Query 045234
Match_columns 299
No_of_seqs 275 out of 756
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 11:09:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045234hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1946 RNA polymerase I trans 99.9 1E-28 2.2E-33 227.6 5.9 157 128-287 3-180 (240)
2 PF02201 SWIB: SWIB/MDM2 domai 99.7 1.3E-18 2.9E-23 134.3 3.1 63 216-282 9-76 (76)
3 smart00151 SWIB SWI complex, B 99.7 4.2E-17 9.1E-22 126.3 5.5 64 216-282 9-76 (77)
4 COG5531 SWIB-domain-containing 99.5 4.6E-15 1E-19 136.7 5.9 69 212-283 125-197 (237)
5 PRK14724 DNA topoisomerase III 99.5 3.1E-14 6.7E-19 153.3 5.1 62 216-281 920-986 (987)
6 PRK06319 DNA topoisomerase I/S 98.8 2.7E-09 5.8E-14 114.2 2.7 64 216-282 792-859 (860)
7 KOG2570 SWI/SNF transcription 98.3 4E-07 8.8E-12 89.8 4.2 66 216-284 213-282 (420)
8 smart00249 PHD PHD zinc finger 98.2 1.2E-06 2.6E-11 59.0 3.3 44 16-61 1-47 (47)
9 COG5034 TNG2 Chromatin remodel 98.1 2E-06 4.4E-11 80.4 2.5 46 11-60 218-266 (271)
10 KOG4299 PHD Zn-finger protein 98.0 3E-06 6.6E-11 87.1 1.7 51 14-66 253-307 (613)
11 KOG1973 Chromatin remodeling p 97.9 6.1E-06 1.3E-10 78.0 2.2 46 12-60 217-264 (274)
12 KOG0383 Predicted helicase [Ge 97.8 7.9E-06 1.7E-10 85.8 1.7 70 33-104 1-91 (696)
13 PF00628 PHD: PHD-finger; Int 97.7 6.2E-06 1.4E-10 58.1 -0.1 43 16-60 1-47 (51)
14 KOG1244 Predicted transcriptio 97.7 1.2E-05 2.6E-10 76.1 0.9 95 11-108 221-332 (336)
15 KOG1081 Transcription factor N 97.7 3.8E-05 8.2E-10 77.7 4.1 143 5-165 80-230 (463)
16 KOG0383 Predicted helicase [Ge 97.6 1.6E-05 3.4E-10 83.7 1.2 51 12-65 45-95 (696)
17 KOG4299 PHD Zn-finger protein 97.6 3.1E-05 6.8E-10 79.8 2.3 52 62-113 255-311 (613)
18 KOG4443 Putative transcription 97.5 2.9E-05 6.3E-10 80.5 1.3 92 13-107 17-118 (694)
19 KOG1512 PHD Zn-finger protein 97.4 6.1E-05 1.3E-09 71.9 1.3 87 14-105 258-361 (381)
20 KOG0956 PHD finger protein AF1 96.8 0.00067 1.4E-08 71.1 2.1 60 17-81 8-72 (900)
21 KOG0954 PHD finger protein [Ge 96.8 0.00061 1.3E-08 71.8 1.8 45 12-61 269-318 (893)
22 KOG1244 Predicted transcriptio 96.6 0.0013 2.9E-08 62.5 2.5 43 14-59 281-326 (336)
23 PF15446 zf-PHD-like: PHD/FYVE 96.5 0.002 4.4E-08 57.4 3.3 72 16-89 1-142 (175)
24 KOG1473 Nucleosome remodeling 96.5 0.0015 3.3E-08 71.5 2.5 62 12-78 342-403 (1414)
25 smart00249 PHD PHD zinc finger 96.4 0.0026 5.6E-08 42.5 2.3 43 62-104 1-47 (47)
26 KOG1512 PHD Zn-finger protein 96.2 0.0021 4.6E-08 61.6 1.7 41 15-60 315-358 (381)
27 KOG0955 PHD finger protein BR1 96.1 0.0049 1.1E-07 67.8 4.2 63 11-83 216-285 (1051)
28 PF00628 PHD: PHD-finger; Int 96.1 0.0026 5.7E-08 44.6 1.4 45 62-106 1-50 (51)
29 KOG0825 PHD Zn-finger protein 95.4 0.0093 2E-07 63.6 2.5 44 14-60 215-262 (1134)
30 KOG4443 Putative transcription 95.3 0.0093 2E-07 62.4 2.1 69 16-87 70-153 (694)
31 PF13771 zf-HC5HC2H: PHD-like 94.3 0.019 4.1E-07 44.6 1.2 48 14-61 36-89 (90)
32 cd04718 BAH_plant_2 BAH, or Br 93.3 0.06 1.3E-06 47.1 2.4 30 37-67 1-30 (148)
33 KOG0825 PHD Zn-finger protein 93.2 0.049 1.1E-06 58.4 2.1 46 61-107 216-266 (1134)
34 COG5141 PHD zinc finger-contai 93.1 0.054 1.2E-06 55.5 2.2 58 14-81 193-257 (669)
35 KOG3362 Predicted BBOX Zn-fing 89.4 0.16 3.5E-06 44.4 1.1 43 36-87 103-146 (156)
36 PF13832 zf-HC5HC2H_2: PHD-zin 89.4 0.21 4.5E-06 40.4 1.6 34 13-46 54-88 (110)
37 KOG0957 PHD finger protein [Ge 88.2 0.39 8.4E-06 49.6 3.0 62 15-83 120-194 (707)
38 PF13831 PHD_2: PHD-finger; PD 85.9 0.29 6.2E-06 32.9 0.4 32 24-59 2-33 (36)
39 KOG0957 PHD finger protein [Ge 85.0 0.38 8.1E-06 49.7 1.0 45 60-104 544-595 (707)
40 KOG1245 Chromatin remodeling c 84.8 0.23 5E-06 56.7 -0.7 46 12-60 1106-1154(1404)
41 KOG4323 Polycomb-like PHD Zn-f 82.9 0.57 1.2E-05 47.8 1.2 47 16-69 170-224 (464)
42 KOG4628 Predicted E3 ubiquitin 81.7 0.94 2E-05 44.8 2.2 43 15-69 230-276 (348)
43 KOG4323 Polycomb-like PHD Zn-f 81.7 0.6 1.3E-05 47.7 0.9 97 13-114 82-231 (464)
44 PF11793 FANCL_C: FANCL C-term 78.2 1 2.2E-05 34.3 1.0 32 14-45 2-39 (70)
45 KOG3612 PHD Zn-finger protein 77.6 1.8 3.9E-05 45.1 2.8 53 12-68 58-110 (588)
46 PF14446 Prok-RING_1: Prokaryo 76.1 1.5 3.2E-05 32.4 1.3 30 15-46 6-39 (54)
47 KOG0955 PHD finger protein BR1 75.9 1.3 2.8E-05 49.4 1.4 41 62-105 221-267 (1051)
48 cd04718 BAH_plant_2 BAH, or Br 75.8 1.5 3.3E-05 38.5 1.5 25 80-105 1-25 (148)
49 PF04438 zf-HIT: HIT zinc fing 74.3 0.9 2E-05 29.4 -0.2 24 59-82 1-24 (30)
50 PF13832 zf-HC5HC2H_2: PHD-zin 73.9 2.2 4.7E-05 34.3 1.9 74 16-91 2-90 (110)
51 KOG2522 Filamentous baseplate 70.3 5.7 0.00012 40.8 4.2 46 220-266 369-418 (560)
52 COG5141 PHD zinc finger-contai 70.1 1.9 4.1E-05 44.7 0.8 33 14-46 303-336 (669)
53 PF06524 NOA36: NOA36 protein; 68.0 4.4 9.6E-05 38.9 2.8 44 62-105 173-216 (314)
54 KOG1973 Chromatin remodeling p 61.1 5.4 0.00012 37.9 2.0 49 51-106 215-267 (274)
55 cd05502 Bromo_tif1_like Bromod 56.1 7.2 0.00016 31.7 1.7 40 103-149 8-47 (109)
56 cd05519 Bromo_SNF2 Bromodomain 55.6 8.5 0.00018 31.0 2.0 45 103-149 4-50 (103)
57 PF10497 zf-4CXXC_R1: Zinc-fin 52.6 4 8.8E-05 33.6 -0.3 32 75-106 34-69 (105)
58 smart00064 FYVE Protein presen 50.9 11 0.00023 27.7 1.8 45 62-106 12-64 (68)
59 KOG1245 Chromatin remodeling c 49.7 4.2 9.2E-05 46.9 -0.9 47 62-109 1110-1160(1404)
60 cd05515 Bromo_polybromo_V Brom 47.9 13 0.00029 30.1 2.0 45 103-149 4-50 (105)
61 PF09889 DUF2116: Uncharacteri 46.8 15 0.00032 27.6 1.9 21 94-114 13-34 (59)
62 cd05495 Bromo_cbp_like Bromodo 44.3 17 0.00036 29.7 2.1 15 135-149 36-50 (108)
63 KOG1473 Nucleosome remodeling 44.0 7 0.00015 44.1 -0.3 46 13-59 427-474 (1414)
64 KOG3576 Ovo and related transc 43.8 4.2 9E-05 38.0 -1.7 54 23-90 114-192 (267)
65 PF03107 C1_2: C1 domain; Int 41.8 20 0.00042 22.8 1.7 24 62-85 2-29 (30)
66 KOG0956 PHD finger protein AF1 40.8 13 0.00027 40.2 1.0 36 70-108 21-58 (900)
67 cd05496 Bromo_WDR9_II Bromodom 39.0 20 0.00042 30.1 1.7 41 103-149 9-49 (119)
68 KOG1734 Predicted RING-contain 37.9 20 0.00044 34.8 1.8 66 61-142 225-301 (328)
69 PF10367 Vps39_2: Vacuolar sor 37.6 18 0.00039 28.2 1.2 32 11-44 75-108 (109)
70 PF02318 FYVE_2: FYVE-type zin 37.5 17 0.00037 30.1 1.1 48 60-111 54-107 (118)
71 PF15446 zf-PHD-like: PHD/FYVE 37.3 14 0.0003 33.3 0.6 27 63-89 2-35 (175)
72 PF13901 DUF4206: Domain of un 37.2 26 0.00057 31.7 2.4 29 70-108 171-199 (202)
73 cd05503 Bromo_BAZ2A_B_like Bro 35.9 24 0.00051 28.1 1.7 41 103-149 4-44 (97)
74 cd05517 Bromo_polybromo_II Bro 35.8 24 0.00051 28.6 1.7 42 104-149 5-50 (103)
75 cd00065 FYVE FYVE domain; Zinc 35.4 20 0.00043 25.2 1.1 44 62-105 4-55 (57)
76 PF07649 C1_3: C1-like domain; 35.4 13 0.00027 23.5 0.0 24 62-85 2-29 (30)
77 cd05505 Bromo_WSTF_like Bromod 32.1 30 0.00066 27.7 1.7 41 103-149 4-44 (97)
78 PF03380 DUF282: Caenorhabditi 31.5 32 0.00069 23.9 1.5 23 29-56 2-24 (39)
79 cd05521 Bromo_Rsc1_2_I Bromodo 30.2 32 0.0007 28.1 1.6 42 104-149 6-51 (106)
80 cd05524 Bromo_polybromo_I Brom 30.1 29 0.00062 28.6 1.3 43 103-149 6-52 (113)
81 COG5222 Uncharacterized conser 30.0 11 0.00025 36.9 -1.2 49 62-114 276-326 (427)
82 PF00641 zf-RanBP: Zn-finger i 29.0 33 0.00072 21.5 1.2 25 53-79 2-26 (30)
83 COG5082 AIR1 Arginine methyltr 28.5 43 0.00092 30.7 2.2 50 12-73 58-110 (190)
84 cd05494 Bromodomain_1 Bromodom 27.4 33 0.00071 28.5 1.2 42 101-149 5-49 (114)
85 PLN02915 cellulose synthase A 27.4 39 0.00085 38.1 2.1 57 56-116 11-75 (1044)
86 KOG1671 Ubiquinol cytochrome c 27.2 41 0.00088 31.2 1.9 21 39-61 155-175 (210)
87 cd05497 Bromo_Brdt_I_like Brom 27.1 40 0.00087 27.5 1.7 24 123-149 25-51 (107)
88 cd05507 Bromo_brd8_like Bromod 26.9 38 0.00081 27.4 1.5 40 104-149 8-47 (104)
89 PF13639 zf-RING_2: Ring finge 26.5 19 0.00041 24.2 -0.3 30 15-46 1-33 (44)
90 cd05500 Bromo_BDF1_2_I Bromodo 26.3 46 0.001 26.6 1.9 44 103-150 8-51 (103)
91 cd05504 Bromo_Acf1_like Bromod 26.3 41 0.0009 27.8 1.6 43 101-149 14-56 (115)
92 PF00130 C1_1: Phorbol esters/ 25.9 35 0.00077 23.6 1.0 28 62-89 13-46 (53)
93 cd05498 Bromo_Brdt_II_like Bro 25.4 53 0.0012 26.0 2.1 46 103-149 4-49 (102)
94 cd05506 Bromo_plant1 Bromodoma 25.4 55 0.0012 25.8 2.1 42 103-149 4-46 (99)
95 PF07191 zinc-ribbons_6: zinc- 25.2 15 0.00032 28.5 -1.1 37 71-107 17-59 (70)
96 PF08225 Antimicrobial19: Pseu 24.8 82 0.0018 19.2 2.2 19 262-280 4-22 (23)
97 KOG0954 PHD finger protein [Ge 24.5 27 0.00058 38.1 0.2 41 62-105 273-319 (893)
98 PF01363 FYVE: FYVE zinc finge 23.4 52 0.0011 24.1 1.5 48 61-108 10-67 (69)
99 PF00643 zf-B_box: B-box zinc 23.3 19 0.00041 23.9 -0.8 26 62-87 5-31 (42)
100 PHA02929 N1R/p28-like protein; 23.3 32 0.0007 32.4 0.5 30 13-45 173-211 (238)
101 cd05520 Bromo_polybromo_III Br 23.3 58 0.0013 26.3 1.9 25 123-149 26-50 (103)
102 cd05513 Bromo_brd7_like Bromod 23.2 57 0.0012 26.3 1.9 25 123-149 21-45 (98)
103 cd05501 Bromo_SP100C_like Brom 22.6 65 0.0014 26.4 2.1 39 103-149 6-44 (102)
104 PF13842 Tnp_zf-ribbon_2: DDE_ 22.4 63 0.0014 21.1 1.6 22 63-84 3-29 (32)
105 PF13907 DUF4208: Domain of un 22.1 82 0.0018 25.4 2.6 53 208-269 38-99 (100)
106 cd03467 Rieske Rieske domain; 22.0 1E+02 0.0022 23.7 3.1 34 23-62 32-65 (98)
107 COG1997 RPL43A Ribosomal prote 21.5 56 0.0012 26.5 1.5 29 60-88 35-70 (89)
108 cd05522 Bromo_Rsc1_2_II Bromod 21.4 69 0.0015 25.9 2.0 25 123-149 27-51 (104)
109 PF10281 Ish1: Putative stress 21.2 1E+02 0.0022 20.5 2.4 31 212-243 2-38 (38)
110 COG0723 QcrA Rieske Fe-S prote 21.0 57 0.0012 28.5 1.6 22 39-61 110-131 (177)
111 PF15227 zf-C3HC4_4: zinc fing 20.9 22 0.00048 24.3 -0.8 29 75-104 14-42 (42)
112 PF04236 Transp_Tc5_C: Tc5 tra 20.4 64 0.0014 24.4 1.5 26 61-86 28-55 (63)
113 smart00547 ZnF_RBZ Zinc finger 20.3 64 0.0014 19.3 1.2 24 54-79 1-24 (26)
114 PF09463 Opy2: Opy2 protein; 20.2 51 0.0011 22.3 0.8 20 63-82 11-35 (35)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.95 E-value=1e-28 Score=227.56 Aligned_cols=157 Identities=15% Similarity=0.164 Sum_probs=113.9
Q ss_pred CcccccchhhHHhhhccccCCChhhHHHHHHhhhcCCccc--c-ccccccCcccccccccccccccc-ccccc-------
Q 045234 128 GERNRFYFKGYWQKIKEKESLTPENVISAYYLLKKGEMHK--L-VSNTFASYEEEHNLSLCWNKKRK-RSNRK------- 196 (299)
Q Consensus 128 ~~~~e~lfk~yw~~ik~k~~lt~~~l~~a~~~~~~~~~~~--~-~~~~~~~~d~~~~~~~~~~~~~k-~~~~~------- 196 (299)
..+|+++|.+||...+.++.||.++|.+|.+.+.+-...+ . ........++..+....++.+++ +..+.
