Query 007901
Match_columns 585
No_of_seqs 200 out of 330
Neff 3.0
Searched_HMMs 46136
Date Thu Mar 28 16:51:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00451 ZnF_U1 U1-like zinc 98.5 6.3E-08 1.4E-12 68.2 3.3 32 335-366 3-34 (35)
2 PF12874 zf-met: Zinc-finger o 98.4 2.1E-07 4.6E-12 61.7 2.2 25 336-360 1-25 (25)
3 smart00451 ZnF_U1 U1-like zinc 98.4 2.1E-07 4.6E-12 65.5 2.2 33 183-215 3-35 (35)
4 PF12874 zf-met: Zinc-finger o 98.1 1.7E-06 3.7E-11 57.3 1.6 25 184-208 1-25 (25)
5 PF12171 zf-C2H2_jaz: Zinc-fin 98.0 1.8E-06 4E-11 59.0 1.3 27 335-361 1-27 (27)
6 PF12171 zf-C2H2_jaz: Zinc-fin 97.7 1.7E-05 3.8E-10 54.2 1.1 26 184-209 2-27 (27)
7 KOG4727 U1-like Zn-finger prot 97.2 0.0002 4.4E-09 69.7 3.1 36 332-367 72-107 (193)
8 PF06220 zf-U1: U1 zinc finger 97.1 0.00051 1.1E-08 51.6 3.0 33 183-215 3-37 (38)
9 PF06220 zf-U1: U1 zinc finger 96.9 0.00052 1.1E-08 51.6 2.2 33 335-367 3-37 (38)
10 KOG3792 Transcription factor N 96.6 0.0014 3.1E-08 74.2 3.7 41 171-212 182-222 (816)
11 KOG3408 U1-like Zn-finger-cont 96.5 0.0016 3.4E-08 60.6 2.3 38 332-369 54-91 (129)
12 KOG4727 U1-like Zn-finger prot 96.3 0.0025 5.4E-08 62.3 2.6 36 181-216 73-108 (193)
13 KOG0150 Spliceosomal protein F 96.2 0.0023 4.9E-08 67.0 1.6 38 177-214 4-42 (336)
14 KOG3032 Uncharacterized conser 96.0 0.01 2.3E-07 60.3 5.3 59 333-392 33-93 (264)
15 PLN02748 tRNA dimethylallyltra 95.8 0.0047 1E-07 67.4 2.3 36 334-369 417-453 (468)
16 KOG3408 U1-like Zn-finger-cont 94.9 0.013 2.8E-07 54.7 1.8 40 179-218 53-92 (129)
17 KOG3454 U1 snRNP-specific prot 94.8 0.016 3.4E-07 56.2 2.1 34 183-216 3-38 (165)
18 KOG0717 Molecular chaperone (D 94.8 0.017 3.7E-07 63.4 2.5 37 335-371 292-328 (508)
19 KOG0717 Molecular chaperone (D 94.4 0.02 4.3E-07 62.9 1.9 34 184-217 293-326 (508)
20 KOG0227 Splicing factor 3a, su 93.9 0.032 7E-07 55.7 2.0 35 333-367 51-85 (222)
21 PF14968 CCDC84: Coiled coil p 93.5 0.045 9.7E-07 58.0 2.5 31 185-218 1-31 (336)
22 PLN02748 tRNA dimethylallyltra 93.5 0.051 1.1E-06 59.5 3.0 37 182-218 417-454 (468)
23 KOG2785 C2H2-type Zn-finger pr 93.5 0.046 1E-06 58.8 2.5 36 334-369 67-102 (390)
24 PF05918 API5: Apoptosis inhib 93.5 0.022 4.7E-07 63.7 0.0 12 114-125 514-525 (556)
25 COG5188 PRP9 Splicing factor 3 92.9 0.041 9E-07 59.0 1.1 36 182-217 237-272 (470)
26 COG5112 UFD2 U1-like Zn-finger 92.6 0.082 1.8E-06 48.8 2.4 39 332-370 52-90 (126)
27 PF13894 zf-C2H2_4: C2H2-type 92.3 0.1 2.2E-06 33.0 1.9 21 336-356 1-21 (24)
28 KOG3454 U1 snRNP-specific prot 92.2 0.072 1.6E-06 51.8 1.7 33 335-367 3-37 (165)
29 PF12756 zf-C2H2_2: C2H2 type 91.9 0.083 1.8E-06 43.2 1.5 31 335-365 50-80 (100)
30 COG5112 UFD2 U1-like Zn-finger 91.0 0.18 4E-06 46.6 2.8 46 173-218 45-90 (126)
31 COG5246 PRP11 Splicing factor 90.7 0.17 3.6E-06 50.5 2.4 37 333-369 51-87 (222)
32 smart00586 ZnF_DBF Zinc finger 90.7 0.12 2.6E-06 41.4 1.2 30 181-213 3-32 (49)
33 KOG3032 Uncharacterized conser 90.4 0.35 7.7E-06 49.6 4.5 39 179-218 31-69 (264)
34 PF00096 zf-C2H2: Zinc finger, 90.1 0.24 5.1E-06 32.1 2.0 22 336-357 1-22 (23)
35 smart00586 ZnF_DBF Zinc finger 90.0 0.13 2.7E-06 41.3 0.8 30 335-367 5-34 (49)
36 PF07535 zf-DBF: DBF zinc fing 90.0 0.15 3.2E-06 40.8 1.2 29 335-366 5-33 (49)
37 KOG4722 Zn-finger protein [Gen 89.9 0.16 3.4E-06 55.9 1.7 34 334-367 492-525 (672)
38 PF13912 zf-C2H2_6: C2H2-type 89.5 0.25 5.3E-06 33.2 1.8 21 336-356 2-22 (27)
39 KOG0227 Splicing factor 3a, su 89.3 0.2 4.3E-06 50.3 1.7 37 182-218 52-88 (222)
40 PF07535 zf-DBF: DBF zinc fing 88.7 0.27 5.9E-06 39.3 1.8 29 181-212 3-31 (49)
41 COG5188 PRP9 Splicing factor 3 88.5 0.21 4.5E-06 53.9 1.3 35 335-369 238-272 (470)
42 KOG0150 Spliceosomal protein F 87.6 0.29 6.2E-06 51.9 1.7 34 334-367 9-43 (336)
43 PF13912 zf-C2H2_6: C2H2-type 86.2 0.49 1.1E-05 31.8 1.7 20 184-203 2-21 (27)
44 KOG0921 Dosage compensation co 85.6 1 2.2E-05 53.7 4.8 33 118-150 1246-1278(1282)
45 PF05918 API5: Apoptosis inhib 85.1 0.27 5.8E-06 55.3 0.0 12 137-148 544-555 (556)
46 smart00355 ZnF_C2H2 zinc finge 85.1 0.51 1.1E-05 29.7 1.3 24 336-361 1-24 (26)
47 COG5246 PRP11 Splicing factor 84.6 0.68 1.5E-05 46.4 2.5 38 181-218 51-88 (222)
48 PF12756 zf-C2H2_2: C2H2 type 82.9 0.58 1.2E-05 38.3 1.0 32 182-213 49-80 (100)
49 PF13894 zf-C2H2_4: C2H2-type 82.5 0.94 2E-05 28.5 1.7 21 184-204 1-21 (24)
50 KOG4722 Zn-finger protein [Gen 80.0 1.2 2.6E-05 49.4 2.4 68 146-217 457-527 (672)
51 PF00096 zf-C2H2: Zinc finger, 78.4 1.4 3E-05 28.5 1.5 20 185-204 2-21 (23)
52 COG5136 U1 snRNP-specific prot 76.8 1 2.2E-05 44.3 0.8 34 183-216 3-38 (188)
53 smart00355 ZnF_C2H2 zinc finge 75.9 1.9 4.2E-05 27.0 1.6 20 185-204 2-21 (26)
54 COG5136 U1 snRNP-specific prot 75.5 0.9 1.9E-05 44.7 -0.0 31 335-365 3-35 (188)
55 KOG1146 Homeobox protein [Gene 74.9 4.9 0.00011 49.5 5.7 40 179-218 514-553 (1406)
56 KOG3973 Uncharacterized conser 74.9 2.3 4.9E-05 46.3 2.8 7 136-142 445-451 (465)
57 PF11931 DUF3449: Domain of un 74.6 0.98 2.1E-05 45.0 0.0 34 334-367 100-134 (196)
58 PTZ00448 hypothetical protein; 71.2 2.9 6.3E-05 45.4 2.5 38 334-371 313-350 (373)
59 KOG2785 C2H2-type Zn-finger pr 70.0 2.1 4.5E-05 46.6 1.2 37 181-217 66-102 (390)
60 PF13909 zf-H2C2_5: C2H2-type 66.3 4.5 9.7E-05 26.7 1.7 21 336-357 1-21 (24)
61 KOG2837 Protein containing a U 63.3 1.3 2.9E-05 46.5 -1.8 34 335-368 25-58 (309)
62 KOG3973 Uncharacterized conser 58.9 9.5 0.0002 41.8 3.5 27 126-153 431-458 (465)
63 KOG3792 Transcription factor N 57.2 4.2 9.2E-05 47.4 0.6 31 334-364 192-222 (816)
64 PF04988 AKAP95: A-kinase anch 55.8 7.6 0.00016 38.2 2.0 32 336-367 1-32 (165)
65 PTZ00034 40S ribosomal protein 53.0 8.5 0.00018 36.4 1.8 22 124-145 103-124 (124)
66 PF12764 Gly-rich_Ago1: Glycin 51.6 18 0.0004 33.4 3.6 8 142-149 23-30 (104)
67 PTZ00070 40S ribosomal protein 50.9 14 0.0003 38.7 3.0 11 137-147 17-27 (257)
68 PF14968 CCDC84: Coiled coil p 49.3 6.6 0.00014 42.1 0.5 28 337-367 1-28 (336)
69 PF12764 Gly-rich_Ago1: Glycin 47.3 29 0.00062 32.1 4.1 23 121-143 7-30 (104)
70 KOG2505 Ankyrin repeat protein 45.5 16 0.00034 41.6 2.7 72 334-405 65-146 (591)
71 KOG3293 Small nuclear ribonucl 44.9 19 0.00041 34.3 2.7 29 120-149 91-119 (134)
72 PF04988 AKAP95: A-kinase anch 43.4 21 0.00046 35.2 2.9 34 184-217 1-34 (165)
73 PF03194 LUC7: LUC7 N_terminus 42.5 11 0.00025 38.5 1.0 30 335-364 190-222 (254)
74 PF12907 zf-met2: Zinc-binding 42.3 14 0.0003 28.8 1.2 26 184-210 2-30 (40)
75 PRK11634 ATP-dependent RNA hel 41.1 26 0.00056 40.0 3.6 13 132-144 579-591 (629)
76 PF04959 ARS2: Arsenite-resist 40.7 25 0.00054 35.7 3.0 36 334-370 76-111 (214)
77 PHA02768 hypothetical protein; 38.2 17 0.00037 30.0 1.2 26 335-362 5-30 (55)
78 KOG3915 Transcription regulato 38.2 88 0.0019 35.8 6.9 20 198-217 206-227 (641)
79 PTZ00448 hypothetical protein; 37.8 24 0.00053 38.6 2.6 35 183-217 314-348 (373)
80 KOG2837 Protein containing a U 36.3 8.1 0.00018 40.9 -1.2 35 183-217 25-59 (309)
