Query 012121
Match_columns 470
No_of_seqs 184 out of 333
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 23:16:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00451 ZnF_U1 U1-like zinc 98.6 5.2E-08 1.1E-12 67.2 3.1 32 220-251 3-34 (35)
2 PF12874 zf-met: Zinc-finger o 98.5 8.8E-08 1.9E-12 62.1 2.0 25 221-245 1-25 (25)
3 smart00451 ZnF_U1 U1-like zinc 98.4 9.3E-08 2E-12 66.0 2.2 34 67-100 2-35 (35)
4 PF12874 zf-met: Zinc-finger o 98.2 7.3E-07 1.6E-11 57.8 1.6 25 69-93 1-25 (25)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.2 7.4E-07 1.6E-11 59.5 1.2 27 220-246 1-27 (27)
6 PF12171 zf-C2H2_jaz: Zinc-fin 97.9 5E-06 1.1E-10 55.5 1.0 26 69-94 2-27 (27)
7 PF06220 zf-U1: U1 zinc finger 97.5 9.3E-05 2E-09 54.2 2.9 33 68-100 3-37 (38)
8 KOG4727 U1-like Zn-finger prot 97.4 0.0001 2.2E-09 70.1 3.0 34 217-250 72-105 (193)
9 PF06220 zf-U1: U1 zinc finger 97.2 0.00023 4.9E-09 52.2 2.0 33 220-252 3-37 (38)
10 KOG4727 U1-like Zn-finger prot 97.0 0.00045 9.8E-09 65.9 2.6 37 66-102 73-109 (193)
11 KOG0150 Spliceosomal protein F 96.7 0.00073 1.6E-08 69.1 1.7 40 61-100 3-43 (336)
12 KOG3408 U1-like Zn-finger-cont 96.3 0.0022 4.8E-08 58.3 2.1 37 217-253 54-90 (129)
13 KOG3454 U1 snRNP-specific prot 96.3 0.0023 4.9E-08 60.5 2.1 36 68-103 3-40 (165)
14 PLN02748 tRNA dimethylallyltra 96.1 0.0029 6.3E-08 67.7 2.1 35 219-253 417-452 (468)
15 KOG3408 U1-like Zn-finger-cont 95.8 0.0044 9.5E-08 56.4 1.8 40 64-103 53-92 (129)
16 KOG3032 Uncharacterized conser 95.6 0.02 4.2E-07 57.2 5.2 60 217-277 32-93 (264)
17 KOG0717 Molecular chaperone (D 95.5 0.0067 1.5E-07 65.1 1.9 34 69-102 293-326 (508)
18 COG5188 PRP9 Splicing factor 3 95.5 0.0055 1.2E-07 64.1 1.2 36 67-102 237-272 (470)
19 KOG3792 Transcription factor N 95.3 0.0074 1.6E-07 67.4 1.4 33 220-252 235-267 (816)
20 KOG0717 Molecular chaperone (D 95.2 0.011 2.4E-07 63.6 2.5 37 221-257 293-329 (508)
21 KOG0227 Splicing factor 3a, su 94.7 0.017 3.6E-07 56.4 1.9 36 217-252 50-85 (222)
22 KOG2785 C2H2-type Zn-finger pr 94.1 0.03 6.4E-07 59.0 2.4 36 219-254 67-102 (390)
23 PF14968 CCDC84: Coiled coil p 93.9 0.051 1.1E-06 56.4 3.5 30 70-102 1-30 (336)
24 KOG3454 U1 snRNP-specific prot 93.8 0.025 5.4E-07 53.7 0.9 33 220-252 3-37 (165)
25 PLN02748 tRNA dimethylallyltra 93.4 0.054 1.2E-06 58.3 2.9 37 67-103 417-454 (468)
26 PF13894 zf-C2H2_4: C2H2-type 93.4 0.054 1.2E-06 33.4 1.7 21 221-241 1-21 (24)
27 COG5112 UFD2 U1-like Zn-finger 93.1 0.08 1.7E-06 47.7 2.9 43 61-103 48-90 (126)
28 PF12756 zf-C2H2_2: C2H2 type 92.4 0.064 1.4E-06 43.1 1.4 31 220-250 50-80 (100)
29 PF00096 zf-C2H2: Zinc finger, 92.0 0.11 2.4E-06 32.8 1.8 22 221-242 1-22 (23)
30 smart00586 ZnF_DBF Zinc finger 91.9 0.076 1.6E-06 41.5 1.1 29 66-97 3-31 (49)
31 PF13912 zf-C2H2_6: C2H2-type 91.3 0.13 2.8E-06 33.7 1.6 22 220-241 1-22 (27)
32 COG5112 UFD2 U1-like Zn-finger 91.2 0.11 2.4E-06 46.8 1.6 37 218-254 53-89 (126)
33 smart00586 ZnF_DBF Zinc finger 91.2 0.077 1.7E-06 41.4 0.5 30 220-252 5-34 (49)
34 KOG3032 Uncharacterized conser 91.2 0.33 7.1E-06 48.8 5.0 41 62-103 29-69 (264)
35 PF07535 zf-DBF: DBF zinc fing 91.0 0.095 2.1E-06 40.8 0.9 30 220-252 5-34 (49)
36 COG5246 PRP11 Splicing factor 91.0 0.15 3.3E-06 49.7 2.4 38 217-254 50-87 (222)
37 PF07535 zf-DBF: DBF zinc fing 90.0 0.19 4.1E-06 39.1 1.7 29 66-97 3-31 (49)
38 COG5136 U1 snRNP-specific prot 89.9 0.13 2.8E-06 49.2 0.9 35 68-102 3-39 (188)
39 COG5188 PRP9 Splicing factor 3 89.7 0.15 3.3E-06 53.8 1.4 36 219-254 237-272 (470)
40 PF13912 zf-C2H2_6: C2H2-type 89.5 0.27 5.8E-06 32.2 2.0 20 69-88 2-21 (27)
41 KOG0227 Splicing factor 3a, su 89.3 0.24 5.1E-06 48.6 2.2 38 66-103 51-88 (222)
42 PF13894 zf-C2H2_4: C2H2-type 87.8 0.38 8.3E-06 29.5 1.7 21 69-89 1-21 (24)
43 smart00355 ZnF_C2H2 zinc finge 87.3 0.31 6.7E-06 30.0 1.1 24 221-246 1-24 (26)
44 KOG0150 Spliceosomal protein F 87.0 0.31 6.7E-06 50.5 1.5 34 219-252 9-43 (336)
45 COG5246 PRP11 Splicing factor 86.2 0.55 1.2E-05 45.9 2.6 38 66-103 51-88 (222)
46 PF12756 zf-C2H2_2: C2H2 type 85.5 0.37 8E-06 38.7 0.9 32 67-98 49-80 (100)
47 KOG4722 Zn-finger protein [Gen 84.9 0.46 1E-05 51.4 1.6 34 219-252 492-525 (672)
48 KOG3792 Transcription factor N 84.3 0.87 1.9E-05 51.7 3.4 35 217-251 356-390 (816)
49 PF11931 DUF3449: Domain of un 83.4 0.35 7.7E-06 47.0 0.0 34 219-252 100-134 (196)
50 KOG1146 Homeobox protein [Gene 82.9 2.2 4.8E-05 51.3 6.1 44 60-103 510-553 (1406)
51 PF00096 zf-C2H2: Zinc finger, 82.3 0.98 2.1E-05 28.4 1.7 21 69-89 1-21 (23)
52 COG5136 U1 snRNP-specific prot 79.2 0.58 1.3E-05 44.9 -0.1 31 220-250 3-35 (188)
53 smart00355 ZnF_C2H2 zinc finge 78.5 1.5 3.2E-05 26.9 1.6 20 70-89 2-21 (26)
54 KOG2785 C2H2-type Zn-finger pr 76.1 1.2 2.7E-05 47.3 1.2 37 66-102 66-102 (390)
55 PF13909 zf-H2C2_5: C2H2-type 75.5 2 4.3E-05 27.6 1.6 20 221-241 1-20 (24)
56 PTZ00448 hypothetical protein; 73.2 2.4 5.1E-05 45.1 2.4 34 219-252 313-346 (373)
57 KOG4722 Zn-finger protein [Gen 70.6 2.5 5.5E-05 46.0 1.9 47 57-103 481-528 (672)
58 KOG2837 Protein containing a U 69.1 0.89 1.9E-05 46.7 -1.7 36 219-254 24-59 (309)
59 PF14968 CCDC84: Coiled coil p 56.6 4.4 9.6E-05 42.5 0.6 28 222-252 1-28 (336)
60 KOG2837 Protein containing a U 56.3 2.8 6E-05 43.2 -0.9 37 66-102 23-59 (309)
61 PF04988 AKAP95: A-kinase anch 55.8 7.3 0.00016 37.4 1.8 32 221-252 1-32 (165)
62 KOG3623 Homeobox transcription 54.2 6.8 0.00015 45.2 1.6 64 218-283 307-370 (1007)
63 PHA02768 hypothetical protein; 49.4 8.8 0.00019 30.8 1.1 27 219-247 4-30 (55)
64 PTZ00448 hypothetical protein; 47.1 14 0.00031 39.4 2.5 35 68-102 314-348 (373)
65 KOG2636 Splicing factor 3a, su 45.8 12 0.00026 41.0 1.8 34 218-251 399-433 (497)
66 PF11931 DUF3449: Domain of un 45.4 7 0.00015 38.3 0.0 38 66-103 99-137 (196)
67 PF04988 AKAP95: A-kinase anch 45.3 19 0.00041 34.7 2.8 33 69-101 1-33 (165)
68 PTZ00070 40S ribosomal protein 44.4 16 0.00036 37.2 2.4 20 62-81 36-55 (257)
69 PF03194 LUC7: LUC7 N_terminus 43.4 11 0.00023 37.9 0.9 30 220-249 190-222 (254)
70 PHA00616 hypothetical protein 42.8 12 0.00025 28.9 0.8 21 220-240 1-21 (44)
71 KOG1994 Predicted RNA binding 41.1 15 0.00032 37.4 1.5 26 66-91 237-262 (268)
72 KOG3623 Homeobox transcription 39.3 9.9 0.00021 44.0 -0.0 25 219-243 949-973 (1007)
73 KOG2505 Ankyrin repeat protein 38.4 26 0.00055 39.2 2.9 57 45-101 42-99 (591)
74 KOG1074 Transcriptional repres 37.0 13 0.00028 43.5 0.4 29 217-245 630-658 (958)
75 PF03194 LUC7: LUC7 N_terminus 36.8 19 0.00041 36.1 1.5 34 66-99 188-224 (254)
76 PF12907 zf-met2: Zinc-binding 36.7 14 0.0003 28.0 0.4 23 221-243 2-27 (40)
