Query 012461
Match_columns 463
No_of_seqs 179 out of 200
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 02:53:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012461hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12874 zf-met: Zinc-finger o 98.3 4.2E-07 9.1E-12 59.0 2.2 25 344-368 1-25 (25)
2 smart00451 ZnF_U1 U1-like zinc 98.3 8.2E-07 1.8E-11 61.5 3.4 33 343-375 3-35 (35)
3 PF12874 zf-met: Zinc-finger o 98.2 5.4E-07 1.2E-11 58.4 1.6 25 209-233 1-25 (25)
4 smart00451 ZnF_U1 U1-like zinc 98.0 2.9E-06 6.4E-11 58.7 2.4 32 208-239 3-34 (35)
5 KOG3792 Transcription factor N 97.9 3.7E-06 8E-11 92.6 0.8 90 204-386 189-278 (816)
6 PF12171 zf-C2H2_jaz: Zinc-fin 97.7 2.1E-05 4.5E-10 52.5 2.0 27 343-369 1-27 (27)
7 PF12171 zf-C2H2_jaz: Zinc-fin 97.6 3E-05 6.4E-10 51.7 1.4 27 208-234 1-27 (27)
8 PF06220 zf-U1: U1 zinc finger 96.8 0.0012 2.6E-08 48.2 2.9 33 343-375 3-37 (38)
9 KOG4727 U1-like Zn-finger prot 96.7 0.0011 2.5E-08 62.9 2.9 36 340-375 72-107 (193)
10 PF06220 zf-U1: U1 zinc finger 96.0 0.005 1.1E-07 45.0 2.5 33 207-239 2-36 (38)
11 KOG2785 C2H2-type Zn-finger pr 95.3 0.019 4.1E-07 60.4 4.3 100 208-377 3-102 (390)
12 KOG3032 Uncharacterized conser 94.5 0.048 1E-06 54.3 4.5 50 341-391 33-82 (264)
13 KOG4727 U1-like Zn-finger prot 94.3 0.03 6.6E-07 53.5 2.6 37 207-243 74-110 (193)
14 PF14968 CCDC84: Coiled coil p 93.3 0.071 1.5E-06 55.5 3.5 39 340-378 55-99 (336)
15 KOG0227 Splicing factor 3a, su 93.1 0.048 1.1E-06 53.0 1.8 36 341-376 51-86 (222)
16 KOG3408 U1-like Zn-finger-cont 92.5 0.091 2E-06 47.8 2.6 36 341-376 55-90 (129)
17 PLN02748 tRNA dimethylallyltra 92.4 0.096 2.1E-06 56.7 3.0 37 342-378 417-454 (468)
18 smart00586 ZnF_DBF Zinc finger 92.3 0.057 1.2E-06 41.8 0.9 29 206-237 3-31 (49)
19 KOG0717 Molecular chaperone (D 92.3 0.079 1.7E-06 57.2 2.2 37 342-378 291-327 (508)
20 KOG0717 Molecular chaperone (D 92.1 0.11 2.4E-06 56.2 2.9 37 208-244 292-328 (508)
21 KOG0227 Splicing factor 3a, su 92.0 0.15 3.2E-06 49.7 3.5 39 201-239 46-84 (222)
22 PLN02748 tRNA dimethylallyltra 91.9 0.11 2.4E-06 56.2 2.9 37 206-242 416-453 (468)
23 KOG4722 Zn-finger protein [Gen 91.8 0.09 2E-06 56.3 2.0 33 344-376 494-526 (672)
24 COG5246 PRP11 Splicing factor 91.6 0.13 2.9E-06 49.8 2.7 41 199-239 44-84 (222)
25 KOG3032 Uncharacterized conser 91.5 0.31 6.8E-06 48.7 5.2 39 202-241 29-67 (264)
26 PF07535 zf-DBF: DBF zinc fing 91.1 0.13 2.7E-06 39.9 1.6 29 206-237 3-31 (49)
27 KOG3792 Transcription factor N 91.0 0.087 1.9E-06 59.3 0.9 35 340-374 356-390 (816)
28 PF13894 zf-C2H2_4: C2H2-type 90.6 0.21 4.5E-06 30.8 2.0 21 344-364 1-21 (24)
29 PF12756 zf-C2H2_2: C2H2 type 90.3 0.15 3.2E-06 41.5 1.5 36 204-239 46-81 (100)
30 PF07535 zf-DBF: DBF zinc fing 89.9 0.23 5.1E-06 38.4 2.2 28 342-372 4-31 (49)
31 smart00586 ZnF_DBF Zinc finger 89.5 0.16 3.6E-06 39.3 1.0 28 343-373 5-32 (49)
32 PF13894 zf-C2H2_4: C2H2-type 89.4 0.23 4.9E-06 30.6 1.4 21 209-229 1-21 (24)
33 KOG0150 Spliceosomal protein F 89.1 0.2 4.4E-06 51.7 1.6 36 204-239 6-42 (336)
34 COG5246 PRP11 Splicing factor 88.3 0.37 7.9E-06 46.8 2.7 37 340-376 50-86 (222)
35 KOG3408 U1-like Zn-finger-cont 88.3 0.29 6.4E-06 44.6 1.9 34 208-241 57-90 (129)
36 KOG3454 U1 snRNP-specific prot 87.5 0.36 7.8E-06 45.8 2.2 32 343-374 3-36 (165)
37 PF00096 zf-C2H2: Zinc finger, 87.0 0.51 1.1E-05 29.6 2.0 22 344-365 1-22 (23)
38 PF13912 zf-C2H2_6: C2H2-type 85.2 0.61 1.3E-05 30.4 1.8 21 344-364 2-22 (27)
39 PF12756 zf-C2H2_2: C2H2 type 84.6 0.56 1.2E-05 38.1 1.6 32 342-373 49-80 (100)
40 KOG0150 Spliceosomal protein F 83.0 0.75 1.6E-05 47.7 2.1 34 341-374 8-42 (336)
41 PF00096 zf-C2H2: Zinc finger, 82.6 0.78 1.7E-05 28.8 1.4 22 209-230 1-22 (23)
42 KOG3454 U1 snRNP-specific prot 82.6 0.68 1.5E-05 44.0 1.5 32 208-239 3-36 (165)
43 KOG2785 C2H2-type Zn-finger pr 81.6 1.2 2.7E-05 47.2 3.1 39 204-242 64-102 (390)
44 smart00355 ZnF_C2H2 zinc finge 81.2 1.3 2.9E-05 27.2 2.1 21 344-364 1-21 (26)
45 PF13912 zf-C2H2_6: C2H2-type 79.8 1.3 2.9E-05 28.8 1.7 21 209-229 2-22 (27)
46 COG5188 PRP9 Splicing factor 3 79.4 0.83 1.8E-05 48.3 1.0 33 207-239 237-269 (470)
47 KOG4722 Zn-finger protein [Gen 79.1 1.1 2.4E-05 48.4 1.9 33 208-240 493-525 (672)
48 KOG2837 Protein containing a U 76.5 0.37 8.1E-06 49.2 -2.4 39 340-378 22-60 (309)
49 smart00355 ZnF_C2H2 zinc finge 74.3 1.9 4.1E-05 26.5 1.3 21 209-229 1-21 (26)
50 PF11931 DUF3449: Domain of un 74.0 1 2.2E-05 43.9 0.0 38 341-378 99-137 (196)
51 COG5188 PRP9 Splicing factor 3 72.1 1.8 4E-05 45.8 1.3 35 342-376 237-271 (470)
52 COG5112 UFD2 U1-like Zn-finger 72.0 2.3 5E-05 38.2 1.7 35 208-242 55-89 (126)
53 PF09237 GAGA: GAGA factor; I 65.9 5.9 0.00013 31.4 2.6 28 202-229 18-45 (54)
54 COG5112 UFD2 U1-like Zn-finger 63.2 4.2 9E-05 36.7 1.5 37 342-378 54-90 (126)
55 KOG1146 Homeobox protein [Gene 61.6 4.9 0.00011 48.6 2.2 36 207-242 517-552 (1406)
56 KOG1146 Homeobox protein [Gene 60.9 11 0.00024 45.8 4.8 92 206-379 463-554 (1406)
57 PF10107 Endonuc_Holl: Endonuc 60.3 27 0.00058 33.3 6.3 58 75-134 48-111 (156)
58 PF11931 DUF3449: Domain of un 60.0 2.9 6.4E-05 40.8 0.0 37 204-240 97-134 (196)
59 PF04988 AKAP95: A-kinase anch 60.0 6.5 0.00014 37.6 2.3 32 209-240 1-32 (165)
60 PF12907 zf-met2: Zinc-binding 59.8 4.5 9.8E-05 30.2 1.0 27 209-235 2-31 (40)
61 PTZ00448 hypothetical protein; 58.8 11 0.00023 40.2 3.9 42 342-383 313-354 (373)
62 PF13909 zf-H2C2_5: C2H2-type 57.7 8.7 0.00019 24.4 1.9 21 344-365 1-21 (24)
63 PF04988 AKAP95: A-kinase anch 57.6 8.2 0.00018 36.9 2.5 32 344-375 1-32 (165)