81 COG1512 Beta-propeller domains 35.4 33 0.00071 35.9 3.0 15 133-147 253-267 (271)
82 PHA00616 hypothetical protein 35.3 19 0.0004 28.7 0.9 23 336-360 2-24 (44)
83 KOG3915 Transcription regulato 33.4 44 0.00096 38.0 3.7 8 523-530 490-497 (641)
84 PF09237 GAGA: GAGA factor; I 32.3 40 0.00086 28.1 2.4 28 177-204 18-45 (54)
85 KOG0116 RasGAP SH3 binding pro 31.8 42 0.0009 37.2 3.2 7 107-113 339-345 (419)
86 KOG2505 Ankyrin repeat protein 31.3 38 0.00082 38.8 2.8 57 159-215 41-98 (591)
87 PF11931 DUF3449: Domain of un 30.8 17 0.00036 36.6 0.0 38 181-218 99-137 (196)
88 KOG0116 RasGAP SH3 binding pro 30.7 44 0.00095 37.0 3.2 9 105-113 341-349 (419)
89 PF12907 zf-met2: Zinc-binding 30.1 22 0.00048 27.7 0.6 26 336-362 2-30 (40)
90 KOG2893 Zn finger protein [Gen 30.1 31 0.00066 36.4 1.8 25 334-358 9-33 (341)
91 PHA00732 hypothetical protein 28.5 33 0.00071 29.6 1.4 21 336-356 2-22 (79)
92 COG4907 Predicted membrane pro 28.3 42 0.00092 38.2 2.6 17 124-140 571-587 (595)
93 KOG0796 Spliceosome subunit [R 26.9 32 0.00069 37.1 1.3 30 335-364 186-218 (319)
94 KOG2636 Splicing factor 3a, su 26.7 37 0.00081 38.2 1.8 38 181-218 247-284 (497)
95 KOG1074 Transcriptional repres 26.7 24 0.00052 42.3 0.4 28 333-360 631-658 (958)
96 KOG1596 Fibrillarin and relate 26.2 72 0.0016 34.0 3.6 10 354-363 191-200 (317)
97 PF03194 LUC7: LUC7 N_terminus 26.0 34 0.00073 35.1 1.3 30 181-210 188-220 (254)
98 KOG3623 Homeobox transcription 25.6 21 0.00046 42.3 -0.3 63 334-398 308-370 (1007)
99 KOG3576 Ovo and related transc 23.3 30 0.00065 35.8 0.3 35 334-368 172-209 (267)
100 KOG3262 H/ACA small nucleolar 23.0 72 0.0016 32.6 2.8 17 125-141 6-22 (215)
101 KOG1146 Homeobox protein [Gene 22.3 66 0.0014 40.5 2.8 41 331-371 514-554 (1406)
102 COG5200 LUC7 U1 snRNP componen 22.2 25 0.00053 36.4 -0.6 41 336-376 186-229 (258)
103 PF09237 GAGA: GAGA factor; I 22.0 51 0.0011 27.5 1.3 22 335-356 24-45 (54)
104 KOG4167 Predicted DNA-binding 21.9 75 0.0016 38.0 3.1 33 332-364 789-821 (907)
105 PHA00616 hypothetical protein 21.9 42 0.0009 26.7 0.8 20 184-203 2-21 (44)
106 PHA02768 hypothetical protein; 20.9 58 0.0012 27.0 1.4 21 184-204 6-26 (55)
107 PF13913 zf-C2HC_2: zinc-finge 20.8 60 0.0013 22.4 1.3 20 336-356 3-22 (25)
108 KOG2893 Zn finger protein [Gen 20.6 48 0.001 35.1 1.1 24 184-207 11-34 (341)
109 KOG0796 Spliceosome subunit [R 20.0 41 0.0009 36.2 0.5 32 181-212 184-218 (319)
No 1
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.54 E-value=6.3e-08 Score=68.23 Aligned_cols=32 Identities=44% Similarity=0.837 Sum_probs=30.6
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhh
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKR 366 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKk 366 (585)
.|+|++|+++|++...+.+|++||||+++|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 59999999999999999999999999999986
No 2
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.36 E-value=2.1e-07 Score=61.69 Aligned_cols=25 Identities=36% Similarity=0.731 Sum_probs=24.5
Q ss_pred EeeeecccccCCHHHHHhhhhhhhH
Q 007901 336 LICELCNVKCESQVVFDSHLVGKKH 360 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~GKKH 360 (585)
|+|++|++.|+++..|++|++|+||
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 7999999999999999999999999
No 3
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.36 E-value=2.1e-07 Score=65.53 Aligned_cols=33 Identities=33% Similarity=0.666 Sum_probs=30.5
Q ss_pred cccccccccccCCHHHHHHHhcCcchHHHHHHH
Q 007901 183 MAWCELCRVDCNTLEILEQHKNGKRHKRNLRTH 215 (585)
Q Consensus 183 ~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraL 215 (585)
.++|++|+++|+++..+.+|+.||+|+++++++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHcC
Confidence 479999999999999999999999999998763
No 4
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.06 E-value=1.7e-06 Score=57.32 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=24.1
Q ss_pred ccccccccccCCHHHHHHHhcCcch
Q 007901 184 AWCELCRVDCNTLEILEQHKNGKRH 208 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~GKKH 208 (585)
++|++|+++|+++.++++|+.||||
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 5899999999999999999999998
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=98.04 E-value=1.8e-06 Score=58.99 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=25.3
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHH
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHL 361 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHq 361 (585)
.|+|.+|++.|+++..|+.|++||+|+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 389999999999999999999999995
No 6
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.66 E-value=1.7e-05 Score=54.18 Aligned_cols=26 Identities=31% Similarity=0.617 Sum_probs=25.1
Q ss_pred ccccccccccCCHHHHHHHhcCcchH
Q 007901 184 AWCELCRVDCNTLEILEQHKNGKRHK 209 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~GKKHK 209 (585)
++|.+|++.|+++.++++|+.||+|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 69999999999999999999999996
No 7
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.24 E-value=0.0002 Score=69.65 Aligned_cols=36 Identities=25% Similarity=0.447 Sum_probs=32.5
Q ss_pred CCCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 332 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 332 ~~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
....|||.+|+..+-.-.+|-.|||||||+.+|--+
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 457899999999999999999999999999998543
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=97.05 E-value=0.00051 Score=51.60 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=21.6
Q ss_pred ccccccccccc--CCHHHHHHHhcCcchHHHHHHH
Q 007901 183 MAWCELCRVDC--NTLEILEQHKNGKRHKRNLRTH 215 (585)
Q Consensus 183 ~~yCdVCkVsc--NSpsqaqsHy~GKKHKKNLraL 215 (585)
-.||+.|+++| +++..-..|..|+||+.|+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 36999999999 5667879999999999999863
No 9
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=96.95 E-value=0.00052 Score=51.58 Aligned_cols=33 Identities=33% Similarity=0.561 Sum_probs=21.5
Q ss_pred CEeeeeccccc--CCHHHHHhhhhhhhHHHHHhhh
Q 007901 335 PLICELCNVKC--ESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 335 ~l~CeLCNV~c--NSe~~~qsHL~GKKHqkKLKkl 367 (585)
.+||+.|++++ ++...-+.|..|+||+.++++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 58999999999 5666779999999999999863
No 10
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=96.64 E-value=0.0014 Score=74.20 Aligned_cols=41 Identities=20% Similarity=0.553 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCcccccccccccCCHHHHHHHhcCcchHHHH
Q 007901 171 QVPGAPTRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNL 212 (585)
Q Consensus 171 ~~~~ap~~~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNL 212 (585)
.+|++++ +.-+.+||++|+++|+.++.+..|+.|.||+++.
