Query 045121
Match_columns 202
No_of_seqs 123 out of 139
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 10:03:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12874 zf-met: Zinc-finger o 98.7 1.2E-08 2.6E-13 58.9 2.0 25 137-161 1-25 (25)
2 smart00451 ZnF_U1 U1-like zinc 98.6 3.3E-08 7E-13 61.0 3.0 32 136-167 3-34 (35)
3 PF12874 zf-met: Zinc-finger o 98.6 3.1E-08 6.6E-13 57.1 1.8 25 3-27 1-25 (25)
4 smart00451 ZnF_U1 U1-like zinc 98.4 1.4E-07 3E-12 58.1 2.1 32 2-33 3-34 (35)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.3 4.9E-07 1.1E-11 53.5 2.1 27 136-162 1-27 (27)
6 PF12171 zf-C2H2_jaz: Zinc-fin 98.1 1.5E-06 3.3E-11 51.3 1.5 27 2-28 1-27 (27)
7 PF06220 zf-U1: U1 zinc finger 97.5 0.0001 2.2E-09 47.6 2.7 32 136-167 3-36 (38)
8 KOG4727 U1-like Zn-finger prot 97.4 8.5E-05 1.8E-09 62.6 2.6 35 132-166 71-105 (193)
9 KOG3408 U1-like Zn-finger-cont 96.7 0.0018 4E-08 51.9 3.6 39 132-170 53-91 (129)
10 PF06220 zf-U1: U1 zinc finger 96.7 0.0017 3.6E-08 41.8 2.7 32 2-33 3-36 (38)
11 KOG4727 U1-like Zn-finger prot 96.1 0.0034 7.4E-08 53.1 2.2 32 3-34 76-107 (193)
12 PF12756 zf-C2H2_2: C2H2 type 95.7 0.0047 1E-07 44.6 1.0 31 136-166 50-80 (100)
13 PF14968 CCDC84: Coiled coil p 95.3 0.0093 2E-07 55.0 2.0 43 133-175 55-104 (336)
14 KOG3792 Transcription factor N 95.2 0.0087 1.9E-07 59.7 1.4 45 133-177 232-276 (816)
15 KOG3032 Uncharacterized conser 95.0 0.028 6E-07 49.7 4.0 37 132-169 31-67 (264)
16 PLN02748 tRNA dimethylallyltra 95.0 0.017 3.6E-07 55.4 2.9 36 135-170 417-453 (468)
17 PF13894 zf-C2H2_4: C2H2-type 95.0 0.017 3.6E-07 31.5 1.8 21 3-23 1-21 (24)
18 KOG0717 Molecular chaperone (D 95.0 0.017 3.6E-07 55.4 2.6 36 136-171 292-327 (508)
19 smart00586 ZnF_DBF Zinc finger 94.9 0.011 2.4E-07 40.3 1.0 28 136-166 5-32 (49)
20 PF07535 zf-DBF: DBF zinc fing 94.7 0.02 4.4E-07 38.9 1.9 28 135-165 4-31 (49)
21 KOG0227 Splicing factor 3a, su 94.6 0.027 5.8E-07 48.6 2.8 36 2-37 53-88 (222)
22 KOG3454 U1 snRNP-specific prot 94.5 0.021 4.5E-07 47.9 1.9 31 136-166 3-35 (165)
23 PF13894 zf-C2H2_4: C2H2-type 94.2 0.031 6.7E-07 30.4 1.5 21 137-157 1-21 (24)
24 smart00586 ZnF_DBF Zinc finger 94.1 0.021 4.5E-07 39.0 0.8 27 2-31 5-31 (49)
25 KOG0717 Molecular chaperone (D 94.1 0.034 7.3E-07 53.4 2.4 34 3-36 293-326 (508)
26 KOG4722 Zn-finger protein [Gen 93.8 0.032 6.9E-07 53.4 1.8 33 137-169 494-526 (672)
27 PF00096 zf-C2H2: Zinc finger, 93.8 0.038 8.3E-07 30.6 1.5 21 3-23 1-21 (23)
28 COG5112 UFD2 U1-like Zn-finger 93.4 0.042 9E-07 43.5 1.5 38 134-171 53-90 (126)
29 PF07535 zf-DBF: DBF zinc fing 93.3 0.041 8.9E-07 37.4 1.2 27 2-31 5-31 (49)
30 PF13912 zf-C2H2_6: C2H2-type 93.3 0.067 1.5E-06 30.8 1.9 22 2-23 1-22 (27)
31 PF12756 zf-C2H2_2: C2H2 type 93.1 0.046 9.9E-07 39.4 1.3 31 2-32 50-80 (100)
32 KOG0227 Splicing factor 3a, su 93.0 0.065 1.4E-06 46.3 2.2 38 132-169 49-86 (222)
33 PF00096 zf-C2H2: Zinc finger, 92.9 0.065 1.4E-06 29.6 1.5 22 137-158 1-22 (23)
34 KOG2785 C2H2-type Zn-finger pr 92.9 0.061 1.3E-06 50.3 2.1 37 134-170 66-102 (390)
35 COG5246 PRP11 Splicing factor 92.7 0.078 1.7E-06 45.6 2.3 33 2-34 53-85 (222)
36 PF13912 zf-C2H2_6: C2H2-type 92.7 0.077 1.7E-06 30.5 1.6 22 136-157 1-22 (27)
37 COG5188 PRP9 Splicing factor 3 91.8 0.079 1.7E-06 49.6 1.4 36 135-170 237-272 (470)
38 COG5246 PRP11 Splicing factor 91.7 0.17 3.7E-06 43.5 3.2 39 131-169 48-86 (222)
39 KOG3032 Uncharacterized conser 90.8 0.2 4.4E-06 44.4 2.8 34 2-36 35-68 (264)
40 smart00355 ZnF_C2H2 zinc finge 90.8 0.15 3.2E-06 27.8 1.3 21 3-23 1-21 (26)
41 KOG1146 Homeobox protein [Gene 90.3 0.24 5.2E-06 52.7 3.4 35 2-36 518-552 (1406)
42 PF13909 zf-H2C2_5: C2H2-type 90.2 0.18 4E-06 28.3 1.4 20 3-23 1-20 (24)
43 KOG3408 U1-like Zn-finger-cont 89.7 0.2 4.4E-06 40.3 1.8 35 2-36 57-91 (129)
44 KOG3454 U1 snRNP-specific prot 89.6 0.21 4.5E-06 41.9 1.8 32 2-33 3-36 (165)
45 KOG3792 Transcription factor N 89.4 0.12 2.7E-06 51.8 0.4 47 120-166 341-389 (816)
46 smart00355 ZnF_C2H2 zinc finge 88.7 0.31 6.6E-06 26.4 1.6 21 137-157 1-21 (26)
47 KOG0150 Spliceosomal protein F 86.8 0.39 8.4E-06 44.1 1.9 34 135-168 9-43 (336)
48 PF09237 GAGA: GAGA factor; I 85.7 0.51 1.1E-05 32.8 1.6 21 3-23 25-45 (54)
49 KOG4722 Zn-finger protein [Gen 85.6 0.46 1E-05 45.7 1.8 33 4-36 495-527 (672)
50 KOG2837 Protein containing a U 84.9 0.19 4.1E-06 45.5 -1.1 39 134-172 23-61 (309)
51 PF04988 AKAP95: A-kinase anch 83.7 0.97 2.1E-05 38.0 2.7 138 3-184 1-140 (165)
52 COG5136 U1 snRNP-specific prot 83.3 0.4 8.7E-06 40.5 0.3 31 136-166 3-35 (188)
53 COG5112 UFD2 U1-like Zn-finger 81.9 0.87 1.9E-05 36.1 1.7 35 2-36 55-89 (126)
54 PF13909 zf-H2C2_5: C2H2-type 81.4 1 2.2E-05 25.2 1.4 20 137-157 1-20 (24)
55 PF04988 AKAP95: A-kinase anch 80.6 1.2 2.7E-05 37.4 2.2 32 137-168 1-32 (165)
56 PF12013 DUF3505: Protein of u 76.7 2 4.3E-05 32.7 2.2 60 135-195 10-74 (109)
57 KOG0150 Spliceosomal protein F 76.5 1.3 2.9E-05 40.7 1.4 31 3-33 11-42 (336)
58 PF11931 DUF3449: Domain of un 76.5 0.81 1.8E-05 39.4 0.0 36 1-36 100-136 (196)
59 COG5188 PRP9 Splicing factor 3 72.8 1.7 3.7E-05 40.9 1.1 35 135-169 373-408 (470)
60 smart00734 ZnF_Rad18 Rad18-lik 71.3 2.6 5.6E-05 24.8 1.3 19 4-23 3-21 (26)
61 KOG2785 C2H2-type Zn-finger pr 68.4 2.4 5.3E-05 39.9 1.1 35 1-35 67-101 (390)
62 PF12907 zf-met2: Zinc-binding 67.9 2.5 5.4E-05 27.6 0.8 24 3-26 2-28 (40)
63 PF03194 LUC7: LUC7 N_terminus 66.1 3.2 6.9E-05 36.8 1.3 27 136-162 190-219 (254)
64 PHA00616 hypothetical protein 65.7 2.8 6E-05 28.0 0.7 21 2-22 1-21 (44)
65 PF11931 DUF3449: Domain of un 65.5 2 4.4E-05 37.0 0.0 36 134-169 99-135 (196)
66 PF12013 DUF3505: Protein of u 65.3 17 0.00038 27.4 5.2 29 3-32 12-40 (109)
67 PF14968 CCDC84: Coiled coil p 64.2 3.2 7E-05 38.5 1.1 29 138-169 1-29 (336)
68 PF09237 GAGA: GAGA factor; I 63.9 5.8 0.00013 27.6 2.0 26 132-157 20-45 (54)
69 KOG2837 Protein containing a U 59.3 2.3 5.1E-05 38.6 -0.7 35 2-36 25-59 (309)
70 PHA00732 hypothetical protein 57.5 7.3 0.00016 28.6 1.8 22 2-23 1-22 (79)
71 KOG1146 Homeobox protein [Gene 56.2 20 0.00044 38.9 5.3 40 134-173 516-555 (1406)
72 PHA02768 hypothetical protein; 55.9 6.9 0.00015 27.3 1.3 25 136-162 5-29 (55)
73 PTZ00448 hypothetical protein; 53.6 14 0.00031 34.8 3.4 35 136-170 314-348 (373)
74 PF12907 zf-met2: Zinc-binding 51.0 7.5 0.00016 25.4 0.8 23 137-159 2-27 (40)
75 KOG1994 Predicted RNA binding 50.2 10 0.00022 33.8 1.8 26 133-158 236-261 (268)
76 PHA02768 hypothetical protein; 49.3 9.7 0.00021 26.5 1.2 24 3-28 6-29 (55)
77 COG5067 DBF4 Protein kinase es 47.5 6.7 0.00015 37.5 0.2 28 135-165 421-448 (468)
78 KOG2636 Splicing factor 3a, su 47.0 12 0.00025 36.4 1.7 36 134-169 399-435 (497)
79 KOG0796 Spliceosome subunit [R 46.2 11 0.00023 34.9 1.3 28 136-163 186-216 (319)
80 KOG2893 Zn finger protein [Gen 44.8 13 0.00028 33.7 1.6 28 133-160 7-34 (341)
81 KOG2505 Ankyrin repeat protein 43.4 14 0.00031 36.3 1.7 31 2-32 66-96 (591)
82 PTZ00448 hypothetical protein; 42.9 18 0.00038 34.2 2.2 35 2-36 314-348 (373)