64 KOG2837 Protein containing a U 56.6 2.8 6E-05 43.1 -0.8 32 208-239 25-56 (309)
65 PF13909 zf-H2C2_5: C2H2-type 54.4 8 0.00017 24.6 1.4 20 209-229 1-20 (24)
66 COG5136 U1 snRNP-specific prot 50.7 5.1 0.00011 38.4 -0.0 30 343-372 3-34 (188)
67 PF12013 DUF3505: Protein of u 50.6 44 0.00095 28.8 5.7 32 206-238 9-40 (109)
68 PF11830 DUF3350: Domain of un 44.7 59 0.0013 26.2 5.0 16 53-68 29-44 (56)
69 KOG1994 Predicted RNA binding 44.5 13 0.00028 37.5 1.7 26 206-231 237-262 (268)
70 PF03194 LUC7: LUC7 N_terminus 42.0 14 0.0003 37.3 1.4 32 204-235 186-220 (254)
71 KOG2893 Zn finger protein [Gen 36.2 18 0.00038 37.0 1.2 56 340-396 7-68 (341)
72 KOG2893 Zn finger protein [Gen 34.2 22 0.00047 36.4 1.5 30 202-232 5-34 (341)
73 KOG2505 Ankyrin repeat protein 33.3 25 0.00053 39.2 1.8 33 207-239 65-97 (591)
74 PF08776 VASP_tetra: VASP tetr 33.2 60 0.0013 24.6 3.2 8 61-68 6-13 (40)
75 KOG2636 Splicing factor 3a, su 32.0 23 0.00051 38.8 1.4 38 341-378 399-437 (497)
76 COG4741 Predicted secreted end 31.6 2.4E+02 0.0053 27.2 7.8 68 53-125 41-112 (175)
77 KOG0796 Spliceosome subunit [R 31.4 17 0.00037 38.1 0.2 39 205-243 183-230 (319)
78 PF04959 ARS2: Arsenite-resist 28.6 50 0.0011 32.8 2.9 41 201-242 70-110 (214)
79 KOG4167 Predicted DNA-binding 28.6 2E+02 0.0044 33.8 7.9 34 204-239 788-821 (907)
80 PHA02768 hypothetical protein; 27.6 39 0.00084 27.0 1.6 26 342-369 4-29 (55)
81 PF04959 ARS2: Arsenite-resist 25.8 61 0.0013 32.2 3.0 37 341-378 75-111 (214)
82 smart00734 ZnF_Rad18 Rad18-lik 25.2 54 0.0012 22.1 1.7 19 345-364 3-21 (26)
83 COG5200 LUC7 U1 snRNP componen 24.5 28 0.0006 35.0 0.3 31 206-236 183-216 (258)
84 COG5136 U1 snRNP-specific prot 23.5 31 0.00066 33.3 0.4 32 208-239 3-36 (188)
85 KOG2391 Vacuolar sorting prote 22.7 4.4E+02 0.0096 28.4 8.5 39 52-90 217-255 (365)
86 PHA00616 hypothetical protein 22.6 41 0.00088 25.8 0.8 21 344-364 2-22 (44)
87 PF12037 DUF3523: Domain of un 21.3 1.1E+02 0.0023 31.8 3.7 70 13-82 1-72 (276)
88 PF14968 CCDC84: Coiled coil p 21.0 43 0.00093 35.4 0.9 28 345-375 1-28 (336)
89 PHA00732 hypothetical protein 20.9 71 0.0015 26.8 2.0 22 344-365 2-23 (79)
90 PF09237 GAGA: GAGA factor; I 20.8 85 0.0018 25.1 2.3 25 340-364 21-45 (54)
91 PTZ00448 hypothetical protein; 20.7 62 0.0013 34.7 2.0 32 208-239 314-345 (373)
No 1
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.29 E-value=4.2e-07 Score=58.97 Aligned_cols=25 Identities=36% Similarity=0.701 Sum_probs=24.4
Q ss_pred eeccccccccCCHHHHHHhhhhhhH
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRGKKH 368 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~GkKH 368 (463)
|+|.+|++.|+++..|.+|++|++|
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 7899999999999999999999999
No 2
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.26 E-value=8.2e-07 Score=61.52 Aligned_cols=33 Identities=30% Similarity=0.639 Sum_probs=30.7
Q ss_pred ceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461 343 KFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES 375 (463)
Q Consensus 343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~ 375 (463)
.|+|++|++.|++...+..|++|++|..+++++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHcC
Confidence 588999999999999999999999999999763
No 3
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.22 E-value=5.4e-07 Score=58.44 Aligned_cols=25 Identities=44% Similarity=0.850 Sum_probs=24.5
Q ss_pred eeccccccccCCHHHHHHhhcccch
Q 012461 209 WSCALCQVSATSERGLDEHLQGKKH 233 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLqGKrH 233 (463)
|+|.||+++|+++..|+.|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 8999999999999999999999998
No 4
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.03 E-value=2.9e-06 Score=58.73 Aligned_cols=32 Identities=41% Similarity=0.735 Sum_probs=30.1
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
.++|++|++.|++...+..|+.|++|+.+++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 58999999999999999999999999999864
No 5
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=97.87 E-value=3.7e-06 Score=92.58 Aligned_cols=90 Identities=24% Similarity=0.356 Sum_probs=73.1
Q ss_pred cCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccc
Q 012461 204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEES 283 (463)
Q Consensus 204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~es 283 (463)
...+..+|.+|++.|++.+++.+||+|.||+++... +
T Consensus 189 ~laqL~~~kw~k~~a~G~qs~re~lr~~r~l~krvp---t---------------------------------------- 225 (816)
T KOG3792|consen 189 RLAQLHYCKWCKISAAGPQTYREHLRGQKHLKKEVP---T---------------------------------------- 225 (816)
T ss_pred HHHHhhhhHHHHHhccccHHHHHHHHHHHHHHhccC---C----------------------------------------
Confidence 445688999999999999999999999999998521 0
Q ss_pred ccccccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhh
Q 012461 284 TEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHK 363 (463)
Q Consensus 284 l~~~~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL 363 (463)
.+..+. -...+.|++|.++|++.+-|..||
T Consensus 226 -------~~~~kg-------------------------------------------w~~el~cEksi~tcs~pd~~g~al 255 (816)
T KOG3792|consen 226 -------NGPLKG-------------------------------------------WPLELHCEKSIVTCSGPDAYGAAL 255 (816)
T ss_pred -------CCCccc-------------------------------------------chHHHHHHHhhccccCccchHHHH
Confidence 000000 114567999999999999999999
Q ss_pred hhhhHHHHHHhhhcCCCCcCCCC
Q 012461 364 RGKKHIARSNESKKNDDAVPATS 386 (463)
Q Consensus 364 ~GkKH~aklk~~~~~gk~Vp~~s 386 (463)
+|.+|....+.+...|++|+.-.