T Consensus 182 dR~K~~~-~laqL~~~kw~k~~a~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 182 DRPKAPP-RLAQLHYCKWCKISAAGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred ccccCch-HHHHhhhhHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 5566666 5678899999999999999999999999999987
No 11
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=96.48 E-value=0.0016 Score=60.64 Aligned_cols=38 Identities=21% Similarity=0.276 Sum_probs=35.4
Q ss_pred CCCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcc
Q 007901 332 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 369 (585)
Q Consensus 332 ~~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g 369 (585)
..+.|||-.|...|.+..+|..|+++|.|+++||++.+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 45799999999999999999999999999999999963
No 12
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=96.29 E-value=0.0025 Score=62.30 Aligned_cols=36 Identities=28% Similarity=0.478 Sum_probs=32.0
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHHHH
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHA 216 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLq 216 (585)
...+||+||+..|--...+..|++||+|++|+.-+.
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSM 108 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHHhhhh
Confidence 456799999999999999999999999999987554
No 13
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=96.15 E-value=0.0023 Score=67.00 Aligned_cols=38 Identities=26% Similarity=0.576 Sum_probs=34.4
Q ss_pred CCCCCCccccccccccc-CCHHHHHHHhcCcchHHHHHH
Q 007901 177 TRPPPPMAWCELCRVDC-NTLEILEQHKNGKRHKRNLRT 214 (585)
Q Consensus 177 ~~~p~~~~yCdVCkVsc-NSpsqaqsHy~GKKHKKNLra 214 (585)
-|.+.+..||++|+++| +++.....|-.||||+-+|++
T Consensus 4 YWkS~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 4 YWKSQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred hhhhccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 48888999999999999 788888999999999999874
No 14
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.97 E-value=0.01 Score=60.34 Aligned_cols=59 Identities=27% Similarity=0.439 Sum_probs=46.1
Q ss_pred CCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhc--ccccccccccccccCCCCCCCCCc
Q 007901 333 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFH--GHRALYGEAALQSLYPASFNSLSS 392 (585)
Q Consensus 333 ~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~--g~q~l~g~~glQ~~~Ppn~~a~sn 392 (585)
.+.+.|-|||+-.- +..+..|.+||||..++-++. +.+.....++..+..|+.+|+.+.
T Consensus 33 sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~k~~~T~~p~~p~spn~kts 93 (264)
T KOG3032|consen 33 SGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVAKTRPTKIPALPKSPNSKTS 93 (264)
T ss_pred CCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhcccccCcCccCccCCCCCCcccc
Confidence 46899999999999 999999999999999988776 222222225667778888888774
No 15
>PLN02748 tRNA dimethylallyltransferase
Probab=95.82 E-value=0.0047 Score=67.37 Aligned_cols=36 Identities=22% Similarity=0.477 Sum_probs=32.7
Q ss_pred CCEeeeeccc-ccCCHHHHHhhhhhhhHHHHHhhhcc
Q 007901 334 IPLICELCNV-KCESQVVFDSHLVGKKHLANVKRFHG 369 (585)
Q Consensus 334 ~~l~CeLCNV-~cNSe~~~qsHL~GKKHqkKLKkl~g 369 (585)
..|.|++|+. .++++..++.|++||+|+++|++...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 5678999998 89999999999999999999998754
No 16
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=94.93 E-value=0.013 Score=54.67 Aligned_cols=40 Identities=23% Similarity=0.340 Sum_probs=36.1
Q ss_pred CCCCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 179 PPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 179 ~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
+--..+||-.|...|.+..++..|..+|.|+|+|+.|...
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~ 92 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREV 92 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccC
Confidence 3356789999999999999999999999999999999853
No 17
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=94.83 E-value=0.016 Score=56.22 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=29.9
Q ss_pred ccccccccccc--CCHHHHHHHhcCcchHHHHHHHH
Q 007901 183 MAWCELCRVDC--NTLEILEQHKNGKRHKRNLRTHA 216 (585)
Q Consensus 183 ~~yCdVCkVsc--NSpsqaqsHy~GKKHKKNLraLq 216 (585)
-.||+.|+..+ .|.++-++|+.|+||++|++...
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY 38 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYY 38 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHH
Confidence 35899999876 59999999999999999998554
No 18
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.81 E-value=0.017 Score=63.40 Aligned_cols=37 Identities=30% Similarity=0.454 Sum_probs=33.6
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcccc
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHR 371 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~q 371 (585)
.+||-+||.+|-|+-+|..|.+.|||.++|.++.+++
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqem 328 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQEM 328 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHHH
Confidence 3999999999999999999999999999998885443
No 19
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.41 E-value=0.02 Score=62.88 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=32.7
Q ss_pred ccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 184 AWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
+||-+|+.+|-|+-++..|-+.|||++||+.|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999874
No 20
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=93.90 E-value=0.032 Score=55.66 Aligned_cols=35 Identities=29% Similarity=0.431 Sum_probs=32.5
Q ss_pred CCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 333 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 333 ~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
.+.|.|.||+-.-+++..|-.|..||||+.+|-+.
T Consensus 51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred CcceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 47899999999999999999999999999998765
No 21
>PF14968 CCDC84: Coiled coil protein 84
Probab=93.54 E-value=0.045 Score=57.97 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=26.6
Q ss_pred cccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 185 WCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 185 yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
||.||+.++.. -+-|.-+++|+++|+.+-..
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L~r 31 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFLSR 31 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHHHH
Confidence 89999999876 67899999999999987543
No 22
>PLN02748 tRNA dimethylallyltransferase
Probab=93.54 E-value=0.051 Score=59.54 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=32.5
Q ss_pred Cccccccccc-ccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 182 PMAWCELCRV-DCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 182 ~~~yCdVCkV-scNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
....|++|+. .++++.+-+.|+.||+|+++++++...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 3446999998 799999999999999999999988653
No 23
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=93.48 E-value=0.046 Score=58.77 Aligned_cols=36 Identities=31% Similarity=0.530 Sum_probs=32.9
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcc
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 369 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g 369 (585)
..++|.+||..+-|+..+..||+.|||..+++++..
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred cceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 368999999999999999999999999999988643
No 24
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=93.46 E-value=0.022 Score=63.69 Aligned_cols=12 Identities=17% Similarity=0.263 Sum_probs=0.0
Q ss_pred ccCCCCCCCccC
Q 007901 114 SVRPQFGQSACR 125 (585)
Q Consensus 114 ~~~~~~g~~~~~ 125 (585)
-..||.|....+
T Consensus 514 ~y~~p~~k~ss~ 525 (556)
T PF05918_consen 514 QYVPPSGKYSSN 525 (556)
T ss_dssp ------------
T ss_pred ccCCCCCCCcCC
Confidence 345666554433
No 25
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=92.94 E-value=0.041 Score=59.04 Aligned_cols=36 Identities=25% Similarity=0.561 Sum_probs=33.0
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 182 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 182 ~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
+.+||.+|..+|....+++.|+.||+|.|++++.+.