T Consensus 3 ~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~~k~~~~k~~~~~~~~~~~~~ 82 (240)
T KOG1946|consen 3 SLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALPVKGSKKKKRGSKTRSRKPKS 82 (240)
T ss_pred chhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccccccccccccccccccccCcc
Confidence 4589999999999999999999999999999998865531 1 11111222223333334443333 11111
Q ss_pred ccCccccccccccchhhhH-HHHHHHHHHhhhh-----hhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH-
Q 045234 197 TSGKKEKSSRSYYMRVRWY-LEMQKMLKLHART-----LQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR- 269 (299)
Q Consensus 197 ~~~k~~k~~~~~~~~~gw~-~eL~~fl~~~g~~-----lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~- 269 (299)
...+..+..+... ++|| ..|+.|+..+++. |||+ +|+++||+|||+||||||.||+.|+||++|+.||++
T Consensus 83 ~~~~~~~~~~~~~--~~~g~~kl~~ls~~L~~~~G~~~lsR~-~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k 159 (240)
T KOG1946|consen 83 LESSGEKNKKKKK--ASWGSTKLIPLSPSLARFVGTSELSRT-DVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKK 159 (240)
T ss_pred cccccccchhccc--cCcCcccccccCHHHHhhcccccccHH-HHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccC
Confidence 0001111112222 6699 8888888888654 9999 999999999999999999999999999999999997
Q ss_pred ---HhhhHHHHhcccCCCCCC
Q 045234 270 ---NHHLQGLLNTMEFLPTCH 287 (299)
Q Consensus 270 ---~f~m~klL~~H~~~p~~~ 287 (299)
||+|++||++||+.+.=.
T Consensus 160 ~v~~fem~KLL~~H~~~~~d~ 180 (240)
T KOG1946|consen 160 RVGMFEMLKLLTKHFLKNQDM 180 (240)
T ss_pred ccceeeHHHHHHHhccCcccc
Confidence 999999999999876543
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.73 E-value=1.3e-18 Score=134.31 Aligned_cols=63 Identities=11% Similarity=0.084 Sum_probs=56.6
Q ss_pred HHHHHHHHHhhhh-hhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH----HhhhHHHHhcccC
Q 045234 216 LEMQKMLKLHART-LQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR----NHHLQGLLNTMEF 282 (299)
Q Consensus 216 ~eL~~fl~~~g~~-lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~----~f~m~klL~~H~~ 282 (299)
++|++|+ |.+ +||. +|++.||+|||+||||||+||+.|+||++|+.||+. +|+|+++|.+|++
T Consensus 9 ~~L~~~l---g~~~~sr~-~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 9 PELAEFL---GEDELSRS-EVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp HHHHHHT---T-SCEEHH-HHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred HHHHHHh---CCCCCCHH-HHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence 6777776 444 9999 999999999999999999999999999999999998 9999999999974
No 3
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.68 E-value=4.2e-17 Score=126.26 Aligned_cols=64 Identities=9% Similarity=0.074 Sum_probs=59.5
Q ss_pred HHHHHHHHHhhhhhhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH----HhhhHHHHhcccC
Q 045234 216 LEMQKMLKLHARTLQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR----NHHLQGLLNTMEF 282 (299)
Q Consensus 216 ~eL~~fl~~~g~~lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~----~f~m~klL~~H~~ 282 (299)
++|++|+|. ..++|. +|++.||+|||+||||||.+|+.|+||+.|++|||+ +++|+++|++|+.
T Consensus 9 ~~L~~~lg~--~~~tr~-ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~ 76 (77)
T smart00151 9 PELAKVLGA--PEMTRT-EIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLI 76 (77)
T ss_pred HHHHHHhCC--CcCcHH-HHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcC
Confidence 789999862 349999 999999999999999999999999999999999997 9999999999975
No 4
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.55 E-value=4.6e-15 Score=136.67 Aligned_cols=69 Identities=9% Similarity=-0.015 Sum_probs=62.4
Q ss_pred hhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHH-H---HhhhHHHHhcccCC
Q 045234 212 VRWYLEMQKMLKLHARTLQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYL-R---NHHLQGLLNTMEFL 283 (299)
Q Consensus 212 ~gw~~eL~~fl~~~g~~lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~-~---~f~m~klL~~H~~~ 283 (299)
+...+.|+.|||. .+++|+ |||+.||+|||+||||||.|||.|+||++|+.||| . ||+|.++|.+|++.
T Consensus 125 ~~lS~~La~ilG~--~~~tr~-~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~ 197 (237)
T COG5531 125 VKLSPKLAAILGL--EPGTRP-EAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIK 197 (237)
T ss_pred eecCHHHHHHhCC--CCCCcc-HHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceec
Confidence 4445889999852 349999 99999999999999999999999999999999999 4 99999999999986
No 5
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.47 E-value=3.1e-14 Score=153.34 Aligned_cols=62 Identities=5% Similarity=0.013 Sum_probs=59.0
Q ss_pred HHHHHHHHHhhhh-hhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH----HhhhHHHHhccc
Q 045234 216 LEMQKMLKLHART-LQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR----NHHLQGLLNTME 281 (299)
Q Consensus 216 ~eL~~fl~~~g~~-lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~----~f~m~klL~~H~ 281 (299)
++|++||+ .+ ++|+ +|++.||+|||+||||||.|||.|+||++|+.|||+ ||+|+++|++|+
T Consensus 920 ~~La~~lg---~~~~~r~-~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl 986 (987)
T PRK14724 920 AALAAVIG---AEPVARP-EVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHL 986 (987)
T ss_pred HHHHHHhC---CCcCCHH-HHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhc
Confidence 89999984 44 9999 999999999999999999999999999999999997 999999999996
No 6
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=98.77 E-value=2.7e-09 Score=114.22 Aligned_cols=64 Identities=6% Similarity=-0.080 Sum_probs=57.9
Q ss_pred HHHHHHHHHhhhhhhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH----HhhhHHHHhcccC
Q 045234 216 LEMQKMLKLHARTLQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR----NHHLQGLLNTMEF 282 (299)
Q Consensus 216 ~eL~~fl~~~g~~lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~----~f~m~klL~~H~~ 282 (299)
++|.+|++. ..++|. +|++.||+|||+|+||||.+|+.|+||++|+.||++ +|.|+++|+.|+.
T Consensus 792 ~~La~~~g~--~~~sr~-~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~ 859 (860)
T PRK06319 792 PALAAMIGA--EPVGRG-EATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI 859 (860)
T ss_pred cccccccCc--CccCch-HHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence 677778742 249999 999999999999999999999999999999999997 8899999999975
No 7
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=98.33 E-value=4e-07 Score=89.79 Aligned_cols=66 Identities=17% Similarity=0.117 Sum_probs=58.1
Q ss_pred HHHHHHHHHhhhhhhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH----HhhhHHHHhcccCCC
Q 045234 216 LEMQKMLKLHARTLQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR----NHHLQGLLNTMEFLP 284 (299)
Q Consensus 216 ~eL~~fl~~~g~~lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~----~f~m~klL~~H~~~p 284 (299)
+.|+..||.. +=+|+ +||..||.|||.|+||||.++..|.||.-|+.+||. +.++..+|++|+.-|
T Consensus 213 p~La~lLGi~--t~Trp-~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~ 282 (420)
T KOG2570|consen 213 PRLANLLGIH--TGTRP-DIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPP 282 (420)
T ss_pred HHHHHHhhhc--cCcch-HHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCC
Confidence 8888888743 46788 999999999999999999999999999999999998 777888898877544
No 8
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.05 E-value=2e-06 Score=80.39 Aligned_cols=46 Identities=41% Similarity=0.961 Sum_probs=40.9
Q ss_pred cccccccceeccC--CceeeeCCCCCCC-cccccccCCCccccCCCCCeeccC
Q 045234 11 EISEIWCFKCKHG--GELRLCDNTRCLK-VYHPECVDKDESFLAAKTKWICNW 60 (299)
Q Consensus 11 ~~~ed~C~vC~dG--GeLv~CD~~~CPk-aYH~~Cl~~~~~~~~~~g~W~Cp~ 60 (299)
++++-||| |..+ |++|-||..+|++ .||..|||+..+ |.|.||||-
T Consensus 218 e~e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~p---PKG~WYC~e 266 (271)
T COG5034 218 EGEELYCF-CQQVSYGQMVACDNANCKREWFHLECVGLKEP---PKGKWYCPE 266 (271)
T ss_pred cCceeEEE-ecccccccceecCCCCCchhheeccccccCCC---CCCcEeCHH
Confidence 45677899 9875 9999999999998 999999999877 999999983
No 10
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.95 E-value=3e-06 Score=87.11 Aligned_cols=51 Identities=22% Similarity=0.515 Sum_probs=41.7
Q ss_pred ccccceeccCCce---eeeCCCCCCCcccccccCCCcc-ccCCCCCeeccCCccccc
Q 045234 14 EIWCFKCKHGGEL---RLCDNTRCLKVYHPECVDKDES-FLAAKTKWICNWHFCGVC 66 (299)
Q Consensus 14 ed~C~vC~dGGeL---v~CD~~~CPkaYH~~Cl~~~~~-~~~~~g~W~Cp~H~C~~C 66 (299)
++||+.|...|.. +||| +||++||..||.|+.. .-.|.|.|+||.|-|.+=
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD--~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCD--GCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccccccceeec--CCchHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 4599999999877 9999 9999999999998622 124899999997666543
No 11
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.87 E-value=6.1e-06 Score=77.98 Aligned_cols=46 Identities=28% Similarity=0.586 Sum_probs=38.0
Q ss_pred cccccccee-ccCCceeeeCCCCCC-CcccccccCCCccccCCCCCeeccC
Q 045234 12 ISEIWCFKC-KHGGELRLCDNTRCL-KVYHPECVDKDESFLAAKTKWICNW 60 (299)
Q Consensus 12 ~~ed~C~vC-~dGGeLv~CD~~~CP-kaYH~~Cl~~~~~~~~~~g~W~Cp~ 60 (299)
++.-||+.. ...|++|-||..+|| ..||..|||+... |.|.||||.
T Consensus 217 ~e~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~---PkgkWyC~~ 264 (274)
T KOG1973|consen 217 DEPTYCICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKTK---PKGKWYCPR 264 (274)
T ss_pred CCCEEEEecccccccccccCCCCCCcceEEEeccccccC---CCCcccchh
Confidence 345566643 348999999988899 8999999999876 999999993
No 12
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.79 E-value=7.9e-06 Score=85.85 Aligned_cols=70 Identities=21% Similarity=0.538 Sum_probs=56.2
Q ss_pred CCCCcccccccCCCccccCCCCCeeccCC--------------------ccccccCCc-eeccccCCCCCCCcccCcccc
Q 045234 33 RCLKVYHPECVDKDESFLAAKTKWICNWH--------------------FCGVCRKAS-KFYCFCCPSAVCKTCLYDIQF 91 (299)
Q Consensus 33 ~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H--------------------~C~~C~~~~-~~~C~~Cp~s~c~~CL~~~~~ 91 (299)
.|||+||..|+.+... ..++++|.||.+ .|.+|+.++ ++.|++||.|||..|+.++..
T Consensus 1 ~~~r~~~~~~~~p~~~-~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~ 79 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLK-EEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGELLWCDTCPASFHASCLGPPLT 79 (696)
T ss_pred CCCcccCcCCCCcccc-cCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCC
Confidence 4899999999997543 346899999953 699999985 678999999999999986655
Q ss_pred ccccCCccccccc
Q 045234 92 ALVKENKGFCNSC 104 (299)
Q Consensus 92 ~~v~~~~~~C~~C 104 (299)
.. +...|.|.+|
T Consensus 80 ~~-p~~~~~c~Rc 91 (696)
T KOG0383|consen 80 PQ-PNGEFICPRC 91 (696)
T ss_pred cC-Cccceeeeee
Confidence 43 4334999887
No 13
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.74 E-value=6.2e-06 Score=58.10 Aligned_cols=43 Identities=33% Similarity=0.802 Sum_probs=33.7
Q ss_pred ccceecc---CCceeeeCCCCCCCcccccccCCCccc-cCCCCCeeccC
Q 045234 16 WCFKCKH---GGELRLCDNTRCLKVYHPECVDKDESF-LAAKTKWICNW 60 (299)
Q Consensus 16 ~C~vC~d---GGeLv~CD~~~CPkaYH~~Cl~~~~~~-~~~~g~W~Cp~ 60 (299)
+|.+|+. ++++|.|+ .|.+.||..|+++.... ..+.+.|+||.
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~~~~H~~C~~~~~~~~~~~~~~w~C~~ 47 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCNRWYHQECVGPPEKAEEIPSGDWYCPN 47 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTSCEEETTTSTSSHSHHSHHSSSBSSHH
T ss_pred eCcCCCCcCCCCCeEEcC--CCChhhCcccCCCChhhccCCCCcEECcC
Confidence 4778876 78999999 99999999999986431 11345899983
No 14
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.68 E-value=1.2e-05 Score=76.10 Aligned_cols=95 Identities=23% Similarity=0.512 Sum_probs=75.6
Q ss_pred cccccccceeccC----------CceeeeCCCCCCCcccccccCCCcc--ccCCCCCeeccCC-ccccccCC----ceec
Q 045234 11 EISEIWCFKCKHG----------GELRLCDNTRCLKVYHPECVDKDES--FLAAKTKWICNWH-FCGVCRKA----SKFY 73 (299)
Q Consensus 11 ~~~ed~C~vC~dG----------GeLv~CD~~~CPkaYH~~Cl~~~~~--~~~~~g~W~Cp~H-~C~~C~~~----~~~~ 73 (299)
.....+|--|..+ -+||-|. .|.|+=|+.||..+.. .....=+|.|--+ .|.+||-. .++.