T Consensus 256 Rrv~ec~~skL~~k~G~gi~d~c 278 (816)
T KOG3792|consen 256 RRVKECKVSKLHKKLGKGIPDPC 278 (816)
T ss_pred HHHHHhhhhcccccCCCCCCCcc
Confidence 99999999999999998876543
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=97.70 E-value=2.1e-05 Score=52.47 Aligned_cols=27 Identities=30% Similarity=0.621 Sum_probs=25.1
Q ss_pred ceeccccccccCCHHHHHHhhhhhhHH
Q 012461 343 KFWCEDCQVGTHSAVVMEGHKRGKKHI 369 (463)
Q Consensus 343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~ 369 (463)
.|+|.+|++.|+++..|..|++|++|+
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 378999999999999999999999996
No 7
>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=97.58 E-value=3e-05 Score=51.71 Aligned_cols=27 Identities=37% Similarity=0.728 Sum_probs=25.4
Q ss_pred ceeccccccccCCHHHHHHhhcccchH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHK 234 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHK 234 (463)
.|+|.+|+..|.++..|.+|+.||+||
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 379999999999999999999999997
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=96.78 E-value=0.0012 Score=48.20 Aligned_cols=33 Identities=24% Similarity=0.541 Sum_probs=21.4
Q ss_pred ceecccccccc--CCHHHHHHhhhhhhHHHHHHhh
Q 012461 343 KFWCEDCQVGT--HSAVVMEGHKRGKKHIARSNES 375 (463)
Q Consensus 343 ~~~C~lCnV~c--tS~~~~~sHL~GkKH~aklk~~ 375 (463)
.+||+.|++.+ ++...-..|.+|+||+.++++.
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 48999999999 5667779999999999999763
No 9
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=96.69 E-value=0.0011 Score=62.88 Aligned_cols=36 Identities=25% Similarity=0.459 Sum_probs=32.3
Q ss_pred cCCceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES 375 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~ 375 (463)
+..-|+|.+|+-.+-.-.+|..|||||+|+.++.-.
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 457799999999999999999999999999998544
No 10
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=96.04 E-value=0.005 Score=44.96 Aligned_cols=33 Identities=24% Similarity=0.366 Sum_probs=20.9
Q ss_pred Cceecccccccc--CCHHHHHHhhcccchHHHHHH
Q 012461 207 KEWSCALCQVSA--TSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 207 k~w~C~LC~Vt~--tSe~~L~~HLqGKrHKkk~e~ 239 (463)
+.++|+.|++.+ ++...=..|++|.+|+.+++.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred cCeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 468999999999 566777999999999999865
No 11
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=95.27 E-value=0.019 Score=60.37 Aligned_cols=100 Identities=18% Similarity=0.303 Sum_probs=69.0
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccccccc
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVN 287 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~esl~~~ 287 (463)
-++|.-|+|.|.+...-+-|+.--=|+=|+.. +.| ++|.-+- +- +
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKR-kVA---------~lPPIta----------------------E~--F- 47 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKR-KVA---------SLPPITA----------------------EE--F- 47 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHh-Hhh---------cCCCcCH----------------------HH--H-
Confidence 46899999999999999999999999999877 333 2222110 00 0
Q ss_pred ccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhhhhhh
Q 012461 288 KAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKK 367 (463)
Q Consensus 288 ~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL~GkK 367 (463)
..+.++.+.. +.+.++ .....+.|.+|+..+.|...+..||..++
T Consensus 48 -----~~k~~s~~~~-----------~~~~~e-------------------~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~ 92 (390)
T KOG2785|consen 48 -----NEKVLSDDSE-----------KEENLE-------------------EAESVVYCEACNKSFASPKAHENHLKSKK 92 (390)
T ss_pred -----hHHHhhhhhh-----------hhhhhh-------------------hcccceehHHhhccccChhhHHHHHHHhh
Confidence 0000100000 000011 13478899999999999999999999999
Q ss_pred HHHHHHhhhc
Q 012461 368 HIARSNESKK 377 (463)
Q Consensus 368 H~aklk~~~~ 377 (463)
|..++..+..
T Consensus 93 h~~~~~~~~r 102 (390)
T KOG2785|consen 93 HVENLSNHQR 102 (390)
T ss_pred cchhhhhhhc
Confidence 9999999875
No 12
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.46 E-value=0.048 Score=54.29 Aligned_cols=50 Identities=22% Similarity=0.286 Sum_probs=38.4
Q ss_pred CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcCCCCcCCCCCcccC
Q 012461 341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIV 391 (463)
Q Consensus 341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~gk~Vp~~s~~~~~ 391 (463)
+..+.|-+|||-.- +.....|++|++|.-++..++-.|.-|.-..+|+|.
T Consensus 33 sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~k~~~T~~p 82 (264)
T KOG3032|consen 33 SGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVAKTRPTKIP 82 (264)
T ss_pred CCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhcccccCcCccCc
Confidence 46789999999999 999999999999999998887443333333444433
No 13
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=94.27 E-value=0.03 Score=53.47 Aligned_cols=37 Identities=22% Similarity=0.489 Sum_probs=33.4
Q ss_pred CceeccccccccCCHHHHHHhhcccchHHHHHHHHHH
Q 012461 207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRA 243 (463)
Q Consensus 207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a 243 (463)
.-+||.||.-.+-.-..|.+|++||+|+-|+..+.+.
T Consensus 74 ~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm~v 110 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSMRV 110 (193)
T ss_pred CceeeeecceeehhhHHHHHHhccHHHHHHHhhhhcc
Confidence 3689999999999999999999999999999986554
No 14
>PF14968 CCDC84: Coiled coil protein 84
Probab=93.34 E-value=0.071 Score=55.53 Aligned_cols=39 Identities=15% Similarity=0.257 Sum_probs=30.7
Q ss_pred cCCceeccccccccCCH------HHHHHhhhhhhHHHHHHhhhcC
Q 012461 340 KKFKFWCEDCQVGTHSA------VVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~------~~~~sHL~GkKH~aklk~~~~~ 378 (463)
....|||-.|+....-- ..+..||.+.-|+++++...-.
T Consensus 55 ~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~ 99 (336)
T PF14968_consen 55 HRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFWWK 99 (336)
T ss_pred ccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHHHH
Confidence 45789999997665533 4678899999999999998443
No 15
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=93.11 E-value=0.048 Score=52.97 Aligned_cols=36 Identities=22% Similarity=0.269 Sum_probs=32.4
Q ss_pred CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461 341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK 376 (463)
Q Consensus 341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~ 376 (463)
...+-|.||.-.-+++..|..|++||||+.+|-+-.
T Consensus 51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarra 86 (222)
T KOG0227|consen 51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRA 86 (222)
T ss_pred CcceeehhhhhhhcchhhhhhhhccchhhHHHHHHH
Confidence 378999999999999999999999999999886553
No 16
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=92.55 E-value=0.091 Score=47.77 Aligned_cols=36 Identities=25% Similarity=0.378 Sum_probs=34.0
Q ss_pred CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461 341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK 376 (463)
Q Consensus 341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~ 376 (463)
...|+|-.|.-.|-+..+|..|+.||.|.++||.+.
