Query 008421
Match_columns 566
No_of_seqs 324 out of 2101
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 11:56:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1244 Predicted transcriptio 99.5 1.9E-15 4.1E-20 149.4 1.0 100 411-513 222-330 (336)
2 KOG0955 PHD finger protein BR1 99.1 7.3E-11 1.6E-15 137.5 4.3 144 293-449 216-361 (1051)
3 KOG1512 PHD Zn-finger protein 99.0 4.5E-11 9.7E-16 119.3 1.1 94 412-512 257-361 (381)
4 KOG4443 Putative transcription 99.0 6.8E-11 1.5E-15 129.6 2.2 100 411-513 16-117 (694)
5 KOG0954 PHD finger protein [Ge 99.0 6.1E-11 1.3E-15 130.8 1.8 139 295-450 270-412 (893)
6 KOG0956 PHD finger protein AF1 99.0 2.6E-10 5.7E-15 124.9 5.0 188 298-512 7-204 (900)
7 COG5141 PHD zinc finger-contai 99.0 1.5E-10 3.3E-15 122.6 0.9 141 296-450 193-335 (669)
8 KOG0957 PHD finger protein [Ge 98.9 3E-10 6.4E-15 120.7 2.2 142 298-448 121-272 (707)
9 KOG4299 PHD Zn-finger protein 98.9 7.4E-10 1.6E-14 121.4 3.5 51 296-346 253-305 (613)
10 KOG4299 PHD Zn-finger protein 98.9 2.5E-09 5.5E-14 117.3 6.0 48 466-513 255-304 (613)
11 KOG1244 Predicted transcriptio 98.7 7.6E-09 1.6E-13 103.1 2.1 48 298-345 283-330 (336)
12 PF00628 PHD: PHD-finger; Int 98.6 8.5E-09 1.8E-13 78.9 0.3 48 298-345 1-50 (51)
13 KOG0825 PHD Zn-finger protein 98.6 2.1E-08 4.6E-13 111.4 1.8 52 296-347 215-267 (1134)
14 PF00628 PHD: PHD-finger; Int 98.5 2.4E-08 5.2E-13 76.4 -0.4 47 467-513 2-50 (51)
15 KOG4443 Putative transcription 98.4 1.1E-07 2.3E-12 105.0 2.9 48 298-345 70-117 (694)
16 KOG0825 PHD Zn-finger protein 98.4 1.8E-07 3.9E-12 104.2 3.6 49 465-513 216-265 (1134)
17 smart00249 PHD PHD zinc finger 98.3 3.5E-07 7.5E-12 67.6 3.2 46 298-343 1-47 (47)
18 cd05502 Bromo_tif1_like Bromod 98.3 9.1E-07 2E-11 78.7 6.3 93 165-259 6-107 (109)
19 cd05505 Bromo_WSTF_like Bromod 98.3 7.4E-07 1.6E-11 77.8 5.3 85 166-253 3-95 (97)
20 KOG0383 Predicted helicase [Ge 98.3 3.5E-07 7.5E-12 103.6 4.1 47 295-344 46-92 (696)
21 smart00249 PHD PHD zinc finger 98.3 5.1E-07 1.1E-11 66.7 3.5 45 467-511 2-47 (47)
22 cd05503 Bromo_BAZ2A_B_like Bro 98.2 1.7E-06 3.7E-11 75.4 5.1 86 166-253 3-95 (97)
23 cd05497 Bromo_Brdt_I_like Brom 98.2 1.9E-06 4.2E-11 76.5 5.0 61 192-254 40-103 (107)
24 cd05509 Bromo_gcn5_like Bromod 98.2 2.5E-06 5.5E-11 74.7 5.7 90 165-256 3-99 (101)
25 cd05496 Bromo_WDR9_II Bromodom 98.2 3.1E-06 6.7E-11 76.6 5.7 93 165-260 7-108 (119)
