Query 041577
Match_columns 237
No_of_seqs 147 out of 319
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:35:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041577.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041577hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12874 zf-met: Zinc-finger o 98.6 2E-08 4.3E-13 58.6 2.5 25 155-179 1-25 (25)
2 smart00451 ZnF_U1 U1-like zinc 98.6 5.8E-08 1.3E-12 60.7 3.2 32 154-185 3-34 (35)
3 PF12874 zf-met: Zinc-finger o 98.6 4.2E-08 9E-13 57.2 2.3 25 35-59 1-25 (25)
4 smart00451 ZnF_U1 U1-like zinc 98.4 1.5E-07 3.2E-12 58.9 2.7 32 34-65 3-34 (35)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.3 3.9E-07 8.4E-12 54.4 1.7 27 154-180 1-27 (27)
6 PF12171 zf-C2H2_jaz: Zinc-fin 98.1 1.5E-06 3.2E-11 51.8 1.6 26 35-60 2-27 (27)
7 KOG3792 Transcription factor N 97.7 7.6E-05 1.6E-09 74.7 6.4 35 150-184 355-389 (816)
8 PF06220 zf-U1: U1 zinc finger 97.4 0.0002 4.3E-09 46.4 3.1 32 154-185 3-36 (38)
9 KOG4727 U1-like Zn-finger prot 97.3 0.00019 4.1E-09 60.9 3.0 42 25-66 66-107 (193)
10 KOG4727 U1-like Zn-finger prot 97.1 0.00031 6.8E-09 59.6 2.9 36 152-187 73-108 (193)
11 PF06220 zf-U1: U1 zinc finger 97.0 0.0007 1.5E-08 43.9 3.1 32 34-65 3-36 (38)
12 KOG2785 C2H2-type Zn-finger pr 96.5 0.0034 7.3E-08 59.2 4.4 99 34-187 3-101 (390)
13 PF12756 zf-C2H2_2: C2H2 type 96.2 0.0015 3.2E-08 48.6 0.6 32 154-185 50-81 (100)
14 PLN02748 tRNA dimethylallyltra 96.2 0.0036 7.8E-08 60.9 3.4 37 153-189 417-454 (468)
15 PF14968 CCDC84: Coiled coil p 95.9 0.0041 8.9E-08 58.1 2.1 38 152-189 56-99 (336)
16 KOG0717 Molecular chaperone (D 95.8 0.0064 1.4E-07 58.8 2.6 36 154-189 292-327 (508)
17 KOG3408 U1-like Zn-finger-cont 95.6 0.0075 1.6E-07 48.6 2.2 36 153-188 56-91 (129)
18 smart00586 ZnF_DBF Zinc finger 95.4 0.0084 1.8E-07 41.0 1.6 30 152-184 3-32 (49)
19 KOG3032 Uncharacterized conser 95.4 0.031 6.7E-07 49.8 5.4 37 152-189 33-69 (264)
20 KOG0227 Splicing factor 3a, su 95.1 0.015 3.3E-07 50.4 2.5 41 152-192 51-91 (222)
21 PLN02748 tRNA dimethylallyltra 95.0 0.019 4.2E-07 55.9 3.3 36 33-68 417-453 (468)
22 PF07535 zf-DBF: DBF zinc fing 95.0 0.02 4.3E-07 39.2 2.4 29 152-183 3-31 (49)
23 PF13894 zf-C2H2_4: C2H2-type 95.0 0.019 4E-07 31.8 1.9 21 155-175 1-21 (24)
24 smart00586 ZnF_DBF Zinc finger 95.0 0.014 2.9E-07 40.0 1.5 29 32-63 3-31 (49)
25 KOG3408 U1-like Zn-finger-cont 94.8 0.02 4.3E-07 46.2 2.2 36 33-68 56-91 (129)
26 PF07535 zf-DBF: DBF zinc fing 94.6 0.028 6E-07 38.5 2.3 29 32-63 3-31 (49)
27 PF00096 zf-C2H2: Zinc finger, 94.5 0.028 6E-07 31.5 1.8 22 155-176 1-22 (23)
28 KOG0717 Molecular chaperone (D 94.2 0.031 6.7E-07 54.2 2.6 35 34-68 292-326 (508)
29 KOG3454 U1 snRNP-specific prot 93.8 0.036 7.7E-07 46.8 1.8 33 34-66 3-37 (165)
30 PF13912 zf-C2H2_6: C2H2-type 93.7 0.058 1.3E-06 31.4 2.1 23 154-176 1-23 (27)
31 PF13894 zf-C2H2_4: C2H2-type 93.4 0.062 1.3E-06 29.6 1.9 21 35-55 1-21 (24)
32 KOG3454 U1 snRNP-specific prot 93.0 0.068 1.5E-06 45.2 2.3 32 154-185 3-36 (165)
33 KOG4722 Zn-finger protein [Gen 92.9 0.061 1.3E-06 51.8 2.1 34 154-187 493-526 (672)
34 KOG0227 Splicing factor 3a, su 92.1 0.12 2.6E-06 44.9 2.7 36 33-68 52-87 (222)
35 PF13912 zf-C2H2_6: C2H2-type 92.0 0.13 2.9E-06 29.8 2.1 21 35-55 2-22 (27)
36 smart00355 ZnF_C2H2 zinc finge 91.2 0.17 3.7E-06 28.0 1.9 21 155-175 1-21 (26)
37 KOG3032 Uncharacterized conser 91.1 0.24 5.1E-06 44.3 3.5 41 27-68 28-68 (264)
38 PF00096 zf-C2H2: Zinc finger, 90.9 0.17 3.7E-06 28.1 1.7 21 35-55 1-21 (23)
39 COG5112 UFD2 U1-like Zn-finger 90.5 0.16 3.5E-06 40.3 1.8 37 153-189 54-90 (126)
40 COG5112 UFD2 U1-like Zn-finger 89.9 0.33 7.1E-06 38.6 3.0 36 33-68 54-89 (126)
41 KOG0150 Spliceosomal protein F 89.1 0.24 5.1E-06 45.9 2.0 33 34-66 10-43 (336)
42 COG5188 PRP9 Splicing factor 3 88.8 0.21 4.5E-06 47.2 1.4 33 153-185 237-269 (470)
43 PF12756 zf-C2H2_2: C2H2 type 88.8 0.21 4.6E-06 36.8 1.2 32 33-64 49-80 (100)
44 KOG0150 Spliceosomal protein F 88.1 0.25 5.4E-06 45.8 1.4 33 153-185 9-42 (336)
45 COG5246 PRP11 Splicing factor 88.1 0.47 1E-05 41.1 3.0 35 152-186 51-85 (222)
46 COG5246 PRP11 Splicing factor 87.3 0.52 1.1E-05 40.8 2.8 36 33-68 52-87 (222)
47 PF04988 AKAP95: A-kinase anch 86.7 0.6 1.3E-05 39.6 2.8 32 155-186 1-32 (165)
48 smart00355 ZnF_C2H2 zinc finge 86.4 0.52 1.1E-05 25.9 1.7 21 35-55 1-21 (26)
49 COG5188 PRP9 Splicing factor 3 86.0 0.39 8.5E-06 45.4 1.5 34 33-66 237-270 (470)
50 KOG4722 Zn-finger protein [Gen 85.5 0.51 1.1E-05 45.7 2.1 35 33-67 492-526 (672)
51 PF11931 DUF3449: Domain of un 84.8 0.28 6.1E-06 42.7 0.0 39 153-191 100-139 (196)
52 KOG2837 Protein containing a U 84.2 0.21 4.5E-06 45.6 -1.1 39 153-191 24-62 (309)
53 PF13909 zf-H2C2_5: C2H2-type 84.0 0.87 1.9E-05 25.7 1.8 20 155-175 1-20 (24)
54 KOG1146 Homeobox protein [Gene 82.4 1.8 4E-05 46.9 4.8 41 153-193 517-557 (1406)
55 KOG1146 Homeobox protein [Gene 81.6 0.79 1.7E-05 49.6 1.8 33 154-186 1328-1360(1406)
56 PF04988 AKAP95: A-kinase anch 80.9 1.5 3.3E-05 37.2 2.9 33 35-67 1-33 (165)
57 PTZ00448 hypothetical protein; 79.3 1.6 3.4E-05 41.5 2.7 34 154-187 314-347 (373)
58 COG5136 U1 snRNP-specific prot 77.6 0.82 1.8E-05 38.8 0.3 32 154-185 3-36 (188)
59 KOG2837 Protein containing a U 77.5 0.56 1.2E-05 42.9 -0.8 36 33-68 24-59 (309)
60 PTZ00448 hypothetical protein; 73.1 2.8 6.1E-05 39.9 2.6 34 34-67 314-347 (373)
61 PHA00616 hypothetical protein 71.0 2.4 5.2E-05 28.4 1.2 21 155-175 2-22 (44)
62 KOG2505 Ankyrin repeat protein 70.8 3.3 7.2E-05 41.0 2.6 33 33-65 65-97 (591)
63 PF11931 DUF3449: Domain of un 70.4 1.4 3E-05 38.4 0.0 36 33-68 100-136 (196)
64 KOG3792 Transcription factor N 68.3 1.5 3.2E-05 44.9 -0.3 79 154-232 193-272 (816)
65 PF12907 zf-met2: Zinc-binding 68.2 2.7 5.9E-05 27.6 1.0 23 35-57 2-27 (40)
66 PHA02768 hypothetical protein; 68.0 3.3 7.1E-05 29.0 1.4 25 154-180 5-29 (55)
67 PF12013 DUF3505: Protein of u 67.4 15 0.00033 28.3 5.3 28 33-61 10-37 (109)
68 COG5136 U1 snRNP-specific prot 66.3 2.4 5.2E-05 36.1 0.5 32 34-65 3-36 (188)
69 smart00734 ZnF_Rad18 Rad18-lik 65.1 5.1 0.00011 23.6 1.7 20 155-175 2-21 (26)
70 PF09237 GAGA: GAGA factor; I 63.9 5.2 0.00011 27.8 1.8 23 33-55 23-45 (54)
71 PF09237 GAGA: GAGA factor; I 63.5 5 0.00011 27.9 1.6 23 153-175 23-45 (54)