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 378999999999999999999999999999999886
No 17
>PLN02748 tRNA dimethylallyltransferase
Probab=92.39 E-value=0.096 Score=56.71 Aligned_cols=37 Identities=30% Similarity=0.467 Sum_probs=33.3
Q ss_pred Cceecccccc-ccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 342 FKFWCEDCQV-GTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 342 ~~~~C~lCnV-~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
..+.|++|+. ++.++...+.|++|++|+++++...+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~ 454 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK 454 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence 4567999998 899999999999999999999987654
No 18
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=92.34 E-value=0.057 Score=41.85 Aligned_cols=29 Identities=28% Similarity=0.450 Sum_probs=25.0
Q ss_pred CCceeccccccccCCHHHHHHhhcccchHHHH
Q 012461 206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKE 237 (463)
Q Consensus 206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~ 237 (463)
.+.-||+.|++.+. .|..|+.+++|++=.
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhccHHHHHHH
Confidence 35679999999987 799999999999753
No 19
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=92.27 E-value=0.079 Score=57.21 Aligned_cols=37 Identities=22% Similarity=0.395 Sum_probs=33.8
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
..++|-+|+.+|-|+.+|..|.+.|||..+|.++..+
T Consensus 291 e~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 291 EVLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred CceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 3499999999999999999999999999999888654
No 20
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=92.05 E-value=0.11 Score=56.18 Aligned_cols=37 Identities=35% Similarity=0.496 Sum_probs=34.1
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHHHHHHh
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQ 244 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~ 244 (463)
.+||.+|+-+|-|+..|..|-+.|+|+.+++.|....
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqem 328 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQEM 328 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHHH
Confidence 4999999999999999999999999999999977543
No 21
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=92.02 E-value=0.15 Score=49.68 Aligned_cols=39 Identities=28% Similarity=0.473 Sum_probs=34.2
Q ss_pred ccccCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 201 MSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 201 ~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
..+.--..+.|.||...-.++..+.-|++||||+.|++.
T Consensus 46 ~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlar 84 (222)
T KOG0227|consen 46 FMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLAR 84 (222)
T ss_pred hhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHH
Confidence 334455578999999999999999999999999999987
No 22
>PLN02748 tRNA dimethylallyltransferase
Probab=91.94 E-value=0.11 Score=56.17 Aligned_cols=37 Identities=19% Similarity=0.430 Sum_probs=32.3
Q ss_pred CCceecccccc-ccCCHHHHHHhhcccchHHHHHHHHH
Q 012461 206 TKEWSCALCQV-SATSERGLDEHLQGKKHKAKEAGLLR 242 (463)
Q Consensus 206 ~k~w~C~LC~V-t~tSe~~L~~HLqGKrHKkk~e~L~~ 242 (463)
-+..+|++|+. ++.++..-+.|+.||+||+++..+.+
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 34557999998 89999999999999999999988544
No 23
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=91.80 E-value=0.09 Score=56.34 Aligned_cols=33 Identities=33% Similarity=0.403 Sum_probs=30.3
Q ss_pred eeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK 376 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~ 376 (463)
--|++|||...|++.|-+|..|+||+..|..+.
T Consensus 494 kqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 494 KQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 469999999999999999999999999987664
No 24
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=91.65 E-value=0.13 Score=49.77 Aligned_cols=41 Identities=32% Similarity=0.618 Sum_probs=36.3
Q ss_pred ccccccCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 199 PLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 199 p~~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
|...+.--..+.|-||+..--++..+..|++||+|+-++..
T Consensus 44 Pyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~r 84 (222)
T COG5246 44 PYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSR 84 (222)
T ss_pred cchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHH
Confidence 45555666789999999999999999999999999999887
No 25
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.53 E-value=0.31 Score=48.69 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=35.6
Q ss_pred cccCCCceeccccccccCCHHHHHHhhcccchHHHHHHHH
Q 012461 202 SSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLL 241 (463)
Q Consensus 202 ~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~ 241 (463)
..+......|.||+|-.- +....-|..||+|+.+++.|+
T Consensus 29 kyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 29 KYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred ccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHH
Confidence 346677899999999999 999999999999999999987
No 26
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=91.05 E-value=0.13 Score=39.86 Aligned_cols=29 Identities=34% Similarity=0.591 Sum_probs=24.9
Q ss_pred CCceeccccccccCCHHHHHHhhcccchHHHH
Q 012461 206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKE 237 (463)
Q Consensus 206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~ 237 (463)
.+.-||+.|++.+. .|..|+++++|++=.
T Consensus 3 ~k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 3 KKPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 35679999999998 599999999999753
No 27
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=91.02 E-value=0.087 Score=59.28 Aligned_cols=35 Identities=23% Similarity=0.491 Sum_probs=31.1
Q ss_pred cCCceeccccccccCCHHHHHHhhhhhhHHHHHHh
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNE 374 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~ 374 (463)
+...|.|.+|+-.|+....-..||+|.||.-.-++
T Consensus 356 K~~~f~cKlcdckf~d~nak~mhl~grRhrLQYk~ 390 (816)
T KOG3792|consen 356 KLLRFHCKLCDCKFNDPNAKEMHLKGRRHRLQYKQ 390 (816)
T ss_pred chHhhhhhhhcCCCCCcchHHhhhhcccccceecc
Confidence 45789999999999999999999999999866654
No 28
>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=90.57 E-value=0.21 Score=30.80 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=17.6
Q ss_pred eeccccccccCCHHHHHHhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~ 364 (463)
|.|.+|+..+.+...|..|+.
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 579999999999999999985
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.28 E-value=0.15 Score=41.47 Aligned_cols=36 Identities=28% Similarity=0.620 Sum_probs=27.3
Q ss_pred cCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
+....|.|.+|...+.+...|+.|++.+.|+.....
T Consensus 46 ~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~~ 81 (100)
T PF12756_consen 46 KVKESFRCPYCNKTFRSREALQEHMRSKHHKKRNSE 81 (100)
T ss_dssp ---SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred ccCCCCCCCccCCCCcCHHHHHHHHcCccCCCcccc
Confidence 444479999999999999999999999999986443
No 30
>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=89.91 E-value=0.23 Score=38.41 Aligned_cols=28 Identities=29% Similarity=0.478 Sum_probs=24.3
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHH
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARS 372 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~akl 372 (463)
..-+|+.|.+.+. +|..|+.+.+|++-.
T Consensus 4 k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 4 KPGYCENCRVKYD---DLEEHIQSEKHRKFA 31 (49)
T ss_pred CCccCccccchhh---hHHHHhCCHHHHHHH
Confidence 4457999999998 699999999999765
No 31
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=89.47 E-value=0.16 Score=39.32 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=24.1
Q ss_pred ceeccccccccCCHHHHHHhhhhhhHHHHHH
Q 012461 343 KFWCEDCQVGTHSAVVMEGHKRGKKHIARSN 373 (463)
Q Consensus 343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk 373 (463)
.-+|+.|.+.+. +|..|+.+.+|++-.+
T Consensus 5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 5 PGYCENCREKYD---DLETHLLSEKHRRFAE 32 (49)
T ss_pred CcccccHhHHHh---hHHHHhccHHHHHHHc
Confidence 457999999987 8999999999997553
No 32
>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=89.35 E-value=0.23 Score=30.63 Aligned_cols=21 Identities=29% Similarity=0.714 Sum_probs=17.7
Q ss_pred eeccccccccCCHHHHHHhhc
Q 012461 209 WSCALCQVSATSERGLDEHLQ 229 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLq 229 (463)
|.|.+|...+.+...|+.|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 689999999999999999985
No 33
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=89.05 E-value=0.2 Score=51.72 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=31.6
Q ss_pred cCCCceecccccccc-CCHHHHHHhhcccchHHHHHH
Q 012461 204 KKTKEWSCALCQVSA-TSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 204 k~~k~w~C~LC~Vt~-tSe~~L~~HLqGKrHKkk~e~ 239 (463)
+.+...+|++|+|=+ +.......|-+|||||.+++.