T Consensus 221 a~Pn~YCDFclgdsr~nkkt~~peelvscs--dcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllf 298 (336)
T KOG1244|consen 221 AQPNPYCDFCLGDSRENKKTGMPEELVSCS--DCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLF 298 (336)
T ss_pred ccCCcccceeccccccccccCCchhhcchh--hcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEe
Confidence 4567889999643 2899999 9999999999987532 1113457999865 78999965 4799
Q ss_pred cccCCCCCCCcccCccccccccCCcccccccHHHH
Q 045234 74 CFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELA 108 (299)
Q Consensus 74 C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~ 108 (299)
|+-|.+.||..||.++..+. +.+.|-|--|++..
T Consensus 299 cddcdrgyhmyclsppm~ep-pegswsc~KOG~~~ 332 (336)
T KOG1244|consen 299 CDDCDRGYHMYCLSPPMVEP-PEGSWSCHLCLEEL 332 (336)
T ss_pred ecccCCceeeEecCCCcCCC-CCCchhHHHHHHHH
Confidence 99999999999999886554 88999999998754
No 15
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=97.66 E-value=3.8e-05 Score=77.65 Aligned_cols=143 Identities=13% Similarity=0.051 Sum_probs=91.0
Q ss_pred cccccccccccccceeccCCceeeeC------CCCCCCcccccccCC--CccccCCCCCeeccCCccccccCCceecccc
Q 045234 5 KRLKKEEISEIWCFKCKHGGELRLCD------NTRCLKVYHPECVDK--DESFLAAKTKWICNWHFCGVCRKASKFYCFC 76 (299)
Q Consensus 5 ~krk~~~~~ed~C~vC~dGGeLv~CD------~~~CPkaYH~~Cl~~--~~~~~~~~g~W~Cp~H~C~~C~~~~~~~C~~ 76 (299)
+-++.+..+.++||+|.+||.+++|+ ++.||.+||+.|+.. +..++.....|.|-|+.|..+..-.-+.|..
T Consensus 80 ~~~~~~~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~~~~~c~~~~~d~~~~~~~~~~~~vw~~vg~~~~~~c~vc~~ 159 (463)
T KOG1081|consen 80 GSRRHPKIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPAQLEKCSKRCTDCRAFKKREVGDLVWSKVGEYPWWPCMVCHD 159 (463)
T ss_pred CchhccCCCcchhccccCCCccceeccccccccccCcCccCcccccCCcceeeeccccceeEEeEEcCcccccccceecC
Confidence 34566778899999999999999999 999999999999998 5555556778999988887776544222222
Q ss_pred CCCCCCCcccCccccccccCCcccccccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCChhhHHHH
Q 045234 77 CPSAVCKTCLYDIQFALVKENKGFCNSCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLTPENVISA 156 (299)
Q Consensus 77 Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt~~~l~~a 156 (299)
..++ +. .. .+ +..+..| ..+..+...... .| ++.+ ...++++.||..-+.....+......|
T Consensus 160 --~~~~---~~----~~-~~-~~~f~~~-~~~~~~~~~~~~--~g-~~~~---~l~~~~~~~s~~~~~~~~~~~r~~~~~ 221 (463)
T KOG1081|consen 160 --PLLP---KG----MK-HD-HVNFFGC-YAWTHEKRVFPY--EG-QSSK---LIPHSKKPASTMSEKIKEAKARFGKLK 221 (463)
T ss_pred --cccc---hh----hc-cc-cceeccc-hhhHHHhhhhhc--cc-hHHH---hhhhccccchhhhhhhhcccchhhhcc
Confidence 2222 11 11 11 2333444 455544443333 11 4555 333778888887777666665555555
Q ss_pred HHhhhcCCc
Q 045234 157 YYLLKKGEM 165 (299)
Q Consensus 157 ~~~~~~~~~ 165 (299)
...+++...
T Consensus 222 ~q~~~~~~~ 230 (463)
T KOG1081|consen 222 AQWEAGIKQ 230 (463)
T ss_pred cchhhccch
Confidence 555555543
No 16
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.65 E-value=1.6e-05 Score=83.67 Aligned_cols=51 Identities=29% Similarity=0.682 Sum_probs=41.2
Q ss_pred ccccccceeccCCceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCcccc
Q 045234 12 ISEIWCFKCKHGGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGV 65 (299)
Q Consensus 12 ~~ed~C~vC~dGGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~ 65 (299)
.+...|.+|++||++++|| .||.+||..|++++... .|.+.|.||++.|+.
T Consensus 45 ~~~e~c~ic~~~g~~l~c~--tC~~s~h~~cl~~pl~~-~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 45 AEQEACRICADGGELLWCD--TCPASFHASCLGPPLTP-QPNGEFICPRCFCPK 95 (696)
T ss_pred hhhhhhhhhcCCCcEEEec--cccHHHHHHccCCCCCc-CCccceeeeeeccCC
Confidence 3457899999999999999 99999999999976442 366669999654443
No 17
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.58 E-value=3.1e-05 Score=79.81 Aligned_cols=52 Identities=23% Similarity=0.519 Sum_probs=41.4
Q ss_pred ccccccCCce----eccccCCCCCCCcccCcc-ccccccCCcccccccHHHHHHHHh
Q 045234 62 FCGVCRKASK----FYCFCCPSAVCKTCLYDI-QFALVKENKGFCNSCLELAWLIET 113 (299)
Q Consensus 62 ~C~~C~~~~~----~~C~~Cp~s~c~~CL~~~-~~~~v~~~~~~C~~C~~l~~~le~ 113 (299)
+|..|++... +.|+.||.+||..||.++ ..+.++.+.|+|..|.-.....+.
T Consensus 255 fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in~~ 311 (613)
T KOG4299|consen 255 FCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPK 311 (613)
T ss_pred HHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccc
Confidence 7999998865 589999999999999977 456678899999999654444333
No 18
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.53 E-value=2.9e-05 Score=80.46 Aligned_cols=92 Identities=23% Similarity=0.493 Sum_probs=67.3
Q ss_pred cccccceeccC-----CceeeeCCCCCCCcccccccCCCccccCCCCCeeccCC-ccccccCCc----eeccccCCCCCC
Q 045234 13 SEIWCFKCKHG-----GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWH-FCGVCRKAS----KFYCFCCPSAVC 82 (299)
Q Consensus 13 ~ed~C~vC~dG-----GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H-~C~~C~~~~----~~~C~~Cp~s~c 82 (299)
....|++|+.. |.|+-|. .|-..||+.||..-..-..-.+.|.||.| .|-.|+.+. ...|..|..|||
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~--~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvsyh 94 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACS--DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVSYH 94 (694)
T ss_pred hhhhhhhhccccccccCcchhhh--hhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCccccccccccccccc
Confidence 35678888764 4788999 99999999999942211112345999976 577777543 578999999999
Q ss_pred CcccCccccccccCCcccccccHHH
Q 045234 83 KTCLYDIQFALVKENKGFCNSCLEL 107 (299)
Q Consensus 83 ~~CL~~~~~~~v~~~~~~C~~C~~l 107 (299)
..|+.++.-. |..+.|+|..|.+.
T Consensus 95 ~yc~~P~~~~-v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 95 CYCQKPPNDK-VPSGPWLCKKCTRC 118 (694)
T ss_pred ccccCCcccc-ccCcccccHHHHhh
Confidence 9999976443 56778888766544
No 19
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.38 E-value=6.1e-05 Score=71.90 Aligned_cols=87 Identities=17% Similarity=0.368 Sum_probs=69.0
Q ss_pred ccccceeccCC---------ceeeeCCCCCCCcccccccCCCccc--cCCCCCeeccCC-ccccccCCc----eeccccC
Q 045234 14 EIWCFKCKHGG---------ELRLCDNTRCLKVYHPECVDKDESF--LAAKTKWICNWH-FCGVCRKAS----KFYCFCC 77 (299)
Q Consensus 14 ed~C~vC~dGG---------eLv~CD~~~CPkaYH~~Cl~~~~~~--~~~~g~W~Cp~H-~C~~C~~~~----~~~C~~C 77 (299)
...|.+|.+|- .+|+|. .|--+||+.|+...... +...=.|.|-.| .|.+|+.+. .+.|+.|
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~--~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~C 335 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCK--PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIESEHLFCDVC 335 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeec--ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccchheeccccc
Confidence 45699998873 799999 99999999999976431 123446999865 799999884 6889999
Q ss_pred CCCCCCcccCccccccccCCccccc-ccH
Q 045234 78 PSAVCKTCLYDIQFALVKENKGFCN-SCL 105 (299)
Q Consensus 78 p~s~c~~CL~~~~~~~v~~~~~~C~-~C~ 105 (299)
...||-.|+.- -.++.+.|.|. .|.
T Consensus 336 DRG~HT~CVGL---~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 336 DRGPHTLCVGL---QDLPRGEWICDMRCR 361 (381)
T ss_pred cCCCCcccccc---ccccCccchhhhHHH
Confidence 99999999863 34578899997 564
No 20
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.76 E-value=0.00067 Score=71.10 Aligned_cols=60 Identities=27% Similarity=0.681 Sum_probs=50.3
Q ss_pred cceeccC-C----ceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCccccccCCceeccccCCCCC
Q 045234 17 CFKCKHG-G----ELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGVCRKASKFYCFCCPSAV 81 (299)
Q Consensus 17 C~vC~dG-G----eLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~~~~~~C~~Cp~s~ 81 (299)
|.||-|. | -||.||..+|--|.|.+|-++... |.|.|||. -|-.-.+.+.++|.-||..+
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqV---PtGpWfCr--KCesqeraarvrCeLCP~kd 72 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQV---PTGPWFCR--KCESQERAARVRCELCPHKD 72 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEec---CCCchhhh--hhhhhhhhccceeecccCcc
Confidence 8999984 3 899999999999999999999877 99999886 34444556789999999764
No 21
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.76 E-value=0.00061 Score=71.78 Aligned_cols=45 Identities=24% Similarity=0.635 Sum_probs=38.9
Q ss_pred ccccccceeccC-----CceeeeCCCCCCCcccccccCCCccccCCCCCeeccCC
Q 045234 12 ISEIWCFKCKHG-----GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWH 61 (299)
Q Consensus 12 ~~ed~C~vC~dG-----GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H 61 (299)
.++-.|-||.-+ -++|.|| .|--.-|.+|.|+... |+|.|.|.+|
T Consensus 269 dedviCDvCrspD~e~~neMVfCd--~Cn~cVHqaCyGIle~---p~gpWlCr~C 318 (893)
T KOG0954|consen 269 DEDVICDVCRSPDSEEANEMVFCD--KCNICVHQACYGILEV---PEGPWLCRTC 318 (893)
T ss_pred cccceeceecCCCccccceeEEec--cchhHHHHhhhceeec---CCCCeeehhc
Confidence 456679999865 5999999 9999999999999877 8999999865
No 22
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.57 E-value=0.0013 Score=62.51 Aligned_cols=43 Identities=26% Similarity=0.663 Sum_probs=34.9
Q ss_pred ccccceecc---CCceeeeCCCCCCCcccccccCCCccccCCCCCeecc
Q 045234 14 EIWCFKCKH---GGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICN 59 (299)
Q Consensus 14 ed~C~vC~d---GGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp 59 (299)
--+|.+|+. ..+|+.|| .|.|.||..||.|+.. ..|+|.|.|-
T Consensus 281 ck~csicgtsenddqllfcd--dcdrgyhmyclsppm~-eppegswsc~ 326 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQLLFCD--DCDRGYHMYCLSPPMV-EPPEGSWSCH 326 (336)
T ss_pred cceeccccCcCCCceeEeec--ccCCceeeEecCCCcC-CCCCCchhHH
Confidence 346777764 35899999 9999999999999765 4599999984
No 23
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.54 E-value=0.002 Score=57.36 Aligned_cols=72 Identities=25% Similarity=0.546 Sum_probs=51.2
Q ss_pred ccceecc------CCceeeeCCCCCCCcccccccCCCccc---c--CCCCCee----------------ccCC-cccccc
Q 045234 16 WCFKCKH------GGELRLCDNTRCLKVYHPECVDKDESF---L--AAKTKWI----------------CNWH-FCGVCR 67 (299)
Q Consensus 16 ~C~vC~d------GGeLv~CD~~~CPkaYH~~Cl~~~~~~---~--~~~g~W~----------------Cp~H-~C~~C~ 67 (299)
.|.+|+. -|.||.|- +|..+||..|||+-... + ...+.|+ -|.| .|..|.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQ--GCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~C~ 78 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQ--GCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMCQQCK 78 (175)
T ss_pred CcccccCCCCCccCCCeEEcC--ccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcccccC
Confidence 4777842 37999999 99999999999975421 0 0122332 3333 688885
Q ss_pred CC------------------------------------------ceeccccCCCCCCCcccCcc
Q 045234 68 KA------------------------------------------SKFYCFCCPSAVCKTCLYDI 89 (299)
Q Consensus 68 ~~------------------------------------------~~~~C~~Cp~s~c~~CL~~~ 89 (299)
.. .+|+|..|-.+||..+|++.
T Consensus 79 ~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 79 KPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPP 142 (175)
T ss_pred CCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCC
Confidence 41 16999999999999999975
No 24
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=96.48 E-value=0.0015 Score=71.50 Aligned_cols=62 Identities=26% Similarity=0.566 Sum_probs=52.3
Q ss_pred ccccccceeccCCceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCccccccCCceeccccCC
Q 045234 12 ISEIWCFKCKHGGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGVCRKASKFYCFCCP 78 (299)
Q Consensus 12 ~~ed~C~vC~dGGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~~~~~~C~~Cp 78 (299)
.-+|.|-+|.|+|.++||. +||++||..|+.++.- ..+...|.|- .|.+|+.++...|..-+
T Consensus 342 ~~ddhcrf~~d~~~~lc~E--t~prvvhlEcv~hP~~-~~~s~~~e~e--vc~~hkvngvvd~vl~~ 403 (1414)
T KOG1473|consen 342 EYDDHCRFCHDLGDLLCCE--TCPRVVHLECVFHPRF-AVPSAFWECE--VCNIHKVNGVVDCVLPP 403 (1414)
T ss_pred eecccccccCcccceeecc--cCCceEEeeecCCccc-cCCCccchhh--hhhhhccCcccccccCh
Confidence 4478999999999999999 9999999999997642 3488899997 78888888777776655
No 25
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.23 E-value=0.0021 Score=61.63 Aligned_cols=41 Identities=29% Similarity=0.657 Sum_probs=35.3
Q ss_pred cccceeccC---CceeeeCCCCCCCcccccccCCCccccCCCCCeeccC
Q 045234 15 IWCFKCKHG---GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNW 60 (299)
Q Consensus 15 d~C~vC~dG---GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~ 60 (299)
..|.+|+.+ .+++.|| .|.|.||..|||+... |.|.|+|-.