72 KOG1994 Predicted RNA binding 60.6 5.5 0.00012 35.7 1.8 26 32-57 237-262 (268)
73 KOG2462 C2H2-type Zn-finger pr 55.5 6.8 0.00015 35.9 1.6 25 153-177 214-238 (279)
74 PHA00732 hypothetical protein 55.5 9 0.0002 28.5 2.0 22 155-176 2-23 (79)
75 PF12907 zf-met2: Zinc-binding 54.2 6.3 0.00014 25.8 0.8 23 155-177 2-27 (40)
76 KOG1074 Transcriptional repres 52.7 5.2 0.00011 41.8 0.4 31 153-183 632-662 (958)
77 KOG3608 Zn finger proteins [Ge 52.0 9.1 0.0002 36.6 1.8 22 33-54 236-257 (467)
78 KOG2505 Ankyrin repeat protein 50.9 13 0.00028 36.9 2.7 34 153-186 65-98 (591)
79 PF03194 LUC7: LUC7 N_terminus 50.8 9.2 0.0002 34.4 1.6 30 32-61 188-220 (254)
80 KOG2893 Zn finger protein [Gen 48.2 11 0.00023 34.3 1.6 25 153-177 9-33 (341)
81 COG5067 DBF4 Protein kinase es 45.2 6.8 0.00015 37.7 -0.1 30 152-184 420-449 (468)
82 PF13913 zf-C2HC_2: zinc-finge 44.9 17 0.00038 21.0 1.6 20 155-175 3-22 (25)
83 PF14968 CCDC84: Coiled coil p 43.9 19 0.0004 34.0 2.5 37 29-66 54-96 (336)
84 KOG2785 C2H2-type Zn-finger pr 42.5 21 0.00046 34.2 2.7 35 154-188 3-37 (390)
85 KOG3576 Ovo and related transc 42.4 13 0.00028 33.1 1.2 35 153-187 172-209 (267)
86 KOG3576 Ovo and related transc 38.8 32 0.00069 30.7 3.0 25 152-176 210-234 (267)
87 PF04959 ARS2: Arsenite-resist 38.2 34 0.00074 30.2 3.2 38 152-190 75-112 (214)
88 KOG2482 Predicted C2H2-type Zn 36.5 13 0.00028 35.3 0.3 31 152-182 193-223 (423)
89 PF03194 LUC7: LUC7 N_terminus 36.4 19 0.00042 32.4 1.4 30 152-181 188-220 (254)
90 PHA02768 hypothetical protein; 36.3 22 0.00048 24.9 1.3 21 35-55 6-26 (55)
91 COG5067 DBF4 Protein kinase es 33.9 23 0.00051 34.2 1.6 29 33-64 421-449 (468)
92 KOG1994 Predicted RNA binding 33.4 25 0.00055 31.6 1.6 26 153-178 238-263 (268)
93 KOG3993 Transcription factor ( 32.1 26 0.00057 34.2 1.6 82 34-174 295-376 (500)
94 KOG2636 Splicing factor 3a, su 31.0 19 0.00041 35.3 0.5 40 153-192 400-440 (497)
95 PHA00733 hypothetical protein 29.0 44 0.00096 26.9 2.2 23 153-175 72-94 (128)
96 KOG2384 Major histocompatibili 28.3 23 0.0005 31.2 0.4 37 152-189 82-118 (223)
97 KOG0796 Spliceosome subunit [R 27.7 26 0.00057 32.8 0.7 32 31-62 183-217 (319)
98 PHA00732 hypothetical protein 26.9 45 0.00098 24.7 1.8 21 35-55 2-22 (79)
99 PF12013 DUF3505: Protein of u 24.9 50 0.0011 25.3 1.8 28 153-181 10-37 (109)
100 PF13465 zf-H2C2_2: Zinc-finge 24.6 43 0.00093 19.2 1.0 13 153-165 13-25 (26)
101 PF05477 SURF2: Surfeit locus 23.7 1E+02 0.0022 27.9 3.7 39 31-69 76-115 (244)
102 PF05605 zf-Di19: Drought indu 23.4 63 0.0014 21.7 1.9 22 154-176 2-23 (54)
103 COG4049 Uncharacterized protei 22.2 41 0.00089 23.9 0.7 22 154-175 17-38 (65)
104 PHA00733 hypothetical protein 20.3 71 0.0015 25.7 1.9 22 154-175 99-120 (128)
No 1
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.64 E-value=2e-08 Score=58.57 Aligned_cols=25 Identities=36% Similarity=0.820 Sum_probs=24.5
Q ss_pred eeccccccccCCHHHHHHHhcChhH
Q 041577 155 WSCALCQVSAPTERGLDEHLQGRKH 179 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~GkkH 179 (237)
|+|.+|++.|+++.+|.+|++|++|
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 7999999999999999999999998
No 2
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.56 E-value=5.8e-08 Score=60.74 Aligned_cols=32 Identities=38% Similarity=0.755 Sum_probs=30.3
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~ 185 (237)
.|+|++|++.|++...+..|++|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58999999999999999999999999999875
No 3
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.56 E-value=4.2e-08 Score=57.18 Aligned_cols=25 Identities=40% Similarity=0.765 Sum_probs=24.5
Q ss_pred eeccccccccCCHHHHHHHhcChhh
Q 041577 35 WSCVLCQVSATTERDLDVHLQGKKH 59 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~GkKH 59 (237)
|+|+||+++|+++.+|+.|++|++|
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 7999999999999999999999998
No 4
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.44 E-value=1.5e-07 Score=58.85 Aligned_cols=32 Identities=44% Similarity=0.746 Sum_probs=29.9
Q ss_pred ceeccccccccCCHHHHHHHhcChhhHHHHHH
Q 041577 34 EWSCVLCQVSATTERDLDVHLQGKKHKAKEKL 65 (237)
Q Consensus 34 ~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~ 65 (237)
.++|++|++.|+++..+..|+.|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58899999999999999999999999999874
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=98.28 E-value=3.9e-07 Score=54.38 Aligned_cols=27 Identities=30% Similarity=0.700 Sum_probs=25.3
Q ss_pred ceeccccccccCCHHHHHHHhcChhHH
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHK 180 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~ 180 (237)
.|+|.+|++.|+++.+|+.|++|++|+
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 489999999999999999999999996
No 6
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.09 E-value=1.5e-06 Score=51.84 Aligned_cols=26 Identities=35% Similarity=0.676 Sum_probs=25.3
Q ss_pred eeccccccccCCHHHHHHHhcChhhH
Q 041577 35 WSCVLCQVSATTERDLDVHLQGKKHK 60 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~GkKHk 60 (237)
+||.+|++.|+++.+|+.|+.|++|+
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 79999999999999999999999996
No 7
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=97.68 E-value=7.6e-05 Score=74.69 Aligned_cols=35 Identities=26% Similarity=0.565 Sum_probs=31.3
Q ss_pred CCCCceeccccccccCCHHHHHHHhcChhHHHHHH
Q 041577 150 NKPKEWSCALCQVSAPTERGLDEHLQGRKHKAKVA 184 (237)
Q Consensus 150 k~~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~ 184 (237)
++...|.|.+|+..|+....-++||+|+||+-..+
T Consensus 355 gK~~~f~cKlcdckf~d~nak~mhl~grRhrLQYk 389 (816)
T KOG3792|consen 355 GKLLRFHCKLCDCKFNDPNAKEMHLKGRRHRLQYK 389 (816)
T ss_pred cchHhhhhhhhcCCCCCcchHHhhhhcccccceec
Confidence 34558999999999999999999999999987766
No 8
>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=97.36 E-value=0.0002 Score=46.45 Aligned_cols=32 Identities=25% Similarity=0.444 Sum_probs=20.6
Q ss_pred ceecccccccc--CCHHHHHHHhcChhHHHHHHh
Q 041577 154 EWSCALCQVSA--PTERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 154 ~~~C~lC~v~~--~s~~~l~~Hl~GkkH~~~~~~ 185 (237)
.+||+.|++.+ ++...-..|..|.+|+.+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 58999999999 455677999999999999875