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 457999999999999999999999999999987765
No 26
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=92.57 E-value=0.082 Score=48.85 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=35.4
Q ss_pred CCCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhccc
Q 007901 332 GVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGH 370 (585)
Q Consensus 332 ~~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~ 370 (585)
..+.+||.-|...|.++..|-.|.+||-|+.++|++.+-
T Consensus 52 GlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 357899999999999999999999999999999998553
No 27
>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=92.26 E-value=0.1 Score=32.98 Aligned_cols=21 Identities=19% Similarity=0.529 Sum_probs=17.7
Q ss_pred EeeeecccccCCHHHHHhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLV 356 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~ 356 (585)
|.|.+|+..|.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 679999999999999999985
No 28
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=92.23 E-value=0.072 Score=51.76 Aligned_cols=33 Identities=33% Similarity=0.603 Sum_probs=28.0
Q ss_pred CEeeeeccccc--CCHHHHHhhhhhhhHHHHHhhh
Q 007901 335 PLICELCNVKC--ESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 335 ~l~CeLCNV~c--NSe~~~qsHL~GKKHqkKLKkl 367 (585)
.|||+-|+... .|..+=+.|+.|+||++++|--
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~Y 37 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDY 37 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHH
Confidence 48999999555 5777999999999999998654
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.93 E-value=0.083 Score=43.23 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=26.5
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHh
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVK 365 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLK 365 (585)
.+.|.+|+..|.+...|..||+.+.|++...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 5999999999999999999999999988654
No 30
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=90.97 E-value=0.18 Score=46.62 Aligned_cols=46 Identities=30% Similarity=0.441 Sum_probs=39.1
Q ss_pred CCCCCCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 173 PGAPTRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 173 ~~ap~~~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
|-.|.-+--..+||--|..-|.++..|..|..||-|+++++.|..-
T Consensus 45 p~Dp~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 45 PYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCCCCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 3344545567789999999999999999999999999999999864
No 31
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=90.70 E-value=0.17 Score=50.52 Aligned_cols=37 Identities=30% Similarity=0.455 Sum_probs=33.2
Q ss_pred CCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcc
Q 007901 333 VIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 369 (585)
Q Consensus 333 ~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g 369 (585)
.+.|.|.||+-.--++..+..|+.||||+.++.+.+.
T Consensus 51 ~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~ 87 (222)
T COG5246 51 TGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSE 87 (222)
T ss_pred CCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHH
Confidence 4689999999999999999999999999999877633
No 32
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=90.67 E-value=0.12 Score=41.45 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=24.8
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHH
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLR 213 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLr 213 (585)
+...||+.|.+.|. .|..|+.++||++=.+
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 35679999999997 6888999999997433
No 33
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.39 E-value=0.35 Score=49.65 Aligned_cols=39 Identities=18% Similarity=0.385 Sum_probs=34.9
Q ss_pred CCCCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 179 PPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 179 ~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
-+.....|-||++-.- +..-..|.+||||+-++..|+..
T Consensus 31 n~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~ 69 (264)
T KOG3032|consen 31 NESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSR 69 (264)
T ss_pred CCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhh
Confidence 4566789999999998 99999999999999999999843
No 34
>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=90.06 E-value=0.24 Score=32.10 Aligned_cols=22 Identities=18% Similarity=0.455 Sum_probs=20.3
Q ss_pred EeeeecccccCCHHHHHhhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLVG 357 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~G 357 (585)
|.|..|+..|++...|..|++-
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 6799999999999999999864
No 35
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=90.03 E-value=0.13 Score=41.34 Aligned_cols=30 Identities=30% Similarity=0.538 Sum_probs=25.4
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
.-||+.|.+.|. .|..|+.++||++=.+..
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~~~ 34 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFAENN 34 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHHcCc
Confidence 469999999997 789999999998866543
No 36
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=89.98 E-value=0.15 Score=40.80 Aligned_cols=29 Identities=31% Similarity=0.589 Sum_probs=25.1
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhh
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKR 366 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKk 366 (585)
.-||+.|.+.|. .|..|+.+++|++-...
T Consensus 5 ~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA~~ 33 (49)
T PF07535_consen 5 PGYCENCRVKYD---DLEEHIQSEKHRKFAEN 33 (49)
T ss_pred CccCccccchhh---hHHHHhCCHHHHHHHcC
Confidence 469999999998 59999999999886644
No 37
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=89.90 E-value=0.16 Score=55.91 Aligned_cols=34 Identities=35% Similarity=0.567 Sum_probs=31.2
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
....|.||||-.+|++.|-+|.+|+||+--|+.+
T Consensus 492 rkkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 492 RKKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 3568999999999999999999999999988876
No 38
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=89.49 E-value=0.25 Score=33.20 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=19.8
Q ss_pred EeeeecccccCCHHHHHhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLV 356 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~ 356 (585)
|.|..|+..|++...|..|++
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 789999999999999999993
No 39
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=89.33 E-value=0.2 Score=50.26 Aligned_cols=37 Identities=30% Similarity=0.373 Sum_probs=32.6
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 182 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 182 ~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
...-|.||.-.-+++..+..|..||||+-||.+-.+.
T Consensus 52 G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa~ 88 (222)
T KOG0227|consen 52 GKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAK 88 (222)
T ss_pred cceeehhhhhhhcchhhhhhhhccchhhHHHHHHHHH
Confidence 4456999999999999999999999999999876654
No 40
>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=88.74 E-value=0.27 Score=39.30 Aligned_cols=29 Identities=31% Similarity=0.692 Sum_probs=24.6
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHH
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNL 212 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNL 212 (585)
....||+.|.+.|.+ |..|+.+++|++=.
T Consensus 3 ~k~GYCE~C~~ky~~---l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 3 KKPGYCENCRVKYDD---LEEHIQSEKHRKFA 31 (49)
T ss_pred CCCccCccccchhhh---HHHHhCCHHHHHHH
Confidence 356799999999985 88999999999654
No 41
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=88.46 E-value=0.21 Score=53.89 Aligned_cols=35 Identities=26% Similarity=0.450 Sum_probs=31.9
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcc
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKRFHG 369 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g 369 (585)
.+||..|..+|....+|..|+.||.|.+..+....
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 59999999999999999999999999998877544
No 42
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=87.57 E-value=0.29 Score=51.89 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=29.6
Q ss_pred CCEeeeeccccc-CCHHHHHhhhhhhhHHHHHhhh
Q 007901 334 IPLICELCNVKC-ESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 334 ~~l~CeLCNV~c-NSe~~~qsHL~GKKHqkKLKkl 367 (585)
..+||++|.|++ |....-+.|=.||+|+.+|.+.
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 468999999987 5677899999999999988665
No 43
>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=86.23 E-value=0.49 Score=31.76 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=18.9
Q ss_pred ccccccccccCCHHHHHHHh
Q 007901 184 AWCELCRVDCNTLEILEQHK 203 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy 203 (585)
+.|++|+..|.+...|..|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCccCCccCChhHHHHHh
Confidence 47999999999999999998
No 44
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=85.64 E-value=1 Score=53.73 Aligned_cols=33 Identities=30% Similarity=0.331 Sum_probs=13.4
Q ss_pred CCCCCccCCCCcCCCCcccCCCccccCCcCCCC
Q 007901 118 QFGQSACRGGGRKGGKPFRRGGRLVGRGRGHGA 150 (585)
Q Consensus 118 ~~g~~~~~g~~~~~g~~~~~~gr~~g~grg~~~ 150 (585)
|-|-.+++||..|||+..+|||.|||.|+++|+
T Consensus 1246 pgggyrgsGGfgrgggrgagggGgfg~G~~Gg~ 1278 (1282)
T KOG0921|consen 1246 PGGGYRGSGGFGRGGGRGAGGGGGFGGGGRGGN 1278 (1282)
T ss_pred CCCCccCCCCcCCCCCCCCCCCCCCCCCCcccc
Confidence 333333334444444444444444444444433
No 45
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=85.13 E-value=0.27 Score=55.28 Aligned_cols=12 Identities=67% Similarity=1.099 Sum_probs=0.0
Q ss_pred CCCccccCCcCC
Q 007901 137 RGGRLVGRGRGH 148 (585)
Q Consensus 137 ~~gr~~g~grg~ 148 (585)
|||||+|+|||+
T Consensus 544 ggg~grg~~r~~ 555 (556)
T PF05918_consen 544 GGGRGRGRGRGF 555 (556)
T ss_dssp ------------
T ss_pred CCCCCCcccccC
Confidence 666777777764
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=85.12 E-value=0.51 Score=29.74 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=20.9
Q ss_pred EeeeecccccCCHHHHHhhhhhhhHH
Q 007901 336 LICELCNVKCESQVVFDSHLVGKKHL 361 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~GKKHq 361 (585)
+.|..|...|++...|..|+. +|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~--~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR--THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH--Hhc
Confidence 469999999999999999997 553
No 47
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=84.60 E-value=0.68 Score=46.36 Aligned_cols=38 Identities=26% Similarity=0.400 Sum_probs=33.0
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
-..+-|.+|+-.--++..+..|..||||+-|+.+-++.
T Consensus 51 ~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~e 88 (222)
T COG5246 51 TGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEE 88 (222)
T ss_pred CCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHH
Confidence 34567999999999999999999999999999877554
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=82.88 E-value=0.58 Score=38.30 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=26.6
Q ss_pred CcccccccccccCCHHHHHHHhcCcchHHHHH
Q 007901 182 PMAWCELCRVDCNTLEILEQHKNGKRHKRNLR 213 (585)
Q Consensus 182 ~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLr 213 (585)
..+.|.+|+..|.+...+..|...+.|++...