T Consensus 6 kS~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 6 KSQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred hhccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 456688999999987 778889999999999999886
No 34
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=88.30 E-value=0.37 Score=46.81 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=32.7
Q ss_pred cCCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK 376 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~ 376 (463)
....|.|.+|+-.-.++..|..|+.||||+-++-+-.
T Consensus 50 h~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs 86 (222)
T COG5246 50 HTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRS 86 (222)
T ss_pred CCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHH
Confidence 3478999999999999999999999999998876553
No 35
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=88.25 E-value=0.29 Score=44.57 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=32.2
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLL 241 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~ 241 (463)
.+||-.|---|.++++|+.|+.+|.||..+..|.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 6899999999999999999999999999998864
No 36
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=87.53 E-value=0.36 Score=45.83 Aligned_cols=32 Identities=25% Similarity=0.560 Sum_probs=26.8
Q ss_pred ceecccccccc--CCHHHHHHhhhhhhHHHHHHh
Q 012461 343 KFWCEDCQVGT--HSAVVMEGHKRGKKHIARSNE 374 (463)
Q Consensus 343 ~~~C~lCnV~c--tS~~~~~sHL~GkKH~aklk~ 374 (463)
.++|+-|++.. .|..+=..|+.|+||+.+++-
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 57899999544 578899999999999988753
No 37
>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=86.96 E-value=0.51 Score=29.63 Aligned_cols=22 Identities=23% Similarity=0.388 Sum_probs=20.1
Q ss_pred eeccccccccCCHHHHHHhhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRG 365 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~G 365 (463)
|.|..|+..|.+...|..|++-
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 5699999999999999999874
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=85.25 E-value=0.61 Score=30.42 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=19.7
Q ss_pred eeccccccccCCHHHHHHhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~ 364 (463)
+.|.+|+..|.+...|..|++
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 679999999999999999984
No 39
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=84.58 E-value=0.56 Score=38.09 Aligned_cols=32 Identities=28% Similarity=0.466 Sum_probs=26.8
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHHH
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSN 373 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk 373 (463)
..|.|.+|+..|.+...|..|++.+.|.....
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 36899999999999999999999999987653
No 40
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=82.96 E-value=0.75 Score=47.67 Aligned_cols=34 Identities=24% Similarity=0.492 Sum_probs=28.0
Q ss_pred CCceecccccccc-CCHHHHHHhhhhhhHHHHHHh
Q 012461 341 KFKFWCEDCQVGT-HSAVVMEGHKRGKKHIARSNE 374 (463)
Q Consensus 341 ~~~~~C~lCnV~c-tS~~~~~sHL~GkKH~aklk~ 374 (463)
....||++|.|.+ +.......|-+|++|+.+|.+
T Consensus 8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 3567899999987 457788999999999988743
No 41
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=82.61 E-value=0.78 Score=28.78 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=20.0
Q ss_pred eeccccccccCCHHHHHHhhcc
Q 012461 209 WSCALCQVSATSERGLDEHLQG 230 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLqG 230 (463)
|.|..|...|++...|+.|++-
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5799999999999999999863
No 42
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=82.59 E-value=0.68 Score=44.01 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=27.9
Q ss_pred ceecccccc--ccCCHHHHHHhhcccchHHHHHH
Q 012461 208 EWSCALCQV--SATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 208 ~w~C~LC~V--t~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
.+||+.|++ +=+|.++=+.||.|++|+.++..
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 579999984 44899999999999999999874
No 43
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=81.58 E-value=1.2 Score=47.22 Aligned_cols=39 Identities=26% Similarity=0.391 Sum_probs=35.2
Q ss_pred cCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461 204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR 242 (463)
Q Consensus 204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~ 242 (463)
+.....+|.+|+-.+.|+....+||..|+|+.++....+
T Consensus 64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 64 EAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred hcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 445678999999999999999999999999999998765
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=81.23 E-value=1.3 Score=27.18 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=19.3
Q ss_pred eeccccccccCCHHHHHHhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~ 364 (463)
+.|..|...|++...|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 359999999999999999987
No 45
>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=79.79 E-value=1.3 Score=28.82 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=19.6
Q ss_pred eeccccccccCCHHHHHHhhc
Q 012461 209 WSCALCQVSATSERGLDEHLQ 229 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLq 229 (463)
..|.+|+..|.+...|..|++
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 579999999999999999994
No 46
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=79.37 E-value=0.83 Score=48.27 Aligned_cols=33 Identities=24% Similarity=0.493 Sum_probs=29.9
Q ss_pred CceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
...||.+|+--|..-+++..||.||+|.++...
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~ 269 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQG 269 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhh
Confidence 456999999999999999999999999998765
No 47
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=79.13 E-value=1.1 Score=48.38 Aligned_cols=33 Identities=36% Similarity=0.576 Sum_probs=30.2
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGL 240 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L 240 (463)
..-|.||+|-.+|+.-|-+|..|++|+..+..|
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 446999999999999999999999999988774
No 48
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=76.51 E-value=0.37 Score=49.16 Aligned_cols=39 Identities=18% Similarity=0.313 Sum_probs=35.0
Q ss_pred cCCceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
++..|+|.+|+..|+.+.-|.+|+...-|++.+.+...+
T Consensus 22 QKlRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~~N 60 (309)
T KOG2837|consen 22 QKLRWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFALN 60 (309)
T ss_pred HHHHHHHHHHHHHhccccccccccCCHHHHHHHHHHHhC
Confidence 347899999999999999999999999999999777554
No 49
>smart00355 ZnF_C2H2 zinc finger.
Probab=74.29 E-value=1.9 Score=26.49 Aligned_cols=21 Identities=29% Similarity=0.645 Sum_probs=19.2
Q ss_pred eeccccccccCCHHHHHHhhc
Q 012461 209 WSCALCQVSATSERGLDEHLQ 229 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLq 229 (463)
+.|..|..+|.+...|+.|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 369999999999999999987
No 50
>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=73.97 E-value=1 Score=43.90 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=0.0
Q ss_pred CCceecccc-ccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 341 KFKFWCEDC-QVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 341 ~~~~~C~lC-nV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
...|.|+|| |.+.-+..+|..|.+..||+.=|+.+.-.
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 357799999 88999999999999999999888776543
No 51
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=72.12 E-value=1.8 Score=45.80 Aligned_cols=35 Identities=26% Similarity=0.440 Sum_probs=30.7
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK 376 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~ 376 (463)
..++|..|...|..-.+|.+|+.||.|.+..+...
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~ 271 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKE 271 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhh
Confidence 46799999999999999999999999998775543
No 52
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=72.03 E-value=2.3 Score=38.24 Aligned_cols=35 Identities=31% Similarity=0.478 Sum_probs=31.9
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR 242 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~ 242 (463)
.+||--|---|.++..|..|+.||-|+..+..|..