No 9
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.28 E-value=0.00019 Score=60.92 Aligned_cols=42 Identities=21% Similarity=0.407 Sum_probs=36.2
Q ss_pred CCCCCCCCCceeccccccccCCHHHHHHHhcChhhHHHHHHH
Q 041577 25 PSTSSNKSKEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLL 66 (237)
Q Consensus 25 ~~~~~kk~~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l 66 (237)
+..+..+.--+||+||+..+--..+|.+|++|++|+.++..+
T Consensus 66 k~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 66 KSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 344556667899999999999999999999999999998753
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.14 E-value=0.00031 Score=59.58 Aligned_cols=36 Identities=17% Similarity=0.480 Sum_probs=32.7
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhhh
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLL 187 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~ 187 (237)
...|||.||+..|-...+|..||+|++|+.++..+.
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSM 108 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHHhhhh
Confidence 458999999999999999999999999999987653
No 11
>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=97.03 E-value=0.0007 Score=43.86 Aligned_cols=32 Identities=25% Similarity=0.348 Sum_probs=20.1
Q ss_pred ceecccccccc--CCHHHHHHHhcChhhHHHHHH
Q 041577 34 EWSCVLCQVSA--TTERDLDVHLQGKKHKAKEKL 65 (237)
Q Consensus 34 ~~~C~vC~Vs~--tSe~~l~~Hl~GkKHk~k~~~ 65 (237)
.+||+.|++.+ ++...-..|..|.+|+.+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 47899999999 455666899999999999874
No 12
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=96.46 E-value=0.0034 Score=59.21 Aligned_cols=99 Identities=16% Similarity=0.253 Sum_probs=67.5
Q ss_pred ceeccccccccCCHHHHHHHhcChhhHHHHHHHhhhhhccCCCCcccccccccccccCCCCcchhhhhcccccccccccc
Q 041577 34 EWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRDLKMCINSTSKKATESRDSADQEMKPNVEDESVKANKTVVGLDQKL 113 (237)
Q Consensus 34 ~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~~k~~~~p~s~k~~~~~~~~~~e~~~~~~~~~~q~~~~~~~~~~~~ 113 (237)
.++|.-|+|.|.+...-..||.--+|+=+|+..-++ +.+++ .+-++ ..+
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~----------lPPIt------------aE~F~---------~k~ 51 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVAS----------LPPIT------------AEEFN---------EKV 51 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhc----------CCCcC------------HHHHh---------HHH
Confidence 478999999999999999999999999999864432 11111 11100 000
Q ss_pred cCCcccccCCCCCCCCCCCccCCCCCCCCCCCccCCCCCCceeccccccccCCHHHHHHHhcChhHHHHHHhhh
Q 041577 114 EGGQTLQVKPNSNPCGSDQKTATPPAGSGELPLTNSNKPKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLL 187 (237)
Q Consensus 114 ~g~~~~Q~kp~~n~~g~~~k~~~~~~~~ge~~~~~~k~~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~ 187 (237)
+. ... +...........++|.+|+..+-|...+..||..++|..++....
T Consensus 52 ------~s-------------~~~-----~~~~~~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~ 101 (390)
T KOG2785|consen 52 ------LS-------------DDS-----EKEENLEEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQ 101 (390)
T ss_pred ------hh-------------hhh-----hhhhhhhhcccceehHHhhccccChhhHHHHHHHhhcchhhhhhh
Confidence 00 000 000001123458999999999999999999999999999998864
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.24 E-value=0.0015 Score=48.57 Aligned_cols=32 Identities=22% Similarity=0.616 Sum_probs=26.6
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~ 185 (237)
.|.|.+|+..|.+...|..||+.+.|......
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~~ 81 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNSE 81 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcccc
Confidence 69999999999999999999999999887543
No 14
>PLN02748 tRNA dimethylallyltransferase
Probab=96.24 E-value=0.0036 Score=60.94 Aligned_cols=37 Identities=24% Similarity=0.512 Sum_probs=33.3
Q ss_pred Cceecccccc-ccCCHHHHHHHhcChhHHHHHHhhhhc
Q 041577 153 KEWSCALCQV-SAPTERGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 153 ~~~~C~lC~v-~~~s~~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
..+.|++|+. .++++.+++.|++|++|+++++.++..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 4678999998 899999999999999999999988643
No 15
>PF14968 CCDC84: Coiled coil protein 84
Probab=95.92 E-value=0.0041 Score=58.11 Aligned_cols=38 Identities=21% Similarity=0.459 Sum_probs=31.1
Q ss_pred CCceeccccccccCCH------HHHHHHhcChhHHHHHHhhhhc
Q 041577 152 PKEWSCALCQVSAPTE------RGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~------~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
...|||-.|...+.-- ..+..||.+..|++++++.-.+
T Consensus 56 ~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~ 99 (336)
T PF14968_consen 56 RNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFWWK 99 (336)
T ss_pred cceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHHHH
Confidence 4589999998777644 4789999999999999987443
No 16
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=95.76 E-value=0.0064 Score=58.79 Aligned_cols=36 Identities=33% Similarity=0.576 Sum_probs=33.7
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhhhhc
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
.+||-+|+.+|-|+.+|..|.+.++|+.+|+.|+..
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 499999999999999999999999999999998744
No 17
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=95.62 E-value=0.0075 Score=48.61 Aligned_cols=36 Identities=22% Similarity=0.421 Sum_probs=34.1
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHhhhh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLR 188 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~ 188 (237)
..|||-.|-..|-++..|..|++++.|+++|+.|+.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 489999999999999999999999999999999974
No 18
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=95.44 E-value=0.0084 Score=41.05 Aligned_cols=30 Identities=27% Similarity=0.412 Sum_probs=25.7
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHH
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVA 184 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~ 184 (237)
++.-||+.|.+.|. .|+.|+.+++|+.-..
