHCGe~q~l~~~e~~~~~g~~~~--~~-~~~~~~c~h~~~~i~~----------~~~~~gv~~~~g~~~~dg 289 (611)
T COG5525 228 VPCPHCGEEQQLKFGEKSGPRGLKDT--PA-EAAFIQCEHCGCVIRP----------KLNGRGVCLRTGEWIRDG 289 (611)
T ss_pred eeCCCCCchhhccccccCCCcCcccc--hh-hhhhhhccccCceeee----------eccCccchhccCCcCCCc
Confidence 49999999876653 1112211111 11 3345689999997766 267777777766665554
No 107
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=28.34 E-value=26 Score=19.36 Aligned_cols=25 Identities=28% Similarity=0.648 Sum_probs=11.2
Q ss_pred CccccCCCCCCCceeecCCCCcccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
..|..|+++.|= .+...++|..|+.
T Consensus 3 p~Cp~C~se~~y----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY----EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E----E-SSSEEETTTTE
T ss_pred CCCCCCCCccee----ccCCEEeCCcccc
Confidence 368888876653 2233688988875
No 108
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=27.76 E-value=43 Score=24.74 Aligned_cols=32 Identities=28% Similarity=0.317 Sum_probs=21.6
Q ss_pred CCCCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 4 QFGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 4 ~~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
..|..++|.+||+...-|=+. ..+|..||--+
T Consensus 5 elGtKr~Cp~cg~kFYDLnk~----p~vcP~cg~~~ 36 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLNRR----PAVSPYTGEQF 36 (129)
T ss_pred hhCccccCCCcCccccccCCC----CccCCCcCCcc
Confidence 346678888888766655542 35888888754
No 109
>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=27.56 E-value=70 Score=20.76 Aligned_cols=41 Identities=24% Similarity=0.472 Sum_probs=30.8
Q ss_pred CcccccCCCCCCcceecCC--CCC--cccchhhhhHHhhCCCCCc
Q psy15323 62 GLCCTNCGTRMTTLWRRNN--DGE--PVCNACGLYYKLHNVNRPL 102 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~--~g~--~lCnaCgly~~~~~~~Rp~ 102 (139)
...|..|....|-.--=++ ..+ ++|-+|--||..-+..|-+
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred CCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 4679999998877544222 233 8999999999998888766
No 110
>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=27.34 E-value=51 Score=26.06 Aligned_cols=52 Identities=27% Similarity=0.522 Sum_probs=33.2
Q ss_pred cccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCc-ceecC
Q psy15323 11 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTT-LWRRN 79 (139)
Q Consensus 11 C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~-~Wr~~ 79 (139)
|..||....|+-. -||..|.+... ++.... ....-.+|..|+.-..+ .|...
T Consensus 1 C~~CG~~~~~~~~------~lC~~C~~~~~------~i~ei~-----~~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 1 CPRCGREIEPLID------GLCPDCYLKRF------DIIEIP-----DRIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CCCCCCCCCCccc------ccChHHhcccC------CeeecC-----CccCceECCCCCCEECCCEeeec
Confidence 7889975555433 39999998431 111111 11234589999998876 89877
No 111
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=26.95 E-value=54 Score=26.55 Aligned_cols=20 Identities=30% Similarity=0.396 Sum_probs=12.7
Q ss_pred cccccCCCCCCcceecCCCC
Q psy15323 63 LCCTNCGTRMTTLWRRNNDG 82 (139)
Q Consensus 63 ~~C~~C~t~~t~~Wr~~~~g 82 (139)
..|.+|++..|-..++|-+|
T Consensus 369 ~~c~~c~~~~~~~~~~~~~~ 388 (389)
T PRK11788 369 WHCPSCKAWETIKPIRGLDG 388 (389)
T ss_pred eECcCCCCccCcCCcccCCC
Confidence 35777777666666666554
No 112
>PHA02942 putative transposase; Provisional
Probab=26.40 E-value=50 Score=28.25 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=19.7
Q ss_pred CCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
....|+.||.....+ ....+.|..||..
T Consensus 324 TSq~Cs~CG~~~~~l----~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEI----AHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcC----CCCEEECCCCCCE
Confidence 567899999765432 1225899999984
No 113
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=26.35 E-value=8.1 Score=21.71 Aligned_cols=28 Identities=25% Similarity=0.442 Sum_probs=15.5
Q ss_pred CccccCCCCCCCceeecCCCCccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACG 36 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCg 36 (139)
.+|..||-..-......-.+..+|-.|.