77 PF12764 Gly-rich_Ago1: Glycin 36.4 51 0.0011 29.8 3.9 28 6-34 3-30 (104)
78 KOG2893 Zn finger protein [Gen 36.1 21 0.00045 36.7 1.7 24 220-243 10-33 (341)
79 PF12907 zf-met2: Zinc-binding 36.0 20 0.00043 27.1 1.2 26 69-95 2-30 (40)
80 PHA00732 hypothetical protein 36.0 20 0.00043 30.2 1.3 21 221-241 2-22 (79)
81 PF04959 ARS2: Arsenite-resist 34.5 26 0.00057 34.7 2.0 41 219-260 76-116 (214)
82 KOG2505 Ankyrin repeat protein 34.3 29 0.00063 38.8 2.5 52 219-270 65-116 (591)
83 KOG3293 Small nuclear ribonucl 33.8 53 0.0012 30.6 3.7 8 7-14 93-100 (134)
84 PHA02768 hypothetical protein; 31.8 30 0.00065 27.8 1.6 22 68-89 5-26 (55)
85 KOG3915 Transcription regulato 30.8 56 0.0012 36.5 3.9 12 83-94 206-217 (641)
86 PF12764 Gly-rich_Ago1: Glycin 30.5 1E+02 0.0023 27.8 4.9 20 9-28 10-30 (104)
87 PF09237 GAGA: GAGA factor; I 30.5 45 0.00098 26.9 2.4 27 62-88 18-44 (54)
88 KOG0796 Spliceosome subunit [R 28.7 32 0.0007 36.2 1.7 37 65-101 183-222 (319)
89 KOG2893 Zn finger protein [Gen 28.1 27 0.00059 35.9 1.0 24 68-91 10-33 (341)
90 PRK10590 ATP-dependent RNA hel 27.6 72 0.0016 33.6 4.0 6 22-27 402-407 (456)
91 KOG4167 Predicted DNA-binding 27.6 83 0.0018 36.8 4.7 44 217-260 789-832 (907)
92 PHA00616 hypothetical protein 27.3 29 0.00062 26.8 0.8 20 69-88 2-21 (44)
93 KOG0796 Spliceosome subunit [R 26.9 31 0.00067 36.3 1.1 29 221-249 187-218 (319)
94 PF13913 zf-C2HC_2: zinc-finge 26.4 49 0.0011 22.2 1.7 20 69-89 3-22 (25)
95 PF13465 zf-H2C2_2: Zinc-finge 25.6 48 0.001 22.0 1.5 13 219-231 13-25 (26)
96 KOG2384 Major histocompatibili 24.6 20 0.00042 35.9 -0.7 34 218-252 82-115 (223)
97 PRK11634 ATP-dependent RNA hel 24.4 60 0.0013 36.4 2.9 13 17-29 579-591 (629)
98 smart00734 ZnF_Rad18 Rad18-lik 24.1 53 0.0012 22.3 1.5 20 69-89 2-21 (26)
99 KOG3576 Ovo and related transc 23.4 29 0.00062 35.1 0.2 44 218-261 171-217 (267)
100 KOG2384 Major histocompatibili 23.4 21 0.00046 35.6 -0.7 36 64-101 80-116 (223)
101 PF09237 GAGA: GAGA factor; I 23.4 44 0.00095 27.0 1.2 22 220-241 24-45 (54)
102 COG5200 LUC7 U1 snRNP componen 22.0 35 0.00076 34.5 0.5 32 221-252 186-220 (258)
103 KOG1146 Homeobox protein [Gene 21.1 66 0.0014 39.6 2.5 39 216-254 514-552 (1406)
104 KOG1994 Predicted RNA binding 20.8 62 0.0013 33.1 1.9 26 218-243 237-262 (268)
No 1
>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=98.56 E-value=5.2e-08 Score=67.24 Aligned_cols=32 Identities=44% Similarity=0.837 Sum_probs=30.6
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHHHHHhh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHLANVKR 251 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk 251 (470)
.|+|++|+++|++...|.+|++||||+++|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 68999999999999999999999999999976
No 2
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.45 E-value=8.8e-08 Score=62.12 Aligned_cols=25 Identities=36% Similarity=0.731 Sum_probs=24.5
Q ss_pred EEeeecccccCcHHHHHhhhhhhhH
Q 012121 221 LICELCNVKCESQVVFDSHLVGKKH 245 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~GKKH 245 (470)
|+|+||++.|+++..|++|++|+||
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 3
>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=98.45 E-value=9.3e-08 Score=65.98 Aligned_cols=34 Identities=32% Similarity=0.631 Sum_probs=30.9
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHHhH
Q 012121 67 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTH 100 (470)
Q Consensus 67 ~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkL 100 (470)
..+||++|+++|++...+.+|+.||+|+++++++
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHHcC
Confidence 3579999999999999999999999999998753
No 4
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.18 E-value=7.3e-07 Score=57.81 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=24.3
Q ss_pred ccccccccccCCHHHHHHHhcCcch
Q 012121 69 AWCELCRVDCNTLEILEQHKNGKRH 93 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~GKKH 93 (470)
|+|++|+++|+++.+|++|+.|++|
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 6899999999999999999999998
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=98.15 E-value=7.4e-07 Score=59.51 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=25.3
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHH
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHL 246 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~ 246 (470)
.|||.+|+..|+++.+|++|++||+|+
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 489999999999999999999999995
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=97.86 E-value=5e-06 Score=55.54 Aligned_cols=26 Identities=31% Similarity=0.617 Sum_probs=25.1
Q ss_pred ccccccccccCCHHHHHHHhcCcchH
Q 012121 69 AWCELCRVDCNTLEILEQHKNGKRHK 94 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~GKKHk 94 (470)
+||.+|++.|+++.++++|+.||+|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 69999999999999999999999996
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=9.3e-05 Score=54.20 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=21.9
Q ss_pred ccccccccccc--CCHHHHHHHhcCcchHHHHHhH
Q 012121 68 MAWCELCRVDC--NTLEILEQHKNGKRHKRNLRTH 100 (470)
Q Consensus 68 ~~yC~VCnVsF--nSpsqaqsHy~GKKHkKNLrkL 100 (470)
-+||+.|+++| +++..-..|..|.+|+.+++.+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 47999999999 6777889999999999999864
No 8
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.40 E-value=0.0001 Score=70.11 Aligned_cols=34 Identities=26% Similarity=0.517 Sum_probs=31.4
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHh
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVK 250 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklK 250 (470)
....|||.|||..+-...+|-.|||||+|+.+|-
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 3569999999999999999999999999999884
No 9
>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=97.17 E-value=0.00023 Score=52.17 Aligned_cols=33 Identities=33% Similarity=0.561 Sum_probs=21.3
Q ss_pred CEEeeeccccc--CcHHHHHhhhhhhhHHHHHhhh
Q 012121 220 PLICELCNVKC--ESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 220 ~~~CeLCNV~c--nSe~~~~sHL~GKKH~kklKk~ 252 (470)
.|||+.|++++ ++...-+.|..|+||+.++++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 68999999999 4556779999999999999763
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=96.97 E-value=0.00045 Score=65.86 Aligned_cols=37 Identities=27% Similarity=0.462 Sum_probs=33.0
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
...+||+||+..|.-...|..|++||+|++|+.-+..