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLLSEKHRRFAE 32 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhccHHHHHHHc
Confidence 35678999999998 7999999999998654
No 19
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.40 E-value=0.031 Score=49.75 Aligned_cols=37 Identities=22% Similarity=0.463 Sum_probs=33.7
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhhhhc
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
...+.|-||++-.- +..+..|.+|++|+..+..|+-.
T Consensus 33 sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~ 69 (264)
T KOG3032|consen 33 SGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSR 69 (264)
T ss_pred CCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhh
Confidence 34789999999999 99999999999999999999843
No 20
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.09 E-value=0.015 Score=50.38 Aligned_cols=41 Identities=24% Similarity=0.447 Sum_probs=34.9
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhhhhccCC
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRDKKR 192 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~k 192 (237)
...|-|.||.-.-+++..|..|.+|+||+.+|..-.+...+
T Consensus 51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~e~k 91 (222)
T KOG0227|consen 51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAKEAK 91 (222)
T ss_pred CcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHHHhh
Confidence 34799999999999999999999999999998776544433
No 21
>PLN02748 tRNA dimethylallyltransferase
Probab=95.01 E-value=0.019 Score=55.95 Aligned_cols=36 Identities=19% Similarity=0.489 Sum_probs=32.3
Q ss_pred Cceecccccc-ccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQV-SATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~V-s~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
...+|++|+. ++.++.+-+.|+.||+|+++++.++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 4557999998 89999999999999999999987764
No 22
>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=95.00 E-value=0.02 Score=39.21 Aligned_cols=29 Identities=34% Similarity=0.567 Sum_probs=25.1
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHH
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKV 183 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~ 183 (237)
++.-||+.|.+.+. .|+.|+.+.+|+.-.
T Consensus 3 ~k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 3 KKPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 34668999999998 599999999999865
No 23
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.98 E-value=0.019 Score=31.80 Aligned_cols=21 Identities=24% Similarity=0.692 Sum_probs=17.7
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
|.|.+|+..|.+...|..|+.
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 24
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=94.97 E-value=0.014 Score=40.03 Aligned_cols=29 Identities=31% Similarity=0.482 Sum_probs=24.8
Q ss_pred CCceeccccccccCCHHHHHHHhcChhhHHHH
Q 041577 32 SKEWSCVLCQVSATTERDLDVHLQGKKHKAKE 63 (237)
Q Consensus 32 ~~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~ 63 (237)
++..||++|.+.|. +|..|+.+++|++=.
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 34679999999996 789999999999753
No 25
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=94.77 E-value=0.02 Score=46.24 Aligned_cols=36 Identities=28% Similarity=0.525 Sum_probs=34.0
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
..+||-.|.--|-++..|..|+.++.|+++++.|+.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 578999999999999999999999999999999874
No 26
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=94.60 E-value=0.028 Score=38.47 Aligned_cols=29 Identities=34% Similarity=0.559 Sum_probs=25.0
Q ss_pred CCceeccccccccCCHHHHHHHhcChhhHHHH
Q 041577 32 SKEWSCVLCQVSATTERDLDVHLQGKKHKAKE 63 (237)
Q Consensus 32 ~~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~ 63 (237)
++..||+.|.+.|. +|..|+.+.+|+.=.
T Consensus 3 ~k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 3 KKPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 45679999999997 589999999999754
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=94.48 E-value=0.028 Score=31.48 Aligned_cols=22 Identities=23% Similarity=0.682 Sum_probs=20.1
Q ss_pred eeccccccccCCHHHHHHHhcC
Q 041577 155 WSCALCQVSAPTERGLDEHLQG 176 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~G 176 (237)
|.|.+|+..|.+...|..|++-
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 6799999999999999999863
No 28
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.23 E-value=0.031 Score=54.18 Aligned_cols=35 Identities=37% Similarity=0.562 Sum_probs=32.8
Q ss_pred ceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 34 EWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 34 ~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
.+||-||+-+|-|+.++..|.+.++|+.+|+.|+.
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 49999999999999999999999999999998863
No 29
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=93.78 E-value=0.036 Score=46.84 Aligned_cols=33 Identities=27% Similarity=0.404 Sum_probs=28.5
Q ss_pred ceeccccccccC--CHHHHHHHhcChhhHHHHHHH
Q 041577 34 EWSCVLCQVSAT--TERDLDVHLQGKKHKAKEKLL 66 (237)
Q Consensus 34 ~~~C~vC~Vs~t--Se~~l~~Hl~GkKHk~k~~~l 66 (237)
.+||+.|++-.| |.++-..|+.|+||+.+++..
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 579999996655 889999999999999998753
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=93.65 E-value=0.058 Score=31.36 Aligned_cols=23 Identities=22% Similarity=0.468 Sum_probs=20.7
Q ss_pred ceeccccccccCCHHHHHHHhcC
Q 041577 154 EWSCALCQVSAPTERGLDEHLQG 176 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~G 176 (237)
.+.|.+|+..|.+...|..|++-
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 37899999999999999999953
No 31
>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=93.44 E-value=0.062 Score=29.58 Aligned_cols=21 Identities=24% Similarity=0.675 Sum_probs=17.4
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
|.|++|+..|.+...|..|+.
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 679999999999999999974
No 32
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=92.96 E-value=0.068 Score=45.17 Aligned_cols=32 Identities=28% Similarity=0.495 Sum_probs=27.1
Q ss_pred ceeccccccccC--CHHHHHHHhcChhHHHHHHh
Q 041577 154 EWSCALCQVSAP--TERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 154 ~~~C~lC~v~~~--s~~~l~~Hl~GkkH~~~~~~ 185 (237)
.|||+.|++..| |.+.-..|+.|++|+++++.
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 589999996554 66789999999999999764
No 33
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=92.89 E-value=0.061 Score=51.85 Aligned_cols=34 Identities=38% Similarity=0.645 Sum_probs=31.5
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhhh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLL 187 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~ 187 (237)
.-.|.+|||...|+.-|-+|..|++|+..|..+-
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 5589999999999999999999999999998864
No 34
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=92.11 E-value=0.12 Score=44.93 Aligned_cols=36 Identities=28% Similarity=0.429 Sum_probs=32.2
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
..+-|.+|.-.-+++..+..|.+|+||+.+++...+
T Consensus 52 G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa 87 (222)
T KOG0227|consen 52 GKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAA 87 (222)
T ss_pred cceeehhhhhhhcchhhhhhhhccchhhHHHHHHHH
Confidence 577899999999999999999999999999875543
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=92.01 E-value=0.13 Score=29.78 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=19.5
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+.|++|+.+|.+...|..|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 579999999999999999984
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=91.17 E-value=0.17 Score=27.97 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=19.4
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
+.|..|...|++...|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 469999999999999999987
No 37
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.07 E-value=0.24 Score=44.27 Aligned_cols=41 Identities=29% Similarity=0.494 Sum_probs=35.8
Q ss_pred CCCCCCCceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 27 TSSNKSKEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 27 ~~~kk~~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
........+.|-||+|-.- +.....|..|++|+.++..|+.
T Consensus 28 akyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs 68 (264)
T KOG3032|consen 28 AKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKS 68 (264)
T ss_pred hccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHh
Confidence 3344457899999999998 9999999999999999999984
No 38
>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=90.89 E-value=0.17 Score=28.15 Aligned_cols=21 Identities=24% Similarity=0.705 Sum_probs=19.3
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+.|.+|+..|.+...|..|..