T Consensus 315 ~lC~IC~~P~~E~E~~FCD--~CDRG~HT~CVGL~~l---P~G~WICD~ 358 (381)
T KOG1512|consen 315 ELCRICLGPVIESEHLFCD--VCDRGPHTLCVGLQDL---PRGEWICDM 358 (381)
T ss_pred HhhhccCCcccchheeccc--cccCCCCccccccccc---cCccchhhh
Confidence 357788764 5999999 8999999999999887 999999963
No 27
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.14 E-value=0.0049 Score=67.79 Aligned_cols=63 Identities=25% Similarity=0.625 Sum_probs=47.5
Q ss_pred cccccccceeccC-----CceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCccccccCC--ceeccccCCCCCCC
Q 045234 11 EISEIWCFKCKHG-----GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGVCRKA--SKFYCFCCPSAVCK 83 (299)
Q Consensus 11 ~~~ed~C~vC~dG-----GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~~--~~~~C~~Cp~s~c~ 83 (299)
.+.+.+|.||.+| -.+|.|| .|-.++|..|.|.... |+|.|.|-. |.-. ....|..||.+-+.
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cygi~~i---peg~WlCr~-----Cl~s~~~~v~c~~cp~~~gA 285 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYGIPFI---PEGQWLCRR-----CLQSPQRPVRCLLCPSKGGA 285 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcC--CCcchhhhhccCCCCC---CCCcEeehh-----hccCcCcccceEeccCCCCc
Confidence 4667889999987 3689999 9999999999996544 999999864 4332 23567777765443
No 28
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=96.13 E-value=0.0026 Score=44.60 Aligned_cols=45 Identities=20% Similarity=0.532 Sum_probs=34.7
Q ss_pred ccccccCC----ceeccccCCCCCCCcccCccccc-cccCCcccccccHH
Q 045234 62 FCGVCRKA----SKFYCFCCPSAVCKTCLYDIQFA-LVKENKGFCNSCLE 106 (299)
Q Consensus 62 ~C~~C~~~----~~~~C~~Cp~s~c~~CL~~~~~~-~v~~~~~~C~~C~~ 106 (299)
+|.+|+.. .++.|..|...||..|+..+... .+....|+|+.|.+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 36778773 36889999999999999977553 23455999999864
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.38 E-value=0.0093 Score=63.65 Aligned_cols=44 Identities=41% Similarity=0.778 Sum_probs=35.2
Q ss_pred ccccceeccC---CceeeeCCCCCCCc-ccccccCCCccccCCCCCeeccC
Q 045234 14 EIWCFKCKHG---GELRLCDNTRCLKV-YHPECVDKDESFLAAKTKWICNW 60 (299)
Q Consensus 14 ed~C~vC~dG---GeLv~CD~~~CPka-YH~~Cl~~~~~~~~~~g~W~Cp~ 60 (299)
.--|-+|.-. --||+|| .|-.+ ||..||+++.. ..|-+.|||+.
T Consensus 215 ~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~-eiP~~eWYC~N 262 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLS-ESPVNEWYCTN 262 (1134)
T ss_pred cccceeeccCChHHhheeec--ccccceeeccccCcccc-cccccceecCc
Confidence 3459999753 3688999 99999 99999999753 23889999995
No 30
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=95.30 E-value=0.0093 Score=62.43 Aligned_cols=69 Identities=28% Similarity=0.676 Sum_probs=51.3
Q ss_pred ccceec---cCCceeeeCCCCCCCcccccccCCCccccCCCCCeeccCC-ccccccCC--c--------eeccccCCC-C
Q 045234 16 WCFKCK---HGGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWH-FCGVCRKA--S--------KFYCFCCPS-A 80 (299)
Q Consensus 16 ~C~vC~---dGGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H-~C~~C~~~--~--------~~~C~~Cp~-s 80 (299)
+|..|+ |.+.++.|+ .|--+||-.|..|.... .+.+.|.|+|| .|..|... + ...|..|.. +
T Consensus 70 vCe~c~~~gD~~kf~~Ck--~cDvsyh~yc~~P~~~~-v~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s~~ 146 (694)
T KOG4443|consen 70 VCEACGTTGDPKKFLLCK--RCDVSYHCYCQKPPNDK-VPSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCASLS 146 (694)
T ss_pred eeeeccccCCcccccccc--cccccccccccCCcccc-ccCcccccHHHHhhhhccccccccchhhhccCcccccccccc
Confidence 456665 445899999 99999999999985432 38999999987 47777653 1 345777776 7
Q ss_pred CCCcccC
Q 045234 81 VCKTCLY 87 (299)
Q Consensus 81 ~c~~CL~ 87 (299)
||..|+.
T Consensus 147 ~cPvc~~ 153 (694)
T KOG4443|consen 147 YCPVCLI 153 (694)
T ss_pred cCchHHH
Confidence 7776665
No 31
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=94.34 E-value=0.019 Score=44.65 Aligned_cols=48 Identities=27% Similarity=0.617 Sum_probs=36.6
Q ss_pred ccccceeccC-CceeeeCCCCCCCcccccccCCCccccCC-----CCCeeccCC
Q 045234 14 EIWCFKCKHG-GELRLCDNTRCLKVYHPECVDKDESFLAA-----KTKWICNWH 61 (299)
Q Consensus 14 ed~C~vC~dG-GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~-----~g~W~Cp~H 61 (299)
...|.+|+.. |-.|-|..++|.+.||+.|.-.....+.. .-..+||.|
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C~~H 89 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFCPKH 89 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEChhc
Confidence 3569999998 99999999999999999999864332111 235667766
No 32
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=93.26 E-value=0.06 Score=47.15 Aligned_cols=30 Identities=17% Similarity=0.373 Sum_probs=22.1
Q ss_pred cccccccCCCccccCCCCCeeccCCcccccc
Q 045234 37 VYHPECVDKDESFLAAKTKWICNWHFCGVCR 67 (299)
Q Consensus 37 aYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~ 67 (299)
.||..||.|+.. ..|+|+|+||.|.-...+
T Consensus 1 g~H~~CL~Ppl~-~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 1 GFHLCCLRPPLK-EVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CcccccCCCCCC-CCCCCCcCCCCCcCCCCC
Confidence 389999998754 349999999964444443
No 33
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.19 E-value=0.049 Score=58.39 Aligned_cols=46 Identities=22% Similarity=0.439 Sum_probs=39.5
Q ss_pred CccccccCCc----eeccccCCCC-CCCcccCccccccccCCcccccccHHH
Q 045234 61 HFCGVCRKAS----KFYCFCCPSA-VCKTCLYDIQFALVKENKGFCNSCLEL 107 (299)
Q Consensus 61 H~C~~C~~~~----~~~C~~Cp~s-~c~~CL~~~~~~~v~~~~~~C~~C~~l 107 (299)
..|.+|+... +++|+.|-.. ||.+||++...+ ++.+.|+|.+|.-+
T Consensus 216 ~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~e-iP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 216 VKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSE-SPVNEWYCTNCSLL 266 (1134)
T ss_pred ccceeeccCChHHhheeecccccceeeccccCccccc-ccccceecCcchhh
Confidence 4799999873 6899999999 999999988766 48899999999644
No 34
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=93.15 E-value=0.054 Score=55.49 Aligned_cols=58 Identities=26% Similarity=0.606 Sum_probs=42.8
Q ss_pred ccccceeccC-----CceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCcccccc--CCceeccccCCCCC
Q 045234 14 EIWCFKCKHG-----GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGVCR--KASKFYCFCCPSAV 81 (299)
Q Consensus 14 ed~C~vC~dG-----GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~--~~~~~~C~~Cp~s~ 81 (299)
++.|.+|... .-+|.|| +|--+-|..|-|.... |+|.|.|-. |= ......|..||.+-
T Consensus 193 d~~C~~c~~t~~eN~naiVfCd--gC~i~VHq~CYGI~f~---peG~WlCrk-----Ci~~~~~i~~C~fCps~d 257 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCD--GCEICVHQSCYGIQFL---PEGFWLCRK-----CIYGEYQIRCCSFCPSSD 257 (669)
T ss_pred hhhhHhccccccCCcceEEEec--Ccchhhhhhcccceec---Ccchhhhhh-----hcccccceeEEEeccCCC
Confidence 4567888653 3689999 9999999999999866 999998863 42 22345577777653
No 35
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=89.38 E-value=0.16 Score=44.40 Aligned_cols=43 Identities=30% Similarity=0.636 Sum_probs=34.1
Q ss_pred CcccccccCCCccccCCCCCeeccCCccccccCCceeccccCCCCCC-CcccC
Q 045234 36 KVYHPECVDKDESFLAAKTKWICNWHFCGVCRKASKFYCFCCPSAVC-KTCLY 87 (299)
Q Consensus 36 kaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~~~~~~C~~Cp~s~c-~~CL~ 87 (299)
..||..+..+... =+.++|.+||-.+.|.|..|...|| ..|+.
T Consensus 103 ~~Y~~~~a~p~~K---------P~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 103 PNYHTAYAKPSFK---------PLRKFCAVCGYDSKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred cchhhcccCCCCC---------CcchhhhhcCCCchhHHHhcCCceeechhhh
Confidence 4688888877543 1468999999999999999999999 46654
No 36
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=89.38 E-value=0.21 Score=40.36 Aligned_cols=34 Identities=29% Similarity=0.757 Sum_probs=29.3
Q ss_pred cccccceecc-CCceeeeCCCCCCCcccccccCCC
Q 045234 13 SEIWCFKCKH-GGELRLCDNTRCLKVYHPECVDKD 46 (299)
Q Consensus 13 ~ed~C~vC~d-GGeLv~CD~~~CPkaYH~~Cl~~~ 46 (299)
....|.+|+. +|-++-|...+|..+||+.|.-..
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 4567999998 688999998889999999998653
No 37
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=88.22 E-value=0.39 Score=49.57 Aligned_cols=62 Identities=26% Similarity=0.584 Sum_probs=44.5
Q ss_pred cccceec-----cCCceeeeCCCCCCCcccccccCCCccccC-------CCCCeeccCCccccccCC-ceeccccCCCCC
Q 045234 15 IWCFKCK-----HGGELRLCDNTRCLKVYHPECVDKDESFLA-------AKTKWICNWHFCGVCRKA-SKFYCFCCPSAV 81 (299)
Q Consensus 15 d~C~vC~-----dGGeLv~CD~~~CPkaYH~~Cl~~~~~~~~-------~~g~W~Cp~H~C~~C~~~-~~~~C~~Cp~s~ 81 (299)
..|.||. |.|++|-|| .|.-..|..|-|..+.... ....|+|-- |.-+ ++-.|..||..|
T Consensus 120 ~iCcVClg~rs~da~ei~qCd--~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCea-----C~~Gvs~P~CElCPn~~ 192 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCD--KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEA-----CLYGVSLPHCELCPNRF 192 (707)
T ss_pred eEEEEeecCccccccceeecc--ccCceecccccccccccccCCCCccCCCCchhhhh-----HhcCCCCCccccCCCcC
Confidence 3799996 468999999 9999999999997632111 225787764 5544 347788888876
Q ss_pred CC
Q 045234 82 CK 83 (299)
Q Consensus 82 c~ 83 (299)
-.
T Consensus 193 Gi 194 (707)
T KOG0957|consen 193 GI 194 (707)
T ss_pred Cc
Confidence 43
No 38
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=85.90 E-value=0.29 Score=32.94 Aligned_cols=32 Identities=28% Similarity=0.728 Sum_probs=17.3
Q ss_pred CceeeeCCCCCCCcccccccCCCccccCCCCCeecc
Q 045234 24 GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICN 59 (299)
Q Consensus 24 GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp 59 (299)
..|+.|+ +|.-+.|..|-|..... ....|+|-
T Consensus 2 n~ll~C~--~C~v~VH~~CYGv~~~~--~~~~W~C~ 33 (36)
T PF13831_consen 2 NPLLFCD--NCNVAVHQSCYGVSEVP--DGDDWLCD 33 (36)
T ss_dssp CEEEE-S--SS--EEEHHHHT-SS----SS-----H
T ss_pred CceEEeC--CCCCcCChhhCCcccCC--CCCcEECC
Confidence 3689999 99999999999987662 33379985
No 39
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=85.05 E-value=0.38 Score=49.68 Aligned_cols=45 Identities=27% Similarity=0.449 Sum_probs=35.5
Q ss_pred CCccccccCCc----eeccccCCCCCCCcccCcccccccc---CCccccccc
Q 045234 60 WHFCGVCRKAS----KFYCFCCPSAVCKTCLYDIQFALVK---ENKGFCNSC 104 (299)
Q Consensus 60 ~H~C~~C~~~~----~~~C~~Cp~s~c~~CL~~~~~~~v~---~~~~~C~~C 104 (299)
.-.|.+|++.. +..|++|-..||.+||.+++.-..+ .-.|.|+-|
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccc
Confidence 34788999974 5789999999999999988654433 346889988
No 40
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=84.78 E-value=0.23 Score=56.73 Aligned_cols=46 Identities=26% Similarity=0.644 Sum_probs=37.3
Q ss_pred ccccccceeccCC---ceeeeCCCCCCCcccccccCCCccccCCCCCeeccC
Q 045234 12 ISEIWCFKCKHGG---ELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNW 60 (299)
Q Consensus 12 ~~ed~C~vC~dGG---eLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~ 60 (299)
...-.|.+|.-.+ .+++|+ .|-..||..|+.+... ..+.++|.||+
T Consensus 1106 ~~~~~c~~cr~k~~~~~m~lc~--~c~~~~h~~C~rp~~~-~~~~~dW~C~~ 1154 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQDEKMLLCD--ECLSGFHLFCLRPALS-SVPPGDWMCPS 1154 (1404)
T ss_pred cchhhhhhhhhcccchhhhhhH--hhhhhHHHHhhhhhhc-cCCcCCccCCc
Confidence 3456799998654 679999 9999999999998644 23889999995
No 41
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=82.88 E-value=0.57 Score=47.85 Aligned_cols=47 Identities=30% Similarity=0.733 Sum_probs=35.8
Q ss_pred ccceeccCC-----ceeeeCCCCCCCcccccccCCCc---cccCCCCCeeccCCccccccCC
Q 045234 16 WCFKCKHGG-----ELRLCDNTRCLKVYHPECVDKDE---SFLAAKTKWICNWHFCGVCRKA 69 (299)
Q Consensus 16 ~C~vC~dGG-----eLv~CD~~~CPkaYH~~Cl~~~~---~~~~~~g~W~Cp~H~C~~C~~~ 69 (299)
.|.||.-|| .+|-|+ .|-..||..|.-+.. .+-.+...|+|- +|..+
T Consensus 170 qc~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~-----~C~~~ 224 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPLIKDELAGDPFYEWFCD-----VCNRG 224 (464)
T ss_pred eeeeeecCCcCccceeeeec--ccccHHHHHhccCCCCHhhccCccceEeeh-----hhccc
Confidence 499998665 899999 999999999998743 223467789874 56543
No 42
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.69 E-value=0.94 Score=44.78 Aligned_cols=43 Identities=28% Similarity=0.743 Sum_probs=32.7
Q ss_pred cccceeccC---CceeeeCCCCCCCcccccccCCCccccCCCCCeecc-CCccccccCC
Q 045234 15 IWCFKCKHG---GELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICN-WHFCGVCRKA 69 (299)
Q Consensus 15 d~C~vC~dG---GeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp-~H~C~~C~~~ 69 (299)
+.|.+|.+. |+.+.=- .|--.||..|+++ |.=. +|+|++|+..