26 cd05506 Bromo_plant1 Bromodoma 98.1 2.7E-06 6E-11 74.2 4.9 86 165-253 2-97 (99)
27 cd05501 Bromo_SP100C_like Brom 98.1 4.4E-06 9.6E-11 73.5 5.9 89 167-258 6-99 (102)
28 KOG1474 Transcription initiati 98.1 3E-06 6.5E-11 96.8 5.6 93 165-260 224-326 (640)
29 KOG0383 Predicted helicase [Ge 98.1 1.6E-06 3.6E-11 98.3 3.3 44 466-512 49-92 (696)
30 cd05495 Bromo_cbp_like Bromodo 98.1 4.1E-06 8.9E-11 74.5 4.9 90 165-256 5-104 (108)
31 KOG1512 PHD Zn-finger protein 98.1 1.4E-06 3E-11 87.7 1.8 46 298-345 316-362 (381)
32 cd05499 Bromo_BDF1_2_II Bromod 98.1 4.4E-06 9.4E-11 73.4 4.8 86 166-253 3-100 (102)
33 cd05504 Bromo_Acf1_like Bromod 98.1 6.6E-06 1.4E-10 74.1 5.8 92 163-257 12-111 (115)
34 KOG0957 PHD finger protein [Ge 98.0 4.9E-06 1.1E-10 89.2 4.9 50 298-347 546-599 (707)
35 cd04718 BAH_plant_2 BAH, or Br 98.0 3.3E-06 7.2E-11 78.5 2.5 28 320-347 1-28 (148)
36 PF00439 Bromodomain: Bromodom 98.0 9.3E-06 2E-10 68.1 4.9 76 168-245 1-83 (84)
37 cd05498 Bromo_Brdt_II_like Bro 98.0 9.8E-06 2.1E-10 71.1 5.0 86 166-253 3-100 (102)
38 cd05524 Bromo_polybromo_I Brom 98.0 1.5E-05 3.2E-10 71.6 6.0 64 197-261 45-111 (113)
39 cd05507 Bromo_brd8_like Bromod 97.9 1.4E-05 3.1E-10 70.6 5.7 87 164-253 4-98 (104)
40 KOG1973 Chromatin remodeling p 97.9 3.9E-06 8.4E-11 86.5 2.3 45 296-346 221-268 (274)
41 cd05500 Bromo_BDF1_2_I Bromodo 97.9 1.5E-05 3.3E-10 70.2 5.5 87 165-253 6-101 (103)
42 cd05516 Bromo_SNF2L2 Bromodoma 97.9 2.2E-05 4.7E-10 69.8 6.5 89 165-255 3-104 (107)
43 cd05508 Bromo_RACK7 Bromodomai 97.9 1.7E-05 3.6E-10 69.6 5.1 59 192-252 35-96 (99)
44 cd05515 Bromo_polybromo_V Brom 97.8 3.1E-05 6.8E-10 68.5 6.1 57 196-253 42-101 (105)
45 cd05510 Bromo_SPT7_like Bromod 97.8 3.5E-05 7.6E-10 69.1 5.9 91 163-255 7-106 (112)
46 cd05519 Bromo_SNF2 Bromodomain 97.8 3.5E-05 7.7E-10 67.9 5.6 56 196-252 42-100 (103)
47 smart00297 BROMO bromo domain. 97.8 3.7E-05 7.9E-10 67.4 5.7 63 192-256 40-105 (107)
48 cd05513 Bromo_brd7_like Bromod 97.8 3E-05 6.6E-10 67.8 4.5 83 166-250 4-93 (98)
49 cd04369 Bromodomain Bromodomai 97.7 4.7E-05 1E-09 64.7 5.5 85 166-252 3-96 (99)
50 cd04718 BAH_plant_2 BAH, or Br 97.7 1.6E-05 3.5E-10 74.0 2.5 26 488-513 1-26 (148)
51 cd05529 Bromo_WDR9_I_like Brom 97.7 4.6E-05 1E-09 69.9 5.4 88 165-254 26-124 (128)
52 cd05512 Bromo_brd1_like Bromod 97.7 3.2E-05 7E-10 67.7 3.9 58 192-251 34-94 (98)
53 cd05525 Bromo_ASH1 Bromodomain 97.7 4.7E-05 1E-09 67.6 5.0 56 196-252 44-102 (106)