83 KOG2636 Splicing factor 3a, su 42.5 12 0.00025 36.4 1.0 36 1-36 400-436 (497)
84 PHA00732 hypothetical protein 41.2 18 0.0004 26.5 1.7 21 137-157 2-22 (79)
85 PF03194 LUC7: LUC7 N_terminus 40.6 14 0.00031 32.7 1.2 28 4-31 192-222 (254)
86 PF04959 ARS2: Arsenite-resist 40.0 26 0.00056 30.6 2.6 34 2-36 77-110 (214)
87 PHA00733 hypothetical protein 36.7 23 0.0005 28.1 1.7 22 2-23 73-94 (128)
88 PF13913 zf-C2HC_2: zinc-finge 36.6 24 0.00051 20.3 1.3 18 4-22 4-21 (25)
89 PF05477 SURF2: Surfeit locus 36.4 43 0.00092 29.9 3.5 39 132-170 75-114 (244)
90 KOG3608 Zn finger proteins [Ge 36.1 20 0.00044 34.0 1.5 28 134-162 350-377 (467)
91 PF05605 zf-Di19: Drought indu 35.3 25 0.00054 23.4 1.5 21 2-23 2-22 (54)
92 COG5200 LUC7 U1 snRNP componen 31.3 25 0.00053 31.2 1.1 26 138-163 187-215 (258)
93 COG5136 U1 snRNP-specific prot 28.8 21 0.00045 30.4 0.3 31 2-32 3-35 (188)
94 KOG3608 Zn finger proteins [Ge 26.2 39 0.00086 32.2 1.6 26 134-159 261-286 (467)
95 PF13465 zf-H2C2_2: Zinc-finge 25.5 34 0.00075 19.5 0.7 12 2-13 14-25 (26)
96 KOG2462 C2H2-type Zn-finger pr 24.8 38 0.00082 30.8 1.2 24 135-158 214-237 (279)
97 KOG0796 Spliceosome subunit [R 24.6 34 0.00074 31.7 0.9 33 4-36 188-229 (319)
98 PF13821 DUF4187: Domain of un 24.1 50 0.0011 22.7 1.5 26 133-158 24-49 (55)
99 KOG2482 Predicted C2H2-type Zn 23.5 36 0.00078 32.2 0.8 34 132-165 330-363 (423)
100 PF04959 ARS2: Arsenite-resist 22.6 78 0.0017 27.6 2.7 37 133-170 74-110 (214)
101 KOG4118 Uncharacterized conser 22.5 28 0.00061 25.4 -0.1 23 3-25 39-61 (74)
102 KOG3576 Ovo and related transc 22.4 37 0.0008 30.1 0.6 29 2-30 117-149 (267)
103 KOG2462 C2H2-type Zn-finger pr 22.3 45 0.00098 30.4 1.2 22 2-23 215-236 (279)
104 KOG2384 Major histocompatibili 22.2 42 0.0009 29.5 0.9 37 132-169 80-116 (223)
105 KOG3576 Ovo and related transc 22.0 26 0.00057 31.0 -0.3 35 135-169 172-209 (267)
106 COG4049 Uncharacterized protei 21.2 39 0.00084 24.1 0.4 23 135-157 16-38 (65)
107 KOG2505 Ankyrin repeat protein 20.7 78 0.0017 31.4 2.5 35 135-169 65-99 (591)
108 cd00350 rubredoxin_like Rubred 20.6 41 0.00089 20.4 0.4 9 2-10 17-25 (33)
No 1
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.66 E-value=1.2e-08 Score=58.87 Aligned_cols=25 Identities=32% Similarity=0.630 Sum_probs=24.5
Q ss_pred eecccccccCCCHHHHHhhhcchhH
Q 045121 137 FWCEVFQVGTHSAVVMEGHKRGKKH 161 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~GkKH 161 (202)
|+|++|++.|+++..|.+|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 7999999999999999999999999
No 2
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.61 E-value=3.3e-08 Score=60.97 Aligned_cols=32 Identities=28% Similarity=0.580 Sum_probs=30.3
Q ss_pred ceecccccccCCCHHHHHhhhcchhHHHHhhh
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHMARSNG 167 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~ 167 (202)
.|||++|++.|++...+..|++|++|..+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 48999999999999999999999999999875
No 3
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.56 E-value=3.1e-08 Score=57.14 Aligned_cols=25 Identities=40% Similarity=0.809 Sum_probs=24.6
Q ss_pred eeccccccccCCHHHHHHhhcCcch
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKH 27 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkH 27 (202)
|+|.||+++|+++..|..|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 8999999999999999999999998
No 4
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.41 E-value=1.4e-07 Score=58.11 Aligned_cols=32 Identities=41% Similarity=0.763 Sum_probs=30.0
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKD 33 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~ 33 (202)
.|+|.+|+++|+++..+.+|+.|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58999999999999999999999999999864
No 5
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.27 E-value=4.9e-07 Score=53.47 Aligned_cols=27 Identities=26% Similarity=0.486 Sum_probs=25.2
Q ss_pred ceecccccccCCCHHHHHhhhcchhHH
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHM 162 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~ 162 (202)
.|+|.+|+..|.++..|..|++|++|+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 389999999999999999999999995
No 6
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.08 E-value=1.5e-06 Score=51.31 Aligned_cols=27 Identities=33% Similarity=0.703 Sum_probs=25.4
Q ss_pred ceeccccccccCCHHHHHHhhcCcchH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHK 28 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk 28 (202)
.|+|.+|+..|.++..|.+|+.|++||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 489999999999999999999999997
No 7
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=97.47 E-value=0.0001 Score=47.55 Aligned_cols=32 Identities=22% Similarity=0.437 Sum_probs=20.7
Q ss_pred ceecccccccC--CCHHHHHhhhcchhHHHHhhh
Q 045121 136 EFWCEVFQVGT--HSAVVMEGHKRGKKHMARSNG 167 (202)
Q Consensus 136 ~~~Ce~C~v~~--~se~~~~~Hl~GkKH~~k~~~ 167 (202)
.+||+.|++.+ ++...=..|.+|++|+.+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 48999999999 555677999999999999875
No 8
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.44 E-value=8.5e-05 Score=62.65 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=31.8
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHhh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~ 166 (202)
-..+-|||.||+-.+-...+|..|+|||+|+.++-
T Consensus 71 sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 71 SQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred cccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 34578999999999999999999999999998875
No 9
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=96.68 E-value=0.0018 Score=51.87 Aligned_cols=39 Identities=21% Similarity=0.201 Sum_probs=35.8
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
.-...|||-.|.--|-++.+|..|++||.|.++|+++.+
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 345679999999999999999999999999999999975
No 10
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=96.66 E-value=0.0017 Score=41.84 Aligned_cols=32 Identities=31% Similarity=0.440 Sum_probs=20.3
Q ss_pred ceeccccccccC--CHHHHHHhhcCcchHHHHHH
Q 045121 2 DWSCALCQVSTT--SKRDLDEHLHGKKHKARKKD 33 (202)
Q Consensus 2 ~w~C~lC~vt~t--se~~l~~Hl~GkkHk~~~e~ 33 (202)
.++|+.|++.++ +...-..|+.|.+|+.+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 489999999994 44566999999999999874
No 11
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=96.10 E-value=0.0034 Score=53.11 Aligned_cols=32 Identities=22% Similarity=0.521 Sum_probs=30.1
Q ss_pred eeccccccccCCHHHHHHhhcCcchHHHHHHH
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKHKARKKDY 34 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l 34 (202)
|+|.||.-++-.-..+.+|++||+|+.++..+
T Consensus 76 yyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred eeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 79999999999999999999999999998754
No 12