T Consensus 230 ~~CaIClEdY~~GdklRiL--PC~H~FH~~CIDp----------WL~~~r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRIL--PCSHKFHVNCIDP----------WLTQTRTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCeeeEe--cCCCchhhccchh----------hHhhcCccCCCCCCc
Confidence 589999873 6555445 7888999999987 4444 4789999863
No 43
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=81.67 E-value=0.6 Score=47.68 Aligned_cols=97 Identities=19% Similarity=0.218 Sum_probs=65.2
Q ss_pred cccccceecc-----CCceeeeCCCCCCCcccccccCCCccccCCCCCeecc----------------------------
Q 045234 13 SEIWCFKCKH-----GGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICN---------------------------- 59 (299)
Q Consensus 13 ~ed~C~vC~d-----GGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp---------------------------- 59 (299)
++-.|-+|.- +-+++.|+ .|-+.||..|-.+... ..+.|.+.
T Consensus 82 ~e~~~nv~~s~~~~p~~e~~~~~--r~~~~~~q~~~i~~~~---~~~~~~~~~c~~~~~~~~g~a~K~g~~a~~~l~y~~ 156 (464)
T KOG4323|consen 82 SELNPNVLTSETVLPENEKVICG--RCKSGYHQGCNIPRFP---SLDIGESTECVFPIFSQEGGALKKGRLARPSLPYPE 156 (464)
T ss_pred cccCCcccccccccCchhhhhhh--hhccCcccccCccCcC---cCCccccccccccccccccccccccccccccccCcc
Confidence 4555777753 34788899 8999999999876432 22222222
Q ss_pred -----------CCccccccCC------ceeccccCCCCCCCcccCccccccc---cCCcccccccHHHHHHHHhh
Q 045234 60 -----------WHFCGVCRKA------SKFYCFCCPSAVCKTCLYDIQFALV---KENKGFCNSCLELAWLIETK 114 (299)
Q Consensus 60 -----------~H~C~~C~~~------~~~~C~~Cp~s~c~~CL~~~~~~~v---~~~~~~C~~C~~l~~~le~~ 114 (299)
.--|.+|..+ ..+.|..|-.-||..|..+..-... +.-.|||..|.+--..+..+
T Consensus 157 ~~l~wD~~~~~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~ 231 (464)
T KOG4323|consen 157 ASLDWDSGHKVNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRL 231 (464)
T ss_pred cccccCccccccceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhcccc
Confidence 1248888754 3688999999999999986532211 55689999997655444443
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=78.23 E-value=1 Score=34.28 Aligned_cols=32 Identities=34% Similarity=0.685 Sum_probs=13.5
Q ss_pred ccccceecc----CCc--eeeeCCCCCCCcccccccCC
Q 045234 14 EIWCFKCKH----GGE--LRLCDNTRCLKVYHPECVDK 45 (299)
Q Consensus 14 ed~C~vC~d----GGe--Lv~CD~~~CPkaYH~~Cl~~ 45 (299)
+..|.||.. +|+ .+.|+...|.+.||..||..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~ 39 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSE 39 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHH
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHH
Confidence 456889974 343 48899999999999999974
No 45
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=77.55 E-value=1.8 Score=45.07 Aligned_cols=53 Identities=17% Similarity=0.281 Sum_probs=42.9
Q ss_pred ccccccceeccCCceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCccccccC
Q 045234 12 ISEIWCFKCKHGGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHFCGVCRK 68 (299)
Q Consensus 12 ~~ed~C~vC~dGGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~ 68 (299)
..+.+||.|.-.|..+.|+ -|-++||..|+.+....-.....|-|| .|..|..
T Consensus 58 N~d~~cfechlpg~vl~c~--vc~Rs~h~~c~sp~~q~r~~s~p~~~p--~p~s~k~ 110 (588)
T KOG3612|consen 58 NIDPFCFECHLPGAVLKCI--VCHRSFHENCQSPDPQKRNYSVPSDKP--QPYSFKV 110 (588)
T ss_pred CCCcccccccCCcceeeee--hhhccccccccCcchhhccccccccCC--cccccCC
Confidence 4577899999999999999 899999999999865533456779999 4666643
No 46
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.05 E-value=1.5 Score=32.39 Aligned_cols=30 Identities=30% Similarity=0.784 Sum_probs=25.7
Q ss_pred cccceecc----CCceeeeCCCCCCCcccccccCCC
Q 045234 15 IWCFKCKH----GGELRLCDNTRCLKVYHPECVDKD 46 (299)
Q Consensus 15 d~C~vC~d----GGeLv~CD~~~CPkaYH~~Cl~~~ 46 (299)
..|.+|++ ++++|.|. .|-..||..|....
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp--~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCP--ECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECC--CCCCcccHHHHhhC
Confidence 45899985 78999999 99999999998653
No 47
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=75.86 E-value=1.3 Score=49.38 Aligned_cols=41 Identities=27% Similarity=0.719 Sum_probs=34.3
Q ss_pred ccccccCC------ceeccccCCCCCCCcccCccccccccCCcccccccH
Q 045234 62 FCGVCRKA------SKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCL 105 (299)
Q Consensus 62 ~C~~C~~~------~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~ 105 (299)
.|.+|.+. ..+.|+-|..++|..|.. ...++++.|+|.+|+
T Consensus 221 ~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg---i~~ipeg~WlCr~Cl 267 (1051)
T KOG0955|consen 221 VCCICLDGECQNSNVIVFCDGCNLAVHQECYG---IPFIPEGQWLCRRCL 267 (1051)
T ss_pred cceeecccccCCCceEEEcCCCcchhhhhccC---CCCCCCCcEeehhhc
Confidence 68899875 368899999999999987 233589999999996
No 48
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=75.82 E-value=1.5 Score=38.47 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=21.5
Q ss_pred CCCCcccCccccccccCCcccccccH
Q 045234 80 AVCKTCLYDIQFALVKENKGFCNSCL 105 (299)
Q Consensus 80 s~c~~CL~~~~~~~v~~~~~~C~~C~ 105 (299)
.||..||.+++. .++.+.|+|+.|.
T Consensus 1 g~H~~CL~Ppl~-~~P~g~W~Cp~C~ 25 (148)
T cd04718 1 GFHLCCLRPPLK-EVPEGDWICPFCE 25 (148)
T ss_pred CcccccCCCCCC-CCCCCCcCCCCCc
Confidence 489999999865 4689999999996
No 49
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=74.32 E-value=0.9 Score=29.44 Aligned_cols=24 Identities=29% Similarity=0.845 Sum_probs=17.0
Q ss_pred cCCccccccCCceeccccCCCCCC
Q 045234 59 NWHFCGVCRKASKFYCFCCPSAVC 82 (299)
Q Consensus 59 p~H~C~~C~~~~~~~C~~Cp~s~c 82 (299)
|.+.|.+|+..+.|.|..|...||
T Consensus 1 ~~~~C~vC~~~~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 1 PRKLCSVCGNPAKYRCPRCGARYC 24 (30)
T ss_dssp --EEETSSSSEESEE-TTT--EES
T ss_pred CcCCCccCcCCCEEECCCcCCcee
Confidence 456899999988999999988877
No 50
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=73.92 E-value=2.2 Score=34.33 Aligned_cols=74 Identities=19% Similarity=0.214 Sum_probs=46.7
Q ss_pred ccceeccCCceeeeCCCCCCCcccccccCCCcc--ccCC--CCCee----c---cCCccccccCC--ceecccc--CCCC
Q 045234 16 WCFKCKHGGELRLCDNTRCLKVYHPECVDKDES--FLAA--KTKWI----C---NWHFCGVCRKA--SKFYCFC--CPSA 80 (299)
Q Consensus 16 ~C~vC~dGGeLv~CD~~~CPkaYH~~Cl~~~~~--~~~~--~g~W~----C---p~H~C~~C~~~--~~~~C~~--Cp~s 80 (299)
.|.+|...|.++--. .--...|..|.-.... +..+ ...+. = -...|.+|++. ....|.. |..+
T Consensus 2 ~C~lC~~~~Galk~t--~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~~~C~iC~~~~G~~i~C~~~~C~~~ 79 (110)
T PF13832_consen 2 SCVLCPKRGGALKRT--SDGQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFKLKCSICGKSGGACIKCSHPGCSTA 79 (110)
T ss_pred ccEeCCCCCCcccCc--cCCcEEEeEccceeCccEEeechhcCcccceeecchhcCCcCcCCCCCCceeEEcCCCCCCcC
Confidence 488898765555444 3467889999875321 1000 00000 0 13578999985 4688999 9999
Q ss_pred CCCcccCcccc
Q 045234 81 VCKTCLYDIQF 91 (299)
Q Consensus 81 ~c~~CL~~~~~ 91 (299)
||..|.....+
T Consensus 80 fH~~CA~~~g~ 90 (110)
T PF13832_consen 80 FHPTCARKAGL 90 (110)
T ss_pred CCHHHHHHCCC
Confidence 99999876543
No 51
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=70.29 E-value=5.7 Score=40.81 Aligned_cols=46 Identities=7% Similarity=-0.018 Sum_probs=37.3
Q ss_pred HHHHHhhhh----hhhhhhHHHHHHHHhhhcccCCcCCCCeeecchhhHHH
Q 045234 220 KMLKLHART----LQEQNNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNL 266 (299)
Q Consensus 220 ~fl~~~g~~----lsr~~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~l 266 (299)
+.+...|.+ +.-. ||...|..||..|||-|+.||-.|+-|+=|-..
T Consensus 369 ~Lf~evg~~kg~lyt~s-eir~~V~kYi~knnLad~~nKg~VrLDpILfd~ 418 (560)
T KOG2522|consen 369 DLFKEVGLAKGTLYTSS-EIRSAVSKYISKNNLADTKNKGKVRLDPILFDM 418 (560)
T ss_pred HHHHhcCccccceeeHH-HHHHHHHHHhhhhhccccccCCcEEeccHHHHH
Confidence 445555544 6677 999999999999999999999999888877654
No 52
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=70.10 E-value=1.9 Score=44.66 Aligned_cols=33 Identities=30% Similarity=0.822 Sum_probs=29.1
Q ss_pred ccccceecc-CCceeeeCCCCCCCcccccccCCC
Q 045234 14 EIWCFKCKH-GGELRLCDNTRCLKVYHPECVDKD 46 (299)
Q Consensus 14 ed~C~vC~d-GGeLv~CD~~~CPkaYH~~Cl~~~ 46 (299)
.-.|.+|+. ||.-|.|..++|.+|||.+|.-.-
T Consensus 303 kl~C~iCk~~~GtcIqCs~~nC~~aYHVtCArra 336 (669)
T COG5141 303 KLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRA 336 (669)
T ss_pred hheeeEEcccCcceeeecccchhhhhhhhhhhhc
Confidence 456999986 899999999999999999998753
No 53
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=68.02 E-value=4.4 Score=38.94 Aligned_cols=44 Identities=20% Similarity=0.529 Sum_probs=38.2
Q ss_pred ccccccCCceeccccCCCCCCCcccCccccccccCCcccccccH
Q 045234 62 FCGVCRKASKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCL 105 (299)
Q Consensus 62 ~C~~C~~~~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~ 105 (299)
-|.+|.+.+.+.|..|-..||..+++...|...++....|+.|.
T Consensus 173 KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 173 KCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred cccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 46689999999999999999999999877776677788999994
No 54
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=61.10 E-value=5.4 Score=37.90 Aligned_cols=49 Identities=20% Similarity=0.352 Sum_probs=34.1
Q ss_pred CCCCCeeccCCccccccCCc-eecccc--CC-CCCCCcccCccccccccCCcccccccHH
Q 045234 51 AAKTKWICNWHFCGVCRKAS-KFYCFC--CP-SAVCKTCLYDIQFALVKENKGFCNSCLE 106 (299)
Q Consensus 51 ~~~g~W~Cp~H~C~~C~~~~-~~~C~~--Cp-~s~c~~CL~~~~~~~v~~~~~~C~~C~~ 106 (299)
.++..|+|+ |. |...+ ..-|+. || .=||..|+.= ..-+.++|||+.|..
T Consensus 215 d~~e~~yC~---Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL---~~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 215 DPDEPTYCI---CN-QVSYGKMIGCDNPGCPIEWFHFTCVGL---KTKPKGKWYCPRCKA 267 (274)
T ss_pred CCCCCEEEE---ec-ccccccccccCCCCCCcceEEEecccc---ccCCCCcccchhhhh
Confidence 466778885 44 44443 456877 99 7799999852 223677899999964
No 55
>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=56.11 E-value=7.2 Score=31.71 Aligned_cols=40 Identities=15% Similarity=0.112 Sum_probs=28.5
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|-+..... .|.+ ++...+.+||++|+.+++|+
T Consensus 8 ~c~~il~~l~~~~~s~----~F~~---pv~~~~p~Y~~iI~~PmdL~ 47 (109)
T cd05502 8 KCERLLLELYCHELSL----PFHE---PVSPSVPNYYKIIKTPMDLS 47 (109)
T ss_pred HHHHHHHHHHhCCCCh----hhcC---CCCCCCCCHHHHCCCCccHH
Confidence 4777777666642222 7877 44447999999999999874
No 56
>cd05519 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=55.60 E-value=8.5 Score=30.96 Aligned_cols=45 Identities=16% Similarity=0.114 Sum_probs=30.4
Q ss_pred ccHHHHHHHHhhccCCCCCC--CCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGF--DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~--df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.+++..|.+..+.+.... .|.+ . +-...+.+||++|+.+++|+
T Consensus 4 ~~~~i~~~v~~~~~~~~~~~~~~F~~-~-p~~~~~pdYy~iIk~Pmdl~ 50 (103)
T cd05519 4 AMLEIYDAVLNCEDETGRKLSELFLE-K-PSKKLYPDYYVIIKRPIALD 50 (103)
T ss_pred HHHHHHHHHHHhcCcCCCchhHHhcC-C-CCCCCCcCHHHHcCCCcCHH
Confidence 47788888887764322222 7766 3 22445789999999999874
No 57
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=52.55 E-value=4 Score=33.58 Aligned_cols=32 Identities=19% Similarity=0.425 Sum_probs=22.1
Q ss_pred ccCCCCCCCcccCcccc----ccccCCcccccccHH
Q 045234 75 FCCPSAVCKTCLYDIQF----ALVKENKGFCNSCLE 106 (299)
Q Consensus 75 ~~Cp~s~c~~CL~~~~~----~~v~~~~~~C~~C~~ 106 (299)
..|...||..||...-- +.+....|.|+.|..
T Consensus 34 ~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 34 RGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred ccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 33488999999985532 223567899998764
No 58
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=49.68 E-value=4.2 Score=46.88 Aligned_cols=47 Identities=28% Similarity=0.497 Sum_probs=38.4
Q ss_pred ccccccCCc----eeccccCCCCCCCcccCccccccccCCcccccccHHHHH
Q 045234 62 FCGVCRKAS----KFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELAW 109 (299)
Q Consensus 62 ~C~~C~~~~----~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~ 109 (299)
.|.+|.+.. .+.|..|-..||..|+++..- .++...|+|+.|..-..