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~ 31 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQ 31 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHh
Confidence 4588888655544444445666776664
No 114
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.90 E-value=52 Score=19.24 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=14.5
Q ss_pred ccccCCCCCCCceeecCCCCccccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.|.+||+..+-. .....+.|..||-.
T Consensus 5 ~C~~CG~~~~~~---~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGREVELD---EYGTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCCEEEEC---CCCCceECCCCCCe
Confidence 578888643221 11125678888764
No 115
>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=25.81 E-value=56 Score=25.33 Aligned_cols=32 Identities=25% Similarity=0.528 Sum_probs=22.2
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGL 37 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgl 37 (139)
+.-..|..||......+-.-.+|.++|..|.-
T Consensus 145 p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 145 LDLDKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred cccCccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 44568999998433344344468899999975
No 116
>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=25.75 E-value=34 Score=26.63 Aligned_cols=29 Identities=31% Similarity=0.781 Sum_probs=23.5
Q ss_pred ccccCCCCCCCceeecCCCC---ccccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGH---YLCNACGLY 38 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~---~lCnaCgly 38 (139)
.|.+||..-..++++-..+. +.|..|+-.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 69999999888999865552 689999874
No 117
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=25.45 E-value=41 Score=19.64 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=19.9
Q ss_pred ccccCCCCCCCceeecCCCC-ccccccccc
Q psy15323 10 ECVNCGAISTPLWRRDGTGH-YLCNACGLY 38 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~-~lCnaCgly 38 (139)
.|..|....++.|+=..-.. -||.+|...
T Consensus 2 ~C~~C~~~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 2 TCNECKHHVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred cCCCCCCcCCCceECCCCcchhhHHHHhCC
Confidence 47778777778888554333 388888764
No 118
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=25.36 E-value=21 Score=29.44 Aligned_cols=41 Identities=22% Similarity=0.568 Sum_probs=22.9
Q ss_pred cccccccc-cccccCC----------CCCCCCCc--cchhhccccCcccccCCC
Q psy15323 30 YLCNACGL-YHKMNGM----------NRPLVKPS--KRLTATRRLGLCCTNCGT 70 (139)
Q Consensus 30 ~lCnaCgl-y~k~hg~----------nRP~~kps--KR~~atk~~~~~C~~C~t 70 (139)
.+|-.|++ +++..|. ..|+.... ..........+.|+||+.
T Consensus 196 ~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~ 249 (272)
T COG3183 196 TVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHK 249 (272)
T ss_pred ceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHH
Confidence 79999999 6666662 23443322 222333445556666654
No 119
>KOG0703|consensus
Probab=25.27 E-value=36 Score=28.37 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=25.8
Q ss_pred cCcccccCCCCCCcceecCCCCCcccchhh
Q psy15323 61 LGLCCTNCGTRMTTLWRRNNDGEPVCNACG 90 (139)
Q Consensus 61 ~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCg 90 (139)
....|+.|++. .|.|-.-+-|-.+|--|.
T Consensus 24 ~N~~CADC~a~-~P~WaSwnlGvFiC~~C~ 52 (287)
T KOG0703|consen 24 DNKVCADCGAK-GPRWASWNLGVFICLRCA 52 (287)
T ss_pred ccCcccccCCC-CCCeEEeecCeEEEeecc
Confidence 37789999997 999988888988999997
No 120
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=25.08 E-value=58 Score=17.22 Aligned_cols=8 Identities=38% Similarity=1.157 Sum_probs=3.9
Q ss_pred cccccccc
Q psy15323 30 YLCNACGL 37 (139)
Q Consensus 30 ~lCnaCgl 37 (139)
..|..||.
T Consensus 15 ~~Cp~CG~ 22 (26)
T PF10571_consen 15 KFCPHCGY 22 (26)
T ss_pred CcCCCCCC
Confidence 34555554
No 121
>PRK12495 hypothetical protein; Provisional
Probab=24.61 E-value=40 Score=27.15 Aligned_cols=31 Identities=26% Similarity=0.683 Sum_probs=23.9
Q ss_pred CCCCCccccCCCCCCCceeecCCCCccccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHK 40 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k 40 (139)
.+....|..|| .||.+. .|..+|..|+-..-
T Consensus 39 tmsa~hC~~CG---~PIpa~--pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 39 TMTNAHCDECG---DPIFRH--DGQEFCPTCQQPVT 69 (226)
T ss_pred ccchhhccccc---CcccCC--CCeeECCCCCCccc
Confidence 34577899999 777743 78899999997643
No 122
>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=24.15 E-value=39 Score=23.00 Aligned_cols=34 Identities=32% Similarity=0.605 Sum_probs=24.6
Q ss_pred CCCCCccccCCCCCCCceeecCCCCccccccccccccc
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 42 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~h 42 (139)
-++...|..|+...+-.+- |...|+||..+++..