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.66 E-value=0.0047 Score=44.64 Aligned_cols=31 Identities=26% Similarity=0.417 Sum_probs=26.2
Q ss_pred ceecccccccCCCHHHHHhhhcchhHHHHhh
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~ 166 (202)
.|.|.+|+..+.+...|..|++.+.|.....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 5899999999999999999999999977644
No 13
>PF14968 CCDC84: Coiled coil protein 84
Probab=95.33 E-value=0.0093 Score=54.97 Aligned_cols=43 Identities=16% Similarity=0.226 Sum_probs=33.4
Q ss_pred cCcceecccccccCCCH------HHHHhhhcchhHHHHhhhh-hhCCCCC
Q 045121 133 ENFEFWCEVFQVGTHSA------VVMEGHKRGKKHMARSNGS-RKNNEAV 175 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se------~~~~~Hl~GkKH~~k~~~~-~~~~~~~ 175 (202)
....|||-+|+.-...- ..+..||.+--|++++++. .+++-.+
T Consensus 55 ~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~~g~~~ 104 (336)
T PF14968_consen 55 HRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFWWKNGADM 104 (336)
T ss_pred ccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHHHHcCCCc
Confidence 45679999999876544 4688999999999999998 4444444
No 14
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=95.18 E-value=0.0087 Score=59.72 Aligned_cols=45 Identities=20% Similarity=0.141 Sum_probs=39.0
Q ss_pred cCcceecccccccCCCHHHHHhhhcchhHHHHhhhhhhCCCCCCC
Q 045121 133 ENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRKNNEAVPL 177 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~~~~~~~~ 177 (202)
+.+.+.|++|-++|++-.-+..||+|-+|..-.+-+...|.+.+.
T Consensus 232 w~~el~cEksi~tcs~pd~~g~alRrv~ec~~skL~~k~G~gi~d 276 (816)
T KOG3792|consen 232 WPLELHCEKSIVTCSGPDAYGAALRRVKECKVSKLHKKLGKGIPD 276 (816)
T ss_pred chHHHHHHHhhccccCccchHHHHHHHHHhhhhcccccCCCCCCC
Confidence 445679999999999999999999999999999888877776554
No 15
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.05 E-value=0.028 Score=49.71 Aligned_cols=37 Identities=22% Similarity=0.305 Sum_probs=33.5
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
..+..+.|.||||-.- +.....|.+||+|..+|..+.
T Consensus 31 n~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 31 NESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred CCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHH
Confidence 3456889999999999 999999999999999998887
No 16
>PLN02748 tRNA dimethylallyltransferase
Probab=95.04 E-value=0.017 Score=55.37 Aligned_cols=36 Identities=25% Similarity=0.353 Sum_probs=32.5
Q ss_pred cceecccccc-cCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 135 FEFWCEVFQV-GTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 135 ~~~~Ce~C~v-~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
..+.|++|+. .+..+..-+.|++||+|+++++....
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 4567999998 89999999999999999999997764
No 17
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.02 E-value=0.017 Score=31.55 Aligned_cols=21 Identities=33% Similarity=0.789 Sum_probs=17.7
Q ss_pred eeccccccccCCHHHHHHhhc
Q 045121 3 WSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~ 23 (202)
|.|.+|..++.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 789999999999999999974
No 18
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.96 E-value=0.017 Score=55.40 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=33.5
Q ss_pred ceecccccccCCCHHHHHhhhcchhHHHHhhhhhhC
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRKN 171 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~~ 171 (202)
.+||-+|+.+|-|+..|..|-+.|||..+|..+.+.
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 389999999999999999999999999999988763
No 19
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=94.91 E-value=0.011 Score=40.30 Aligned_cols=28 Identities=21% Similarity=0.227 Sum_probs=23.8
Q ss_pred ceecccccccCCCHHHHHhhhcchhHHHHhh
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~ 166 (202)
.-|||.|.+.+. +|..|+.+++|++=..
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFAE 32 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHHc
Confidence 359999999986 7999999999986543
No 20
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=94.75 E-value=0.02 Score=38.94 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=24.2
Q ss_pred cceecccccccCCCHHHHHhhhcchhHHHHh
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRGKKHMARS 165 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~ 165 (202)
..-|||.|.+.+. +|..|+.+.+|++=.
T Consensus 4 k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 4 KPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 3469999999997 599999999998755
No 21
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.63 E-value=0.027 Score=48.61 Aligned_cols=36 Identities=22% Similarity=0.423 Sum_probs=32.1
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLEM 37 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~~ 37 (202)
.|-|-||...-.+|..+..|++||||+.|++.-.++
T Consensus 53 ~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~ 88 (222)
T KOG0227|consen 53 KYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAK 88 (222)
T ss_pred ceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHH
Confidence 478999999999999999999999999999865543
No 22
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=94.55 E-value=0.021 Score=47.86 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=26.8
Q ss_pred ceeccccccc--CCCHHHHHhhhcchhHHHHhh
Q 045121 136 EFWCEVFQVG--THSAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 136 ~~~Ce~C~v~--~~se~~~~~Hl~GkKH~~k~~ 166 (202)
.|||+.|++. =.|.++=..|+.|+||+.+++
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHH
Confidence 4899999954 457889999999999998886
No 23
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.19 E-value=0.031 Score=30.44 Aligned_cols=21 Identities=24% Similarity=0.384 Sum_probs=17.6
Q ss_pred eecccccccCCCHHHHHhhhc
Q 045121 137 FWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
|.|++|+..+.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 679999999999999999985
No 24
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=94.08 E-value=0.021 Score=38.97 Aligned_cols=27 Identities=30% Similarity=0.493 Sum_probs=23.6
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARK 31 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~ 31 (202)
+.+|++|.+.+. +|..|+.+++|+.=.
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHH
Confidence 458999999986 799999999999844
No 25
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.034 Score=53.37 Aligned_cols=34 Identities=29% Similarity=0.536 Sum_probs=32.6
Q ss_pred eeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
++|-+|.-+|-|+..|..|-..|+|+.+|+.|+.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 7999999999999999999999999999998875
No 26
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=93.84 E-value=0.032 Score=53.37 Aligned_cols=33 Identities=27% Similarity=0.301 Sum_probs=30.8
Q ss_pred eecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 137 FWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
--|++|||-..|++.|-+|..|+||+..|+.+.