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 579999999999999999975
No 39
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=90.53 E-value=0.16 Score=40.26 Aligned_cols=37 Identities=30% Similarity=0.404 Sum_probs=34.5
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHhhhhc
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
..+||--|...|-++..|..|..|+-|+++++.|++-
T Consensus 54 GqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 4799999999999999999999999999999999754
No 40
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=89.93 E-value=0.33 Score=38.56 Aligned_cols=36 Identities=36% Similarity=0.541 Sum_probs=33.9
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
..+||=-|.--|-++..|..|..|+-|+++++.|+.
T Consensus 54 GqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 678999999999999999999999999999998875
No 41
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=89.08 E-value=0.24 Score=45.89 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=28.0
Q ss_pred ceeccccccccC-CHHHHHHHhcChhhHHHHHHH
Q 041577 34 EWSCVLCQVSAT-TERDLDVHLQGKKHKAKEKLL 66 (237)
Q Consensus 34 ~~~C~vC~Vs~t-Se~~l~~Hl~GkKHk~k~~~l 66 (237)
..||++|+|.+- .......|-.|++|+.+|+..
T Consensus 10 kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 10 KKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred chhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 457999999884 667778999999999999764
No 42
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=88.77 E-value=0.21 Score=47.20 Aligned_cols=33 Identities=21% Similarity=0.452 Sum_probs=29.7
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~ 185 (237)
..+||..|+..|.-...++.|+.|++|.+..+.
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~ 269 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQG 269 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhh
Confidence 478999999999999999999999999987654
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.76 E-value=0.21 Score=36.77 Aligned_cols=32 Identities=22% Similarity=0.584 Sum_probs=26.7
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHH
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEK 64 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~ 64 (237)
..|.|.+|+..|.+...|..|+....|.....
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 46999999999999999999999999987643
No 44
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=88.10 E-value=0.25 Score=45.76 Aligned_cols=33 Identities=24% Similarity=0.463 Sum_probs=27.5
Q ss_pred CceeccccccccC-CHHHHHHHhcChhHHHHHHh
Q 041577 153 KEWSCALCQVSAP-TERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 153 ~~~~C~lC~v~~~-s~~~l~~Hl~GkkH~~~~~~ 185 (237)
...||++|+|.+- ....-..|-+|+||+.+|++
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 3678999999885 45688899999999999854
No 45
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=88.09 E-value=0.47 Score=41.08 Aligned_cols=35 Identities=29% Similarity=0.530 Sum_probs=31.6
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhh
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGL 186 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~ 186 (237)
...|-|.||+-.--++..+..|+.|+||..++..-
T Consensus 51 ~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 51 TGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred CCcEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 35899999999999999999999999999987654
No 46
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=87.28 E-value=0.52 Score=40.81 Aligned_cols=36 Identities=31% Similarity=0.544 Sum_probs=32.6
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
..+.|-+|+-.--++..+..|..|+||+.++....+
T Consensus 52 Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~ 87 (222)
T COG5246 52 GKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSE 87 (222)
T ss_pred CcEEeeeeccccccHHHHHHhhccchhhhhHHHHHH
Confidence 678999999999999999999999999999876644
No 47
>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=86.69 E-value=0.6 Score=39.56 Aligned_cols=32 Identities=22% Similarity=0.651 Sum_probs=29.5
Q ss_pred eeccccccccCCHHHHHHHhcChhHHHHHHhh
Q 041577 155 WSCALCQVSAPTERGLDEHLQGRKHKAKVAGL 186 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~ 186 (237)
|.|.+|..+.--+..|+.||.++=|+..++-+
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 67999999999999999999999999887665
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=86.44 E-value=0.52 Score=25.89 Aligned_cols=21 Identities=19% Similarity=0.501 Sum_probs=19.1
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+.|.+|..+|++...|..|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 359999999999999999986
No 49
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=86.03 E-value=0.39 Score=45.42 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=30.4
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHH
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLL 66 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l 66 (237)
...||.+|+--|....+|+.|+.|+.|.+.....
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~ 270 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGK 270 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhh
Confidence 4679999999999999999999999999887644
No 50
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=85.53 E-value=0.51 Score=45.69 Aligned_cols=35 Identities=31% Similarity=0.513 Sum_probs=30.6
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLR 67 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~ 67 (237)
..--|++|+|-..|+.-|-+|..|+||+..+..+-
T Consensus 492 rkkqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 492 RKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 34469999999999999999999999998887653
No 51
>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=84.81 E-value=0.28 Score=42.71 Aligned_cols=39 Identities=21% Similarity=0.418 Sum_probs=0.0
Q ss_pred Cceecccc-ccccCCHHHHHHHhcChhHHHHHHhhhhccC
Q 041577 153 KEWSCALC-QVSAPTERGLDEHLQGRKHKAKVAGLLRDKK 191 (237)
Q Consensus 153 ~~~~C~lC-~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~ 191 (237)
..|.|+|| |.++-....++.|++..||.--|+-|.-..-
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~nt 139 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIPNT 139 (196)
T ss_dssp ----------------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCCCc
Confidence 47899999 7777799999999999999999999876643
No 52
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=84.18 E-value=0.21 Score=45.58 Aligned_cols=39 Identities=21% Similarity=0.474 Sum_probs=34.8
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHhhhhccC
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRDKK 191 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~ 191 (237)
-.|||-+|+..|+.+..|..|+...-|++.+........
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~Np~ 62 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFALNPG 62 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHhCcc
Confidence 489999999999999999999999999999887765443
No 53
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=83.96 E-value=0.87 Score=25.66 Aligned_cols=20 Identities=30% Similarity=0.762 Sum_probs=16.1
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
|.|..|+-.++ +..|..|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 57999999998 999999986
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=82.37 E-value=1.8 Score=46.93 Aligned_cols=41 Identities=24% Similarity=0.423 Sum_probs=36.7
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHhhhhccCCC
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRDKKRC 193 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~k~ 193 (237)
..+.|..|++.++....|-.||+.-.|+.+++...+.....
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~ 557 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQ 557 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccc
Confidence 47899999999999999999999999999998887776643
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=81.59 E-value=0.79 Score=49.60 Aligned_cols=33 Identities=24% Similarity=0.495 Sum_probs=28.0
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGL 186 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~ 186 (237)
.++|.+|+|.+.++..|+.|++..-|+.+..--
T Consensus 1328 ~~~c~~c~~~~~~~~alqihm~~~~~~~kt~~~ 1360 (1406)
T KOG1146|consen 1328 TYHCLACEVLLSGREALQIHMRSSAHRRKTAPP 1360 (1406)
T ss_pred cccchHHHhhcchhHHHHHHHHHhhhcccCCCC
Confidence 445999999999999999999999888765443
No 56
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=80.89 E-value=1.5 Score=37.17 Aligned_cols=33 Identities=27% Similarity=0.683 Sum_probs=30.7
Q ss_pred eeccccccccCCHHHHHHHhcChhhHHHHHHHh
Q 041577 35 WSCVLCQVSATTERDLDVHLQGKKHKAKEKLLR 67 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~ 67 (237)
++|++|+.+.--+..++.||.++=|+..++.+.
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 479999999999999999999999999998874
No 57
>PTZ00448 hypothetical protein; Provisional
Probab=79.27 E-value=1.6 Score=41.52 Aligned_cols=34 Identities=12% Similarity=0.226 Sum_probs=31.4
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhhh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLL 187 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~ 187 (237)
.|.|..|++.|.+......|++.-+|+=+|+..-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 6889999999999999999999999999998753
No 58
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=77.58 E-value=0.82 Score=38.81 Aligned_cols=32 Identities=19% Similarity=0.248 Sum_probs=26.5
Q ss_pred ceeccccccccCC--HHHHHHHhcChhHHHHHHh
Q 041577 154 EWSCALCQVSAPT--ERGLDEHLQGRKHKAKVAG 185 (237)
Q Consensus 154 ~~~C~lC~v~~~s--~~~l~~Hl~GkkH~~~~~~ 185 (237)
.|+|+.|++..+. .+.-.+|+-|++|..+.+.