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm~ 109 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSMR 109 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHHhhhhc
Confidence 4789999999999999999999999999999876543
No 11
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=96.69 E-value=0.00073 Score=69.12 Aligned_cols=40 Identities=25% Similarity=0.548 Sum_probs=36.4
Q ss_pred CCCCCCCccccccccccc-CCHHHHHHHhcCcchHHHHHhH
Q 012121 61 PTRPPPPMAWCELCRVDC-NTLEILEQHKNGKRHKRNLRTH 100 (470)
Q Consensus 61 ~~~~p~~~~yC~VCnVsF-nSpsqaqsHy~GKKHkKNLrkL 100 (470)
-.|.+....||++|++|| +++...+.|-.||||+-+|.+.
T Consensus 3 eYWkS~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 3 EYWKSQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred hhhhhccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 469999999999999999 7888889999999999999854
No 12
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=96.31 E-value=0.0022 Score=58.29 Aligned_cols=37 Identities=22% Similarity=0.291 Sum_probs=34.8
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhc
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFH 253 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~ 253 (470)
....|||-.|.-.|.+..+|+.|+++|.|+++||++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 3579999999999999999999999999999999985
No 13
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=96.26 E-value=0.0023 Score=60.48 Aligned_cols=36 Identities=22% Similarity=0.542 Sum_probs=31.9
Q ss_pred ccccccccccc--CCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 68 MAWCELCRVDC--NTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 68 ~~yC~VCnVsF--nSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
-+||+.|+.++ +|.++-.+|+.|+||++|++-+...
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY~k 40 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYYQK 40 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHHHH
Confidence 46899999887 6999999999999999999977644
No 14
>PLN02748 tRNA dimethylallyltransferase
Probab=96.10 E-value=0.0029 Score=67.70 Aligned_cols=35 Identities=23% Similarity=0.500 Sum_probs=32.4
Q ss_pred CCEEeeeccc-ccCcHHHHHhhhhhhhHHHHHhhhc
Q 012121 219 IPLICELCNV-KCESQVVFDSHLVGKKHLANVKRFH 253 (470)
Q Consensus 219 ~~~~CeLCNV-~cnSe~~~~sHL~GKKH~kklKk~~ 253 (470)
..|+|++|+. .++++.+++.|++|++|++++++..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~ 452 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLK 452 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHH
Confidence 5788999998 8999999999999999999999864
No 15
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=95.85 E-value=0.0044 Score=56.40 Aligned_cols=40 Identities=23% Similarity=0.340 Sum_probs=35.8
Q ss_pred CCCCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 64 PPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 64 ~p~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
+--..+||-.|...|.+..++..|+.+|.|+++++.|...
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~ 92 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREV 92 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccC
Confidence 3356789999999999999999999999999999999753
No 16
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.56 E-value=0.02 Score=57.19 Aligned_cols=60 Identities=25% Similarity=0.393 Sum_probs=45.1
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc--cccccccccccccCCCCCCCCCc
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG--HRALYGEAALQSLYPASFNSLSS 277 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g--~~~l~g~~~lq~~~P~n~sa~s~ 277 (470)
..+.+.|-|||+-.- +..++.|.+||||...+-++.. .+-.-..+.+.+-.|+.+|+.+.
T Consensus 32 ~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~k~~~T~~p~~p~spn~kts 93 (264)
T KOG3032|consen 32 ESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVAKTRPTKIPALPKSPNSKTS 93 (264)
T ss_pred CCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhcccccCcCccCccCCCCCCcccc
Confidence 347899999999999 9999999999999999877752 22222225566667777777664
No 17
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=95.49 E-value=0.0067 Score=65.12 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=32.7
Q ss_pred ccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 69 AWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
.||.||+++|.|+-++..|-..|||++||+.|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999874
No 18
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=95.48 E-value=0.0055 Score=64.12 Aligned_cols=36 Identities=25% Similarity=0.561 Sum_probs=33.3
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 67 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 67 ~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
+.+||.+|..||....+|+.|+.||.|.|+.++...
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 568999999999999999999999999999987765
No 19
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=95.26 E-value=0.0074 Score=67.40 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=30.1
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
.|+|++|-++||+.+-+..||.+-+|.+..+.+
T Consensus 235 el~cEksi~tcs~pd~~g~alRrv~ec~~skL~ 267 (816)
T KOG3792|consen 235 ELHCEKSIVTCSGPDAYGAALRRVKECKVSKLH 267 (816)
T ss_pred HHHHHHhhccccCccchHHHHHHHHHhhhhccc
Confidence 469999999999999999999999999887665
No 20
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=95.25 E-value=0.011 Score=63.56 Aligned_cols=37 Identities=30% Similarity=0.470 Sum_probs=33.9
Q ss_pred EEeeecccccCcHHHHHhhhhhhhHHHHHhhhccccc
Q 012121 221 LICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRA 257 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g~~~ 257 (470)
+||-+||.+|-|+-+|..|.+.|||..+|.++.+.+.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqemE 329 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQEME 329 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998865443
No 21
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.70 E-value=0.017 Score=56.36 Aligned_cols=36 Identities=28% Similarity=0.406 Sum_probs=32.8
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
...+|.|.||+-.-+++..|-.|..||||+.+|.+.
T Consensus 50 h~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 50 HLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred cCcceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 346899999999999999999999999999998764
No 22
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=94.14 E-value=0.03 Score=58.96 Aligned_cols=36 Identities=31% Similarity=0.530 Sum_probs=33.0
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
..++|.+|+..+-|+..+..||..|||..+++++..
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred cceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 468999999999999999999999999999988643
No 23
>PF14968 CCDC84: Coiled coil protein 84
Probab=93.88 E-value=0.051 Score=56.42 Aligned_cols=30 Identities=23% Similarity=0.621 Sum_probs=26.1
Q ss_pred cccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 70 WCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 70 yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
||.||++.+.. -+-|.-+++|+++|+.+-.