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~-~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALS-SVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhc-cCCcCCccCCccchhhh
Confidence 688998763 588999999999999998754 45788899999965553
No 60
>cd05515 Bromo_polybromo_V Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=47.89 E-value=13 Score=30.10 Aligned_cols=45 Identities=13% Similarity=0.060 Sum_probs=30.0
Q ss_pred ccHHHHHHHHhhccCCCCCC--CCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGF--DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~--df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|.+..+...... .|.. . +-...+.+||++|+.+++|+
T Consensus 4 ~~~~~~~~i~~~~d~~~~~~a~~F~~-~-p~~~~~pdYy~iIk~PmdL~ 50 (105)
T cd05515 4 KLWELYNAVKNYTDGRGRRLSLIFMR-L-PSKSEYPDYYDVIKKPIDME 50 (105)
T ss_pred HHHHHHHHHHHhhCcCCCcccHHhcc-C-CCcccCCcHHHHcCCCcCHH
Confidence 46777777877766532222 6755 2 22334679999999999874
No 61
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=46.82 E-value=15 Score=27.58 Aligned_cols=21 Identities=19% Similarity=0.502 Sum_probs=15.5
Q ss_pred ccCCccccc-ccHHHHHHHHhh
Q 045234 94 VKENKGFCN-SCLELAWLIETK 114 (299)
Q Consensus 94 v~~~~~~C~-~C~~l~~~le~~ 114 (299)
++.+.-||+ .|.+.+..-++.
T Consensus 13 Ip~~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 13 IPPDESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcchhhhCHHHHHHHHHHHHH
Confidence 566788996 898887666554
No 62
>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=44.26 E-value=17 Score=29.72 Aligned_cols=15 Identities=20% Similarity=0.474 Sum_probs=13.2
Q ss_pred hhhHHhhhccccCCC
Q 045234 135 FKGYWQKIKEKESLT 149 (299)
Q Consensus 135 fk~yw~~ik~k~~lt 149 (299)
+.+||++||.+++|+
T Consensus 36 ~pdY~~iIk~PmDL~ 50 (108)
T cd05495 36 IPDYFDIVKNPMDLS 50 (108)
T ss_pred CCcHHHHhCCCCCHH
Confidence 579999999999874
No 63
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=43.97 E-value=7 Score=44.15 Aligned_cols=46 Identities=15% Similarity=0.213 Sum_probs=36.5
Q ss_pred cccccceeccCCceeeeCCCCCCCcccc-cccCCCcc-ccCCCCCeecc
Q 045234 13 SEIWCFKCKHGGELRLCDNTRCLKVYHP-ECVDKDES-FLAAKTKWICN 59 (299)
Q Consensus 13 ~ed~C~vC~dGGeLv~CD~~~CPkaYH~-~Cl~~~~~-~~~~~g~W~Cp 59 (299)
..+-|++|+..|-+++|+. +||.+||+ .||+.+.. ..-+++-|.|+
T Consensus 427 i~rrl~Ie~~det~l~yys-T~pqly~ll~cLd~~~~e~~L~d~i~~~~ 474 (1414)
T KOG1473|consen 427 ISRRLRIEGMDETLLWYYS-TCPQLYHLLRCLDRTYVEMYLCDGIWERR 474 (1414)
T ss_pred eeeeeEEecCCCcEEEEec-CcHHHHHHHHHhchHHHHHhhccchhhhH
Confidence 4567999999999999993 49999999 99995321 12378899998
No 64
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=43.85 E-value=4.2 Score=38.01 Aligned_cols=54 Identities=24% Similarity=0.607 Sum_probs=39.3
Q ss_pred CCceeeeCCCCCCCcc--------cccccCCCccccCCCCCeeccCCccccccCC-----------------ceeccccC
Q 045234 23 GGELRLCDNTRCLKVY--------HPECVDKDESFLAAKTKWICNWHFCGVCRKA-----------------SKFYCFCC 77 (299)
Q Consensus 23 GGeLv~CD~~~CPkaY--------H~~Cl~~~~~~~~~~g~W~Cp~H~C~~C~~~-----------------~~~~C~~C 77 (299)
++++..|+ -|.|.| |..|..... +|.|..||++ .-|.|..|
T Consensus 114 d~d~ftCr--vCgK~F~lQRmlnrh~kch~~vk------------r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c 179 (267)
T KOG3576|consen 114 DQDSFTCR--VCGKKFGLQRMLNRHLKCHSDVK------------RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLC 179 (267)
T ss_pred CCCeeeee--hhhhhhhHHHHHHHHhhhccHHH------------HHHHhhccCcccchhhhhhhhccccCccccchhhh
Confidence 37888898 899988 445555432 4678899985 13889999
Q ss_pred CCCCCCcccCccc
Q 045234 78 PSAVCKTCLYDIQ 90 (299)
Q Consensus 78 p~s~c~~CL~~~~ 90 (299)
.+||-..|--+.-
T Consensus 180 ~kaftqrcslesh 192 (267)
T KOG3576|consen 180 EKAFTQRCSLESH 192 (267)
T ss_pred hHHHHhhccHHHH
Confidence 9999888865443
No 65
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=41.82 E-value=20 Score=22.81 Aligned_cols=24 Identities=29% Similarity=0.776 Sum_probs=19.2
Q ss_pred ccccccCC---c-eeccccCCCCCCCcc
Q 045234 62 FCGVCRKA---S-KFYCFCCPSAVCKTC 85 (299)
Q Consensus 62 ~C~~C~~~---~-~~~C~~Cp~s~c~~C 85 (299)
.|.+|++. . .|.|..|...+|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 57888875 4 678999998888877
No 66
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=40.85 E-value=13 Score=40.24 Aligned_cols=36 Identities=28% Similarity=0.602 Sum_probs=27.7
Q ss_pred ceecc--ccCCCCCCCcccCccccccccCCcccccccHHHH
Q 045234 70 SKFYC--FCCPSAVCKTCLYDIQFALVKENKGFCNSCLELA 108 (299)
Q Consensus 70 ~~~~C--~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~ 108 (299)
.+..| ..|..|+|..|.. ...|+.+.|||.+|...-
T Consensus 21 PLVYCDG~nCsVAVHQaCYG---IvqVPtGpWfCrKCesqe 58 (900)
T KOG0956|consen 21 PLVYCDGHNCSVAVHQACYG---IVQVPTGPWFCRKCESQE 58 (900)
T ss_pred ceeeecCCCceeeeehhcce---eEecCCCchhhhhhhhhh
Confidence 35566 5788999999974 456789999999997543
No 67
>cd05496 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=38.97 E-value=20 Score=30.09 Aligned_cols=41 Identities=20% Similarity=0.155 Sum_probs=26.2
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|..+...|.+...+ ..|.. .-.. .-+.+||++|+.+|+|+
T Consensus 9 ~c~~il~~l~~~~~s----~~F~~-PVd~-~~~pdY~~iIk~PmDL~ 49 (119)
T cd05496 9 QCKELVNLMWDCEDS----EPFRQ-PVDL-LKYPDYRDIIDTPMDLG 49 (119)
T ss_pred HHHHHHHHHHhCCcc----ccccC-CCCh-hhcCcHHHHhCCcccHH
Confidence 466666666554332 26776 2221 23789999999999884
No 68
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.93 E-value=20 Score=34.75 Aligned_cols=66 Identities=21% Similarity=0.306 Sum_probs=43.7
Q ss_pred CccccccCCc-----------eeccccCCCCCCCcccCccccccccCCcccccccHHHHHHHHhhccCCCCCCCCCCCCc
Q 045234 61 HFCGVCRKAS-----------KFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELAWLIETKKDVNYDGFDRSDAGE 129 (299)
Q Consensus 61 H~C~~C~~~~-----------~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~~le~~~~~~~~~~df~d~~~ 129 (299)
..|.+||..- ...=..|...||..|+++= . +-+.+-+|+-|.+-+-+-.. |++
T Consensus 225 ~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGW--c-ivGKkqtCPYCKekVdl~rm----------fsn--- 288 (328)
T KOG1734|consen 225 SVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGW--C-IVGKKQTCPYCKEKVDLKRM----------FSN--- 288 (328)
T ss_pred chhHhhcchheeecchhhhhhhheeeecccchHHHhhhhh--e-eecCCCCCchHHHHhhHhhh----------ccC---
Confidence 3688999751 2334678899999999864 2 35788999999865443322 344
Q ss_pred ccccchhhHHhhh
Q 045234 130 RNRFYFKGYWQKI 142 (299)
Q Consensus 130 ~~e~lfk~yw~~i 142 (299)
+||--.--|.++|
T Consensus 289 pWekph~~yg~Ll 301 (328)
T KOG1734|consen 289 PWEKPHVWYGQLL 301 (328)
T ss_pred ccccchhHHHHHH
Confidence 6665555555554
No 69
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=37.62 E-value=18 Score=28.22 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=22.4
Q ss_pred cccccccceecc--CCceeeeCCCCCCCcccccccC
Q 045234 11 EISEIWCFKCKH--GGELRLCDNTRCLKVYHPECVD 44 (299)
Q Consensus 11 ~~~ed~C~vC~d--GGeLv~CD~~~CPkaYH~~Cl~ 44 (299)
...+..|.+|+. |...+.-- .|..+||..|..
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEe--CCCeEEeccccc
Confidence 455777999987 33443333 567999999975
No 70
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=37.50 E-value=17 Score=30.08 Aligned_cols=48 Identities=29% Similarity=0.489 Sum_probs=33.4
Q ss_pred CCccccccCC------ceeccccCCCCCCCcccCccccccccCCcccccccHHHHHHH
Q 045234 60 WHFCGVCRKA------SKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELAWLI 111 (299)
Q Consensus 60 ~H~C~~C~~~------~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~~l 111 (299)
.+.|..|+.+ ....|..|...+|..|--. ......|.|.-|.+...+.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~----~~~~~~WlC~vC~k~rel~ 107 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY----SKKEPIWLCKVCQKQRELK 107 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE----TSSSCCEEEHHHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc----CCCCCCEEChhhHHHHHHH
Confidence 4567788764 2467999999999998653 2256789999998766554
No 71
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=37.29 E-value=14 Score=33.33 Aligned_cols=27 Identities=37% Similarity=0.789 Sum_probs=21.6
Q ss_pred ccccc-------CCceeccccCCCCCCCcccCcc
Q 045234 63 CGVCR-------KASKFYCFCCPSAVCKTCLYDI 89 (299)
Q Consensus 63 C~~C~-------~~~~~~C~~Cp~s~c~~CL~~~ 89 (299)
|..|+ ++.+..|.-|..|||..||...
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~R 35 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPR 35 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCCc
Confidence 66673 2357899999999999999854
No 72
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=37.17 E-value=26 Score=31.74 Aligned_cols=29 Identities=24% Similarity=0.561 Sum_probs=23.1
Q ss_pred ceeccccCCCCCCCcccCccccccccCCcccccccHHHH
Q 045234 70 SKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELA 108 (299)
Q Consensus 70 ~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~ 108 (299)
...+|..|.+-||..|... .-|+.|.++.
T Consensus 171 ~~~~C~~C~~v~H~~C~~~----------~~CpkC~R~~ 199 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFRK----------KSCPKCARRQ 199 (202)
T ss_pred CeeeCCcCccccchhhcCC----------CCCCCcHhHh
Confidence 4578999999999999873 2399998764
No 73
>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.87 E-value=24 Score=28.10 Aligned_cols=41 Identities=17% Similarity=0.181 Sum_probs=25.4
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|.+..... .|.+ .-+- -.+.+||++|+.+++|+
T Consensus 4 ~c~~il~~l~~~~~~~----~F~~-pv~~-~~~p~Y~~iIk~PmdL~ 44 (97)
T cd05503 4 LCETILDEMEAHEDAW----PFLE-PVNT-KLVPGYRKIIKKPMDFS 44 (97)
T ss_pred HHHHHHHHHHcCCCch----hhcC-CCCc-cccCCHHHHhCCCCCHH
Confidence 3666665555543222 6765 2221 24689999999999874
No 74
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=35.80 E-value=24 Score=28.63 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=27.6
Q ss_pred cHHHHHHHHhhccCCCCCC----CCCCCCcccccchhhHHhhhccccCCC
Q 045234 104 CLELAWLIETKKDVNYDGF----DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 104 C~~l~~~le~~~~~~~~~~----df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
|.++...|.+..+. .|. .|.. . +-...+.+||++|+.+++|+
T Consensus 5 ~~~l~~~i~~~~d~--~gr~~~~~F~~-l-p~~~~~pdYy~vI~~PmdL~ 50 (103)
T cd05517 5 LEQLLEAVMTATDP--SGRLISELFQK-L-PSKVLYPDYYAVIKEPIDLK 50 (103)
T ss_pred HHHHHHHHHHhhCc--CCCChhHHHhc-C-CCCCCCCCHHHHcCCCcCHH
Confidence 55666666665443 333 6654 2 33456889999999999874
No 75
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=35.45 E-value=20 Score=25.21 Aligned_cols=44 Identities=23% Similarity=0.489 Sum_probs=28.0
Q ss_pred ccccccCC-----ceeccccCCCCCCCcccCccccccc---cCCcccccccH
Q 045234 62 FCGVCRKA-----SKFYCFCCPSAVCKTCLYDIQFALV---KENKGFCNSCL 105 (299)
Q Consensus 62 ~C~~C~~~-----~~~~C~~Cp~s~c~~CL~~~~~~~v---~~~~~~C~~C~ 105 (299)
.|..|++. ....|..|...||..|......... ....-.|..|.
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~ 55 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCY 55 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHh
Confidence 46677664 3477889999999999986543321 12234666664
No 76
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=35.39 E-value=13 Score=23.54 Aligned_cols=24 Identities=25% Similarity=0.635 Sum_probs=10.7
Q ss_pred ccccccCC----ceeccccCCCCCCCcc
Q 045234 62 FCGVCRKA----SKFYCFCCPSAVCKTC 85 (299)
Q Consensus 62 ~C~~C~~~----~~~~C~~Cp~s~c~~C 85 (299)
.|..|++. ..|.|..|...+|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 47788875 3689999999888776
No 77
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=32.06 E-value=30 Score=27.75 Aligned_cols=41 Identities=15% Similarity=-0.010 Sum_probs=25.4
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|-+..... .|.. .-+ .--+.+||++|+.+++|+
T Consensus 4 ~c~~il~~l~~~~~s~----~F~~-pv~-~~~~pdY~~iIk~PmDL~ 44 (97)
T cd05505 4 KCEEILSKILKYRFSW----PFRE-PVT-ADEAEDYKKVITNPMDLQ 44 (97)
T ss_pred HHHHHHHHHHhCCCcc----cccC-CCC-hhhcccHHHHcCCcCCHH
Confidence 3566655555433222 6765 222 224789999999999884
No 78
>PF03380 DUF282: Caenorhabditis protein of unknown function, DUF282; InterPro: IPR005044 This family consists of proteins of unknown function found in Caenorhabditis species.