T Consensus 55 qhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 68999999999999999999999999999888543
No 53
>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=65.92 E-value=5.9 Score=31.44 Aligned_cols=28 Identities=25% Similarity=0.563 Sum_probs=19.9
Q ss_pred cccCCCceeccccccccCCHHHHHHhhc
Q 012461 202 SSKKTKEWSCALCQVSATSERGLDEHLQ 229 (463)
Q Consensus 202 ~kk~~k~w~C~LC~Vt~tSe~~L~~HLq 229 (463)
...+.+.-+|.+|...+.+...|.-||.
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 3466778899999999999999999985
No 54
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=63.24 E-value=4.2 Score=36.68 Aligned_cols=37 Identities=24% Similarity=0.413 Sum_probs=34.1
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
..++|--|.--|-++.+|..|+.|+=|..+++.+.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 6789999999999999999999999999999988654
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=61.60 E-value=4.9 Score=48.61 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=31.6
Q ss_pred CceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461 207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR 242 (463)
Q Consensus 207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~ 242 (463)
+..-|..|++++++...|-.||+--+|+.+++.+.+
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~ 552 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEE 552 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHh
Confidence 466799999999999999999999999999776433
No 56
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=60.86 E-value=11 Score=45.77 Aligned_cols=92 Identities=15% Similarity=0.188 Sum_probs=67.4
Q ss_pred CCceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccccc
Q 012461 206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTE 285 (463)
Q Consensus 206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~esl~ 285 (463)
.+...|..|+..+.-+.+|.-|.+-|-|.... .++.+.+..
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~-~~c~~gq~~-------------------------------------- 503 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS-AYCKAGQNH-------------------------------------- 503 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccccccccch-hHhHhcccc--------------------------------------
Confidence 37889999999999999999999999998887 545442110
Q ss_pred ccccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhhhh
Q 012461 286 VNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRG 365 (463)
Q Consensus 286 ~~~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL~G 365 (463)
+... .++++. .....+.|..|+++++....|-.||+.
T Consensus 504 ----~~~a--------------------rg~~~~-------------------~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 504 ----PRLA--------------------RGEVYR-------------------CPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ----cccc--------------------cccccc-------------------CCCCcccceeeeeeeecchHHHHHHHH
Confidence 0000 000000 012567899999999999999999999
Q ss_pred hhHHHHHHhhhcCC
Q 012461 366 KKHIARSNESKKND 379 (463)
Q Consensus 366 kKH~aklk~~~~~g 379 (463)
-+|..+++.....+
T Consensus 541 ~~h~~~lee~~~~~ 554 (1406)
T KOG1146|consen 541 DLHRNELEEAEENA 554 (1406)
T ss_pred HhhHHHHHHHHhcc
Confidence 99999987775553
No 57
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=60.31 E-value=27 Score=33.29 Aligned_cols=58 Identities=24% Similarity=0.264 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh---cCCCchhhhhhcccCCCcccccCCcccccC---CCCCCCC
Q 012461 75 RRLLEEEVRRELMMEREMARASE---MGLSMDERLSMQLHSRYPLMHQLNNRWLED---RFPFPGS 134 (463)
Q Consensus 75 rr~lE~evrrE~~~er~~~~~~~---~g~~~~~~~~~~~~~~~p~~~~~~~~~~~~---~~~~pg~ 134 (463)
+-+||.|...++..-|.-++.+| .+.-..|+|+|.| |-+| ++|-+.++++. +-+|+|.
T Consensus 48 ~~~~~~w~~~~~~~~rkdav~rSravl~Gkv~EqlaP~l-p~F~-ynP~D~RFlG~PVD~IvF~Gl 111 (156)
T PF10107_consen 48 EAELEEWKQKEEKEIRKDAVKRSRAVLKGKVSEQLAPFL-PEFP-YNPKDARFLGSPVDFIVFDGL 111 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcchhHHHhhhcc-CCCC-CChhhheecCCCceEEEEcCC
Confidence 34566666666665565565555 3333578888866 4455 56667777754 4566773
No 58
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=59.99 E-value=2.9 Score=40.83 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=0.0
Q ss_pred cCCCceecccc-ccccCCHHHHHHhhcccchHHHHHHH
Q 012461 204 KKTKEWSCALC-QVSATSERGLDEHLQGKKHKAKEAGL 240 (463)
Q Consensus 204 k~~k~w~C~LC-~Vt~tSe~~L~~HLqGKrHKkk~e~L 240 (463)
....++.|+|| +.+.-+...|..|++.-||.--+..|
T Consensus 97 GL~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcL 134 (196)
T PF11931_consen 97 GLGVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCL 134 (196)
T ss_dssp --------------------------------------
T ss_pred CCCCeeeeEeCCCcceecHHHHHHhcChhHHHccChhc
Confidence 45568999999 67777999999999999999999984
No 59
>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=59.98 E-value=6.5 Score=37.56 Aligned_cols=32 Identities=25% Similarity=0.628 Sum_probs=29.6
Q ss_pred eeccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461 209 WSCALCQVSATSERGLDEHLQGKKHKAKEAGL 240 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L 240 (463)
++|.+|+...--+..+..||+++-|+.-+.-+
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 47999999999999999999999999888775
No 60
>PF12907 zf-met2: Zinc-binding
Probab=59.78 E-value=4.5 Score=30.24 Aligned_cols=27 Identities=33% Similarity=0.635 Sum_probs=22.4
Q ss_pred eeccccc---cccCCHHHHHHhhcccchHH
Q 012461 209 WSCALCQ---VSATSERGLDEHLQGKKHKA 235 (463)
Q Consensus 209 w~C~LC~---Vt~tSe~~L~~HLqGKrHKk 235 (463)
..|.||+ +..+++..|.+|...|--|.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 4699999 77799999999999875553
No 61
>PTZ00448 hypothetical protein; Provisional
Probab=58.81 E-value=11 Score=40.25 Aligned_cols=42 Identities=14% Similarity=0.360 Sum_probs=36.9
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcCCCCcC
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVP 383 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~gk~Vp 383 (463)
..+.|..|++.|.+...+..|...-=|.-+||+......||-
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gLppvs 354 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKMEPIS 354 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCCCCCC
Confidence 468899999999999999999999999999998877655553
No 62
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=57.70 E-value=8.7 Score=24.44 Aligned_cols=21 Identities=19% Similarity=0.498 Sum_probs=16.4
Q ss_pred eeccccccccCCHHHHHHhhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRG 365 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~G 365 (463)
+.|..|+-.++ ...|..|++-
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 46999999998 9999999863
No 63
>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=57.64 E-value=8.2 Score=36.91 Aligned_cols=32 Identities=25% Similarity=0.307 Sum_probs=30.0
Q ss_pred eeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRGKKHIARSNES 375 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~ 375 (463)
|.|.+|.....-+..+..||.++=|+..++-+
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 57999999999999999999999999988777
No 64
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=56.60 E-value=2.8 Score=43.05 Aligned_cols=32 Identities=25% Similarity=0.581 Sum_probs=30.6
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
.|||-.||-.|..+-+|+.|+..--|+..+..
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~ 56 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLLL 56 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHHH
Confidence 79999999999999999999999999998876
No 65
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=54.41 E-value=8 Score=24.59 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=15.9
Q ss_pred eeccccccccCCHHHHHHhhc
Q 012461 209 WSCALCQVSATSERGLDEHLQ 229 (463)
Q Consensus 209 w~C~LC~Vt~tSe~~L~~HLq 229 (463)
.-|.+|.-+++ +..|..|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 35999999998 999999986
No 66
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=50.66 E-value=5.1 Score=38.40 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=24.9
Q ss_pred ceeccccccccC--CHHHHHHhhhhhhHHHHH
Q 012461 343 KFWCEDCQVGTH--SAVVMEGHKRGKKHIARS 372 (463)
Q Consensus 343 ~~~C~lCnV~ct--S~~~~~sHL~GkKH~akl 372 (463)
.++|+.|++..+ +..+-.+|+-|++|..+.