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~d 36 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKD 36 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHH
Confidence 5899999998875 4578899999999887644
No 59
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=77.53 E-value=0.56 Score=42.87 Aligned_cols=36 Identities=22% Similarity=0.493 Sum_probs=33.2
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
-.|||..||-.|..+..|..|++---|++.+.....
T Consensus 24 lRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 24 LRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 589999999999999999999999999999886654
No 60
>PTZ00448 hypothetical protein; Provisional
Probab=73.09 E-value=2.8 Score=39.86 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=30.8
Q ss_pred ceeccccccccCCHHHHHHHhcChhhHHHHHHHh
Q 041577 34 EWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLR 67 (237)
Q Consensus 34 ~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~ 67 (237)
.+.|..|+|.|.+......|+..-.|+-+++..-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 4679999999999999999999999999998643
No 61
>PHA00616 hypothetical protein
Probab=70.98 E-value=2.4 Score=28.36 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=19.5
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
+.|..|+..|...++|..|++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH
Confidence 679999999999999999993
No 62
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=70.79 E-value=3.3 Score=40.95 Aligned_cols=33 Identities=18% Similarity=0.350 Sum_probs=31.3
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHHH
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEKL 65 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~ 65 (237)
..|.|.+|++.|-+-+....||+--.|+-+++.
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Kr 97 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKR 97 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999999999999999875
No 63
>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=70.43 E-value=1.4 Score=38.43 Aligned_cols=36 Identities=22% Similarity=0.399 Sum_probs=0.0
Q ss_pred Cceecccc-ccccCCHHHHHHHhcChhhHHHHHHHhh
Q 041577 33 KEWSCVLC-QVSATTERDLDVHLQGKKHKAKEKLLRD 68 (237)
Q Consensus 33 ~~~~C~vC-~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~ 68 (237)
..+.|.|| +.++-+...|+.|+...+|.--++.|..
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI 136 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGI 136 (196)
T ss_dssp -------------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCC
Confidence 45699999 7788899999999999999999998875
No 64
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=68.30 E-value=1.5 Score=44.87 Aligned_cols=79 Identities=22% Similarity=0.228 Sum_probs=48.4
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhhhhccCCCCCCCCCCCCCCCCC-CCCCCchhhhhhhhhccccccccCc
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRDKKRCSNSIPSTSKKSTES-RDGVGQEMKTKIQEESVNQKVEGGL 232 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~k~~~~~~~~~~~~~~~-~~~~g~~~~~~~~~~~~q~~~~~~~ 232 (237)
..||.+|+++|+....+..||+|.||+.+--.-...-+--.+-+..+.+..+-+ .++.|..+=-..++..+..|.-+|.
T Consensus 193 L~~~kw~k~~a~G~qs~re~lr~~r~l~krvpt~~~~kgw~~el~cEksi~tcs~pd~~g~alRrv~ec~~skL~~k~G~ 272 (816)
T KOG3792|consen 193 LHYCKWCKISAAGPQTYREHLRGQKHLKKEVPTNGPLKGWPLELHCEKSIVTCSGPDAYGAALRRVKECKVSKLHKKLGK 272 (816)
T ss_pred hhhhHHHHHhccccHHHHHHHHHHHHHHhccCCCCCcccchHHHHHHHhhccccCccchHHHHHHHHHhhhhcccccCCC
Confidence 569999999999999999999999999875111111111223333334444422 2244455555666666666665554
No 65
>PF12907 zf-met2: Zinc-binding
Probab=68.23 E-value=2.7 Score=27.55 Aligned_cols=23 Identities=30% Similarity=0.634 Sum_probs=19.9
Q ss_pred eeccccc---cccCCHHHHHHHhcCh
Q 041577 35 WSCVLCQ---VSATTERDLDVHLQGK 57 (237)
Q Consensus 35 ~~C~vC~---Vs~tSe~~l~~Hl~Gk 57 (237)
+.|.||. +..+++.+|.+|+..|
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 4699999 8888999999998754
No 66
>PHA02768 hypothetical protein; Provisional
Probab=68.03 E-value=3.3 Score=29.02 Aligned_cols=25 Identities=20% Similarity=0.531 Sum_probs=22.0
Q ss_pred ceeccccccccCCHHHHHHHhcChhHH
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHK 180 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~ 180 (237)
.|.|+.|+..|+....|..|++- |.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cC
Confidence 57899999999999999999865 55
No 67
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=67.43 E-value=15 Score=28.26 Aligned_cols=28 Identities=21% Similarity=0.513 Sum_probs=23.5
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHH
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKA 61 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~ 61 (237)
+.|.|..|+..+.- ..+..||..+-|..
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHIL 37 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccc
Confidence 68999999988866 77889999887654
No 68
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=66.28 E-value=2.4 Score=36.06 Aligned_cols=32 Identities=25% Similarity=0.317 Sum_probs=27.1
Q ss_pred ceeccccccccC--CHHHHHHHhcChhhHHHHHH
Q 041577 34 EWSCVLCQVSAT--TERDLDVHLQGKKHKAKEKL 65 (237)
Q Consensus 34 ~~~C~vC~Vs~t--Se~~l~~Hl~GkKHk~k~~~ 65 (237)
.++|+.|++..+ +.+.-..|+.|++|....+.
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~d 36 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKD 36 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHH
Confidence 478999999887 66778899999999987764
No 69
>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=65.08 E-value=5.1 Score=23.58 Aligned_cols=20 Identities=25% Similarity=0.569 Sum_probs=17.4
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
..|.+|+..+ ++..++.||.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3599999999 7889999986
No 70
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=63.87 E-value=5.2 Score=27.81 Aligned_cols=23 Identities=26% Similarity=0.587 Sum_probs=16.4
Q ss_pred CceeccccccccCCHHHHHHHhc
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+-..|.+|...+.+...|..|+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHH
Confidence 67799999999999999999873
No 71
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=63.49 E-value=5 Score=27.88 Aligned_cols=23 Identities=26% Similarity=0.616 Sum_probs=16.7
Q ss_pred CceeccccccccCCHHHHHHHhc
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
..-.|.+|...+.+..+|..||.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHH
Confidence 36789999999999999999984
No 72
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=60.63 E-value=5.5 Score=35.72 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=23.8
Q ss_pred CCceeccccccccCCHHHHHHHhcCh
Q 041577 32 SKEWSCVLCQVSATTERDLDVHLQGK 57 (237)
Q Consensus 32 ~~~~~C~vC~Vs~tSe~~l~~Hl~Gk 57 (237)
...|||=+|.+.|.++.+|..|.=|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCCC
Confidence 36899999999999999999999874
No 73
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=55.55 E-value=6.8 Score=35.90 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=22.8
Q ss_pred CceeccccccccCCHHHHHHHhcCh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGR 177 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~Gk 177 (237)
+.|.|..|+..|-..++|.+||+--
T Consensus 214 KPF~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 214 KPFSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred CCccCCcccchhcchHHHHHHHHhh
Confidence 4799999999999999999999854
No 74
>PHA00732 hypothetical protein
Probab=55.50 E-value=9 Score=28.47 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=20.1
Q ss_pred eeccccccccCCHHHHHHHhcC
Q 041577 155 WSCALCQVSAPTERGLDEHLQG 176 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~G 176 (237)
+.|.+|...|++...|..|+..
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 6799999999999999999873
No 75
>PF12907 zf-met2: Zinc-binding
Probab=54.16 E-value=6.3 Score=25.84 Aligned_cols=23 Identities=26% Similarity=0.663 Sum_probs=19.9
Q ss_pred eeccccc---cccCCHHHHHHHhcCh
Q 041577 155 WSCALCQ---VSAPTERGLDEHLQGR 177 (237)
Q Consensus 155 ~~C~lC~---v~~~s~~~l~~Hl~Gk 177 (237)
+.|.||. ....++.+|..|...|
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 5699999 7888999999998765
No 76
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=52.70 E-value=5.2 Score=41.79 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=26.1
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHH
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKV 183 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~ 183 (237)
+.|.|.||+..|+....|..|+.+.|-+--+
T Consensus 632 RPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 632 RPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred CccccccccchhccccchhhcccccccCccc
Confidence 4799999999999999999999997644333
No 77
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=52.04 E-value=9.1 Score=36.57 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=16.5
Q ss_pred CceeccccccccCCHHHHHHHh
Q 041577 33 KEWSCVLCQVSATTERDLDVHL 54 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl 54 (237)
+.+-|..|...|..+..|.+|.