Probab=31.54 E-value=32 Score=23.85 Aligned_cols=23 Identities=26% Similarity=0.778 Sum_probs=17.8
Q ss_pred eCCCCCCCcccccccCCCccccCCCCCe
Q 045234 29 CDNTRCLKVYHPECVDKDESFLAAKTKW 56 (299)
Q Consensus 29 CD~~~CPkaYH~~Cl~~~~~~~~~~g~W 56 (299)
|. .|+++|-..|.|...+ ....|
T Consensus 2 Cs--~C~~iYdt~CqG~g~P---s~~~w 24 (39)
T PF03380_consen 2 CS--VCSKIYDTTCQGFGIP---SLSDW 24 (39)
T ss_pred Cc--ccccccCCCCccCCCC---Ccccc
Confidence 66 8999999999997644 34456
No 79
>cd05521 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.17 E-value=32 Score=28.13 Aligned_cols=42 Identities=26% Similarity=0.112 Sum_probs=25.2
Q ss_pred cHHHHHHHHhhccCCCCCC----CCCCCCcccccchhhHHhhhccccCCC
Q 045234 104 CLELAWLIETKKDVNYDGF----DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 104 C~~l~~~le~~~~~~~~~~----df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
|..+...|.+..+. +|. .|.. .+-.-.+.+||++|+.+++|+
T Consensus 6 ~~~l~~~i~~~~~~--~g~~~~~~F~~--lp~~~~~pdYy~iI~~PmdL~ 51 (106)
T cd05521 6 LKPLYDGIYTLKEE--NGIEIHPIFNV--LPLRKDYPDYYKIIKNPLSLN 51 (106)
T ss_pred HHHHHHHHHhhcCc--CCCCchHhhhc--CCccccCccHHHHhcCCCCHH
Confidence 44555555554433 233 4533 122345789999999999874
No 80
>cd05524 Bromo_polybromo_I Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=30.10 E-value=29 Score=28.62 Aligned_cols=43 Identities=23% Similarity=0.180 Sum_probs=28.9
Q ss_pred ccHHHHHHHHhhccCCCCCC----CCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGF----DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~----df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|..+...|.+.... +|. .|-+ . +..-.+.+||++|+.+++|+
T Consensus 6 ~c~~il~~l~~~~~~--~g~~l~~~F~~-~-p~~~~~PdYy~iI~~Pmdl~ 52 (113)
T cd05524 6 VCQELYDTIRNYKSE--DGRILCESFIR-V-PKRRNEPEYYEVVSNPIDLL 52 (113)
T ss_pred HHHHHHHHHHhhccc--CCCchhHHHhc-C-CCcccCCCHHHHhCCccCHH
Confidence 577888888776544 333 4544 2 22345679999999999874
No 81
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.00 E-value=11 Score=36.93 Aligned_cols=49 Identities=18% Similarity=0.423 Sum_probs=36.9
Q ss_pred ccccccCCceecc--ccCCCCCCCcccCccccccccCCcccccccHHHHHHHHhh
Q 045234 62 FCGVCRKASKFYC--FCCPSAVCKTCLYDIQFALVKENKGFCNSCLELAWLIETK 114 (299)
Q Consensus 62 ~C~~C~~~~~~~C--~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~~le~~ 114 (299)
.|.+|+....--| -+|..-||..|+..+++.+ .+-|+.|.+-..+|+..
T Consensus 276 kCplc~~Llrnp~kT~cC~~~fc~eci~~al~ds----Df~CpnC~rkdvlld~l 326 (427)
T COG5222 276 KCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDS----DFKCPNCSRKDVLLDGL 326 (427)
T ss_pred cCcchhhhhhCcccCccccchHHHHHHhhhhhhc----cccCCCcccccchhhcc
Confidence 5778886543333 4688999999998876655 78899999877777664
No 82
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=29.01 E-value=33 Score=21.51 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=12.4
Q ss_pred CCCeeccCCccccccCCceeccccCCC
Q 045234 53 KTKWICNWHFCGVCRKASKFYCFCCPS 79 (299)
Q Consensus 53 ~g~W~Cp~H~C~~C~~~~~~~C~~Cp~ 79 (299)
.|.|.|+. |..=.......|..|..
T Consensus 2 ~g~W~C~~--C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 2 EGDWKCPS--CTFMNPASRSKCVACGA 26 (30)
T ss_dssp SSSEEETT--TTEEEESSSSB-TTT--
T ss_pred CcCccCCC--CcCCchHHhhhhhCcCC
Confidence 47899973 33323334566666643
No 83
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=28.55 E-value=43 Score=30.70 Aligned_cols=50 Identities=26% Similarity=0.545 Sum_probs=32.6
Q ss_pred ccccccceeccCCceeeeCCCCCCCcccccccCC--CccccCCCCCeeccCC-ccccccCCceec
Q 045234 12 ISEIWCFKCKHGGELRLCDNTRCLKVYHPECVDK--DESFLAAKTKWICNWH-FCGVCRKASKFY 73 (299)
Q Consensus 12 ~~ed~C~vC~dGGeLv~CD~~~CPkaYH~~Cl~~--~~~~~~~~g~W~Cp~H-~C~~C~~~~~~~ 73 (299)
+.+-+|+.|+.-|.+. +.|| |..|-.- +.. ..=.||+- .|..||..+++.
T Consensus 58 ~~~~~C~nCg~~GH~~----~DCP---~~iC~~C~~~~H-----~s~~C~~~~~C~~Cg~~GH~~ 110 (190)
T COG5082 58 EENPVCFNCGQNGHLR----RDCP---HSICYNCSWDGH-----RSNHCPKPKKCYNCGETGHLS 110 (190)
T ss_pred ccccccchhcccCccc----ccCC---hhHhhhcCCCCc-----ccccCCcccccccccccCccc
Confidence 4456799999999987 3699 4544433 211 12346765 788888877654
No 84
>cd05494 Bromodomain_1 Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=27.44 E-value=33 Score=28.46 Aligned_cols=42 Identities=14% Similarity=-0.061 Sum_probs=25.4
Q ss_pred ccccHHHHHHHHhhccCCCCCCCCCCCCccccc---chhhHHhhhccccCCC
Q 045234 101 CNSCLELAWLIETKKDVNYDGFDRSDAGERNRF---YFKGYWQKIKEKESLT 149 (299)
Q Consensus 101 C~~C~~l~~~le~~~~~~~~~~df~d~~~~~e~---lfk~yw~~ik~k~~lt 149 (299)
|..|.+....+..+.... .|.. ++.. -+-+|+++||.+|+|+
T Consensus 5 ~~~~l~~l~~~~~~~~~~----pF~~---PVd~~~~~~pdY~~iIK~PMDL~ 49 (114)
T cd05494 5 LERVLRELKRHRRNEDAW----PFLE---PVNPPRRGAPDYRDVIKRPMSFG 49 (114)
T ss_pred HHHHHHHHHHhhhCCCCC----CcCC---CCCchhcCCCChhhhcCCCCChH
Confidence 344444444444422332 6865 3333 4788999999999984
No 85
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=27.41 E-value=39 Score=38.12 Aligned_cols=57 Identities=21% Similarity=0.399 Sum_probs=42.9
Q ss_pred eeccCCccccccCC--------ceeccccCCCCCCCcccCccccccccCCcccccccHHHHHHHHhhcc
Q 045234 56 WICNWHFCGVCRKA--------SKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCLELAWLIETKKD 116 (299)
Q Consensus 56 W~Cp~H~C~~C~~~--------~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~~l~~~le~~~~ 116 (299)
=.|+.+.|.+||.. ...-|..|....|..|.. ++. +++.-.|++|..-+........
T Consensus 11 ~~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye---ye~-~~g~~~cp~c~t~y~~~~~~~~ 75 (1044)
T PLN02915 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE---YER-SEGNQCCPQCNTRYKRHKGCPR 75 (1044)
T ss_pred cCCCcchhhccccccCcCCCCCEEEEeccCCCccccchhh---hhh-hcCCccCCccCCchhhhcCCCC
Confidence 45788999999985 135699999999999983 443 5667799999877775543333
No 86
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=27.23 E-value=41 Score=31.21 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=16.1
Q ss_pred cccccCCCccccCCCCCeeccCC
Q 045234 39 HPECVDKDESFLAAKTKWICNWH 61 (299)
Q Consensus 39 H~~Cl~~~~~~~~~~g~W~Cp~H 61 (299)
|+.|+.+... ...|.|+||.|
T Consensus 155 hLGCVp~~~A--Gd~gg~~CPCH 175 (210)
T KOG1671|consen 155 HLGCVPIANA--GDYGGYYCPCH 175 (210)
T ss_pred cccccccccc--cccCceecccc
Confidence 9999987544 26789999943
No 87
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=27.11 E-value=40 Score=27.48 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=18.1
Q ss_pred CCCCCCccccc---chhhHHhhhccccCCC
Q 045234 123 DRSDAGERNRF---YFKGYWQKIKEKESLT 149 (299)
Q Consensus 123 df~d~~~~~e~---lfk~yw~~ik~k~~lt 149 (299)
.|.+ ++.. -+.+||++||.+++|+
T Consensus 25 ~F~~---PVd~~~~~~pdY~~iIk~PmDL~ 51 (107)
T cd05497 25 PFQQ---PVDAVKLNLPDYHKIIKTPMDLG 51 (107)
T ss_pred cccC---CCCcccccCCcHHHHHcCcccHH
Confidence 7876 3332 3789999999999884
No 88
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.90 E-value=38 Score=27.38 Aligned_cols=40 Identities=10% Similarity=0.006 Sum_probs=23.9
Q ss_pred cHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 104 CLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 104 C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
|..+...|.+..... .|.. .-+ +-.+.+||++|+.+++|+
T Consensus 8 ~~~il~~l~~~~~a~----~F~~-pV~-~~~~p~Y~~iIk~PmDL~ 47 (104)
T cd05507 8 ILLVYRTLASHRYAS----VFLK-PVT-EDIAPGYHSVVYRPMDLS 47 (104)
T ss_pred HHHHHHHHHcCCCCH----hhcC-CCC-ccccCCHHHHhCCCcCHH
Confidence 444444444432222 6766 222 134678999999999884
No 89
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=26.54 E-value=19 Score=24.20 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=20.9
Q ss_pred cccceeccC---CceeeeCCCCCCCcccccccCCC
Q 045234 15 IWCFKCKHG---GELRLCDNTRCLKVYHPECVDKD 46 (299)
Q Consensus 15 d~C~vC~dG---GeLv~CD~~~CPkaYH~~Cl~~~ 46 (299)
|.|.||.++ ++.+.-- .|.-+||..|+..-
T Consensus 1 d~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKL--PCGHVFHRSCIKEW 33 (44)
T ss_dssp -CETTTTCBHHTTSCEEEE--TTSEEEEHHHHHHH
T ss_pred CCCcCCChhhcCCCeEEEc--cCCCeeCHHHHHHH
Confidence 468888763 4444444 59999999999863
No 90
>cd05500 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.34 E-value=46 Score=26.65 Aligned_cols=44 Identities=16% Similarity=0.027 Sum_probs=28.1
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCCh
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLTP 150 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt~ 150 (299)
.|.++...|.+..... .|.+.-++-...+.+||++|+.+++|+.
T Consensus 8 ~~~~ii~~l~~~~~a~----~F~~pv~~~~~~~p~Y~~~I~~P~dL~t 51 (103)
T cd05500 8 FLLSSIRSLKRLKDAR----PFLVPVDPVKLNIPHYPTIIKKPMDLGT 51 (103)
T ss_pred HHHHHHHHHHcCCCCh----hhcCCCCcccccCCCHHHHhcCCCCHHH
Confidence 3666666666554443 6877111223457899999999998753
No 91
>cd05504 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=26.29 E-value=41 Score=27.76 Aligned_cols=43 Identities=19% Similarity=0.094 Sum_probs=28.2
Q ss_pred ccccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 101 CNSCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 101 C~~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
...|.++...|-...... +|.. .-+ ..-+.+||++|+.+++|+
T Consensus 14 ~~~c~~il~~l~~~~~s~----~F~~-pvd-~~~~pdY~~vI~~PmDL~ 56 (115)
T cd05504 14 LSALEQLLVEIVKHKDSW----PFLR-PVS-KIEVPDYYDIIKKPMDLG 56 (115)
T ss_pred HHHHHHHHHHHHhCCCch----hhcC-CCC-ccccccHHHHhcCcccHH
Confidence 346777776666643332 6755 222 234789999999999874
No 92
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=25.85 E-value=35 Score=23.62 Aligned_cols=28 Identities=32% Similarity=0.794 Sum_probs=21.5
Q ss_pred ccccccCCc------eeccccCCCCCCCcccCcc
Q 045234 62 FCGVCRKAS------KFYCFCCPSAVCKTCLYDI 89 (299)
Q Consensus 62 ~C~~C~~~~------~~~C~~Cp~s~c~~CL~~~ 89 (299)
.|..|++.- -+.|..|....|..|+...
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 678888753 5899999999999999754
No 93
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=25.40 E-value=53 Score=26.04 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=26.2
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|-.... ......|.+.-++-..-+.+||++|+.+++|+
T Consensus 4 ~c~~il~~l~~~~~-~~~a~~F~~pv~~~~~~~p~Y~~~I~~Pmdl~ 49 (102)
T cd05498 4 FCSGILKELFSKKH-KAYAWPFYKPVDPEALGLHDYHDIIKHPMDLS 49 (102)
T ss_pred HHHHHHHHHHhCCC-ccccCcccCcCCccccCCCcHHHHccCCCcHH
Confidence 36666655555411 11111676611122234789999999999874
No 94
>cd05506 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=25.38 E-value=55 Score=25.78 Aligned_cols=42 Identities=17% Similarity=0.048 Sum_probs=26.0
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcc-cccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGER-NRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~-~e~lfk~yw~~ik~k~~lt 149 (299)
.|.++...|-+..... .|.+ .-. -..-+.+||++|+.+++|+
T Consensus 4 ~c~~il~~l~~~~~~~----~F~~-pv~~~~~~~p~Y~~~I~~P~dl~ 46 (99)
T cd05506 4 QCGTLLRKLMKHKWGW----VFNA-PVDVVALGLPDYFDIIKKPMDLG 46 (99)
T ss_pred HHHHHHHHHHhCCCCc----cccC-CCCccccCCCCHHHHHcCCCCHH
Confidence 3666665555543322 6866 221 1234789999999999874
No 95
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=25.18 E-value=15 Score=28.54 Aligned_cols=37 Identities=27% Similarity=0.636 Sum_probs=16.8
Q ss_pred eeccccCCC-----CCCCcccCccccccc-cCCcccccccHHH
Q 045234 71 KFYCFCCPS-----AVCKTCLYDIQFALV-KENKGFCNSCLEL 107 (299)
Q Consensus 71 ~~~C~~Cp~-----s~c~~CL~~~~~~~v-~~~~~~C~~C~~l 107 (299)
.+.|..|.. ++|++|-.+.+.... -....||.+|..|
T Consensus 17 ~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 17 HYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp EEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred EEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 566666653 567777554432211 1236788888654
No 96
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=24.77 E-value=82 Score=19.22 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=16.1
Q ss_pred hhHHHHHHHhhhHHHHhcc
Q 045234 262 NMWNLYLRNHHLQGLLNTM 280 (299)
Q Consensus 262 kL~~lF~~~f~m~klL~~H 280 (299)
.|+.+|..-.+..||++.|
T Consensus 4 tlkkv~qglhe~ikli~nh 22 (23)
T PF08225_consen 4 TLKKVFQGLHEVIKLINNH 22 (23)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 4788888888899999887
No 97
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=24.48 E-value=27 Score=38.08 Aligned_cols=41 Identities=29% Similarity=0.704 Sum_probs=32.0
Q ss_pred ccccccCC------ceeccccCCCCCCCcccCccccccccCCcccccccH
Q 045234 62 FCGVCRKA------SKFYCFCCPSAVCKTCLYDIQFALVKENKGFCNSCL 105 (299)
Q Consensus 62 ~C~~C~~~------~~~~C~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C~ 105 (299)
.|.+|+.+ ....|+.|-.-+|..|.. +..++++.|+|..|.