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 35899999999999999999999999997544
No 49
>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=82.52 E-value=0.94 Score=28.46 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=16.8
Q ss_pred ccccccccccCCHHHHHHHhc
Q 007901 184 AWCELCRVDCNTLEILEQHKN 204 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~ 204 (585)
+-|++|+..|.+...+..|+.
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 359999999999999999974
No 50
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=79.96 E-value=1.2 Score=49.40 Aligned_cols=68 Identities=21% Similarity=0.281 Sum_probs=48.8
Q ss_pred cCCCCCCCCCCCC---cccccCCCCCCCCCCCCCCCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 146 RGHGAISNSTPSA---AVPGQTSSSIPGQVPGAPTRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 146 rg~~~~s~~~p~~---~v~~~as~st~a~~~~ap~~~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
|-||.+-.-++++ |+.+-+++..-++-- . +-....-|++|+|-.+|+.-|-+|..|+||+..|+.+-.
T Consensus 457 ~RH~ek~e~~ke~aadl~qgrhantdyapkl--t--pyerkkqcslcnvlissevylfshvkgrkhqqal~e~~~ 527 (672)
T KOG4722|consen 457 IRHGEKEEPAKEAAADLLQGRHANTDYAPKL--T--PYERKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELLL 527 (672)
T ss_pred HhhhcccCcccccHHHHhccccccccccccc--C--hHHhhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHhc
Confidence 3466555555544 666766666554321 1 235667899999999999999999999999988887754
No 51
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=78.40 E-value=1.4 Score=28.48 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=18.5
Q ss_pred cccccccccCCHHHHHHHhc
Q 007901 185 WCELCRVDCNTLEILEQHKN 204 (585)
Q Consensus 185 yCdVCkVscNSpsqaqsHy~ 204 (585)
-|..|+..|++...|..|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 59999999999999999974
No 52
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=76.76 E-value=1 Score=44.31 Aligned_cols=34 Identities=21% Similarity=0.345 Sum_probs=29.3
Q ss_pred cccccccccccC--CHHHHHHHhcCcchHHHHHHHH
Q 007901 183 MAWCELCRVDCN--TLEILEQHKNGKRHKRNLRTHA 216 (585)
Q Consensus 183 ~~yCdVCkVscN--SpsqaqsHy~GKKHKKNLraLq 216 (585)
-.||+.|+++++ +.++-..|+.|++|..+.+...
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY 38 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYY 38 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHH
Confidence 358999999985 7889999999999999887554
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=75.89 E-value=1.9 Score=27.04 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=18.6
Q ss_pred cccccccccCCHHHHHHHhc
Q 007901 185 WCELCRVDCNTLEILEQHKN 204 (585)
Q Consensus 185 yCdVCkVscNSpsqaqsHy~ 204 (585)
-|..|...|++...+..|..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 59999999999999999986
No 54
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=75.54 E-value=0.9 Score=44.72 Aligned_cols=31 Identities=32% Similarity=0.349 Sum_probs=25.8
Q ss_pred CEeeeecccccCC--HHHHHhhhhhhhHHHHHh
Q 007901 335 PLICELCNVKCES--QVVFDSHLVGKKHLANVK 365 (585)
Q Consensus 335 ~l~CeLCNV~cNS--e~~~qsHL~GKKHqkKLK 365 (585)
.|+|+.|+++.+. ..+-+.|+.|++|..+.+
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~ 35 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRK 35 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHH
Confidence 4899999998875 458899999999976653
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=74.89 E-value=4.9 Score=49.54 Aligned_cols=40 Identities=20% Similarity=0.245 Sum_probs=33.7
Q ss_pred CCCCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 179 PPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 179 ~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
.+....-|.+|++.++....|-.|++--+|+.+++..+..
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~ 553 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEEN 553 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhc
Confidence 3455567999999999999999999999999997776654
No 56
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=74.87 E-value=2.3 Score=46.28 Aligned_cols=7 Identities=43% Similarity=0.487 Sum_probs=2.8
Q ss_pred cCCCccc
Q 007901 136 RRGGRLV 142 (585)
Q Consensus 136 ~~~gr~~ 142 (585)
.|||||+
T Consensus 445 ~gggrgr 451 (465)
T KOG3973|consen 445 DGGGRGR 451 (465)
T ss_pred CCCCCCC
Confidence 3344443
No 57
>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=74.57 E-value=0.98 Score=45.05 Aligned_cols=34 Identities=18% Similarity=0.510 Sum_probs=0.0
Q ss_pred CCEeeeecc-cccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 334 IPLICELCN-VKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 334 ~~l~CeLCN-V~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
..|.|+||. .+.-+...|..|+...||..-||.+
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp -----------------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcChhHHHccChhc
Confidence 479999997 7778999999999999999988876
No 58
>PTZ00448 hypothetical protein; Provisional
Probab=71.15 E-value=2.9 Score=45.38 Aligned_cols=38 Identities=26% Similarity=0.434 Sum_probs=33.7
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcccc
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHR 371 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~q 371 (585)
..|.|..|++.|.+....+.|++.-=|.=+||+.-...
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gL 350 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKM 350 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCC
Confidence 36889999999999999999999999999999874443
No 59
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=69.97 E-value=2.1 Score=46.59 Aligned_cols=37 Identities=27% Similarity=0.545 Sum_probs=33.7
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
+...+|.+|+..|.|+.....|+..|||+.++.++..
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 4567999999999999999999999999999998764
No 60
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=66.28 E-value=4.5 Score=26.67 Aligned_cols=21 Identities=19% Similarity=0.414 Sum_probs=16.4
Q ss_pred EeeeecccccCCHHHHHhhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLVG 357 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~G 357 (585)
|.|..|+-.++ +..|..|++-
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 57999999888 9999999863
No 61
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=63.35 E-value=1.3 Score=46.48 Aligned_cols=34 Identities=21% Similarity=0.570 Sum_probs=31.4
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHHHHhhhc
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLANVKRFH 368 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~ 368 (585)
.|||.+|...|+.+--|+.|....-|++.|..+.
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~ 58 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFA 58 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHHHHH
Confidence 4899999999999999999999999999987653
No 62
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=58.87 E-value=9.5 Score=41.76 Aligned_cols=27 Identities=56% Similarity=0.911 Sum_probs=12.9
Q ss_pred CCCcCCCCcccCCCcc-ccCCcCCCCCCC
Q 007901 126 GGGRKGGKPFRRGGRL-VGRGRGHGAISN 153 (585)
Q Consensus 126 g~~~~~g~~~~~~gr~-~g~grg~~~~s~ 153 (585)
|||++||+ -.||||+ =|||||.|..-|
T Consensus 431 ggg~~ggg-r~gggr~gggrgrgggggrg 458 (465)
T KOG3973|consen 431 GGGRDGGG-RDGGGRDGGGRGRGGGGGRG 458 (465)
T ss_pred CCCCCCCC-CCCCCCCCCCCCCCCCCCCc
Confidence 33444433 3345554 456666664333
No 63
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=57.20 E-value=4.2 Score=47.41 Aligned_cols=31 Identities=26% Similarity=0.567 Sum_probs=28.5
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHH
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANV 364 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKL 364 (585)
.-.||++|.+.||....+..|+.|.||+++-
T Consensus 192 qL~~~kw~k~~a~G~qs~re~lr~~r~l~kr 222 (816)
T KOG3792|consen 192 QLHYCKWCKISAAGPQTYREHLRGQKHLKKE 222 (816)
T ss_pred HhhhhHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 4578999999999999999999999998864
No 64
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=55.76 E-value=7.6 Score=38.22 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=29.9
Q ss_pred EeeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 336 LICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
|.|.+|....--+..+..||.++=|+..|+.+
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 57999999999999999999999999988877
No 65
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=53.00 E-value=8.5 Score=36.38 Aligned_cols=22 Identities=41% Similarity=0.650 Sum_probs=13.6
Q ss_pred cCCCCcCCCCcccCCCccccCC
Q 007901 124 CRGGGRKGGKPFRRGGRLVGRG 145 (585)
Q Consensus 124 ~~g~~~~~g~~~~~~gr~~g~g 145 (585)
.++.++|+|+++||.|||.|||
T Consensus 103 ~~~~~~r~~~~~~~~gr~~~r~ 124 (124)
T PTZ00034 103 TEEEGSRGGRGGRGRGRGYGRG 124 (124)
T ss_pred cccccccCCCCCCCCCCCCCCC
Confidence 3455667777776666666553
No 66
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=51.56 E-value=18 Score=33.36 Aligned_cols=8 Identities=63% Similarity=1.149 Sum_probs=4.2
Q ss_pred ccCCcCCC
Q 007901 142 VGRGRGHG 149 (585)
Q Consensus 142 ~g~grg~~ 149 (585)
.|.|||.+
T Consensus 23 yGggrgg~ 30 (104)
T PF12764_consen 23 YGGGRGGG 30 (104)
T ss_pred CCCCCCCC
Confidence 45555554
No 67
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=50.88 E-value=14 Score=38.67 Aligned_cols=11 Identities=82% Similarity=1.374 Sum_probs=5.1
Q ss_pred CCCccccCCcC
Q 007901 137 RGGRLVGRGRG 147 (585)
Q Consensus 137 ~~gr~~g~grg 147 (585)
+|+||+|||||
T Consensus 17 ~~~~g~~~~~~ 27 (257)
T PTZ00070 17 RGGRGRGRGRG 27 (257)
T ss_pred CCCCCCCCCCC
Confidence 33455444444
No 68
>PF14968 CCDC84: Coiled coil protein 84
Probab=49.26 E-value=6.6 Score=42.13 Aligned_cols=28 Identities=25% Similarity=0.543 Sum_probs=25.4
Q ss_pred eeeecccccCCHHHHHhhhhhhhHHHHHhhh
Q 007901 337 ICELCNVKCESQVVFDSHLVGKKHLANVKRF 367 (585)
Q Consensus 337 ~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl 367 (585)
||.+|...+.. -+-|..+++|+++|+.+
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAF 28 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHH
Confidence 79999998886 89999999999999776
No 69
>PF12764 Gly-rich_Ago1: Glycine-rich region of argonaut; InterPro: IPR024357 This domain is found in the N terminus of some argonaut proteins. Argonaut (AGO) proteins are involved in RNA-mediated post-transcriptional gene silencing [].