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L~ 30 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFLS 30 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHHH
Confidence 89999999876 6789999999999997754
No 24
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=93.75 E-value=0.025 Score=53.65 Aligned_cols=33 Identities=33% Similarity=0.575 Sum_probs=28.0
Q ss_pred CEEeeecccccC--cHHHHHhhhhhhhHHHHHhhh
Q 012121 220 PLICELCNVKCE--SQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 220 ~~~CeLCNV~cn--Se~~~~sHL~GKKH~kklKk~ 252 (470)
.|||+-|+...+ |..+=+.|+.|+||++++|-.
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 589999996665 667999999999999998654
No 25
>PLN02748 tRNA dimethylallyltransferase
Probab=93.41 E-value=0.054 Score=58.26 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=32.6
Q ss_pred Cccccccccc-ccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 67 PMAWCELCRV-DCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 67 ~~~yC~VCnV-sFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
..+.|++|+. .+.++.+-+.|+.|++|++++++.+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 4446999998 799999999999999999999987654
No 26
>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=93.37 E-value=0.054 Score=33.43 Aligned_cols=21 Identities=19% Similarity=0.529 Sum_probs=17.8
Q ss_pred EEeeecccccCcHHHHHhhhh
Q 012121 221 LICELCNVKCESQVVFDSHLV 241 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~ 241 (470)
|.|.+|+..|.+...|..|+.
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 689999999999999999985
No 27
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=93.06 E-value=0.08 Score=47.71 Aligned_cols=43 Identities=30% Similarity=0.446 Sum_probs=37.8
Q ss_pred CCCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 61 PTRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 61 ~~~~p~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
|..+--..+||--|...|.++..|..|..||-|+++++.+..-
T Consensus 48 p~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 48 PELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 4445567899999999999999999999999999999988764
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.43 E-value=0.064 Score=43.08 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=26.5
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHHHHHh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHLANVK 250 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~kklK 250 (470)
.+.|.+|+..|.+...|..||+.+.|++...
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 5899999999999999999999999988754
No 29
>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=91.99 E-value=0.11 Score=32.77 Aligned_cols=22 Identities=18% Similarity=0.455 Sum_probs=20.4
Q ss_pred EEeeecccccCcHHHHHhhhhh
Q 012121 221 LICELCNVKCESQVVFDSHLVG 242 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~G 242 (470)
|.|.+|+..|++...|..|++-
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 6899999999999999999864
No 30
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=91.89 E-value=0.076 Score=41.45 Aligned_cols=29 Identities=31% Similarity=0.549 Sum_probs=24.5
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHH
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNL 97 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNL 97 (470)
++..||+.|.+.|. .|..|+.+++|++=.
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhccHHHHHHH
Confidence 35679999999998 578899999999743
No 31
>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=91.29 E-value=0.13 Score=33.67 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=20.3
Q ss_pred CEEeeecccccCcHHHHHhhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLV 241 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~ 241 (470)
.|.|..|+..|.+...|..|++
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 3789999999999999999993
No 32
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=91.22 E-value=0.11 Score=46.81 Aligned_cols=37 Identities=19% Similarity=0.221 Sum_probs=34.1
Q ss_pred cCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 218 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 218 ~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
...+||--|...|.++..|..|++||-|+.++|++.+
T Consensus 53 lGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 3689999999999999999999999999999998843
No 33
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=91.21 E-value=0.077 Score=41.42 Aligned_cols=30 Identities=30% Similarity=0.538 Sum_probs=25.5
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
.-||++|.+.|. .|..|+.++||++=.+..
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~~~ 34 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFAENN 34 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHHcCc
Confidence 449999999987 789999999998876554
No 34
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.20 E-value=0.33 Score=48.75 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=36.4
Q ss_pred CCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 62 TRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 62 ~~~p~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
+.-+.....|.||++-.. +.....|.+||+|+-++..|+.-
T Consensus 29 kyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~ 69 (264)
T KOG3032|consen 29 KYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSR 69 (264)
T ss_pred ccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhh
Confidence 445677788999999999 99999999999999999999943
No 35
>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=91.05 E-value=0.095 Score=40.79 Aligned_cols=30 Identities=30% Similarity=0.520 Sum_probs=25.4
Q ss_pred CEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
.-||+.|.+.|. .|..|+.+++|++-....
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA~~~ 34 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQSEKHRKFAEND 34 (49)
T ss_pred CccCccccchhh---hHHHHhCCHHHHHHHcCc
Confidence 349999999998 599999999998876543
No 36
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=91.00 E-value=0.15 Score=49.68 Aligned_cols=38 Identities=29% Similarity=0.431 Sum_probs=33.4
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
....|.|.||+-.--++..|..|+.||||+.++.+.+.
T Consensus 50 h~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~ 87 (222)
T COG5246 50 HTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSE 87 (222)
T ss_pred CCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHH
Confidence 45689999999999999999999999999999876533
No 37
>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=89.96 E-value=0.19 Score=39.14 Aligned_cols=29 Identities=31% Similarity=0.692 Sum_probs=24.7
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHH
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNL 97 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNL 97 (470)
.+..||+.|.+.|.+ |..|+.+++|++=.
T Consensus 3 ~k~GYCE~C~~ky~~---l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 3 KKPGYCENCRVKYDD---LEEHIQSEKHRKFA 31 (49)
T ss_pred CCCccCccccchhhh---HHHHhCCHHHHHHH
Confidence 456799999999985 88999999999644
No 38
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=89.93 E-value=0.13 Score=49.21 Aligned_cols=35 Identities=20% Similarity=0.323 Sum_probs=30.4
Q ss_pred ccccccccccc--CCHHHHHHHhcCcchHHHHHhHHh
Q 012121 68 MAWCELCRVDC--NTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 68 ~~yC~VCnVsF--nSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
-+||+.|++|+ ++.++-..|+.|++|..+.+.+..
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY~ 39 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYM 39 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHHH
Confidence 36899999998 588899999999999999886654
No 39
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=89.75 E-value=0.15 Score=53.76 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=32.3
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
..+||..|..+|....+|..|+.||.|.+..+....
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 368999999999999999999999999998877544
No 40
>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=89.52 E-value=0.27 Score=32.17 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=19.0
Q ss_pred ccccccccccCCHHHHHHHh
Q 012121 69 AWCELCRVDCNTLEILEQHK 88 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy 88 (470)
+.|++|+++|.+...|..|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCccCCccCChhHHHHHh
Confidence 56999999999999999998
No 41
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=89.26 E-value=0.24 Score=48.60 Aligned_cols=38 Identities=29% Similarity=0.344 Sum_probs=33.6
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
-..+-|.+|.-.-+++..+..|..||||+-||.+....
T Consensus 51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~ 88 (222)
T KOG0227|consen 51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAK 88 (222)
T ss_pred CcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHH
Confidence 34556999999999999999999999999999988765
No 42
>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=87.79 E-value=0.38 Score=29.52 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=16.9
Q ss_pred ccccccccccCCHHHHHHHhc
Q 012121 69 AWCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~ 89 (470)
+-|.+|+..|.+...+..|+.
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 459999999999999999974
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=87.30 E-value=0.31 Score=30.03 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=21.0
Q ss_pred EEeeecccccCcHHHHHhhhhhhhHH
Q 012121 221 LICELCNVKCESQVVFDSHLVGKKHL 246 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~GKKH~ 246 (470)
|.|..|+..|++...|..|+. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~--~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR--THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH--Hhc
Confidence 469999999999999999997 553
No 44
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=87.01 E-value=0.31 Score=50.55 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=28.8
Q ss_pred CCEEeeeccccc-CcHHHHHhhhhhhhHHHHHhhh
Q 012121 219 IPLICELCNVKC-ESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 219 ~~~~CeLCNV~c-nSe~~~~sHL~GKKH~kklKk~ 252 (470)
..+||++|.|++ +.....+.|=.||||+.+|.+.