T Consensus 3 ~~~~~~C~VCg~~a~g~hy----Gv~sC~aCk~FFRR~ 36 (90)
T cd07169 3 RAEQRTCLICGDRATGLHY----GIISCEGCKGFFKRS 36 (90)
T ss_pred cccCCCCeecCCcCcceEE----CcceehhhHHHHHHH
Confidence 3567789999975554443 456899999988654
No 123
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=23.84 E-value=48 Score=27.70 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=22.2
Q ss_pred CccccCCCCCCCceeecCCCCcccccccccccc
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKM 41 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~ 41 (139)
+.|.+|...+|-- .-.-+.+-+||+|-.+..+
T Consensus 2 ~~C~~C~~~~t~p-~i~fd~~GvC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMPTTRP-GITFDEDGVCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCCCCCC-CeeECCCCCchhhhhHHhh
Confidence 5799999876543 2223445699999998744
No 124
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=23.56 E-value=36 Score=24.23 Aligned_cols=30 Identities=33% Similarity=0.837 Sum_probs=20.9
Q ss_pred ccccCCCCCCc---ceecCCCCCcccchhhhhH
Q psy15323 64 CCTNCGTRMTT---LWRRNNDGEPVCNACGLYY 93 (139)
Q Consensus 64 ~C~~C~t~~t~---~Wr~~~~g~~lCnaCgly~ 93 (139)
-|..|+-.... +--.+.-|...|..||+++
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 48888876655 5444444667899999876
No 125
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=23.52 E-value=55 Score=18.68 Aligned_cols=28 Identities=18% Similarity=0.610 Sum_probs=17.3
Q ss_pred cCcccccCCCCCCcceec--CCCCC--cccchh
Q psy15323 61 LGLCCTNCGTRMTTLWRR--NNDGE--PVCNAC 89 (139)
Q Consensus 61 ~~~~C~~C~t~~t~~Wr~--~~~g~--~lCnaC 89 (139)
+.+.|..|+.++. +-+. +++|. ++|-.|
T Consensus 4 i~v~CP~C~s~~~-v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 4 IDVHCPRCQSTEG-VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred EeeeCCCCCCCCc-ceeCCCCCCCCEeEecCcC
Confidence 3457888888653 3343 44563 788777
No 126
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.37 E-value=36 Score=25.00 Aligned_cols=8 Identities=38% Similarity=1.016 Sum_probs=4.0
Q ss_pred cccccccc
Q psy15323 30 YLCNACGL 37 (139)
Q Consensus 30 ~lCnaCgl 37 (139)
|+|+.|+.
T Consensus 100 Y~Cp~C~~ 107 (147)
T smart00531 100 YKCPNCQS 107 (147)
T ss_pred EECcCCCC
Confidence 45555554
No 127
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) 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. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=23.26 E-value=52 Score=22.58 Aligned_cols=31 Identities=19% Similarity=0.471 Sum_probs=21.2
Q ss_pred CccccCCCCCCCceeecCCCCcccccccccccccC
Q psy15323 9 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNG 43 (139)
Q Consensus 9 ~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg 43 (139)
+.|..|+...+-.+- |.+-|+||..+++..-
T Consensus 1 ~~C~VCg~~a~g~hy----Gv~sC~aC~~FFRR~v 31 (94)
T cd06966 1 KICGVCGDKALGYNF----NAITCESCKAFFRRNA 31 (94)
T ss_pred CCCeeCCCcCcceEE----Ccceeeeehheehhcc
Confidence 368889865444433 4568999999886543
No 128
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) 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. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=23.15 E-value=67 Score=21.57 Aligned_cols=32 Identities=19% Similarity=0.416 Sum_probs=22.6
Q ss_pred CCCccccCCCCCCCceeecCCCCccccccccccccc
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 42 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~h 42 (139)
....|..|+...+-.+- |..-|+||..+++..