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHH
Confidence 4566888888888888877775
No 78
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=50.85 E-value=13 Score=36.95 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=31.4
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHHHHHhh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGL 186 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~ 186 (237)
..|.|..|++.|-+......|++.-.|+-+++.-
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krk 98 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRK 98 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999999999998654
No 79
>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=50.78 E-value=9.2 Score=34.45 Aligned_cols=30 Identities=30% Similarity=0.533 Sum_probs=23.5
Q ss_pred CCceecccccc---ccCCHHHHHHHhcChhhHH
Q 041577 32 SKEWSCVLCQV---SATTERDLDVHLQGKKHKA 61 (237)
Q Consensus 32 ~~~~~C~vC~V---s~tSe~~l~~Hl~GkKHk~ 61 (237)
++.-.|+||.. ..-+..-+.+|+.||.|.-
T Consensus 188 qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 188 QKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cCccchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 45678999983 3346677999999999974
No 80
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=48.17 E-value=11 Score=34.32 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=21.9
Q ss_pred CceeccccccccCCHHHHHHHhcCh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGR 177 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~Gk 177 (237)
..-||..||..|..+..|.+|...+
T Consensus 9 ~kpwcwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred CCceeeecccccchhhhhhhhhhhc
Confidence 3668999999999999999998765
No 81
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=45.18 E-value=6.8 Score=37.73 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=24.8
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHH
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVA 184 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~ 184 (237)
...-||+-|.+.+- .|++|+.|.+|+.-.+
T Consensus 420 tk~GYCENCreky~---~lE~Hi~s~~HrrFAE 449 (468)
T COG5067 420 TKKGYCENCREKYE---SLEQHIVSEKHRRFAE 449 (468)
T ss_pred cccchhHHHHHHHH---HHHHHhhhhhhhhhhh
Confidence 34579999999875 7999999999997644
No 82
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=44.89 E-value=17 Score=20.98 Aligned_cols=20 Identities=20% Similarity=0.501 Sum_probs=15.8
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 155 WSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 155 ~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
..|.+|+-.| ....|+.|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4699999999 5677887753
No 83
>PF14968 CCDC84: Coiled coil protein 84
Probab=43.90 E-value=19 Score=34.03 Aligned_cols=37 Identities=22% Similarity=0.550 Sum_probs=29.3
Q ss_pred CCCCCceeccccccccCCH------HHHHHHhcChhhHHHHHHH
Q 041577 29 SNKSKEWSCVLCQVSATTE------RDLDVHLQGKKHKAKEKLL 66 (237)
Q Consensus 29 ~kk~~~~~C~vC~Vs~tSe------~~l~~Hl~GkKHk~k~~~l 66 (237)
......| |-+|.+...-- ..+..||.+..|+++++++
T Consensus 54 ~~~~~fW-C~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F 96 (336)
T PF14968_consen 54 EHRNRFW-CVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKF 96 (336)
T ss_pred cccceeE-eeCccchhhhccchhhhccHHhhcCCHHHHHHHHHH
Confidence 3444666 99998877544 4678999999999999986
No 84
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=42.52 E-value=21 Score=34.18 Aligned_cols=35 Identities=14% Similarity=0.334 Sum_probs=31.7
Q ss_pred ceeccccccccCCHHHHHHHhcChhHHHHHHhhhh
Q 041577 154 EWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLR 188 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~ 188 (237)
.|-|.-|+|.|.+...-..|+..-+|+=+|+..-+
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA 37 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVA 37 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhh
Confidence 58899999999999999999999999999986543
No 85
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=42.36 E-value=13 Score=33.08 Aligned_cols=35 Identities=23% Similarity=0.522 Sum_probs=27.9
Q ss_pred CceeccccccccCCHHHHHHHhc---ChhHHHHHHhhh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQ---GRKHKAKVAGLL 187 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~---GkkH~~~~~~~~ 187 (237)
..|.|++|+..||-.-.|++||+ |..|+-..++.+
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 47999999999999999999986 666665555444
No 86
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=38.75 E-value=32 Score=30.68 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=21.1
Q ss_pred CCceeccccccccCCHHHHHHHhcC
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQG 176 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~G 176 (237)
.+.|.|+-|..+-.....|..|+.-
T Consensus 210 ~kl~vcedcg~t~~~~e~~~~h~~~ 234 (267)
T KOG3576|consen 210 AKLYVCEDCGYTSERPEVYYLHLKL 234 (267)
T ss_pred hheeeecccCCCCCChhHHHHHHHh
Confidence 3578999999988888899999864
No 87
>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=38.22 E-value=34 Score=30.21 Aligned_cols=38 Identities=24% Similarity=0.487 Sum_probs=29.9
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhhhhcc
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRDK 190 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~ 190 (237)
...|.|.+|...|-...-..-||. .||...|+.++.+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 348999999999999999999998 57999999886543
No 88
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=36.46 E-value=13 Score=35.31 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=28.0
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHH
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAK 182 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~ 182 (237)
...+.|-.|.+.|.....|..||+-|+|++.
T Consensus 193 L~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 193 LERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred HhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 3478999999999999999999999999863
No 89
>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=36.43 E-value=19 Score=32.38 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=22.8
Q ss_pred CCceecccccccc---CCHHHHHHHhcChhHHH
Q 041577 152 PKEWSCALCQVSA---PTERGLDEHLQGRKHKA 181 (237)
Q Consensus 152 ~~~~~C~lC~v~~---~s~~~l~~Hl~GkkH~~ 181 (237)
...-.|+||.... -+..-|..|+.||-|.-
T Consensus 188 qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 188 QKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cCccchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 4467899998433 44557999999999964
No 90
>PHA02768 hypothetical protein; Provisional
Probab=36.29 E-value=22 Score=24.88 Aligned_cols=21 Identities=19% Similarity=0.556 Sum_probs=18.7
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+.|+.|+-.|+..+.|..|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r 26 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLR 26 (55)
T ss_pred cCcchhCCeeccHHHHHHHHH
Confidence 469999999999999988874
No 91
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=33.86 E-value=23 Score=34.19 Aligned_cols=29 Identities=24% Similarity=0.441 Sum_probs=24.8
Q ss_pred CceeccccccccCCHHHHHHHhcChhhHHHHH
Q 041577 33 KEWSCVLCQVSATTERDLDVHLQGKKHKAKEK 64 (237)
Q Consensus 33 ~~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~ 64 (237)
...||+-|.+.+ ..|+.|+.|.+|++=.+
T Consensus 421 k~GYCENCreky---~~lE~Hi~s~~HrrFAE 449 (468)
T COG5067 421 KKGYCENCREKY---ESLEQHIVSEKHRRFAE 449 (468)
T ss_pred ccchhHHHHHHH---HHHHHHhhhhhhhhhhh
Confidence 568999999998 46899999999998644
No 92
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=33.38 E-value=25 Score=31.59 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=23.7
Q ss_pred CceeccccccccCCHHHHHHHhcChh
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRK 178 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~Gkk 178 (237)
..|||-.|.+.+.+..+|..|.=|..