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 468999999988 5677899999999999888543
No 45
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=86.18 E-value=0.55 Score=45.92 Aligned_cols=38 Identities=26% Similarity=0.400 Sum_probs=33.8
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
-..+-|.+|+-.--++..+..|..||||+-|+.+....
T Consensus 51 ~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~e 88 (222)
T COG5246 51 TGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEE 88 (222)
T ss_pred CCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHH
Confidence 34567999999999999999999999999999988654
No 46
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=85.50 E-value=0.37 Score=38.70 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=26.6
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHH
Q 012121 67 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLR 98 (470)
Q Consensus 67 ~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLr 98 (470)
..+.|.+|++.|.+...+..|+..+.|.+...
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 36889999999999999999999999997544
No 47
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=84.88 E-value=0.46 Score=51.36 Aligned_cols=34 Identities=35% Similarity=0.567 Sum_probs=31.2
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
....|.+|||-..|+.-|-+|..|+||+--|+.+
T Consensus 492 rkkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 492 RKKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 4568999999999999999999999999988875
No 48
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=84.28 E-value=0.87 Score=51.69 Aligned_cols=35 Identities=26% Similarity=0.567 Sum_probs=30.9
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhh
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKR 251 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk 251 (470)
....|.|+||+..||..-.-..||+|+||.-..|+
T Consensus 356 K~~~f~cKlcdckf~d~nak~mhl~grRhrLQYk~ 390 (816)
T KOG3792|consen 356 KLLRFHCKLCDCKFNDPNAKEMHLKGRRHRLQYKQ 390 (816)
T ss_pred chHhhhhhhhcCCCCCcchHHhhhhcccccceecc
Confidence 45699999999999999999999999999766664
No 49
>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=83.39 E-value=0.35 Score=47.04 Aligned_cols=34 Identities=18% Similarity=0.510 Sum_probs=0.0
Q ss_pred CCEEeeecc-cccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 219 IPLICELCN-VKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 219 ~~~~CeLCN-V~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
..|.|+||. .++-+...|..|+...||..-|+.+
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp -----------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHccChhc
Confidence 589999997 7788999999999999999888876
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=82.89 E-value=2.2 Score=51.30 Aligned_cols=44 Identities=20% Similarity=0.230 Sum_probs=36.5
Q ss_pred CCCCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 60 APTRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 60 a~~~~p~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
+....+....-|.+|++.++....+-.|++--+|+.+++.+...
T Consensus 510 ~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~ 553 (1406)
T KOG1146|consen 510 EVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEEN 553 (1406)
T ss_pred ccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhc
Confidence 34456667778999999999999999999999999997766654
No 51
>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=82.29 E-value=0.98 Score=28.42 Aligned_cols=21 Identities=19% Similarity=0.412 Sum_probs=18.8
Q ss_pred ccccccccccCCHHHHHHHhc
Q 012121 69 AWCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~ 89 (470)
+-|..|+..|.+...|..|..
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 359999999999999999974
No 52
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=79.25 E-value=0.58 Score=44.91 Aligned_cols=31 Identities=32% Similarity=0.375 Sum_probs=26.0
Q ss_pred CEEeeecccccCcH--HHHHhhhhhhhHHHHHh
Q 012121 220 PLICELCNVKCESQ--VVFDSHLVGKKHLANVK 250 (470)
Q Consensus 220 ~~~CeLCNV~cnSe--~~~~sHL~GKKH~kklK 250 (470)
.|+|+.|+++++.- .+-+.|+.|++|..+.+
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~ 35 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRK 35 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHH
Confidence 58999999998764 48899999999976653
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=78.52 E-value=1.5 Score=26.89 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=18.6
Q ss_pred cccccccccCCHHHHHHHhc
Q 012121 70 WCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 70 yC~VCnVsFnSpsqaqsHy~ 89 (470)
-|..|...|.+...+..|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 59999999999999999986
No 54
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=76.09 E-value=1.2 Score=47.27 Aligned_cols=37 Identities=27% Similarity=0.545 Sum_probs=33.9
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
....||.+|+..|.|+..+..|+..|+|..++.++..
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 4567999999999999999999999999999998765
No 55
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=75.48 E-value=2 Score=27.56 Aligned_cols=20 Identities=20% Similarity=0.451 Sum_probs=16.1
Q ss_pred EEeeecccccCcHHHHHhhhh
Q 012121 221 LICELCNVKCESQVVFDSHLV 241 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~ 241 (470)
|.|..|+-.++ +..|..|+.
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 68999998888 999999986
No 56
>PTZ00448 hypothetical protein; Provisional
Probab=73.21 E-value=2.4 Score=45.06 Aligned_cols=34 Identities=29% Similarity=0.514 Sum_probs=31.8
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
..|.|..|++.|.+...++.|++.-=|.=+||+.
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 3689999999999999999999999999999986
No 57
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=70.60 E-value=2.5 Score=45.97 Aligned_cols=47 Identities=26% Similarity=0.383 Sum_probs=37.8
Q ss_pred CCCCCCCCC-CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 57 VPGAPTRPP-PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 57 ~~~a~~~~p-~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
...||+..| ....-|.+|+|-..|+.-+-+|..|+||+..++.+-..
T Consensus 481 tdyapkltpyerkkqcslcnvlissevylfshvkgrkhqqal~e~~~i 528 (672)
T KOG4722|consen 481 TDYAPKLTPYERKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELLLI 528 (672)
T ss_pred cccccccChHHhhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHhcc
Confidence 345566554 55667999999999999999999999999988876543
No 58
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=69.15 E-value=0.89 Score=46.67 Aligned_cols=36 Identities=19% Similarity=0.524 Sum_probs=32.3
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
..|||.+|...|+.+--|+.|+..--|++.+..+..
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 467999999999999999999999999999876643
No 59
>PF14968 CCDC84: Coiled coil protein 84
Probab=56.58 E-value=4.4 Score=42.47 Aligned_cols=28 Identities=25% Similarity=0.543 Sum_probs=25.4
Q ss_pred EeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 222 ICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 222 ~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
||.+|...+.. -+-|..+++|+++|+.+
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAF 28 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHH
Confidence 79999998875 89999999999999776
No 60
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=56.29 E-value=2.8 Score=43.24 Aligned_cols=37 Identities=22% Similarity=0.427 Sum_probs=32.8
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
.--|||..|+..|+.+.-|.-|.+.--|++.+.-...
T Consensus 23 KlRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 23 KLRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 3468999999999999999999999999998876654
No 61
>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=55.76 E-value=7.3 Score=37.41 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=29.6
Q ss_pred EEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 221 LICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
|.|.+|....--+..+..||.++=|+..++..