T Consensus 494 kqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 494 KQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 469999999999999999999999999998775
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.84 E-value=0.038 Score=30.63 Aligned_cols=21 Identities=33% Similarity=0.806 Sum_probs=19.7
Q ss_pred eeccccccccCCHHHHHHhhc
Q 045121 3 WSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~ 23 (202)
|.|.+|+..|++...|..|..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 689999999999999999975
No 28
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=93.40 E-value=0.042 Score=43.49 Aligned_cols=38 Identities=21% Similarity=0.215 Sum_probs=35.2
Q ss_pred CcceecccccccCCCHHHHHhhhcchhHHHHhhhhhhC
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRKN 171 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~~ 171 (202)
-..+||--|.--|-++..|..|+.|+-|.++++.+++.
T Consensus 53 lGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 35789999999999999999999999999999999863
No 29
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=93.35 E-value=0.041 Score=37.45 Aligned_cols=27 Identities=33% Similarity=0.630 Sum_probs=23.5
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARK 31 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~ 31 (202)
.-+|+.|.+.+. +|..|+.+++|+.=.
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CccCccccchhh---hHHHHhCCHHHHHHH
Confidence 358999999997 599999999999754
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.28 E-value=0.067 Score=30.77 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=20.2
Q ss_pred ceeccccccccCCHHHHHHhhc
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~ 23 (202)
++.|.+|+.+|.+...|..|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC
T ss_pred CCCCCccCCccCChhHHHHHhH
Confidence 4789999999999999999994
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.11 E-value=0.046 Score=39.38 Aligned_cols=31 Identities=32% Similarity=0.718 Sum_probs=26.2
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKK 32 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e 32 (202)
.|.|.+|...|.+...|..|+..+.|.....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 4899999999999999999999999988654
No 32
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=93.01 E-value=0.065 Score=46.29 Aligned_cols=38 Identities=16% Similarity=0.173 Sum_probs=33.4
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
..-..|-|.+|.-.-+++..+..|+.||||+.+|-...
T Consensus 49 Nh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarra 86 (222)
T KOG0227|consen 49 NHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRA 86 (222)
T ss_pred ccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHH
Confidence 33478999999999999999999999999999886654
No 33
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=92.93 E-value=0.065 Score=29.65 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=20.0
Q ss_pred eecccccccCCCHHHHHhhhcc
Q 045121 137 FWCEVFQVGTHSAVVMEGHKRG 158 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~G 158 (202)
|.|+.|+..|.+...|..|++-
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5799999999999999999863
No 34
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=92.92 E-value=0.061 Score=50.35 Aligned_cols=37 Identities=22% Similarity=0.355 Sum_probs=33.9
Q ss_pred CcceecccccccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
.+.++|.+|+-.+.|...+..||..|+|..++.....
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 4668999999999999999999999999999998764
No 35
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=92.72 E-value=0.078 Score=45.56 Aligned_cols=33 Identities=27% Similarity=0.546 Sum_probs=30.3
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDY 34 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l 34 (202)
.+.|-||..+--++..+..|+.||||+.++.+-
T Consensus 53 k~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 53 KYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred cEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 478999999999999999999999999998754
No 36
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=92.71 E-value=0.077 Score=30.51 Aligned_cols=22 Identities=27% Similarity=0.364 Sum_probs=20.1
Q ss_pred ceecccccccCCCHHHHHhhhc
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
.+.|.+|+..|.+...|..|++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC
T ss_pred CCCCCccCCccCChhHHHHHhH
Confidence 3789999999999999999984
No 37
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=91.80 E-value=0.079 Score=49.60 Aligned_cols=36 Identities=22% Similarity=0.349 Sum_probs=32.0
Q ss_pred cceecccccccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
..+||++|+--+....+|+.|+.||.|-+..+..++
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 468999999999999999999999999988876553
No 38
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=91.66 E-value=0.17 Score=43.48 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=34.3
Q ss_pred cccCcceecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 131 LRENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 131 k~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
+.....|.|.+|+-.--++..+..|+.||||..++-..+
T Consensus 48 knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs 86 (222)
T COG5246 48 KNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRS 86 (222)
T ss_pred hcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHH
Confidence 344579999999999999999999999999998887664
No 39
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.77 E-value=0.2 Score=44.38 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=31.8
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
...|.||.|..- +....-|..||+|+.+++.|+.
T Consensus 35 ql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs 68 (264)
T KOG3032|consen 35 QLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKS 68 (264)
T ss_pred CeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHh
Confidence 468999999999 9999999999999999999994
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=90.76 E-value=0.15 Score=27.77 Aligned_cols=21 Identities=33% Similarity=0.651 Sum_probs=19.5
Q ss_pred eeccccccccCCHHHHHHhhc
Q 045121 3 WSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~ 23 (202)
+.|..|..+|.+...|..|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 469999999999999999986
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.33 E-value=0.24 Score=52.67 Aligned_cols=35 Identities=29% Similarity=0.537 Sum_probs=32.1
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
++-|.+|.+++|....|-.||+.-+|+.+++.+..
T Consensus 518 p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~ 552 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEE 552 (1406)
T ss_pred cccceeeeeeeecchHHHHHHHHHhhHHHHHHHHh
Confidence 57899999999999999999999999999776665
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.18 E-value=0.18 Score=28.32 Aligned_cols=20 Identities=40% Similarity=0.860 Sum_probs=16.2
Q ss_pred eeccccccccCCHHHHHHhhc
Q 045121 3 WSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~ 23 (202)
+.|..|..+++ +..|..|+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 57999999999 999999975
No 43
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=89.72 E-value=0.2 Score=40.32 Aligned_cols=35 Identities=29% Similarity=0.476 Sum_probs=32.8
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
.++|=.|.--|-++..|+.|+.||.|+..+..|+.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 57999999999999999999999999999988875
No 44
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=89.62 E-value=0.21 Score=41.95 Aligned_cols=32 Identities=31% Similarity=0.552 Sum_probs=26.8
Q ss_pred ceecccccc--ccCCHHHHHHhhcCcchHHHHHH
Q 045121 2 DWSCALCQV--STTSKRDLDEHLHGKKHKARKKD 33 (202)
Q Consensus 2 ~w~C~lC~v--t~tse~~l~~Hl~GkkHk~~~e~ 33 (202)
.|+|+-|++ |=-|-..-+.|+.|++|+.++..
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 489999994 44577889999999999999864
No 45
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=89.40 E-value=0.12 Score=51.85 Aligned_cols=47 Identities=21% Similarity=0.396 Sum_probs=36.3
Q ss_pred cCCCcc--cccCCcccCcceecccccccCCCHHHHHhhhcchhHHHHhh
Q 045121 120 PTGGTM--RRKLPLRENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 120 ~~G~~~--e~~~~k~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~ 166 (202)
+.|+.. |.+-+..+...|.|.+|+-.|+..-.-..||+|+||.-.-+
T Consensus 341 pvgeE~v~Eekd~~gK~~~f~cKlcdckf~d~nak~mhl~grRhrLQYk 389 (816)
T KOG3792|consen 341 PVGEEYVEEEKDPEGKLLRFHCKLCDCKFNDPNAKEMHLKGRRHRLQYK 389 (816)
T ss_pred CCcccccccccCcccchHhhhhhhhcCCCCCcchHHhhhhcccccceec
Confidence 444442 44444566689999999999999999999999999965444
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=88.73 E-value=0.31 Score=26.44 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=19.3
Q ss_pred eecccccccCCCHHHHHhhhc
Q 045121 137 FWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
+-|..|+..+.+...|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 469999999999999999987
No 47
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=86.76 E-value=0.39 Score=44.12 Aligned_cols=34 Identities=18% Similarity=0.339 Sum_probs=28.1
Q ss_pred cceecccccccCC-CHHHHHhhhcchhHHHHhhhh
Q 045121 135 FEFWCEVFQVGTH-SAVVMEGHKRGKKHMARSNGS 168 (202)
Q Consensus 135 ~~~~Ce~C~v~~~-se~~~~~Hl~GkKH~~k~~~~ 168 (202)
...||++|+|.+. .....+.|-+|++|+.+|.+.