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~ 34 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMR 34 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHH
Confidence 478999998776 567889999999998654
No 67
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=50.59 E-value=44 Score=28.81 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=25.5
Q ss_pred CCceeccccccccCCHHHHHHhhcccchHHHHH
Q 012461 206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKEA 238 (463)
Q Consensus 206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e 238 (463)
-+.|.|..|+....- ..+..||+.+-|..+-.
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~ 40 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQ 40 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHH
Confidence 457999999987766 89999999987765433
No 68
>PF11830 DUF3350: Domain of unknown function (DUF3350); InterPro: IPR021785 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.
Probab=44.67 E-value=59 Score=26.21 Aligned_cols=16 Identities=25% Similarity=0.418 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 012461 53 TIQREIEKERIRHEII 68 (463)
Q Consensus 53 ~l~re~~ke~iR~eii 68 (463)
+-.|+||+-.|.|.||
T Consensus 29 eelR~LWrkAI~QqIl 44 (56)
T PF11830_consen 29 EELRELWRKAIHQQIL 44 (56)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6677899999999998
No 69
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=44.45 E-value=13 Score=37.51 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=23.8
Q ss_pred CCceeccccccccCCHHHHHHhhccc
Q 012461 206 TKEWSCALCQVSATSERGLDEHLQGK 231 (463)
Q Consensus 206 ~k~w~C~LC~Vt~tSe~~L~~HLqGK 231 (463)
..-|||=.|.+.+.++.+|-+||=|-
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCCC
Confidence 46899999999999999999999884
No 70
>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=41.98 E-value=14 Score=37.25 Aligned_cols=32 Identities=28% Similarity=0.604 Sum_probs=25.6
Q ss_pred cCCCceecccccc---ccCCHHHHHHhhcccchHH
Q 012461 204 KKTKEWSCALCQV---SATSERGLDEHLQGKKHKA 235 (463)
Q Consensus 204 k~~k~w~C~LC~V---t~tSe~~L~~HLqGKrHKk 235 (463)
..++.-.|+||.+ ...+..-|.+|+.||-|.-
T Consensus 186 ~~qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 186 QQQKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cccCccchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 3456789999974 4477888999999999964
No 71
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=36.16 E-value=18 Score=36.98 Aligned_cols=56 Identities=20% Similarity=0.245 Sum_probs=38.0
Q ss_pred cCCceeccccccccCCHHHHHHhhhhhhHHHH----HHhhhcCCCCcCCCC--CcccCCCCCC
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIAR----SNESKKNDDAVPATS--SMTIVAPPDP 396 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~ak----lk~~~~~gk~Vp~~s--~~~~~~~~~~ 396 (463)
+-.+-||..||-.|..+..|.+|...| |.+- -|+....|..|.+.- +.+|+.-|+.
T Consensus 7 k~~kpwcwycnrefddekiliqhqkak-hfkchichkkl~sgpglsihcmqvhketid~ip~a 68 (341)
T KOG2893|consen 7 KVDKPWCWYCNREFDDEKILIQHQKAK-HFKCHICHKKLFSGPGLSIHCMQVHKETIDKIPAA 68 (341)
T ss_pred ccCCceeeecccccchhhhhhhhhhhc-cceeeeehhhhccCCCceeehhhhhhhhhhccccc
Confidence 346779999999999999999998764 4432 345566677777653 2334444433
No 72
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=34.22 E-value=22 Score=36.36 Aligned_cols=30 Identities=30% Similarity=0.545 Sum_probs=23.3
Q ss_pred cccCCCceeccccccccCCHHHHHHhhcccc
Q 012461 202 SSKKTKEWSCALCQVSATSERGLDEHLQGKK 232 (463)
Q Consensus 202 ~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKr 232 (463)
+||+.+.| |..|+-.|+.+..|.+|..-|-
T Consensus 5 kkk~~kpw-cwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 5 KKKVDKPW-CWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred ccccCCce-eeecccccchhhhhhhhhhhcc
Confidence 44555565 8999999999999999976653
No 73
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=33.29 E-value=25 Score=39.20 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=31.0
Q ss_pred CceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
..|.|..|+++|.+-....+|++---|+-|+..
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Kr 97 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKR 97 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999999776
No 74
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=33.23 E-value=60 Score=24.55 Aligned_cols=8 Identities=50% Similarity=1.057 Sum_probs=3.6
Q ss_pred HHHHHHHH
Q 012461 61 ERIRHEII 68 (463)
Q Consensus 61 e~iR~eii 68 (463)
+++.+|||
T Consensus 6 e~~KqEIL 13 (40)
T PF08776_consen 6 ERLKQEIL 13 (40)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 44444444
No 75
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.98 E-value=23 Score=38.76 Aligned_cols=38 Identities=13% Similarity=0.160 Sum_probs=32.0
Q ss_pred CCceecccc-ccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 341 KFKFWCEDC-QVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 341 ~~~~~C~lC-nV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
+..|.|+|| |-+..+...|.-|.+-++|.-=++.+.-.
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIp 437 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIP 437 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhHHHHHhhcceecCCC
Confidence 456789999 59999999999999999999777665544
No 76
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=31.60 E-value=2.4e+02 Score=27.22 Aligned_cols=68 Identities=18% Similarity=0.271 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----cCCCchhhhhhcccCCCcccccCCcccc
Q 012461 53 TIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASE----MGLSMDERLSMQLHSRYPLMHQLNNRWL 125 (463)
Q Consensus 53 ~l~re~~ke~iR~eii~~E~a~rr~lE~evrrE~~~er~~~~~~~----~g~~~~~~~~~~~~~~~p~~~~~~~~~~ 125 (463)
+|+++.-.+.+++.+...| +.|.|++|...-+..-|+-|.+.| .|- -.|+|+|.|.. + -++|-+.++.
T Consensus 41 ~l~~~e~~r~v~ea~~~ke--~~~Kl~E~iekkieeaR~dav~kS~~Vi~Gr-VtEqlaPffp~-f-~ynPkD~RfI 112 (175)
T COG4741 41 TLQKAERERLVNEAQARKE--EEWKLKEWIEKKIEEAREDAVRKSRAVILGR-VTEQLAPFFPE-F-KYNPKDARFI 112 (175)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhHHHHhhh-hHhhhcccccC-C-CcCCccceee
Confidence 3444433444555554444 345666655544444466666666 332 23455542221 0 1455555544
No 77
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=31.36 E-value=17 Score=38.11 Aligned_cols=39 Identities=31% Similarity=0.499 Sum_probs=30.4
Q ss_pred CCCceecccccccc---CCHHHHHHhhcccchH------HHHHHHHHH
Q 012461 205 KTKEWSCALCQVSA---TSERGLDEHLQGKKHK------AKEAGLLRA 243 (463)
Q Consensus 205 ~~k~w~C~LC~Vt~---tSe~~L~~HLqGKrHK------kk~e~L~~a 243 (463)
.++.-.|+||.+-. +...=|.+||.||-|- .+++.|+..
T Consensus 183 ~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~ 230 (319)
T KOG0796|consen 183 QQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKE 230 (319)
T ss_pred hhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHH
Confidence 45677999997654 8899999999999995 455665554
No 78
>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=28.60 E-value=50 Score=32.80 Aligned_cols=41 Identities=20% Similarity=0.437 Sum_probs=31.3
Q ss_pred ccccCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461 201 MSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR 242 (463)
Q Consensus 201 ~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~ 242 (463)
.++.....|.|.+|..-|-.+.-...|+. +||..+++.+..