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 68999999999999999999999999888776
No 62
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=54.23 E-value=6.8 Score=45.21 Aligned_cols=64 Identities=22% Similarity=0.225 Sum_probs=46.4
Q ss_pred cCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcccccccccccccccCCCCCCCCCccccccc
Q 012121 218 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYGEAALQSLYPASFNSLSSSVITQV 283 (470)
Q Consensus 218 ~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g~~~l~g~~~lq~~~P~n~sa~s~~~~~q~ 283 (470)
...|-|.-|..-|.....|.+||..||-...+-.+--.++++.+ |+--.+.-.+++.+..++|+
T Consensus 307 EKPfeCpnCkKRFSHSGSySSHmSSKKCIsli~vngr~R~~lKt--~~~Sp~saSsSp~~s~~pq~ 370 (1007)
T KOG3623|consen 307 EKPFECPNCKKRFSHSGSYSSHMSSKKCISLILVNGRNRALLKT--LEKSPGSASSSPRRSPSPQG 370 (1007)
T ss_pred CCCcCCcccccccccCCcccccccccchhhhhcccCcchhhhhh--cccCCcccCCCCCCCCChhH
Confidence 46899999999999999999999999998777666666666665 33333333444555555555
No 63
>PHA02768 hypothetical protein; Provisional
Probab=49.36 E-value=8.8 Score=30.81 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=23.3
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHH
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLA 247 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~k 247 (470)
..|.|+.|+..|+....|..|++= |.+
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~--H~k 30 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRK--HNT 30 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHh--cCC
Confidence 468999999999999999999864 763
No 64
>PTZ00448 hypothetical protein; Provisional
Probab=47.14 E-value=14 Score=39.45 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=31.4
Q ss_pred cccccccccccCCHHHHHHHhcCcchHHHHHhHHh
Q 012121 68 MAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 102 (470)
Q Consensus 68 ~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk~ 102 (470)
.+.|..|++.|.+....+.||..=-|+=|+++.-.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~ 348 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNAR 348 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhc
Confidence 45699999999999999999999999999987654
No 65
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=45.82 E-value=12 Score=41.02 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=29.8
Q ss_pred cCCEEeeecc-cccCcHHHHHhhhhhhhHHHHHhh
Q 012121 218 VIPLICELCN-VKCESQVVFDSHLVGKKHLANVKR 251 (470)
Q Consensus 218 ~~~~~CeLCN-V~cnSe~~~~sHL~GKKH~kklKk 251 (470)
...|.|+||. -+.++...|+.|++=++|.--|+-
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrC 433 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRC 433 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhHHHHHhhccee
Confidence 4689999998 999999999999999999765543
No 66
>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=45.38 E-value=7 Score=38.29 Aligned_cols=38 Identities=24% Similarity=0.261 Sum_probs=0.0
Q ss_pred CCcccccccc-cccCCHHHHHHHhcCcchHHHHHhHHhh
Q 012121 66 PPMAWCELCR-VDCNTLEILEQHKNGKRHKRNLRTHADL 103 (470)
Q Consensus 66 ~~~~yC~VCn-VsFnSpsqaqsHy~GKKHkKNLrkLk~~ 103 (470)
...+.|+||. ..+...-.|+.|....||..-++.|-.+
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~ 137 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIP 137 (196)
T ss_dssp ---------------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCC
Confidence 5567899996 5578999999999999999999999765
No 67
>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=45.27 E-value=19 Score=34.68 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=29.7
Q ss_pred ccccccccccCCHHHHHHHhcCcchHHHHHhHH
Q 012121 69 AWCELCRVDCNTLEILEQHKNGKRHKRNLRTHA 101 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk 101 (470)
+.|.+|+.+--....++.|+.++-|+--++.+.
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~ 33 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQ 33 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHH
Confidence 479999999888899999999999998888874
No 68
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=44.38 E-value=16 Score=37.22 Aligned_cols=20 Identities=10% Similarity=-0.142 Sum_probs=9.3
Q ss_pred CCCCCCcccccccccccCCH
Q 012121 62 TRPPPPMAWCELCRVDCNTL 81 (470)
Q Consensus 62 ~~~p~~~~yC~VCnVsFnSp 81 (470)
.|.|....=.-|=+-..+|-
T Consensus 36 ~W~P~TklGrlVk~gki~s~ 55 (257)
T PTZ00070 36 EWVPVTKLGRLVKAGKITSL 55 (257)
T ss_pred ceeeccchhhhhhcCccccH
Confidence 46665444444444444443
No 69
>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=43.43 E-value=11 Score=37.87 Aligned_cols=30 Identities=27% Similarity=0.507 Sum_probs=23.1
Q ss_pred CEEeeecccccCc---HHHHHhhhhhhhHHHHH
Q 012121 220 PLICELCNVKCES---QVVFDSHLVGKKHLANV 249 (470)
Q Consensus 220 ~~~CeLCNV~cnS---e~~~~sHL~GKKH~kkl 249 (470)
--.|+||...... ..-+..|+.||-|+--+
T Consensus 190 l~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~ 222 (254)
T PF03194_consen 190 LEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYA 222 (254)
T ss_pred ccchhhhhhHHhccchHHHHHHHhccchhhhHH
Confidence 4589999976644 44699999999997543
No 70
>PHA00616 hypothetical protein
Probab=42.83 E-value=12 Score=28.92 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=19.5
Q ss_pred CEEeeecccccCcHHHHHhhh
Q 012121 220 PLICELCNVKCESQVVFDSHL 240 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL 240 (470)
.|.|..|+..|.....|..|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 368999999999999999999
No 71
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=41.07 E-value=15 Score=37.39 Aligned_cols=26 Identities=23% Similarity=0.408 Sum_probs=23.8
Q ss_pred CCcccccccccccCCHHHHHHHhcCc
Q 012121 66 PPMAWCELCRVDCNTLEILEQHKNGK 91 (470)
Q Consensus 66 ~~~~yC~VCnVsFnSpsqaqsHy~GK 91 (470)
...|||-+|.+.|.++..+-.|.-|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCCC
Confidence 56799999999999999999999885
No 72
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=39.29 E-value=9.9 Score=43.97 Aligned_cols=25 Identities=16% Similarity=0.481 Sum_probs=22.8
Q ss_pred CCEEeeecccccCcHHHHHhhhhhh
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGK 243 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GK 243 (470)
..|.|+-|..-|.....|.+||+=+
T Consensus 949 KPfQCdKClKRFSHSGSYSQHMNHR 973 (1007)
T KOG3623|consen 949 KPFQCDKCLKRFSHSGSYSQHMNHR 973 (1007)
T ss_pred CcchhhhhhhhcccccchHhhhccc
Confidence 5799999999999999999999843
No 73
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=38.44 E-value=26 Score=39.18 Aligned_cols=57 Identities=16% Similarity=0.230 Sum_probs=40.0
Q ss_pred ccccCCCCCCCCCCCCCCC-CCCCcccccccccccCCHHHHHHHhcCcchHHHHHhHH
Q 012121 45 VPGQTSSSIPGQVPGAPTR-PPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHA 101 (470)
Q Consensus 45 ~~~~~s~s~~~~~~~a~~~-~p~~~~yC~VCnVsFnSpsqaqsHy~GKKHkKNLrkLk 101 (470)
.+.+||-|......|--.- .....++|..|++.|-+-+....||.---|.-|+++.-
T Consensus 42 ~~~~Tsd~~~~~~e~~~r~~v~sd~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl 99 (591)
T KOG2505|consen 42 IVPETSDSMSLEEEGDMRDSVISDSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKL 99 (591)
T ss_pred cCCcCCCccchhhccchhhhhhcccccccccCCccccHHHHHHHHHHHHHHHHHHHHh
Confidence 3344444444444322211 23467889999999999999999999999999887654
No 74
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=36.97 E-value=13 Score=43.48 Aligned_cols=29 Identities=21% Similarity=0.489 Sum_probs=25.6
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhH
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKH 245 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH 245 (470)
....|.|+||.--|+....|+.||.+-|-
T Consensus 630 GERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 630 GERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred CcCccccccccchhccccchhhccccccc
Confidence 35789999999999999999999998553
No 75
>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=36.75 E-value=19 Score=36.13 Aligned_cols=34 Identities=24% Similarity=0.387 Sum_probs=26.5
Q ss_pred CCccccccccccc---CCHHHHHHHhcCcchHHHHHh
Q 012121 66 PPMAWCELCRVDC---NTLEILEQHKNGKRHKRNLRT 99 (470)
Q Consensus 66 ~~~~yC~VCnVsF---nSpsqaqsHy~GKKHkKNLrk 99 (470)
.....|+||.... .+..=+..||.||.|.-=++-
T Consensus 188 qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~I 224 (254)
T PF03194_consen 188 QKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAKI 224 (254)
T ss_pred cCccchhhhhhHHhccchHHHHHHHhccchhhhHHHH
Confidence 4567899999765 577778999999999854443
No 76
>PF12907 zf-met2: Zinc-binding
Probab=36.66 E-value=14 Score=27.97 Aligned_cols=23 Identities=22% Similarity=0.654 Sum_probs=20.0
Q ss_pred EEeeecc---cccCcHHHHHhhhhhh
Q 012121 221 LICELCN---VKCESQVVFDSHLVGK 243 (470)
Q Consensus 221 ~~CeLCN---V~cnSe~~~~sHL~GK 243 (470)
+.|.||- +...++.+|.+|...|
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 5799999 8888899999998754
No 77
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=36.42 E-value=51 Score=29.77 Aligned_cols=28 Identities=36% Similarity=0.649 Sum_probs=13.1
Q ss_pred CCccCCCCcCCCCcccCCCccccCCCCCC
Q 012121 6 QSACRGGGRKGGKPFRRGGRLVGRGRGHG 34 (470)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 34 (470)
.--|-|+ +|||.+-+||--+.|.|||.+
T Consensus 3 p~eYqgr-GRGgp~~qgG~~~yGggrgg~ 30 (104)
T PF12764_consen 3 PPEYQGR-GRGGPPQQGGRPGYGGGRGGG 30 (104)
T ss_pred Ccccccc-CCCCCcccCCCCCCCCCCCCC
Confidence 3345555 344444443322355566555
No 78
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=36.05 E-value=21 Score=36.74 Aligned_cols=24 Identities=21% Similarity=0.381 Sum_probs=20.7
Q ss_pred CEEeeecccccCcHHHHHhhhhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLVGK 243 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~GK 243 (470)
.-||=.||--|..|..|-+|.+-|
T Consensus 10 kpwcwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhc
Confidence 449999999999999999998754
No 79
>PF12907 zf-met2: Zinc-binding
Probab=36.04 E-value=20 Score=27.13 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=20.1
Q ss_pred ccccccc---cccCCHHHHHHHhcCcchHH
Q 012121 69 AWCELCR---VDCNTLEILEQHKNGKRHKR 95 (470)
Q Consensus 69 ~yC~VCn---VsFnSpsqaqsHy~GKKHkK 95 (470)
+-|.||. +.-.+..+|.+|+..| |-|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK-HpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK-HPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc-CCC
Confidence 4699999 4457889999999865 443
No 80
>PHA00732 hypothetical protein
Probab=35.98 E-value=20 Score=30.19 Aligned_cols=21 Identities=14% Similarity=0.461 Sum_probs=19.7
Q ss_pred EEeeecccccCcHHHHHhhhh
Q 012121 221 LICELCNVKCESQVVFDSHLV 241 (470)
Q Consensus 221 ~~CeLCNV~cnSe~~~~sHL~ 241 (470)
|.|.+|+..|++...|+.|+.