T Consensus 3 ~~~~C~VCg~~~~g~hy----Gv~sC~aC~~FFRR~ 34 (85)
T cd06964 3 IYKPCFVCQDKSSGYHY----GVSACEGCKGFFRRS 34 (85)
T ss_pred cCCCCcccCCcCcccEE----CcceeeeeeeEEeee
Confidence 34579999975554433 456899999988654
No 129
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=22.96 E-value=34 Score=23.49 Aligned_cols=18 Identities=17% Similarity=0.488 Sum_probs=12.2
Q ss_pred ccCcccccCCCCCCccee
Q psy15323 60 RLGLCCTNCGTRMTTLWR 77 (139)
Q Consensus 60 ~~~~~C~~C~t~~t~~Wr 77 (139)
.....|..|++.+.|.|.
T Consensus 36 v~~Q~C~~C~~~~~P~~~ 53 (98)
T PF13695_consen 36 VFGQRCKKCNPLERPYFS 53 (98)
T ss_pred EECCCCCCCCCCCCccCc
Confidence 345567777777777775
No 130
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=22.92 E-value=40 Score=23.92 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=3.7
Q ss_pred cccccccc
Q psy15323 30 YLCNACGL 37 (139)
Q Consensus 30 ~lCnaCgl 37 (139)
..|+.|+-
T Consensus 71 ~~C~~Cg~ 78 (115)
T TIGR00100 71 CECEDCSE 78 (115)
T ss_pred EEcccCCC
Confidence 34444443
No 131
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=22.90 E-value=50 Score=28.27 Aligned_cols=62 Identities=24% Similarity=0.488 Sum_probs=36.8
Q ss_pred CCCCCccccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCc-ceecCCCCC
Q psy15323 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTT-LWRRNNDGE 83 (139)
Q Consensus 5 ~~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~-~Wr~~~~g~ 83 (139)
+.....|..||...-|+- .-||..|.+-. -+..... ....-..|.+|+.-..+ .|-..+.+.
T Consensus 3 ~~~~~~C~~CGr~~~~~~------~~lC~dC~~~~------~~~~~ip-----~~~~v~~C~~Cga~~~~~~W~~~~~~~ 65 (355)
T COG1499 3 DASTILCVRCGRSVDPLI------DGLCGDCYVET------TPLIEIP-----DEVNVEVCRHCGAYRIRGRWVDEEGAN 65 (355)
T ss_pred CCcccEeccCCCcCchhh------ccccHHHHhcc------CccccCC-----CceEEEECCcCCCccCCCcceeccccc
Confidence 345678999997665433 34999999841 1111100 01224579999955544 888744343
No 132
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=22.90 E-value=42 Score=22.21 Aligned_cols=55 Identities=31% Similarity=0.659 Sum_probs=28.0
Q ss_pred ccccCCCCCCCceeecCCCCcccccccccccccCCCCCCCCCccchhhccccCcccccCCCCCCcceecCCCCCcccchh
Q psy15323 10 ECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNAC 89 (139)
Q Consensus 10 ~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~hg~nRP~~kpsKR~~atk~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaC 89 (139)
.|-.|+ ++|=+.+ +.+.|.+|...+.+ ...|.+|+..-.-|--=|.. .++||.|
T Consensus 3 ~CP~C~---~~L~~~~--~~~~C~~C~~~~~~--------------------~a~CPdC~~~Le~LkACGAv-dYFC~~c 56 (70)
T PF07191_consen 3 TCPKCQ---QELEWQG--GHYHCEACQKDYKK--------------------EAFCPDCGQPLEVLKACGAV-DYFCNHC 56 (70)
T ss_dssp B-SSS----SBEEEET--TEEEETTT--EEEE--------------------EEE-TTT-SB-EEEEETTEE-EEE-TTT
T ss_pred cCCCCC---CccEEeC--CEEECcccccccee--------------------cccCCCcccHHHHHHHhccc-ceeeccC
Confidence 467777 4443333 78999999985533 23688888755555322222 2788888
Q ss_pred h
Q psy15323 90 G 90 (139)
Q Consensus 90 g 90 (139)
.