Probab=47.27 E-value=29 Score=32.13 Aligned_cols=23 Identities=48% Similarity=0.721 Sum_probs=15.2
Q ss_pred CCccCCCCc-CCCCcccCCCcccc
Q 007901 121 QSACRGGGR-KGGKPFRRGGRLVG 143 (585)
Q Consensus 121 ~~~~~g~~~-~~g~~~~~~gr~~g 143 (585)
+.+.||+-+ |||++..|||||-+
T Consensus 7 qgrGRGgp~~qgG~~~yGggrgg~ 30 (104)
T PF12764_consen 7 QGRGRGGPPQQGGRPGYGGGRGGG 30 (104)
T ss_pred cccCCCCCcccCCCCCCCCCCCCC
Confidence 334555444 67888888888765
No 70
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=45.50 E-value=16 Score=41.61 Aligned_cols=72 Identities=21% Similarity=0.289 Sum_probs=55.4
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcccccccccccccccCCCCCC----------CCCccccccccCCCC
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYGEAALQSLYPASFN----------SLSSSVITQVQQGVN 403 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~q~l~g~~glQ~~~Ppn~~----------a~sn~~~~q~qqg~~ 403 (585)
..+.|..|++.|-+......|++.-=|.-++|+.--...+++...|-.++--.+. ..|...+.|.++|++
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~edFe~i~s~d~ssiSgsEde~~s~tsSdheq~ek~~d 144 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEEDFEGIISSDLSSISGSEDEAESLTSSDHEQTEKGLD 144 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhhcccccccccccccccCCcchhHHHHHhhh
Confidence 4689999999999999999999999999999998888888887555555444332 333455677788875
Q ss_pred Cc
Q 007901 404 DP 405 (585)
Q Consensus 404 ~~ 405 (585)
-.
T Consensus 145 r~ 146 (591)
T KOG2505|consen 145 RD 146 (591)
T ss_pred hh
Confidence 44
No 71
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=44.91 E-value=19 Score=34.32 Aligned_cols=29 Identities=48% Similarity=0.673 Sum_probs=14.6
Q ss_pred CCCccCCCCcCCCCcccCCCccccCCcCCC
Q 007901 120 GQSACRGGGRKGGKPFRRGGRLVGRGRGHG 149 (585)
Q Consensus 120 g~~~~~g~~~~~g~~~~~~gr~~g~grg~~ 149 (585)
++++.+|+||.+|+ ..++|+++|+|||..
T Consensus 91 ~~~r~~~~grG~gn-g~~~~~~rg~~~g~~ 119 (134)
T KOG3293|consen 91 KQSRDRGRGRGRGN-GNRGGNRRGGGRGGS 119 (134)
T ss_pred hccccccCCcCCCC-CCCCCCcCCCCCCCC
Confidence 46666666663333 333444445555443
No 72
>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=43.39 E-value=21 Score=35.20 Aligned_cols=34 Identities=24% Similarity=0.389 Sum_probs=30.3
Q ss_pred ccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 184 AWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
+.|++|+.+--....++.|+.++-|+--++.+..
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~t 34 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQT 34 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHHh
Confidence 4799999998888999999999999998888843
No 73
>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=42.54 E-value=11 Score=38.47 Aligned_cols=30 Identities=27% Similarity=0.528 Sum_probs=23.2
Q ss_pred CEeeeecccccC---CHHHHHhhhhhhhHHHHH
Q 007901 335 PLICELCNVKCE---SQVVFDSHLVGKKHLANV 364 (585)
Q Consensus 335 ~l~CeLCNV~cN---Se~~~qsHL~GKKHqkKL 364 (585)
...|+||....+ +..-+..|+.||-|+--+
T Consensus 190 l~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~ 222 (254)
T PF03194_consen 190 LEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYA 222 (254)
T ss_pred ccchhhhhhHHhccchHHHHHHHhccchhhhHH
Confidence 468999996664 444699999999996543
No 74
>PF12907 zf-met2: Zinc-binding
Probab=42.29 E-value=14 Score=28.77 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=20.8
Q ss_pred ccccccc---cccCCHHHHHHHhcCcchHH
Q 007901 184 AWCELCR---VDCNTLEILEQHKNGKRHKR 210 (585)
Q Consensus 184 ~yCdVCk---VscNSpsqaqsHy~GKKHKK 210 (585)
+-|.||. +.-.++.+|.+|+..| |-|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK-HpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK-HPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc-CCC
Confidence 5699999 5568999999999865 544
No 75
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=41.08 E-value=26 Score=39.97 Aligned_cols=13 Identities=38% Similarity=0.547 Sum_probs=7.6
Q ss_pred CCcccCCCccccC
Q 007901 132 GKPFRRGGRLVGR 144 (585)
Q Consensus 132 g~~~~~~gr~~g~ 144 (585)
|+.-|+|||+|++
T Consensus 579 ~~~~~~~~~~~~~ 591 (629)
T PRK11634 579 GGERREGGRNFSG 591 (629)
T ss_pred CCCCCCCCcCCCC
Confidence 4455666677643
No 76
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=40.68 E-value=25 Score=35.66 Aligned_cols=36 Identities=19% Similarity=0.341 Sum_probs=28.3
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhccc
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGH 370 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~ 370 (585)
..|.|.+|...|-.+.=...||. +||..+|+.+...
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~e 111 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKE 111 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHH
Confidence 46899999999999999999997 6899999877543
No 77
>PHA02768 hypothetical protein; Provisional
Probab=38.24 E-value=17 Score=30.05 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=22.8
Q ss_pred CEeeeecccccCCHHHHHhhhhhhhHHH
Q 007901 335 PLICELCNVKCESQVVFDSHLVGKKHLA 362 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~GKKHqk 362 (585)
.|.|+.|+..|+....|..|++- |.+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~--H~k 30 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK--HNT 30 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh--cCC
Confidence 58999999999999999999864 763
No 78
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=38.23 E-value=88 Score=35.79 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=13.2
Q ss_pred HHHHHhcCcchH--HHHHHHHh
Q 007901 198 ILEQHKNGKRHK--RNLRTHAD 217 (585)
Q Consensus 198 qaqsHy~GKKHK--KNLraLqa 217 (585)
.+..|+.|--|- -||++|..
T Consensus 206 lFLKhlVGGLHTVYTKLKRLdI 227 (641)
T KOG3915|consen 206 LFLKHLVGGLHTVYTKLKRLDI 227 (641)
T ss_pred HHHHHHhchHHHHHHHhhccce
Confidence 455899999996 34555543
No 79
>PTZ00448 hypothetical protein; Provisional
Probab=37.82 E-value=24 Score=38.59 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=31.1
Q ss_pred cccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 183 MAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 183 ~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
.+.|..|++.|.+....+.||..==|+=||++.-.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~ 348 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNAR 348 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHHHhc
Confidence 45699999999999999999999999999987643
No 80
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=36.26 E-value=8.1 Score=40.91 Aligned_cols=35 Identities=23% Similarity=0.479 Sum_probs=31.7
Q ss_pred cccccccccccCCHHHHHHHhcCcchHHHHHHHHh
Q 007901 183 MAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHAD 217 (585)
Q Consensus 183 ~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa 217 (585)
-|||-+|+..|+.+.-+.-|.+.--|+|.+....+
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~ 59 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFAL 59 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHHHHHh
Confidence 46999999999999999999999999998876654
No 81
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=35.37 E-value=33 Score=35.95 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=7.9
Q ss_pred CcccCCCccccCCcC
Q 007901 133 KPFRRGGRLVGRGRG 147 (585)
Q Consensus 133 ~~~~~~gr~~g~grg 147 (585)
+.|+|||+..|+|++
T Consensus 253 ~gfsgGGgS~GGGGa 267 (271)
T COG1512 253 GGFSGGGGSSGGGGA 267 (271)
T ss_pred CCcCCCCCCCCCCCC
Confidence 345566666655443
No 82
>PHA00616 hypothetical protein
Probab=35.29 E-value=19 Score=28.66 Aligned_cols=23 Identities=17% Similarity=0.164 Sum_probs=20.4
Q ss_pred EeeeecccccCCHHHHHhhhhhhhH
Q 007901 336 LICELCNVKCESQVVFDSHLVGKKH 360 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~GKKH 360 (585)
+-|..|+..|.....|..|+ ++|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~--r~~ 24 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHL--LSV 24 (44)
T ss_pred CccchhhHHHhhHHHHHHHH--HHh
Confidence 67999999999999999999 444
No 83
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=33.36 E-value=44 Score=38.01 Aligned_cols=8 Identities=13% Similarity=0.073 Sum_probs=4.0
Q ss_pred cCCCCCCC
Q 007901 523 SSLENPDN 530 (585)
Q Consensus 523 ~~~~~~~~ 530 (585)
.||-++|.