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 679999999999999999986
No 81
>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=34.54 E-value=26 Score=34.70 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=30.5
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcccccccc
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYG 260 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g~~~l~g 260 (470)
..|.|.+|...|-...=...||. +||..+|......-..|-
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev~~fn 116 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEVEYFN 116 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHHHHHH
Confidence 47899999999999999999997 689999887654433443
No 82
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=34.32 E-value=29 Score=38.78 Aligned_cols=52 Identities=17% Similarity=0.235 Sum_probs=43.8
Q ss_pred CCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcccccccccccccccCCC
Q 012121 219 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYGEAALQSLYPA 270 (470)
Q Consensus 219 ~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g~~~l~g~~~lq~~~P~ 270 (470)
..+.|..|++.|-+......||+.-=|.-++|+.--.+.++...-.-.++-.
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~edFe~i~s~ 116 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEEDFEGIISS 116 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhhc
Confidence 5789999999999999999999999999999998888888877444444444
No 83
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=33.81 E-value=53 Score=30.59 Aligned_cols=8 Identities=63% Similarity=0.833 Sum_probs=3.6
Q ss_pred CccCCCCc
Q 012121 7 SACRGGGR 14 (470)
Q Consensus 7 ~~~~~~~~ 14 (470)
+..+|+||
T Consensus 93 ~r~~~~gr 100 (134)
T KOG3293|consen 93 SRDRGRGR 100 (134)
T ss_pred cccccCCc
Confidence 34444444
No 84
>PHA02768 hypothetical protein; Provisional
Probab=31.82 E-value=30 Score=27.82 Aligned_cols=22 Identities=14% Similarity=0.107 Sum_probs=19.0
Q ss_pred cccccccccccCCHHHHHHHhc
Q 012121 68 MAWCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 68 ~~yC~VCnVsFnSpsqaqsHy~ 89 (470)
.+-|+.|+..|+..+.|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r 26 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLR 26 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHH
Confidence 4579999999999999988873
No 85
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=30.82 E-value=56 Score=36.46 Aligned_cols=12 Identities=25% Similarity=0.407 Sum_probs=8.9
Q ss_pred HHHHHhcCcchH
Q 012121 83 ILEQHKNGKRHK 94 (470)
Q Consensus 83 qaqsHy~GKKHk 94 (470)
.|-.|+.|=-|-
T Consensus 206 lFLKhlVGGLHT 217 (641)
T KOG3915|consen 206 LFLKHLVGGLHT 217 (641)
T ss_pred HHHHHHhchHHH
Confidence 455788888886
No 86
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=30.54 E-value=1e+02 Score=27.82 Aligned_cols=20 Identities=50% Similarity=0.787 Sum_probs=14.6
Q ss_pred cCCCCc-CCCCcccCCCcccc
Q 012121 9 CRGGGR-KGGKPFRRGGRLVG 28 (470)
Q Consensus 9 ~~~~~~-~~~~~~~~~~~~~~ 28 (470)
+||+-+ +||+|..|||||-+
T Consensus 10 GRGgp~~qgG~~~yGggrgg~ 30 (104)
T PF12764_consen 10 GRGGPPQQGGRPGYGGGRGGG 30 (104)
T ss_pred CCCCCcccCCCCCCCCCCCCC
Confidence 566555 78888888888755
No 87
>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=30.47 E-value=45 Score=26.95 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=18.8
Q ss_pred CCCCCCcccccccccccCCHHHHHHHh
Q 012121 62 TRPPPPMAWCELCRVDCNTLEILEQHK 88 (470)
Q Consensus 62 ~~~p~~~~yC~VCnVsFnSpsqaqsHy 88 (470)
...+.....|.+|+..|.+...+.-|+
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHl 44 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHL 44 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHH
T ss_pred hhccCCCCCCCcchhhccchhhHHHHH
Confidence 456778889999999999999998887
No 88
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=28.68 E-value=32 Score=36.16 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=29.2
Q ss_pred CCCccccccccccc---CCHHHHHHHhcCcchHHHHHhHH
Q 012121 65 PPPMAWCELCRVDC---NTLEILEQHKNGKRHKRNLRTHA 101 (470)
Q Consensus 65 p~~~~yC~VCnVsF---nSpsqaqsHy~GKKHkKNLrkLk 101 (470)
..+...|+||...+ .+..=+..|+.||-|.--+.-..
T Consensus 183 ~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~ 222 (319)
T KOG0796|consen 183 QQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIRE 222 (319)
T ss_pred hhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHH
Confidence 34677899999986 58888999999999986555333
No 89
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=28.13 E-value=27 Score=35.95 Aligned_cols=24 Identities=33% Similarity=0.731 Sum_probs=20.8
Q ss_pred cccccccccccCCHHHHHHHhcCc
Q 012121 68 MAWCELCRVDCNTLEILEQHKNGK 91 (470)
Q Consensus 68 ~~yC~VCnVsFnSpsqaqsHy~GK 91 (470)
.-||..||..|..+-.|.+|..-|
T Consensus 10 kpwcwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred Cceeeecccccchhhhhhhhhhhc
Confidence 348999999999999999998654
No 90
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=27.65 E-value=72 Score=33.65 Aligned_cols=6 Identities=50% Similarity=0.612 Sum_probs=2.6
Q ss_pred CCCccc
Q 012121 22 RGGRLV 27 (470)
Q Consensus 22 ~~~~~~ 27 (470)
|||||.