T Consensus 57 ~ 57 (70)
T PF07191_consen 57 H 57 (70)
T ss_dssp T
T ss_pred C
Confidence 4
No 133
>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=21.61 E-value=60 Score=22.05 Aligned_cols=32 Identities=25% Similarity=0.526 Sum_probs=19.9
Q ss_pred CcccccCCCCCCcceecCCCCCcccchhhhhHHhhC
Q psy15323 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHN 97 (139)
Q Consensus 62 ~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~ 97 (139)
...|..|+...+-. --|...|+||...++..-
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 44688887643322 124467999988886543
No 134
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.52 E-value=63 Score=25.49 Aligned_cols=25 Identities=24% Similarity=0.683 Sum_probs=17.9
Q ss_pred CCCCccccCCCCCCCceeecCCCCccccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLY 38 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly 38 (139)
.+...|+.||. +. ...+.|..||..
T Consensus 307 ~tS~~C~~cg~-----~~---~r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH-----LS---GRLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC-----cc---ceeEECCCCCCe
Confidence 35688999997 11 235789999984
No 135
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.25 E-value=69 Score=20.34 Aligned_cols=26 Identities=35% Similarity=0.775 Sum_probs=13.8
Q ss_pred CCCCccccCCCCCCCceeecCCCCcccccccccc
Q psy15323 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYH 39 (139)
Q Consensus 6 ~~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~ 39 (139)
+..-+|.|||...= -+-+|..||.|.
T Consensus 25 ~~~~~c~~cG~~~l--------~Hrvc~~cg~Y~ 50 (57)
T COG0333 25 PTLSVCPNCGEYKL--------PHRVCLKCGYYK 50 (57)
T ss_pred ccceeccCCCCccc--------CceEcCCCCCcc
Confidence 33456777763211 124777777654
No 136
>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=20.48 E-value=47 Score=18.89 Aligned_cols=29 Identities=17% Similarity=0.409 Sum_probs=11.8
Q ss_pred CCccccCCCCCCCceeecCCCCccccccc
Q psy15323 8 GRECVNCGAISTPLWRRDGTGHYLCNACG 36 (139)
Q Consensus 8 ~~~C~nC~~~~tp~WRr~~~g~~lCnaCg 36 (139)
...|..|+....--|=...=+..+|..|-
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred CchHhHhCCHHHHHHHHHhCCcccccccc
Confidence 45788888755554443333455777773
No 137
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=20.30 E-value=77 Score=18.62 Aligned_cols=31 Identities=23% Similarity=0.451 Sum_probs=17.3
Q ss_pred CcccccCCCCC--CcceecCC-CCCcccchhhhh
Q psy15323 62 GLCCTNCGTRM--TTLWRRNN-DGEPVCNACGLY 92 (139)
Q Consensus 62 ~~~C~~C~t~~--t~~Wr~~~-~g~~lCnaCgly 92 (139)
...|..|++.. ...|+=.. ....||.+|+.-
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 45677777732 44565332 345799999864
No 138
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=20.29 E-value=65 Score=27.95 Aligned_cols=38 Identities=18% Similarity=0.423 Sum_probs=30.3
Q ss_pred ccCcccccCCCCCCcceecCCCCCcccchhhhhHHhhCC
Q psy15323 60 RLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNV 98 (139)
Q Consensus 60 ~~~~~C~~C~t~~t~~Wr~~~~g~~lCnaCgly~~~~~~ 98 (139)
.....|..|+.. -|.|=.-+-|-.||..|.-..|..++
T Consensus 20 PgNk~CaDCga~-nPtWASvn~GIFLCl~CSGVHRsLGv 57 (395)
T PLN03114 20 SDNKICFDCNAK-NPTWASVTYGIFLCIDCSAVHRSLGV 57 (395)
T ss_pred cCCCcCccCCCC-CCCceeeccceeehhhhhHhhccCCC
Confidence 456789999985 69999888898999999866655553
No 139
>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=20.13 E-value=49 Score=22.16 Aligned_cols=32 Identities=22% Similarity=0.620 Sum_probs=22.3
Q ss_pred CCCccccCCCCCCCceeecCCCCccccccccccccc
Q psy15323 7 EGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 42 (139)
Q Consensus 7 ~~~~C~nC~~~~tp~WRr~~~g~~lCnaCgly~k~h 42 (139)
+...|..|+...+-.+- |.+-|+||..+++..
T Consensus 2 ~~~~C~VCg~~a~g~hy----Gv~sC~aCk~FFRR~ 33 (82)
T cd07173 2 PQKTCLICGDEASGCHY----GALTCGSCKVFFKRA 33 (82)
T ss_pred CCCCCeecCCcCcceEE----CcchhhhHHHHHHHH
Confidence 34579999965544332 456899999988654
Done!