T Consensus 238 eh~YC~fCG~~y~~~edl~ehCPGvn 263 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHCPGVN 263 (268)
T ss_pred cceEEEEeccccCCHHHHHHhCCCCC
Confidence 48999999999999999999998863
No 93
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=32.07 E-value=26 Score=34.20 Aligned_cols=82 Identities=18% Similarity=0.304 Sum_probs=0.0
Q ss_pred ceeccccccccCCHHHHHHHhcChhhHHHHHHHhhhhhccCCCCcccccccccccccCCCCcchhhhhcccccccccccc
Q 041577 34 EWSCVLCQVSATTERDLDVHLQGKKHKAKEKLLRDLKMCINSTSKKATESRDSADQEMKPNVEDESVKANKTVVGLDQKL 113 (237)
Q Consensus 34 ~~~C~vC~Vs~tSe~~l~~Hl~GkKHk~k~~~l~~~k~~~~p~s~k~~~~~~~~~~e~~~~~~~~~~q~~~~~~~~~~~~ 113 (237)
++.|.-|..-|+....|.+|- |+|+-+-++-++ .....+..-...++.-++...+.|+.+-|
T Consensus 295 EYrCPEC~KVFsCPANLASHR--RWHKPR~eaa~a----------------~~~P~k~~~~~rae~~ea~rsg~dss~gi 356 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHR--RWHKPRPEAAKA----------------GSPPPKQAVETRAEVQEAERSGDDSSSGI 356 (500)
T ss_pred eecCCcccccccCchhhhhhh--cccCCchhhhhc----------------CCCChhhhhhhhhhhhhccccCCcccCce
Q ss_pred cCCcccccCCCCCCCCCCCccCCCCCCCCCCCccCCCCCCceeccccccccCCHHHHHHHh
Q 041577 114 EGGQTLQVKPNSNPCGSDQKTATPPAGSGELPLTNSNKPKEWSCALCQVSAPTERGLDEHL 174 (237)
Q Consensus 114 ~g~~~~Q~kp~~n~~g~~~k~~~~~~~~ge~~~~~~k~~~~~~C~lC~v~~~s~~~l~~Hl 174 (237)
|.|.+|...|.-+.-|.-|+
T Consensus 357 -----------------------------------------~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 357 -----------------------------------------FSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred -----------------------------------------eecHHhhhhhHHHHHHHHhH
No 94
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.03 E-value=19 Score=35.27 Aligned_cols=40 Identities=18% Similarity=0.375 Sum_probs=33.2
Q ss_pred Cceeccccc-cccCCHHHHHHHhcChhHHHHHHhhhhccCC
Q 041577 153 KEWSCALCQ-VSAPTERGLDEHLQGRKHKAKVAGLLRDKKR 192 (237)
Q Consensus 153 ~~~~C~lC~-v~~~s~~~l~~Hl~GkkH~~~~~~~~~~~~k 192 (237)
..|.|+||. -+......++.|++-.||.--++=|..+.-+
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIpnt~ 440 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIPNTS 440 (497)
T ss_pred cccceeeccCccccCcHHHHHHhHHHHHhhcceecCCCCcH
Confidence 467999996 9999999999999999999877766544443
No 95
>PHA00733 hypothetical protein
Probab=28.95 E-value=44 Score=26.86 Aligned_cols=23 Identities=22% Similarity=0.654 Sum_probs=18.9
Q ss_pred CceeccccccccCCHHHHHHHhc
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
..|.|..|...|.+...|..|+.
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHh
Confidence 46788888888888888888876
No 96
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=28.26 E-value=23 Score=31.25 Aligned_cols=37 Identities=14% Similarity=0.394 Sum_probs=27.1
Q ss_pred CCceeccccccccCCHHHHHHHhcChhHHHHHHhhhhc
Q 041577 152 PKEWSCALCQVSAPTERGLDEHLQGRKHKAKVAGLLRD 189 (237)
Q Consensus 152 ~~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~~~~~~~~~ 189 (237)
...+||++|++.+-. +-...|+..--|+-.++.+-+.
T Consensus 82 e~lfyCE~Cd~~ip~-~~~snH~tSttHllsl~~~pa~ 118 (223)
T KOG2384|consen 82 EALFYCEVCDIYIPN-SKKSNHFTSTTHLLSLQHIPAN 118 (223)
T ss_pred CccchhhhhhhhccC-CCCccchhhHHHHhhhccCCCC
Confidence 458999999998753 2334588888888888777533
No 97
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=27.68 E-value=26 Score=32.78 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=24.8
Q ss_pred CCCceecccccccc---CCHHHHHHHhcChhhHHH
Q 041577 31 KSKEWSCVLCQVSA---TTERDLDVHLQGKKHKAK 62 (237)
Q Consensus 31 k~~~~~C~vC~Vs~---tSe~~l~~Hl~GkKHk~k 62 (237)
-++.-.|+||..-. -...=+..||.||-|.--
T Consensus 183 ~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy 217 (319)
T KOG0796|consen 183 QQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGY 217 (319)
T ss_pred hhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHH
Confidence 34577899997544 377889999999999743
No 98
>PHA00732 hypothetical protein
Probab=26.87 E-value=45 Score=24.69 Aligned_cols=21 Identities=24% Similarity=0.547 Sum_probs=18.9
Q ss_pred eeccccccccCCHHHHHHHhc
Q 041577 35 WSCVLCQVSATTERDLDVHLQ 55 (237)
Q Consensus 35 ~~C~vC~Vs~tSe~~l~~Hl~ 55 (237)
+.|.+|.-+|++...|..|..
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 459999999999999999975
No 99
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=24.94 E-value=50 Score=25.33 Aligned_cols=28 Identities=25% Similarity=0.523 Sum_probs=23.6
Q ss_pred CceeccccccccCCHHHHHHHhcChhHHH
Q 041577 153 KEWSCALCQVSAPTERGLDEHLQGRKHKA 181 (237)
Q Consensus 153 ~~~~C~lC~v~~~s~~~l~~Hl~GkkH~~ 181 (237)
..|.|..|+..+.- +.+..||+.+-|..
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHIL 37 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccc
Confidence 47999999988876 99999999876654
No 100
>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=24.65 E-value=43 Score=19.22 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=11.0
Q ss_pred CceeccccccccC
Q 041577 153 KEWSCALCQVSAP 165 (237)
Q Consensus 153 ~~~~C~lC~v~~~ 165 (237)
+.|.|.+|+..|.
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 4699999998875
No 101
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=23.74 E-value=1e+02 Score=27.86 Aligned_cols=39 Identities=13% Similarity=0.284 Sum_probs=29.4
Q ss_pred CCCceeccccccccC-CHHHHHHHhcChhhHHHHHHHhhh
Q 041577 31 KSKEWSCVLCQVSAT-TERDLDVHLQGKKHKAKEKLLRDL 69 (237)
Q Consensus 31 k~~~~~C~vC~Vs~t-Se~~l~~Hl~GkKHk~k~~~l~~~ 69 (237)
....+||.|=.-..| .+.+...|.+|+|-++.|+.....
T Consensus 76 ~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee~ 115 (244)
T PF05477_consen 76 NPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEEC 115 (244)
T ss_pred CCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHHH
Confidence 345666666554444 889999999999999999877653
No 102
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=23.38 E-value=63 Score=21.69 Aligned_cols=22 Identities=27% Similarity=0.590 Sum_probs=16.8
Q ss_pred ceeccccccccCCHHHHHHHhcC
Q 041577 154 EWSCALCQVSAPTERGLDEHLQG 176 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~G 176 (237)
.|.|..|+. -.++..|..|+.-
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 477888888 5668888888753
No 103
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.16 E-value=41 Score=23.88 Aligned_cols=22 Identities=14% Similarity=0.317 Sum_probs=20.5
Q ss_pred ceeccccccccCCHHHHHHHhc
Q 041577 154 EWSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
.+.|..|...|....+|..|.+
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhh
Confidence 6899999999999999999976
No 104
>PHA00733 hypothetical protein
Probab=20.30 E-value=71 Score=25.67 Aligned_cols=22 Identities=14% Similarity=0.281 Sum_probs=19.8
Q ss_pred ceeccccccccCCHHHHHHHhc
Q 041577 154 EWSCALCQVSAPTERGLDEHLQ 175 (237)
Q Consensus 154 ~~~C~lC~v~~~s~~~l~~Hl~ 175 (237)
.+.|.+|...|.....|..|+.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHH
Confidence 4899999999999999998864
Done!