T Consensus 273 iCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG---Ile~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 273 ICDVCRSPDSEEANEMVFCDKCNICVHQACYG---ILEVPEGPWLCRTCA 319 (893)
T ss_pred eeceecCCCccccceeEEeccchhHHHHhhhc---eeecCCCCeeehhcc
Confidence 57888776 257899999999999964 334588999999985
No 98
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=23.36 E-value=52 Score=24.08 Aligned_cols=48 Identities=25% Similarity=0.509 Sum_probs=23.9
Q ss_pred CccccccCC-----ceeccccCCCCCCCcccCcccccc---c--cCCcccccccHHHH
Q 045234 61 HFCGVCRKA-----SKFYCFCCPSAVCKTCLYDIQFAL---V--KENKGFCNSCLELA 108 (299)
Q Consensus 61 H~C~~C~~~-----~~~~C~~Cp~s~c~~CL~~~~~~~---v--~~~~~~C~~C~~l~ 108 (299)
..|.+|++. ....|..|...||..|........ . ....-.|..|...+
T Consensus 10 ~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~ 67 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKL 67 (69)
T ss_dssp SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHH
T ss_pred CcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHh
Confidence 356778775 357899999999999998554322 1 11234677776543
No 99
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=23.33 E-value=19 Score=23.91 Aligned_cols=26 Identities=19% Similarity=0.599 Sum_probs=18.8
Q ss_pred ccccccCC-ceeccccCCCCCCCcccC
Q 045234 62 FCGVCRKA-SKFYCFCCPSAVCKTCLY 87 (299)
Q Consensus 62 ~C~~C~~~-~~~~C~~Cp~s~c~~CL~ 87 (299)
.|..++.. ..+.|..|...+|..|..
T Consensus 5 ~C~~H~~~~~~~~C~~C~~~~C~~C~~ 31 (42)
T PF00643_consen 5 KCPEHPEEPLSLFCEDCNEPLCSECTV 31 (42)
T ss_dssp B-SSTTTSBEEEEETTTTEEEEHHHHH
T ss_pred cCccCCccceEEEecCCCCccCccCCC
Confidence 45566666 678888888888888765
No 100
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.32 E-value=32 Score=32.38 Aligned_cols=30 Identities=27% Similarity=0.434 Sum_probs=20.7
Q ss_pred cccccceeccCCc---------eeeeCCCCCCCcccccccCC
Q 045234 13 SEIWCFKCKHGGE---------LRLCDNTRCLKVYHPECVDK 45 (299)
Q Consensus 13 ~ed~C~vC~dGGe---------Lv~CD~~~CPkaYH~~Cl~~ 45 (299)
.+..|.+|.+.-. .+.- .|.-+||..|+..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~---~C~H~FC~~CI~~ 211 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILS---NCNHVFCIECIDI 211 (238)
T ss_pred CCCCCccCCcccccCccccccceecC---CCCCcccHHHHHH
Confidence 3577999987521 1222 5888999999975
No 101
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=23.26 E-value=58 Score=26.34 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=18.2
Q ss_pred CCCCCCcccccchhhHHhhhccccCCC
Q 045234 123 DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 123 df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.. . +..-.+.+||++|+.+++|+
T Consensus 26 pF~~-~-p~~~~~PdYy~iI~~PmdL~ 50 (103)
T cd05520 26 PFLK-L-PSKRKYPDYYQEIKNPISLQ 50 (103)
T ss_pred hhhc-C-CCcccCCCHHHHcCCCcCHH
Confidence 6755 3 22345789999999999874
No 102
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=23.24 E-value=57 Score=26.29 Aligned_cols=25 Identities=20% Similarity=0.089 Sum_probs=17.6
Q ss_pred CCCCCCcccccchhhHHhhhccccCCC
Q 045234 123 DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 123 df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.. .-. ...+.+||++||.+++|+
T Consensus 21 ~F~~-PV~-~~~~pdY~~vIk~PmDL~ 45 (98)
T cd05513 21 FFAF-PVT-DFIAPGYSSIIKHPMDFS 45 (98)
T ss_pred cccC-cCC-ccccccHHHHHcCccCHH
Confidence 5665 111 335789999999999874
No 103
>cd05501 Bromo_SP100C_like Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=22.62 E-value=65 Score=26.43 Aligned_cols=39 Identities=23% Similarity=0.251 Sum_probs=26.5
Q ss_pred ccHHHHHHHHhhccCCCCCCCCCCCCcccccchhhHHhhhccccCCC
Q 045234 103 SCLELAWLIETKKDVNYDGFDRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 103 ~C~~l~~~le~~~~~~~~~~df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.+|-..|-...++. .|-. ++ ....+|+++||.+|+|+
T Consensus 6 ~ce~il~~l~~~~~s~----~f~~--~p--~~~pdY~~iIk~PMDL~ 44 (102)
T cd05501 6 KCEFLLLKVYCMSKSG----FFIS--KP--YYIRDYCQGIKEPMWLN 44 (102)
T ss_pred HHHHHHHHHHhCcccc----cccC--CC--CCCCchHHHcCCCCCHH
Confidence 4777777777765553 3422 12 35678999999999883
No 104
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=22.39 E-value=63 Score=21.05 Aligned_cols=22 Identities=32% Similarity=0.976 Sum_probs=14.4
Q ss_pred cccccCC-----ceeccccCCCCCCCc
Q 045234 63 CGVCRKA-----SKFYCFCCPSAVCKT 84 (299)
Q Consensus 63 C~~C~~~-----~~~~C~~Cp~s~c~~ 84 (299)
|.+|... +.|.|..|+...|..
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CeECCcCCccceeEEEccCCCCcccCC
Confidence 5556543 568888887766654
No 105
>PF13907 DUF4208: Domain of unknown function (DUF4208)
Probab=22.09 E-value=82 Score=25.39 Aligned_cols=53 Identities=11% Similarity=-0.029 Sum_probs=34.3
Q ss_pred ccchhhhHHHHHHHHHHhhhh----hhhh-----hhHHHHHHHHhhhcccCCcCCCCeeecchhhHHHHHH
Q 045234 208 YYMRVRWYLEMQKMLKLHART----LQEQ-----NNKNTMVACRNHTQEALVKAMQLHVTCHWNMWNLYLR 269 (299)
Q Consensus 208 ~~~~~gw~~eL~~fl~~~g~~----lsr~-----~~v~k~lw~YIk~n~LqdP~~Kr~I~CD~kL~~lF~~ 269 (299)
..+...|+..|-.-|..||+- +... ...-+.||.|+- ..=|.. =++|..+|.+
T Consensus 38 ~l~~~e~a~~lk~~L~~IG~~I~~~l~~~~~~~~~~l~~~LW~fvs---~fwp~~------~~kL~~mY~k 99 (100)
T PF13907_consen 38 GLPRKERAKILKKELLKIGDFIDSILKEYKDDEPEKLRKHLWSFVS---KFWPNK------GKKLHKMYKK 99 (100)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHH---HcCCCC------HHHHHHHHHc
Confidence 334568998888888888864 2211 155789999998 445544 4556666653
No 106
>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.
Probab=22.02 E-value=1e+02 Score=23.72 Aligned_cols=34 Identities=26% Similarity=0.508 Sum_probs=20.3
Q ss_pred CCceeeeCCCCCCCcccccccCCCccccCCCCCeeccCCc
Q 045234 23 GGELRLCDNTRCLKVYHPECVDKDESFLAAKTKWICNWHF 62 (299)
Q Consensus 23 GGeLv~CD~~~CPkaYH~~Cl~~~~~~~~~~g~W~Cp~H~ 62 (299)
+|++...+ ..|| |..|.-.... ...+.+.||+|.
T Consensus 32 ~~~~~a~~-~~Cp---H~g~~l~~~~--~~~~~i~Cp~H~ 65 (98)
T cd03467 32 GGEVYALS-NRCT---HQGCPLSEGE--GEDGCIVCPCHG 65 (98)
T ss_pred CCEEEEEc-CcCC---CCCccCCcCc--cCCCEEEeCCCC
Confidence 35666665 3676 6666432222 256789999874
No 107
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.50 E-value=56 Score=26.50 Aligned_cols=29 Identities=17% Similarity=0.445 Sum_probs=20.6
Q ss_pred CCccccccCC-------ceeccccCCCCCCCcccCc
Q 045234 60 WHFCGVCRKA-------SKFYCFCCPSAVCKTCLYD 88 (299)
Q Consensus 60 ~H~C~~C~~~-------~~~~C~~Cp~s~c~~CL~~ 88 (299)
-|.|+.|++. ..+.|..|...|=.+.-.+
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeeccccccc
Confidence 3678889886 3588999988776555443
No 108
>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=21.41 E-value=69 Score=25.89 Aligned_cols=25 Identities=20% Similarity=0.165 Sum_probs=18.0
Q ss_pred CCCCCCcccccchhhHHhhhccccCCC
Q 045234 123 DRSDAGERNRFYFKGYWQKIKEKESLT 149 (299)
Q Consensus 123 df~d~~~~~e~lfk~yw~~ik~k~~lt 149 (299)
.|.+ .. ....+.+||++|+.+++|+
T Consensus 27 ~F~~-~p-~~~~~pdYy~~I~~Pmdl~ 51 (104)
T cd05522 27 HFEK-LP-DKAREPEYYQEISNPISLD 51 (104)
T ss_pred HHhc-CC-CccccCcHHHHhCCCcCHH
Confidence 6655 22 2336789999999999874
No 109
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=21.25 E-value=1e+02 Score=20.48 Aligned_cols=31 Identities=13% Similarity=0.186 Sum_probs=21.9
Q ss_pred hhhH-HHHHHHHHHhhhh----h-hhhhhHHHHHHHHh
Q 045234 212 VRWY-LEMQKMLKLHART----L-QEQNNKNTMVACRN 243 (299)
Q Consensus 212 ~gw~-~eL~~fl~~~g~~----l-sr~~~v~k~lw~YI 243 (299)
..|. .+|.+||...|-. . +|- +.++.+-+||
T Consensus 2 dtWs~~~L~~wL~~~gi~~~~~~~~rd-~Ll~~~k~~y 38 (38)
T PF10281_consen 2 DTWSDSDLKSWLKSHGIPVPKSAKTRD-ELLKLAKKNY 38 (38)
T ss_pred CCCCHHHHHHHHHHcCCCCCCCCCCHH-HHHHHHHHhC
Confidence 4688 8999999888754 3 566 6666665543
No 110
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=21.01 E-value=57 Score=28.52 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=15.2
Q ss_pred cccccCCCccccCCCCCeeccCC
Q 045234 39 HPECVDKDESFLAAKTKWICNWH 61 (299)
Q Consensus 39 H~~Cl~~~~~~~~~~g~W~Cp~H 61 (299)
|+-|...-. .....+.|.||.|
T Consensus 110 HlGC~~~~~-~~~~~~~~~CPCH 131 (177)
T COG0723 110 HLGCTVPWN-NAGAEGGFFCPCH 131 (177)
T ss_pred CCCCccCcc-cCCCCCeEEccCC
Confidence 888887653 0126789999954
No 111
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=20.87 E-value=22 Score=24.26 Aligned_cols=29 Identities=21% Similarity=0.528 Sum_probs=13.9
Q ss_pred ccCCCCCCCcccCccccccccCCccccccc
Q 045234 75 FCCPSAVCKTCLYDIQFALVKENKGFCNSC 104 (299)
Q Consensus 75 ~~Cp~s~c~~CL~~~~~~~v~~~~~~C~~C 104 (299)
..|..+||..|+....-.. ......|+.|
T Consensus 14 l~CGH~FC~~Cl~~~~~~~-~~~~~~CP~C 42 (42)
T PF15227_consen 14 LPCGHSFCRSCLERLWKEP-SGSGFSCPEC 42 (42)
T ss_dssp -SSSSEEEHHHHHHHHCCS-SSST---SSS
T ss_pred cCCcCHHHHHHHHHHHHcc-CCcCCCCcCC
Confidence 4567888888876432221 2223667665
No 112
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.41 E-value=64 Score=24.40 Aligned_cols=26 Identities=23% Similarity=0.668 Sum_probs=22.2
Q ss_pred Ccccc--ccCCceeccccCCCCCCCccc
Q 045234 61 HFCGV--CRKASKFYCFCCPSAVCKTCL 86 (299)
Q Consensus 61 H~C~~--C~~~~~~~C~~Cp~s~c~~CL 86 (299)
-.|.+ |+..+.++|..|.+.+|..++
T Consensus 28 ~~C~~~gC~~~s~I~C~~Ckk~~Cf~Hf 55 (63)
T PF04236_consen 28 GDCDITGCNNTSFIRCAYCKKSLCFNHF 55 (63)
T ss_pred CcCCCCCCCCcCEEEccccCCcccccce
Confidence 35777 999999999999999998765
No 113
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.31 E-value=64 Score=19.27 Aligned_cols=24 Identities=33% Similarity=0.782 Sum_probs=11.5
Q ss_pred CCeeccCCccccccCCceeccccCCC
Q 045234 54 TKWICNWHFCGVCRKASKFYCFCCPS 79 (299)
Q Consensus 54 g~W~Cp~H~C~~C~~~~~~~C~~Cp~ 79 (299)
++|.|+. |..=.......|..|..
T Consensus 1 g~W~C~~--C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 1 GDWECPA--CTFLNFASRSKCFACGA 24 (26)
T ss_pred CcccCCC--CCCcChhhhccccccCC
Confidence 4688874 22222223445555543
No 114
>PF09463 Opy2: Opy2 protein; InterPro: IPR018571 Opy2p acts as a membrane anchor in the HOG signalling pathway []. This entry represents a conserved N-terminal domain.
Probab=20.17 E-value=51 Score=22.32 Aligned_cols=20 Identities=30% Similarity=0.948 Sum_probs=14.4
Q ss_pred cccccCCc-----eeccccCCCCCC
Q 045234 63 CGVCRKAS-----KFYCFCCPSAVC 82 (299)
Q Consensus 63 C~~C~~~~-----~~~C~~Cp~s~c 82 (299)
|+.|..+. ...|.+||+.||
T Consensus 11 CP~C~~ge~C~~t~~tC~~C~~~~C 35 (35)
T PF09463_consen 11 CPSCPSGEECVLTSQTCTSCPTTYC 35 (35)
T ss_pred CCCCCCCCEEEecCCChhhcccccC
Confidence 44677663 467999998876
Done!