T Consensus 402 ~~~~~~ 407 (456)
T PRK10590 402 GGGRGQ 407 (456)
T ss_pred CCCCCC
Confidence 444443
No 91
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=27.61 E-value=83 Score=36.84 Aligned_cols=44 Identities=11% Similarity=0.175 Sum_probs=32.5
Q ss_pred CcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcccccccc
Q 012121 217 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYG 260 (470)
Q Consensus 217 ~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g~~~l~g 260 (470)
....|.|.+|+..|.-...+..||+--+-+.+-.+.....++|-
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~q~~~~~~~a~~aa~~ 832 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQQEEQQRQKAQKAAFA 832 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999977666665444444444443
No 92
>PHA00616 hypothetical protein
Probab=27.32 E-value=29 Score=26.83 Aligned_cols=20 Identities=15% Similarity=0.097 Sum_probs=18.4
Q ss_pred ccccccccccCCHHHHHHHh
Q 012121 69 AWCELCRVDCNTLEILEQHK 88 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy 88 (470)
.-|..|...|...+.+..|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CccchhhHHHhhHHHHHHHH
Confidence 35999999999999999998
No 93
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=26.88 E-value=31 Score=36.31 Aligned_cols=29 Identities=31% Similarity=0.579 Sum_probs=22.9
Q ss_pred EEeeecccccC---cHHHHHhhhhhhhHHHHH
Q 012121 221 LICELCNVKCE---SQVVFDSHLVGKKHLANV 249 (470)
Q Consensus 221 ~~CeLCNV~cn---Se~~~~sHL~GKKH~kkl 249 (470)
-.|+||.+++. +..-+..||.||-|+--+
T Consensus 187 ~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~ 218 (319)
T KOG0796|consen 187 RVCEVCGAFLSVNDADRRLADHFGGKLHLGYV 218 (319)
T ss_pred hHHHhhhHHHhccchHHHHHHhhcchHHHHHH
Confidence 36999997654 555799999999997544
No 94
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.40 E-value=49 Score=22.20 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=15.4
Q ss_pred ccccccccccCCHHHHHHHhc
Q 012121 69 AWCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~ 89 (470)
.-|.+|+.+| .+..+..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4599999999 5666777753
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=25.62 E-value=48 Score=22.04 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=11.3
Q ss_pred CCEEeeecccccC
Q 012121 219 IPLICELCNVKCE 231 (470)
Q Consensus 219 ~~~~CeLCNV~cn 231 (470)
..|.|.+|+..|.
T Consensus 13 k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 13 KPYKCPYCGKSFS 25 (26)
T ss_dssp SSEEESSSSEEES
T ss_pred CCCCCCCCcCeeC
Confidence 5799999998886
No 96
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=24.62 E-value=20 Score=35.86 Aligned_cols=34 Identities=18% Similarity=0.450 Sum_probs=25.8
Q ss_pred cCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhh
Q 012121 218 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 218 ~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~ 252 (470)
...|||++|++.+-. ...-.|+..--|+-.++..
T Consensus 82 e~lfyCE~Cd~~ip~-~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 82 EALFYCEVCDIYIPN-SKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred CccchhhhhhhhccC-CCCccchhhHHHHhhhccC
Confidence 358999999998763 3445688888898877664
No 97
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=24.37 E-value=60 Score=36.41 Aligned_cols=13 Identities=38% Similarity=0.547 Sum_probs=7.2
Q ss_pred CCcccCCCccccC
Q 012121 17 GKPFRRGGRLVGR 29 (470)
Q Consensus 17 ~~~~~~~~~~~~~ 29 (470)
|+.-|+|||+|++
T Consensus 579 ~~~~~~~~~~~~~ 591 (629)
T PRK11634 579 GGERREGGRNFSG 591 (629)
T ss_pred CCCCCCCCcCCCC
Confidence 3444556666653
No 98
>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=24.10 E-value=53 Score=22.34 Aligned_cols=20 Identities=15% Similarity=0.504 Sum_probs=17.0
Q ss_pred ccccccccccCCHHHHHHHhc
Q 012121 69 AWCELCRVDCNTLEILEQHKN 89 (470)
Q Consensus 69 ~yC~VCnVsFnSpsqaqsHy~ 89 (470)
.-|.||+..+ +...++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3599999999 7788889986
No 99
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.43 E-value=29 Score=35.09 Aligned_cols=44 Identities=25% Similarity=0.422 Sum_probs=32.9
Q ss_pred cCCEEeeecccccCcHHHHHhhhh---hhhHHHHHhhhccccccccc
Q 012121 218 VIPLICELCNVKCESQVVFDSHLV---GKKHLANVKRFHGHRALYGE 261 (470)
Q Consensus 218 ~~~~~CeLCNV~cnSe~~~~sHL~---GKKH~kklKk~~g~~~l~g~ 261 (470)
+..|.|++|+..|+-.-.|.+||. |-.|+--.|+...+.-.+..
T Consensus 171 vrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vced 217 (267)
T KOG3576|consen 171 VRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCED 217 (267)
T ss_pred ccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecc
Confidence 357999999999999999999985 55666666665555555444
No 100
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=23.43 E-value=21 Score=35.61 Aligned_cols=36 Identities=17% Similarity=0.354 Sum_probs=24.2
Q ss_pred CCCCcccccccccccC-CHHHHHHHhcCcchHHHHHhHH
Q 012121 64 PPPPMAWCELCRVDCN-TLEILEQHKNGKRHKRNLRTHA 101 (470)
Q Consensus 64 ~p~~~~yC~VCnVsFn-SpsqaqsHy~GKKHkKNLrkLk 101 (470)
.+...+||++|++.|. ++.. .|...--|.-+++.+-
T Consensus 80 ~~e~lfyCE~Cd~~ip~~~~s--nH~tSttHllsl~~~p 116 (223)
T KOG2384|consen 80 RDEALFYCEVCDIYIPNSKKS--NHFTSTTHLLSLQHIP 116 (223)
T ss_pred CCCccchhhhhhhhccCCCCc--cchhhHHHHhhhccCC
Confidence 3456789999999984 3332 4777777776666554
No 101
>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=23.39 E-value=44 Score=27.04 Aligned_cols=22 Identities=23% Similarity=0.531 Sum_probs=16.5
Q ss_pred CEEeeecccccCcHHHHHhhhh
Q 012121 220 PLICELCNVKCESQVVFDSHLV 241 (470)
Q Consensus 220 ~~~CeLCNV~cnSe~~~~sHL~ 241 (470)
.-.|-+|...|.+...|+.||.
T Consensus 24 PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHH
Confidence 4599999999999999999984
No 102
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=21.98 E-value=35 Score=34.49 Aligned_cols=32 Identities=22% Similarity=0.431 Sum_probs=24.6
Q ss_pred EEeeecccccC---cHHHHHhhhhhhhHHHHHhhh
Q 012121 221 LICELCNVKCE---SQVVFDSHLVGKKHLANVKRF 252 (470)
Q Consensus 221 ~~CeLCNV~cn---Se~~~~sHL~GKKH~kklKk~ 252 (470)
-.|.||.+... ...-+..|++||=|+--+.-.
T Consensus 186 qvC~iCgayLsrlDtdrrladHf~GklHlGy~~~R 220 (258)
T COG5200 186 QVCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVR 220 (258)
T ss_pred hhhhhhhhHHHhcchhhHHHHHhccchhhhHHHHH
Confidence 37999998765 445799999999998665433
No 103
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=21.14 E-value=66 Score=39.64 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=34.4
Q ss_pred CCcCCEEeeecccccCcHHHHHhhhhhhhHHHHHhhhcc
Q 012121 216 KGVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 254 (470)
Q Consensus 216 ~~~~~~~CeLCNV~cnSe~~~~sHL~GKKH~kklKk~~g 254 (470)
.....|.|..||+.++....|-.||..-+|+.+++....
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~ 552 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEE 552 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHh
Confidence 345789999999999999999999999999999877643
No 104
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=20.79 E-value=62 Score=33.10 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=23.0
Q ss_pred cCCEEeeecccccCcHHHHHhhhhhh
Q 012121 218 VIPLICELCNVKCESQVVFDSHLVGK 243 (470)
Q Consensus 218 ~~~~~CeLCNV~cnSe~~~~sHL~GK 243 (470)
..-|||-.|.+.|.++..|-.|-=|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCCC
Confidence 46899999999999999999997663
Done!