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 4569999999874 567889999999999887653
No 48
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=85.68 E-value=0.51 Score=32.78 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=16.4
Q ss_pred eeccccccccCCHHHHHHhhc
Q 045121 3 WSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~ 23 (202)
-+|++|+.++.+...|..||.
T Consensus 25 atCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCcchhhccchhhHHHHHH
Confidence 489999999999999999984
No 49
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=85.60 E-value=0.46 Score=45.70 Aligned_cols=33 Identities=33% Similarity=0.603 Sum_probs=29.1
Q ss_pred eccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 4 SCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 4 ~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
-|+||.|-.+|+.-|-+|..||||+-.+-.+-.
T Consensus 495 qcslcnvlissevylfshvkgrkhqqal~e~~~ 527 (672)
T KOG4722|consen 495 QCSLCNVLISSEVYLFSHVKGRKHQQALNELLL 527 (672)
T ss_pred ccchhhhhhhhhhhhhhhhcchhHHHHHHHHhc
Confidence 599999999999999999999999977665443
No 50
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=84.93 E-value=0.19 Score=45.52 Aligned_cols=39 Identities=13% Similarity=0.179 Sum_probs=35.3
Q ss_pred CcceecccccccCCCHHHHHhhhcchhHHHHhhhhhhCC
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRKNN 172 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~~~ 172 (202)
.+.|||.+|+-+|.++--|.+|...--|++.+.....+.
T Consensus 23 KlRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~Np 61 (309)
T KOG2837|consen 23 KLRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFALNP 61 (309)
T ss_pred HHHHHHHHHHHHhccccccccccCCHHHHHHHHHHHhCc
Confidence 367999999999999999999999999999999887643
No 51
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=83.65 E-value=0.97 Score=38.00 Aligned_cols=138 Identities=16% Similarity=0.263 Sum_probs=79.8
Q ss_pred eeccccccccCCHHHHHHhhcCcchHHHHHHHHHHHhhhccccceeeeeeccCCCCCcccchhhhhcccccccccccccc
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLEMRRCATRKWTVVKMSILNGANWSSEDVHYLIFNNVKAAHYSSSLVK 82 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~~~~~~~~k~~~~~~~i~~~a~~s~e~~~~~~~~n~~~~~~sss~~k 82 (202)
++|++|.+.+--+..+..||.++=|+..+.-+.. +. + +..-+.++.|..+.++... .
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~t--kl--~-------------k~~~dFLqEy~~nk~KKt~------~ 57 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQT--KL--P-------------KKTMDFLQEYMVNKFKKTE------S 57 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHHh--cC--C-------------hHHHHHHHHHHHhhHHHHH------H
Confidence 5899999999999999999999999998887733 11 1 1123344455554222111 0
Q ss_pred ccc-ccCCCCccCCccccccccchhhhccccccccccccCCCcccccCCcccCcceecccccccCCC-HHHHHhhhcchh
Q 045121 83 PRQ-QKNVGGEEDSENKNEELPKKKALNTITQKTTNGIPTGGTMRRKLPLRENFEFWCEVFQVGTHS-AVVMEGHKRGKK 160 (202)
Q Consensus 83 ~~~-qkn~g~~e~~~~k~~~~~k~~~l~~~~k~~~~~~~~G~~~e~~~~k~~~~~~~Ce~C~v~~~s-e~~~~~Hl~GkK 160 (202)
+++ ..+..+ ..+ ++ ..+...|-.++.-+ ++-.-+.|.-|++-.+. -..++.||..--
T Consensus 58 r~~~~~~~~~---------~~~------~i----e~D~~~gig~ehfm--~KVEa~hCsACd~~IP~~~~~vQ~Hl~S~~ 116 (165)
T PF04988_consen 58 RRQQLENSSE---------ASK------QI----EQDVMEGIGQEHFM--KKVEAAHCSACDVFIPMQHSSVQKHLKSQD 116 (165)
T ss_pred HHHHHHHhhh---------ccc------cc----ccchhhhcCHHHHH--HHHHHhhhhHhhhhccCcHHHHHHHhccHH
Confidence 010 000000 000 00 00111111122222 23345699999998876 678899999999
Q ss_pred HHHHhhhhhhCCCCCCCCCCCccc
Q 045121 161 HMARSNGSRKNNEAVPLTTPTTIV 184 (202)
Q Consensus 161 H~~k~~~~~~~~~~~~~~~p~tiv 184 (202)
|..+-+...+..+...+..+++|.
T Consensus 117 H~~Nrr~~~eq~Kr~sl~vA~Sil 140 (165)
T PF04988_consen 117 HNKNRRAMMEQSKRSSLSVARSIL 140 (165)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHh
Confidence 998888666555555555555544
No 52
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=83.29 E-value=0.4 Score=40.48 Aligned_cols=31 Identities=23% Similarity=0.270 Sum_probs=25.9
Q ss_pred ceecccccccCC--CHHHHHhhhcchhHHHHhh
Q 045121 136 EFWCEVFQVGTH--SAVVMEGHKRGKKHMARSN 166 (202)
Q Consensus 136 ~~~Ce~C~v~~~--se~~~~~Hl~GkKH~~k~~ 166 (202)
.|+|+.|++..+ +.++-.+|+-|++|..+.+
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~ 35 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRK 35 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHH
Confidence 479999999875 5778899999999986554
No 53
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=81.90 E-value=0.87 Score=36.13 Aligned_cols=35 Identities=34% Similarity=0.507 Sum_probs=32.5
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
..+|--|---|-++..|..|+.|+-|+..+..|+.
T Consensus 55 qhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 46899999999999999999999999999988887
No 54
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=81.41 E-value=1 Score=25.19 Aligned_cols=20 Identities=15% Similarity=0.295 Sum_probs=16.1
Q ss_pred eecccccccCCCHHHHHhhhc
Q 045121 137 FWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
|.|..|+-.++ +..|..|+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 57999999998 999999975
No 55
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=80.59 E-value=1.2 Score=37.40 Aligned_cols=32 Identities=22% Similarity=0.221 Sum_probs=29.5
Q ss_pred eecccccccCCCHHHHHhhhcchhHHHHhhhh
Q 045121 137 FWCEVFQVGTHSAVVMEGHKRGKKHMARSNGS 168 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~ 168 (202)
|.|.+|..+.--+..|+.||.++-|+..++-+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 67999999999999999999999999777766
No 56
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=76.65 E-value=2 Score=32.68 Aligned_cols=60 Identities=18% Similarity=0.345 Sum_probs=37.6
Q ss_pred cceecccccccCCCHHHHHhhhcchhHHH-Hh--hhhhhCCCCCC--CCCCCcccCCCCCCCCCcc
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRGKKHMA-RS--NGSRKNNEAVP--LTTPTTIVTPSEPTENVED 195 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~-k~--~~~~~~~~~~~--~~~p~tiv~ps~~~~~~~~ 195 (202)
..++|..|.....- ..+..||+.+-|.. .. +.+.+.-..-. ...|..+..|+.+..+|++
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~g 74 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPG 74 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCC
Confidence 35799999988777 88999999986643 22 22322222222 3444556667776666665
No 57
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=76.53 E-value=1.3 Score=40.70 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=26.2
Q ss_pred eeccccccccC-CHHHHHHhhcCcchHHHHHH
Q 045121 3 WSCALCQVSTT-SKRDLDEHLHGKKHKARKKD 33 (202)
Q Consensus 3 w~C~lC~vt~t-se~~l~~Hl~GkkHk~~~e~ 33 (202)
.+|.+|+|=+. .......|-+|+||+.+|+.
T Consensus 11 kfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 11 KFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred hhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 48999999775 46778899999999999873
No 58
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=76.51 E-value=0.81 Score=39.40 Aligned_cols=36 Identities=14% Similarity=0.423 Sum_probs=0.0
Q ss_pred Cceecccc-ccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 1 MDWSCALC-QVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 1 ~~w~C~lC-~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
++|.|+|| ..++-....|..|...-||.--+..|+-
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI 136 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGI 136 (196)
T ss_dssp -------------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCC
Confidence 46899999 6677799999999999999999998887
No 59
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=72.80 E-value=1.7 Score=40.92 Aligned_cols=35 Identities=17% Similarity=0.173 Sum_probs=30.2
Q ss_pred cceeccccc-ccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 135 FEFWCEVFQ-VGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 135 ~~~~Ce~C~-v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
..|-|+||. ...+....|..|.+--+|.--|+-+.