T Consensus 490 gp~i~ada 497 (641)
T KOG3915|consen 490 GPFIFADA 497 (641)
T ss_pred Cccccccc
Confidence 44555554
No 84
>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=32.26 E-value=40 Score=28.11 Aligned_cols=28 Identities=18% Similarity=0.273 Sum_probs=19.2
Q ss_pred CCCCCCcccccccccccCCHHHHHHHhc
Q 007901 177 TRPPPPMAWCELCRVDCNTLEILEQHKN 204 (585)
Q Consensus 177 ~~~p~~~~yCdVCkVscNSpsqaqsHy~ 204 (585)
.+.+.....|.+|...|.+...|.-|+.
T Consensus 18 ~~~S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 18 KSQSEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp CCTTS--EE-TTT--EESSHHHHHHHHH
T ss_pred hhccCCCCCCCcchhhccchhhHHHHHH
Confidence 4467788899999999999999988863
No 85
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=31.75 E-value=42 Score=37.20 Aligned_cols=7 Identities=57% Similarity=0.515 Sum_probs=3.3
Q ss_pred chHhhhc
Q 007901 107 TAAAAQR 113 (585)
Q Consensus 107 ~~~~~~~ 113 (585)
+++++|.
T Consensus 339 ~~~~~~~ 345 (419)
T KOG0116|consen 339 NAAAVQN 345 (419)
T ss_pred ecchhhh
Confidence 4444444
No 86
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=31.34 E-value=38 Score=38.76 Aligned_cols=57 Identities=16% Similarity=0.232 Sum_probs=40.3
Q ss_pred cccccCCCCCCCCCCCCC-CCCCCCcccccccccccCCHHHHHHHhcCcchHHHHHHH
Q 007901 159 AVPGQTSSSIPGQVPGAP-TRPPPPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTH 215 (585)
Q Consensus 159 ~v~~~as~st~a~~~~ap-~~~p~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraL 215 (585)
+.+..|+-|......+.- .-.....+.|..|++.|-+-.....||.--=|+-|+++-
T Consensus 41 ~~~~~Tsd~~~~~~e~~~r~~v~sd~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krk 98 (591)
T KOG2505|consen 41 LIVPETSDSMSLEEEGDMRDSVISDSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRK 98 (591)
T ss_pred hcCCcCCCccchhhccchhhhhhcccccccccCCccccHHHHHHHHHHHHHHHHHHHH
Confidence 344445555444444331 112345679999999999999999999999999988754
No 87
>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=30.76 E-value=17 Score=36.63 Aligned_cols=38 Identities=24% Similarity=0.254 Sum_probs=0.0
Q ss_pred CCccccccccc-ccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 181 PPMAWCELCRV-DCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 181 ~~~~yCdVCkV-scNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
...+.|+||.= ++-....++.|....||..-|+.|-..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~ 137 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIP 137 (196)
T ss_dssp ---------------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCC
Confidence 45678999964 568999999999999999999999775
No 88
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=30.65 E-value=44 Score=37.02 Aligned_cols=9 Identities=11% Similarity=0.143 Sum_probs=3.5
Q ss_pred ccchHhhhc
Q 007901 105 SGTAAAAQR 113 (585)
Q Consensus 105 ~~~~~~~~~ 113 (585)
++.-.+-+.
T Consensus 341 ~~~~~~i~A 349 (419)
T KOG0116|consen 341 AAVQNAIEA 349 (419)
T ss_pred chhhhhhhc
Confidence 444333333
No 89
>PF12907 zf-met2: Zinc-binding
Probab=30.07 E-value=22 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=21.4
Q ss_pred Eeeeecc---cccCCHHHHHhhhhhhhHHH
Q 007901 336 LICELCN---VKCESQVVFDSHLVGKKHLA 362 (585)
Q Consensus 336 l~CeLCN---V~cNSe~~~qsHL~GKKHqk 362 (585)
+.|.||- +...++.+|..|...| |-|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK-HpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK-HPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc-CCC
Confidence 5799999 8888999999998754 443
No 90
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=30.06 E-value=31 Score=36.44 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=21.8
Q ss_pred CCEeeeecccccCCHHHHHhhhhhh
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGK 358 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GK 358 (585)
..-||=.||.-|..|..|-+|.+-|
T Consensus 9 ~kpwcwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 9 DKPWCWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred CCceeeecccccchhhhhhhhhhhc
Confidence 3569999999999999999998765
No 91
>PHA00732 hypothetical protein
Probab=28.52 E-value=33 Score=29.64 Aligned_cols=21 Identities=14% Similarity=0.461 Sum_probs=19.6
Q ss_pred EeeeecccccCCHHHHHhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLV 356 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~ 356 (585)
|.|..|+..|++...|+.|+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 679999999999999999986
No 92
>COG4907 Predicted membrane protein [Function unknown]
Probab=28.34 E-value=42 Score=38.16 Aligned_cols=17 Identities=35% Similarity=0.622 Sum_probs=7.9
Q ss_pred cCCCCcCCCCcccCCCc
Q 007901 124 CRGGGRKGGKPFRRGGR 140 (585)
Q Consensus 124 ~~g~~~~~g~~~~~~gr 140 (585)
+||+.+.||.+|.|||-
T Consensus 571 ~~~~~~GGG~G~~gGg~ 587 (595)
T COG4907 571 RRSSSSGGGGGFSGGGS 587 (595)
T ss_pred ccCCCCCCCCCcCCCCC
Confidence 34444444444444443
No 93
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=26.86 E-value=32 Score=37.06 Aligned_cols=30 Identities=30% Similarity=0.562 Sum_probs=23.5
Q ss_pred CEeeeeccccc---CCHHHHHhhhhhhhHHHHH
Q 007901 335 PLICELCNVKC---ESQVVFDSHLVGKKHLANV 364 (585)
Q Consensus 335 ~l~CeLCNV~c---NSe~~~qsHL~GKKHqkKL 364 (585)
--.|+||.... .+..-+..|+.||-|+--+
T Consensus 186 l~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~ 218 (319)
T KOG0796|consen 186 LRVCEVCGAFLSVNDADRRLADHFGGKLHLGYV 218 (319)
T ss_pred hhHHHhhhHHHhccchHHHHHHhhcchHHHHHH
Confidence 35799999665 4566899999999997544
No 94
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.72 E-value=37 Score=38.25 Aligned_cols=38 Identities=21% Similarity=0.240 Sum_probs=32.0
Q ss_pred CCcccccccccccCCHHHHHHHhcCcchHHHHHHHHhh
Q 007901 181 PPMAWCELCRVDCNTLEILEQHKNGKRHKRNLRTHADL 218 (585)
Q Consensus 181 ~~~~yCdVCkVscNSpsqaqsHy~GKKHKKNLraLqa~ 218 (585)
...++|..|...+.--.++..|.-|+.|-+..+-....