T Consensus 70 ~~e~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ 110 (214)
T PF04959_consen 70 TKEEDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKK 110 (214)
T ss_dssp E-SSSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHH
T ss_pred HHHHcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHH
Confidence 33456668999999999999999999998 789999988654
No 79
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=28.57 E-value=2e+02 Score=33.76 Aligned_cols=34 Identities=21% Similarity=0.386 Sum_probs=26.7
Q ss_pred cCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
..+..+-|.+|.-.|.--..+|-|. |+|+-+.++
T Consensus 788 ~~~giFpCreC~kvF~KiKSrNAHM--K~Hr~q~~~ 821 (907)
T KOG4167|consen 788 DPTGIFPCRECGKVFFKIKSRNAHM--KTHRQQEEQ 821 (907)
T ss_pred CCCceeehHHHHHHHHHHhhhhHHH--HHHHHHHHH
Confidence 4466889999999898888888887 677766654
No 80
>PHA02768 hypothetical protein; Provisional
Probab=27.64 E-value=39 Score=26.99 Aligned_cols=26 Identities=23% Similarity=0.219 Sum_probs=21.6
Q ss_pred CceeccccccccCCHHHHHHhhhhhhHH
Q 012461 342 FKFWCEDCQVGTHSAVVMEGHKRGKKHI 369 (463)
Q Consensus 342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~ 369 (463)
.-|.|+.|...|+..+.|..|++= |.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHh--cC
Confidence 346899999999999999888754 55
No 81
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=25.82 E-value=61 Score=32.16 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=29.1
Q ss_pred CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461 341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN 378 (463)
Q Consensus 341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~ 378 (463)
..+|.|.+|...|-...-..-||. .||...|+..++.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~e 111 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKE 111 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHH
Confidence 467999999999999999999998 5799999877543
No 82
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=25.18 E-value=54 Score=22.09 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=16.8
Q ss_pred eccccccccCCHHHHHHhhh
Q 012461 345 WCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 345 ~C~lCnV~ctS~~~~~sHL~ 364 (463)
.|.+|+... +...++.||.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999998 7889999986
No 83
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=24.47 E-value=28 Score=34.97 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=25.5
Q ss_pred CCceecccccccc---CCHHHHHHhhcccchHHH
Q 012461 206 TKEWSCALCQVSA---TSERGLDEHLQGKKHKAK 236 (463)
Q Consensus 206 ~k~w~C~LC~Vt~---tSe~~L~~HLqGKrHKkk 236 (463)
|+...|.||.+-. +...-|..|+.||-|.--
T Consensus 183 qklqvC~iCgayLsrlDtdrrladHf~GklHlGy 216 (258)
T COG5200 183 QKLQVCGICGAYLSRLDTDRRLADHFNGKLHLGY 216 (258)
T ss_pred hhhhhhhhhhhHHHhcchhhHHHHHhccchhhhH
Confidence 4567899998765 778889999999999753
No 84
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=23.45 E-value=31 Score=33.31 Aligned_cols=32 Identities=19% Similarity=0.275 Sum_probs=27.0
Q ss_pred ceecccccccc--CCHHHHHHhhcccchHHHHHH
Q 012461 208 EWSCALCQVSA--TSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 208 ~w~C~LC~Vt~--tSe~~L~~HLqGKrHKkk~e~ 239 (463)
.++|+.|++-. ++.++-..|+.|++|--..+.
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~d 36 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKD 36 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHH
Confidence 47899999865 788999999999999877654
No 85
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.67 E-value=4.4e+02 Score=28.38 Aligned_cols=39 Identities=15% Similarity=0.061 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012461 52 YTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMER 90 (463)
Q Consensus 52 ~~l~re~~ke~iR~eii~~E~a~rr~lE~evrrE~~~er 90 (463)
+.||+.+++|.-|..-+.+++.++.+--.+-..||.+++
T Consensus 217 eklR~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~ 255 (365)
T KOG2391|consen 217 EKLRRRREEEMERLQAEQESLKRTEEELNIGKQKLVAMK 255 (365)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHH
Confidence 467777777777776666666666554444445554443
No 86
>PHA00616 hypothetical protein
Probab=22.61 E-value=41 Score=25.76 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=19.2
Q ss_pred eeccccccccCCHHHHHHhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~ 364 (463)
+-|..|...|.....|..|++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH
Confidence 569999999999999999994
No 87
>PF12037 DUF3523: Domain of unknown function (DUF3523); InterPro: IPR021911 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with PF00004 from PFAM. This domain has a conserved LER sequence motif.
Probab=21.26 E-value=1.1e+02 Score=31.75 Aligned_cols=70 Identities=13% Similarity=0.168 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCcchhhhhh-hccCCCCCCCCCCcch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012461 13 TPCRSSPSPSSHSLSYFSEQALR-VNYSMDPNFMHNPRDF-YTIQREIEKERIRHEIITAENLRRRLLEEEV 82 (463)
Q Consensus 13 ~~~~~~p~ps~~~~~~~s~~~~r-~~~~~~~~~~~~~~~~-~~l~re~~ke~iR~eii~~E~a~rr~lE~ev 82 (463)
|+||++|+|+.++.+......-+ .+|++||+.+-...-. ++|-+-----..=+-|-..|..++-++.+++
T Consensus 1 p~pp~~~~~~~~~~~~~~~~~~~~~~~~FDP~aLERaAkAlrel~~S~~Ak~afel~k~QE~TkQ~E~~ak~ 72 (276)
T PF12037_consen 1 PSPPSQPGPADSGGSKPRNDNPRTTASGFDPEALERAAKALRELNSSPHAKKAFELMKKQEETKQAELQAKI 72 (276)
T ss_pred CcCCCCCCCCCCCCcCCCCCCCCcccCCCCcHHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHHHHHHHHHH
No 88
>PF14968 CCDC84: Coiled coil protein 84
Probab=21.01 E-value=43 Score=35.41 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=24.2
Q ss_pred eccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461 345 WCEDCQVGTHSAVVMEGHKRGKKHIARSNES 375 (463)
Q Consensus 345 ~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~ 375 (463)
+|.+|+.++.. -.-|..+.+|++.|...
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 69999998875 77899999999998765
No 89
>PHA00732 hypothetical protein
Probab=20.93 E-value=71 Score=26.82 Aligned_cols=22 Identities=27% Similarity=0.508 Sum_probs=19.7
Q ss_pred eeccccccccCCHHHHHHhhhh
Q 012461 344 FWCEDCQVGTHSAVVMEGHKRG 365 (463)
Q Consensus 344 ~~C~lCnV~ctS~~~~~sHL~G 365 (463)
+.|.+|...+++...|..|+..
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 5699999999999999999863
No 90
>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=20.80 E-value=85 Score=25.11 Aligned_cols=25 Identities=12% Similarity=0.141 Sum_probs=17.3
Q ss_pred cCCceeccccccccCCHHHHHHhhh
Q 012461 340 KKFKFWCEDCQVGTHSAVVMEGHKR 364 (463)
Q Consensus 340 ~~~~~~C~lCnV~ctS~~~~~sHL~ 364 (463)
....-.|.+|...|.+.-+|.-||.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHH
Confidence 3456789999999999999999984
No 91
>PTZ00448 hypothetical protein; Provisional
Probab=20.71 E-value=62 Score=34.73 Aligned_cols=32 Identities=13% Similarity=0.315 Sum_probs=29.9
Q ss_pred ceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461 208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAG 239 (463)
Q Consensus 208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~ 239 (463)
..+|..|++.|.+....++|+..-=|+=|+..
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKR 345 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKR 345 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHHH
Confidence 46799999999999999999999999999877
Done!