T Consensus 373 ~ef~CEICgNyvy~GR~~FdrHF~E~rHiygl~clG 408 (470)
T COG5188 373 IEFECEICGNYVYYGRDRFDRHFEEDRHIYGLECLG 408 (470)
T ss_pred cceeeeecccccccchHHHHhhhhhhhhhhheeecc
Confidence 478899998 89999999999999999987666543
No 60
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=71.34 E-value=2.6 Score=24.81 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=17.1
Q ss_pred eccccccccCCHHHHHHhhc
Q 045121 4 SCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 4 ~C~lC~vt~tse~~l~~Hl~ 23 (202)
.|+||+-.. ++..+++||.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699999888 8899999997
No 61
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=68.38 E-value=2.4 Score=39.95 Aligned_cols=35 Identities=26% Similarity=0.351 Sum_probs=31.7
Q ss_pred CceeccccccccCCHHHHHHhhcCcchHHHHHHHH
Q 045121 1 MDWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYL 35 (202)
Q Consensus 1 ~~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~ 35 (202)
+.++|.+|.-.+.|+....+||..|+|+.++..+.
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~ 101 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQ 101 (390)
T ss_pred cceehHHhhccccChhhHHHHHHHhhcchhhhhhh
Confidence 45799999999999999999999999999988644
No 62
>PF12907 zf-met2: Zinc-binding
Probab=67.93 E-value=2.5 Score=27.64 Aligned_cols=24 Identities=33% Similarity=0.691 Sum_probs=20.8
Q ss_pred eeccccc---cccCCHHHHHHhhcCcc
Q 045121 3 WSCALCQ---VSTTSKRDLDEHLHGKK 26 (202)
Q Consensus 3 w~C~lC~---vt~tse~~l~~Hl~Gkk 26 (202)
+.|.||. +.++++..|.+|...|-
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKH 28 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKH 28 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccC
Confidence 5799999 88999999999987653
No 63
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=66.09 E-value=3.2 Score=36.76 Aligned_cols=27 Identities=26% Similarity=0.284 Sum_probs=22.1
Q ss_pred ceeccccccc---CCCHHHHHhhhcchhHH
Q 045121 136 EFWCEVFQVG---THSAVVMEGHKRGKKHM 162 (202)
Q Consensus 136 ~~~Ce~C~v~---~~se~~~~~Hl~GkKH~ 162 (202)
.-.|+||..- ..+..-++.|+.||-|+
T Consensus 190 l~VCeVCGA~Ls~~D~d~RladH~~GK~Hl 219 (254)
T PF03194_consen 190 LEVCEVCGAFLSVGDNDRRLADHFGGKQHL 219 (254)
T ss_pred ccchhhhhhHHhccchHHHHHHHhccchhh
Confidence 4589999943 35667899999999998
No 64
>PHA00616 hypothetical protein
Probab=65.71 E-value=2.8 Score=28.00 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=19.6
Q ss_pred ceeccccccccCCHHHHHHhh
Q 045121 2 DWSCALCQVSTTSKRDLDEHL 22 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl 22 (202)
++.|..|+-.|.....|..|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 468999999999999999999
No 65
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=65.54 E-value=2 Score=36.99 Aligned_cols=36 Identities=17% Similarity=0.166 Sum_probs=0.0
Q ss_pred Ccceeccccccc-CCCHHHHHhhhcchhHHHHhhhhh
Q 045121 134 NFEFWCEVFQVG-THSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 134 ~~~~~Ce~C~v~-~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
+..|.||||.=. .-....|..|....||.-=|+.|.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLG 135 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLG 135 (196)
T ss_dssp -------------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcC
Confidence 357899999654 559999999999999998887765
No 66
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=65.30 E-value=17 Score=27.43 Aligned_cols=29 Identities=21% Similarity=0.557 Sum_probs=23.7
Q ss_pred eeccccccccCCHHHHHHhhcCcchHHHHH
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKHKARKK 32 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e 32 (202)
|.|..|++...- ..+..||..+-|..+-.
T Consensus 12 lIC~~C~~av~~-~~v~~HL~~~H~~~~~~ 40 (109)
T PF12013_consen 12 LICRQCQYAVQP-SEVESHLRKRHHILKSQ 40 (109)
T ss_pred EEeCCCCcccCc-hHHHHHHHHhcccccHH
Confidence 789999987776 88999999987766443
No 67
>PF14968 CCDC84: Coiled coil protein 84
Probab=64.24 E-value=3.2 Score=38.47 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=25.7
Q ss_pred ecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 138 WCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 138 ~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
||++|+..... -..|..+++|+++|..+.
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L 29 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFL 29 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHH
Confidence 79999998877 899999999999988663
No 68
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=63.89 E-value=5.8 Score=27.60 Aligned_cols=26 Identities=8% Similarity=0.084 Sum_probs=18.1
Q ss_pred ccCcceecccccccCCCHHHHHhhhc
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
+.+-.-.|.+|...+.+.-+|..||.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHHH
Confidence 34556799999999999999999984
No 69
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=59.34 E-value=2.3 Score=38.62 Aligned_cols=35 Identities=17% Similarity=0.440 Sum_probs=31.9
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
.|+|-.||-.|..+-.|..|+...-|+..+.....
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 49999999999999999999999999998876554
No 70
>PHA00732 hypothetical protein
Probab=57.52 E-value=7.3 Score=28.64 Aligned_cols=22 Identities=23% Similarity=0.567 Sum_probs=20.1
Q ss_pred ceeccccccccCCHHHHHHhhc
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~ 23 (202)
++.|.+|+.+|++...|..|..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhh
Confidence 4689999999999999999976
No 71
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=56.17 E-value=20 Score=38.87 Aligned_cols=40 Identities=13% Similarity=0.138 Sum_probs=35.0
Q ss_pred CcceecccccccCCCHHHHHhhhcchhHHHHhhhhhhCCC
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRKNNE 173 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~~~~ 173 (202)
-..+.|+.|++.++..-.|-+||.--+|+.+++...++..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g 555 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAG 555 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccc
Confidence 3457899999999999999999999999999888776444
No 72
>PHA02768 hypothetical protein; Provisional
Probab=55.87 E-value=6.9 Score=27.27 Aligned_cols=25 Identities=20% Similarity=0.141 Sum_probs=21.5
Q ss_pred ceecccccccCCCHHHHHhhhcchhHH
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHM 162 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~ 162 (202)
-|-|+.|+-.|+..+.|..|++= |.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC
Confidence 46899999999999999998854 65
No 73
>PTZ00448 hypothetical protein; Provisional
Probab=53.65 E-value=14 Score=34.76 Aligned_cols=35 Identities=11% Similarity=0.247 Sum_probs=32.5
Q ss_pred ceecccccccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 136 EFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 136 ~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
.|.|..|++.|.+....+.|++.==|+-||+....
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~ 348 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNAR 348 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhc
Confidence 57899999999999999999999999999998763
No 74
>PF12907 zf-met2: Zinc-binding
Probab=51.02 E-value=7.5 Score=25.40 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=20.2
Q ss_pred eeccccc---ccCCCHHHHHhhhcch
Q 045121 137 FWCEVFQ---VGTHSAVVMEGHKRGK 159 (202)
Q Consensus 137 ~~Ce~C~---v~~~se~~~~~Hl~Gk 159 (202)
+.|.||. +.+.++..|..|...|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK 27 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK 27 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc
Confidence 4799999 8999999999998754
No 75
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=50.25 E-value=10 Score=33.84 Aligned_cols=26 Identities=12% Similarity=0.226 Sum_probs=23.4
Q ss_pred cCcceecccccccCCCHHHHHhhhcc
Q 045121 133 ENFEFWCEVFQVGTHSAVVMEGHKRG 158 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se~~~~~Hl~G 158 (202)
+...|||-.|.+.+.++.+|-.|.=|
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehCPG 261 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHCPG 261 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhCCC
Confidence 34689999999999999999999877
No 76
>PHA02768 hypothetical protein; Provisional
Probab=49.33 E-value=9.7 Score=26.54 Aligned_cols=24 Identities=21% Similarity=0.617 Sum_probs=20.7
Q ss_pred eeccccccccCCHHHHHHhhcCcchH
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGKKHK 28 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~GkkHk 28 (202)
+.|+.|+-.|+....|..|..= |.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHh--cC
Confidence 6799999999999999999753 55
No 77
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=47.51 E-value=6.7 Score=37.47 Aligned_cols=28 Identities=21% Similarity=0.196 Sum_probs=23.8
Q ss_pred cceecccccccCCCHHHHHhhhcchhHHHHh
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRGKKHMARS 165 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~ 165 (202)
.+-|||-|.+.+ ..|++|+.|++|++-.