T Consensus 247 ~Eel~~~g~erlk~al~alglk~gGt~~~ra~rlf~Tk 284 (497)
T KOG2636|consen 247 VEELYCLGCERLKSALTALGLKCGGTLHERAQRLFSTK 284 (497)
T ss_pred HHHHHhhchhHHHHHHHHHHHhcCCeecHHHHhhhhhc
Confidence 56789999998888888999999999999887776654
No 95
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=26.68 E-value=24 Score=42.28 Aligned_cols=28 Identities=18% Similarity=0.428 Sum_probs=24.6
Q ss_pred CCCEeeeecccccCCHHHHHhhhhhhhH
Q 007901 333 VIPLICELCNVKCESQVVFDSHLVGKKH 360 (585)
Q Consensus 333 ~~~l~CeLCNV~cNSe~~~qsHL~GKKH 360 (585)
...|.|+||.--|+....|+.||.+-|-
T Consensus 631 ERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 631 ERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred cCccccccccchhccccchhhccccccc
Confidence 4689999999999999999999988543
No 96
>KOG1596 consensus Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification]
Probab=26.17 E-value=72 Score=34.04 Aligned_cols=10 Identities=20% Similarity=0.368 Sum_probs=3.7
Q ss_pred hhhhhhHHHH
Q 007901 354 HLVGKKHLAN 363 (585)
Q Consensus 354 HL~GKKHqkK 363 (585)
|..|+.-..+
T Consensus 191 ~rsGRdL~nm 200 (317)
T KOG1596|consen 191 HRSGRDLINM 200 (317)
T ss_pred ccchHHHHHH
Confidence 3333333333
No 97
>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=26.03 E-value=34 Score=35.13 Aligned_cols=30 Identities=27% Similarity=0.443 Sum_probs=23.8
Q ss_pred CCccccccccccc---CCHHHHHHHhcCcchHH
Q 007901 181 PPMAWCELCRVDC---NTLEILEQHKNGKRHKR 210 (585)
Q Consensus 181 ~~~~yCdVCkVsc---NSpsqaqsHy~GKKHKK 210 (585)
.....|+||..-. .+..=+..|+.||-|.-
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 4567899999765 46667889999999964
No 98
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.64 E-value=21 Score=42.34 Aligned_cols=63 Identities=21% Similarity=0.211 Sum_probs=43.6
Q ss_pred CCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcccccccccccccccCCCCCCCCCccccccc
Q 007901 334 IPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHRALYGEAALQSLYPASFNSLSSSVITQV 398 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~q~l~g~~glQ~~~Ppn~~a~sn~~~~q~ 398 (585)
..|-|.-|...|....-|.+||..||=...+-.+--.++++... +--.+.--.++.+..++|.
T Consensus 308 KPfeCpnCkKRFSHSGSySSHmSSKKCIsli~vngr~R~~lKt~--~~Sp~saSsSp~~s~~pq~ 370 (1007)
T KOG3623|consen 308 KPFECPNCKKRFSHSGSYSSHMSSKKCISLILVNGRNRALLKTL--EKSPGSASSSPRRSPSPQG 370 (1007)
T ss_pred CCcCCcccccccccCCcccccccccchhhhhcccCcchhhhhhc--ccCCcccCCCCCCCCChhH
Confidence 35899999999999999999999999987776665555665552 2222222234445556665
No 99
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.27 E-value=30 Score=35.84 Aligned_cols=35 Identities=29% Similarity=0.499 Sum_probs=26.7
Q ss_pred CCEeeeecccccCCHHHHHhhhh---hhhHHHHHhhhc
Q 007901 334 IPLICELCNVKCESQVVFDSHLV---GKKHLANVKRFH 368 (585)
Q Consensus 334 ~~l~CeLCNV~cNSe~~~qsHL~---GKKHqkKLKkl~ 368 (585)
..|.|++|+..|+-...|++|++ |-.|+--.|+..
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr 209 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERR 209 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhh
Confidence 46999999999999999999975 445554444443
No 100
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=22.96 E-value=72 Score=32.59 Aligned_cols=17 Identities=53% Similarity=0.896 Sum_probs=9.6
Q ss_pred CCCCcCCCCcccCCCcc
Q 007901 125 RGGGRKGGKPFRRGGRL 141 (585)
Q Consensus 125 ~g~~~~~g~~~~~~gr~ 141 (585)
.|++.++++.||+|+|+
T Consensus 6 gggg~~g~~gfRgg~gg 22 (215)
T KOG3262|consen 6 GGGGGGGGGGFRGGGGG 22 (215)
T ss_pred CCCCCCCCCCcccCCCC
Confidence 34455555666766554
No 101
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=22.29 E-value=66 Score=40.46 Aligned_cols=41 Identities=17% Similarity=0.246 Sum_probs=35.8
Q ss_pred CCCCCEeeeecccccCCHHHHHhhhhhhhHHHHHhhhcccc
Q 007901 331 KGVIPLICELCNVKCESQVVFDSHLVGKKHLANVKRFHGHR 371 (585)
Q Consensus 331 k~~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKLKkl~g~q 371 (585)
+....+.|..||+.++....|-.||..-+|+.+|+.++...
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~ 554 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENA 554 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhcc
Confidence 45568999999999999999999999999999988775444
No 102
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=22.18 E-value=25 Score=36.44 Aligned_cols=41 Identities=20% Similarity=0.347 Sum_probs=29.1
Q ss_pred EeeeecccccC---CHHHHHhhhhhhhHHHHHhhhccccccccc
Q 007901 336 LICELCNVKCE---SQVVFDSHLVGKKHLANVKRFHGHRALYGE 376 (585)
Q Consensus 336 l~CeLCNV~cN---Se~~~qsHL~GKKHqkKLKkl~g~q~l~g~ 376 (585)
-.|.||.+... ...-+..|++||-|+--++-.+.-.++..-
T Consensus 186 qvC~iCgayLsrlDtdrrladHf~GklHlGy~~~R~dl~~llk~ 229 (258)
T COG5200 186 QVCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVRSDLADLLKK 229 (258)
T ss_pred hhhhhhhhHHHhcchhhHHHHHhccchhhhHHHHHHHHHHHHHH
Confidence 47999997764 455799999999998766554444444433
No 103
>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=22.03 E-value=51 Score=27.50 Aligned_cols=22 Identities=23% Similarity=0.531 Sum_probs=16.5
Q ss_pred CEeeeecccccCCHHHHHhhhh
Q 007901 335 PLICELCNVKCESQVVFDSHLV 356 (585)
Q Consensus 335 ~l~CeLCNV~cNSe~~~qsHL~ 356 (585)
.-.|-+|...|.+...|+.||.
T Consensus 24 PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHH
Confidence 4689999999999999999984
No 104
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=21.92 E-value=75 Score=37.97 Aligned_cols=33 Identities=9% Similarity=0.078 Sum_probs=26.8
Q ss_pred CCCCEeeeecccccCCHHHHHhhhhhhhHHHHH
Q 007901 332 GVIPLICELCNVKCESQVVFDSHLVGKKHLANV 364 (585)
Q Consensus 332 ~~~~l~CeLCNV~cNSe~~~qsHL~GKKHqkKL 364 (585)
..+.|.|.+|...|.-....++||+--+-+.+-
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~q~~~ 821 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQQEEQ 821 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 356899999999999999999999766655533
No 105
>PHA00616 hypothetical protein
Probab=21.86 E-value=42 Score=26.74 Aligned_cols=20 Identities=15% Similarity=0.097 Sum_probs=18.4
Q ss_pred ccccccccccCCHHHHHHHh
Q 007901 184 AWCELCRVDCNTLEILEQHK 203 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy 203 (585)
.-|..|...|.....+..|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CccchhhHHHhhHHHHHHHH
Confidence 35999999999999999998
No 106
>PHA02768 hypothetical protein; Provisional
Probab=20.94 E-value=58 Score=27.03 Aligned_cols=21 Identities=14% Similarity=0.167 Sum_probs=18.4
Q ss_pred ccccccccccCCHHHHHHHhc
Q 007901 184 AWCELCRVDCNTLEILEQHKN 204 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~ 204 (585)
+-|+.|+..|+....|..|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r 26 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLR 26 (55)
T ss_pred cCcchhCCeeccHHHHHHHHH
Confidence 479999999999999987763
No 107
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.83 E-value=60 Score=22.45 Aligned_cols=20 Identities=20% Similarity=0.458 Sum_probs=15.8
Q ss_pred EeeeecccccCCHHHHHhhhh
Q 007901 336 LICELCNVKCESQVVFDSHLV 356 (585)
Q Consensus 336 l~CeLCNV~cNSe~~~qsHL~ 356 (585)
.-|.+|+-.| ..+.+..|+.
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 5777777754
No 108
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.62 E-value=48 Score=35.07 Aligned_cols=24 Identities=33% Similarity=0.758 Sum_probs=21.0
Q ss_pred ccccccccccCCHHHHHHHhcCcc
Q 007901 184 AWCELCRVDCNTLEILEQHKNGKR 207 (585)
Q Consensus 184 ~yCdVCkVscNSpsqaqsHy~GKK 207 (585)
-||..||-.|..+..|.+|..-|-
T Consensus 11 pwcwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred ceeeecccccchhhhhhhhhhhcc
Confidence 499999999999999999987553
No 109
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=20.04 E-value=41 Score=36.22 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=25.9
Q ss_pred CCccccccccccc---CCHHHHHHHhcCcchHHHH
Q 007901 181 PPMAWCELCRVDC---NTLEILEQHKNGKRHKRNL 212 (585)
Q Consensus 181 ~~~~yCdVCkVsc---NSpsqaqsHy~GKKHKKNL 212 (585)
.+...|+||.+.+ .+..=+..|+.||-|.--+
T Consensus 184 qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~ 218 (319)
T KOG0796|consen 184 QKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYV 218 (319)
T ss_pred hhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHH
Confidence 4566899999886 4777888999999997544
Done!