T Consensus 421 k~GYCENCreky---~~lE~Hi~s~~HrrFA 448 (468)
T COG5067 421 KKGYCENCREKY---ESLEQHIVSEKHRRFA 448 (468)
T ss_pred ccchhHHHHHHH---HHHHHHhhhhhhhhhh
Confidence 457999999987 5699999999998644
No 78
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=47.02 E-value=12 Score=36.38 Aligned_cols=36 Identities=14% Similarity=0.180 Sum_probs=30.6
Q ss_pred Ccceeccccc-ccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 134 NFEFWCEVFQ-VGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 134 ~~~~~Ce~C~-v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
+..|.|+||. .+......|+.|.+-++|.-=|+-+.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLG 435 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLG 435 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhHHHHHhhcceecC
Confidence 4578899998 99999999999999999986665543
No 79
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=46.24 E-value=11 Score=34.90 Aligned_cols=28 Identities=25% Similarity=0.267 Sum_probs=23.0
Q ss_pred ceeccccccc---CCCHHHHHhhhcchhHHH
Q 045121 136 EFWCEVFQVG---THSAVVMEGHKRGKKHMA 163 (202)
Q Consensus 136 ~~~Ce~C~v~---~~se~~~~~Hl~GkKH~~ 163 (202)
.-.|+||... .....-++.|++||=|+-
T Consensus 186 l~VCeVCGa~L~~~D~d~RlaDHf~GKlHlG 216 (319)
T KOG0796|consen 186 LRVCEVCGAFLSVNDADRRLADHFGGKLHLG 216 (319)
T ss_pred hhHHHhhhHHHhccchHHHHHHhhcchHHHH
Confidence 3479999864 467788999999999983
No 80
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=44.84 E-value=13 Score=33.65 Aligned_cols=28 Identities=14% Similarity=0.275 Sum_probs=23.8
Q ss_pred cCcceecccccccCCCHHHHHhhhcchh
Q 045121 133 ENFEFWCEVFQVGTHSAVVMEGHKRGKK 160 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se~~~~~Hl~GkK 160 (202)
+..+-||-.||--|.+|..|.+|...|-
T Consensus 7 k~~kpwcwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 7 KVDKPWCWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred ccCCceeeecccccchhhhhhhhhhhcc
Confidence 3456699999999999999999988753
No 81
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=43.38 E-value=14 Score=36.34 Aligned_cols=31 Identities=26% Similarity=0.496 Sum_probs=29.3
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKK 32 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e 32 (202)
.|+|..|+++|-+-.....|...-=|+-|+-
T Consensus 66 ~~~CstCq~~F~s~~eqr~HyksD~HR~N~K 96 (591)
T KOG2505|consen 66 SDQCSTCQIPFGSRQEQREHYKSDWHRFNTK 96 (591)
T ss_pred cccccccCCccccHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999876
No 82
>PTZ00448 hypothetical protein; Provisional
Probab=42.87 E-value=18 Score=34.19 Aligned_cols=35 Identities=14% Similarity=0.281 Sum_probs=30.6
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
.++|..|++.|.+.....+|...-=|+-|+-..-.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~ 348 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNAR 348 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhc
Confidence 36799999999999999999999999999864443
No 83
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=42.48 E-value=12 Score=36.37 Aligned_cols=36 Identities=14% Similarity=0.428 Sum_probs=30.0
Q ss_pred Cceeccccc-cccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 1 MDWSCALCQ-VSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 1 ~~w~C~lC~-vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
++|.|+||+ .+..+..+|+.|..--||.--+.-|+.
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGI 436 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGI 436 (497)
T ss_pred cccceeeccCccccCcHHHHHHhHHHHHhhcceecCC
Confidence 468999997 999999999999999999865544443
No 84
>PHA00732 hypothetical protein
Probab=41.21 E-value=18 Score=26.51 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=19.5
Q ss_pred eecccccccCCCHHHHHhhhc
Q 045121 137 FWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 137 ~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
+-|..|...+++...|..|+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 569999999999999999986
No 85
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=40.56 E-value=14 Score=32.66 Aligned_cols=28 Identities=29% Similarity=0.619 Sum_probs=22.1
Q ss_pred eccccc---cccCCHHHHHHhhcCcchHHHH
Q 045121 4 SCALCQ---VSTTSKRDLDEHLHGKKHKARK 31 (202)
Q Consensus 4 ~C~lC~---vt~tse~~l~~Hl~GkkHk~~~ 31 (202)
.|.||+ +..-++.-|.+|+.||-|.-=.
T Consensus 192 VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~ 222 (254)
T PF03194_consen 192 VCEVCGAFLSVGDNDRRLADHFGGKQHLGYA 222 (254)
T ss_pred chhhhhhHHhccchHHHHHHHhccchhhhHH
Confidence 599996 3445677899999999998754
No 86
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=40.00 E-value=26 Score=30.58 Aligned_cols=34 Identities=21% Similarity=0.533 Sum_probs=27.8
Q ss_pred ceeccccccccCCHHHHHHhhcCcchHHHHHHHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLHGKKHKARKKDYLE 36 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~GkkHk~~~e~l~~ 36 (202)
.|-|.+|..-|-.+.-...|+. .||-.+++.++.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ 110 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKK 110 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHH
Confidence 5999999999999999999997 689999987765
No 87
>PHA00733 hypothetical protein
Probab=36.72 E-value=23 Score=28.10 Aligned_cols=22 Identities=27% Similarity=0.694 Sum_probs=19.6
Q ss_pred ceeccccccccCCHHHHHHhhc
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~ 23 (202)
+|.|..|...|.+...|..|..
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHh
Confidence 6889999999999999988875
No 88
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=36.62 E-value=24 Score=20.34 Aligned_cols=18 Identities=22% Similarity=0.597 Sum_probs=15.1
Q ss_pred eccccccccCCHHHHHHhh
Q 045121 4 SCALCQVSTTSKRDLDEHL 22 (202)
Q Consensus 4 ~C~lC~vt~tse~~l~~Hl 22 (202)
.|.+|+-+| ....|..|.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 599999999 677788885
No 89
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=36.43 E-value=43 Score=29.85 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=29.0
Q ss_pred ccCcceeccccc-ccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 132 RENFEFWCEVFQ-VGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 132 ~~~~~~~Ce~C~-v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
.....+||.|=. ..--+......|++|||-++.|.+..+
T Consensus 75 ~~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee 114 (244)
T PF05477_consen 75 KNPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEE 114 (244)
T ss_pred CCCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHH
Confidence 344678887643 334578999999999999999986543
No 90
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=36.15 E-value=20 Score=34.03 Aligned_cols=28 Identities=21% Similarity=0.189 Sum_probs=24.2
Q ss_pred CcceecccccccCCCHHHHHhhhcchhHH
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGKKHM 162 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~ 162 (202)
...|-|-+|+..+++-..|-.||. |||.
T Consensus 350 p~~Y~CH~Cdr~ft~G~~L~~HL~-kkH~ 377 (467)
T KOG3608|consen 350 PILYACHCCDRFFTSGKSLSAHLM-KKHG 377 (467)
T ss_pred CCceeeecchhhhccchhHHHHHH-Hhhc
Confidence 356889999999999999999997 5665
No 91
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=35.31 E-value=25 Score=23.42 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=15.4
Q ss_pred ceeccccccccCCHHHHHHhhc
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~ 23 (202)
.+.|+.|+. --++..|..|+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~ 22 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCE 22 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHH
Confidence 467888888 566778888863
No 92
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=31.31 E-value=25 Score=31.23 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=21.4
Q ss_pred ecccccccC---CCHHHHHhhhcchhHHH
Q 045121 138 WCEVFQVGT---HSAVVMEGHKRGKKHMA 163 (202)
Q Consensus 138 ~Ce~C~v~~---~se~~~~~Hl~GkKH~~ 163 (202)
.|.||.+-. ...--|+.|++||=|+-
T Consensus 187 vC~iCgayLsrlDtdrrladHf~GklHlG 215 (258)
T COG5200 187 VCGICGAYLSRLDTDRRLADHFNGKLHLG 215 (258)
T ss_pred hhhhhhhHHHhcchhhHHHHHhccchhhh
Confidence 799999754 45667999999999983
No 93
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=28.81 E-value=21 Score=30.36 Aligned_cols=31 Identities=26% Similarity=0.368 Sum_probs=25.0
Q ss_pred ceeccccccccC--CHHHHHHhhcCcchHHHHH
Q 045121 2 DWSCALCQVSTT--SKRDLDEHLHGKKHKARKK 32 (202)
Q Consensus 2 ~w~C~lC~vt~t--se~~l~~Hl~GkkHk~~~e 32 (202)
.|+|+.|++-.| +-..-..|+.|++|-...+
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~ 35 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRK 35 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHH
Confidence 479999987655 4567789999999988665
No 94
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=26.19 E-value=39 Score=32.18 Aligned_cols=26 Identities=19% Similarity=0.226 Sum_probs=22.5
Q ss_pred CcceecccccccCCCHHHHHhhhcch
Q 045121 134 NFEFWCEVFQVGTHSAVVMEGHKRGK 159 (202)
Q Consensus 134 ~~~~~Ce~C~v~~~se~~~~~Hl~Gk 159 (202)
-.-|-|.+|+.+|.+.+.|..|++=|
T Consensus 261 vn~ykCplCdmtc~~~ssL~~H~r~r 286 (467)
T KOG3608|consen 261 VNCYKCPLCDMTCSSASSLTTHIRYR 286 (467)
T ss_pred hhcccccccccCCCChHHHHHHHHhh
Confidence 35688999999999999999999753
No 95
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.54 E-value=34 Score=19.54 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=10.2
Q ss_pred ceeccccccccC
Q 045121 2 DWSCALCQVSTT 13 (202)
Q Consensus 2 ~w~C~lC~vt~t 13 (202)
+|.|++|.-+|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 588999998875
No 96
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=24.84 E-value=38 Score=30.84 Aligned_cols=24 Identities=13% Similarity=0.117 Sum_probs=21.1
Q ss_pred cceecccccccCCCHHHHHhhhcc
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRG 158 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~G 158 (202)
..|-|..|+..|.+.++|+.|+.=
T Consensus 214 KPF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 214 KPFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred CCccCCcccchhcchHHHHHHHHh
Confidence 468999999999999999999863
No 97
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=24.58 E-value=34 Score=31.68 Aligned_cols=33 Identities=24% Similarity=0.550 Sum_probs=24.6
Q ss_pred eccccc---cccCCHHHHHHhhcCcchHH------HHHHHHH
Q 045121 4 SCALCQ---VSTTSKRDLDEHLHGKKHKA------RKKDYLE 36 (202)
Q Consensus 4 ~C~lC~---vt~tse~~l~~Hl~GkkHk~------~~e~l~~ 36 (202)
.|.||+ +-.-...-|.+|+.||-|.- +++.|..
T Consensus 188 VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~ 229 (319)
T KOG0796|consen 188 VCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKK 229 (319)
T ss_pred HHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHH
Confidence 489995 44567788999999999965 5555554
No 98
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.12 E-value=50 Score=22.71 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=22.5
Q ss_pred cCcceecccccccCCCHHHHHhhhcc
Q 045121 133 ENFEFWCEVFQVGTHSAVVMEGHKRG 158 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se~~~~~Hl~G 158 (202)
+...+||--|.+.+.|+..|..|-=|
T Consensus 24 R~~~~YC~~Cg~~Y~d~~dL~~~CPG 49 (55)
T PF13821_consen 24 REEHNYCFWCGTKYDDEEDLERNCPG 49 (55)
T ss_pred HhhCceeeeeCCccCCHHHHHhCCCC
Confidence 35678999999999999999988766
No 99
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=23.50 E-value=36 Score=32.21 Aligned_cols=34 Identities=12% Similarity=0.091 Sum_probs=28.7
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARS 165 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~ 165 (202)
+.+-...|-.|++.|-++..+..|+.--+|+.-+
T Consensus 330 kq~~~~~c~~cd~~F~~e~~l~~hm~e~k~l~i~ 363 (423)
T KOG2482|consen 330 KQKKKSRCAECDLSFWKEPGLLIHMVEDKHLSIL 363 (423)
T ss_pred HHhhccccccccccccCcchhhhhcccccccccc
Confidence 3346789999999999999999999999997543
No 100
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=22.61 E-value=78 Score=27.59 Aligned_cols=37 Identities=14% Similarity=0.186 Sum_probs=28.8
Q ss_pred cCcceecccccccCCCHHHHHhhhcchhHHHHhhhhhh
Q 045121 133 ENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSRK 170 (202)
Q Consensus 133 ~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~~ 170 (202)
...+|.|.+|...|-...-..-|+. .||-..|+.+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ 110 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKK 110 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHH
Confidence 3457999999999999999999997 679988887653
No 101
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.51 E-value=28 Score=25.44 Aligned_cols=23 Identities=22% Similarity=0.661 Sum_probs=20.3
Q ss_pred eeccccccccCCHHHHHHhhcCc
Q 045121 3 WSCALCQVSTTSKRDLDEHLHGK 25 (202)
Q Consensus 3 w~C~lC~vt~tse~~l~~Hl~Gk 25 (202)
+.|+||.+......+|..|..-+
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~k 61 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENK 61 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhc
Confidence 57999999999999999998643
No 102
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=22.36 E-value=37 Score=30.14 Aligned_cols=29 Identities=28% Similarity=0.564 Sum_probs=22.8
Q ss_pred ceeccccccccCCHHHHHHhhc----CcchHHH
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH----GKKHKAR 30 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~----GkkHk~~ 30 (202)
.++|.||+..|+=.+-|+.|+. =|||...
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct 149 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCT 149 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHh
Confidence 4789999999999999998874 3555544
No 103
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.31 E-value=45 Score=30.36 Aligned_cols=22 Identities=23% Similarity=0.640 Sum_probs=16.0
Q ss_pred ceeccccccccCCHHHHHHhhc
Q 045121 2 DWSCALCQVSTTSKRDLDEHLH 23 (202)
Q Consensus 2 ~w~C~lC~vt~tse~~l~~Hl~ 23 (202)
+|.|+.|.-.|.....|.-|++
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred CccCCcccchhcchHHHHHHHH
Confidence 4677777777777777777764
No 104
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=22.18 E-value=42 Score=29.47 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=26.0
Q ss_pred ccCcceecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 132 RENFEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 132 ~~~~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
..+..||||+|++-+..- ---.|...--|+-+++.+.
T Consensus 80 ~~e~lfyCE~Cd~~ip~~-~~snH~tSttHllsl~~~p 116 (223)
T KOG2384|consen 80 RDEALFYCEVCDIYIPNS-KKSNHFTSTTHLLSLQHIP 116 (223)
T ss_pred CCCccchhhhhhhhccCC-CCccchhhHHHHhhhccCC
Confidence 567889999999976541 1235777777877776655
No 105
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=22.00 E-value=26 Score=31.05 Aligned_cols=35 Identities=17% Similarity=0.304 Sum_probs=28.1
Q ss_pred cceecccccccCCCHHHHHhhhc---chhHHHHhhhhh
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKR---GKKHMARSNGSR 169 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~---GkKH~~k~~~~~ 169 (202)
-.|.|++|+..|+-.-.|++||. |-.|+-..++.+
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 46889999999999999999985 667766666554
No 106
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.17 E-value=39 Score=24.07 Aligned_cols=23 Identities=9% Similarity=-0.116 Sum_probs=20.9
Q ss_pred cceecccccccCCCHHHHHhhhc
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKR 157 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~ 157 (202)
..+.|.-|+..|..+.++..|.|
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhh
Confidence 46789999999999999999986
No 107
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=20.71 E-value=78 Score=31.40 Aligned_cols=35 Identities=14% Similarity=0.024 Sum_probs=32.1
Q ss_pred cceecccccccCCCHHHHHhhhcchhHHHHhhhhh
Q 045121 135 FEFWCEVFQVGTHSAVVMEGHKRGKKHMARSNGSR 169 (202)
Q Consensus 135 ~~~~Ce~C~v~~~se~~~~~Hl~GkKH~~k~~~~~ 169 (202)
..|.|..|++.|.|......|+.--=|+-+++...
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl 99 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKL 99 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHh
Confidence 57899999999999999999999999999988754
No 108
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.60 E-value=41 Score=20.44 Aligned_cols=9 Identities=33% Similarity=1.357 Sum_probs=7.1
Q ss_pred ceecccccc
Q 045121 2 DWSCALCQV 10 (202)
Q Consensus 2 ~w~C~lC~v 10 (202)
+|.|++|+.
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 688888876
Done!