54 cd05528 Bromo_AAA Bromodomain; 97.7 4.9E-05 1.1E-09 68.1 5.1 64 192-257 36-106 (112)
55 cd05520 Bromo_polybromo_III Br 97.7 5.4E-05 1.2E-09 66.8 5.0 55 197-252 43-100 (103)
56 cd05518 Bromo_polybromo_IV Bro 97.7 5.4E-05 1.2E-09 66.9 5.0 55 196-251 42-99 (103)
57 cd05517 Bromo_polybromo_II Bro 97.6 0.0001 2.2E-09 65.1 4.9 56 196-252 42-100 (103)
58 cd05511 Bromo_TFIID Bromodomai 97.5 0.00013 2.9E-09 65.3 5.4 65 192-258 33-100 (112)
59 cd05492 Bromo_ZMYND11 Bromodom 97.5 0.00014 3E-09 64.9 5.4 56 192-249 39-97 (109)
60 KOG1473 Nucleosome remodeling 97.5 2.4E-05 5.3E-10 90.7 0.6 47 296-345 344-390 (1414)
61 cd05522 Bromo_Rsc1_2_II Bromod 97.4 0.0002 4.3E-09 63.3 5.0 56 197-253 44-102 (104)
62 COG5034 TNG2 Chromatin remodel 97.4 6.1E-05 1.3E-09 75.2 1.9 41 302-345 226-269 (271)
63 KOG4323 Polycomb-like PHD Zn-f 97.4 0.00019 4.1E-09 78.0 5.4 47 471-517 177-227 (464)
64 PF15446 zf-PHD-like: PHD/FYVE 97.4 0.00022 4.7E-09 67.4 4.6 66 299-364 2-83 (175)
65 KOG1973 Chromatin remodeling p 97.3 6.4E-05 1.4E-09 77.5 1.0 38 474-513 227-267 (274)
66 KOG1245 Chromatin remodeling c 97.3 5.4E-05 1.2E-09 92.5 -0.7 51 297-347 1109-1159(1404)
67 KOG1245 Chromatin remodeling c 97.1 0.00013 2.7E-09 89.4 0.6 50 466-515 1110-1159(1404)
68 cd05521 Bromo_Rsc1_2_I Bromodo 97.1 0.00063 1.4E-08 60.4 4.6 54 196-252 43-99 (106)
69 cd05491 Bromo_TBP7_like Bromod 97.1 0.00072 1.6E-08 60.8 4.8 60 187-248 52-112 (119)
70 PF13831 PHD_2: PHD-finger; PD 97.0 0.00011 2.4E-09 52.5 -0.8 34 309-344 2-36 (36)
71 COG5034 TNG2 Chromatin remodel 96.6 0.0008 1.7E-08 67.4 1.5 35 476-512 231-268 (271)
72 cd05526 Bromo_polybromo_VI Bro 96.6 0.004 8.7E-08 55.7 5.7 62 194-256 41-105 (110)
73 KOG0955 PHD finger protein BR1 96.5 0.0011 2.4E-08 78.7 1.7 49 466-516 221-271 (1051)
74 PF13832 zf-HC5HC2H_2: PHD-zin 95.8 0.0055 1.2E-07 54.3 2.5 86 354-450 2-87 (110)
75 KOG4323 Polycomb-like PHD Zn-f 95.4 0.0048 1E-07 67.3 0.6 49 298-346 170-224 (464)
76 COG5076 Transcription factor i 94.0 0.039 8.4E-07 59.4 3.1 73 190-264 179-254 (371)
77 KOG0954 PHD finger protein [Ge 93.7 0.023 5E-07 64.4 0.8 45 466-512 273-319 (893)
78 PF13831 PHD_2: PHD-finger; PD 92.6 0.012 2.7E-07 42.0 -2.2 33 477-511 2-35 (36)
79 COG5141 PHD zinc finger-contai 92.6 0.05 1.1E-06 59.2 1.2 46 466-513 195-242 (669)
80 KOG0956 PHD finger protein AF1 92.4 0.055 1.2E-06 61.0 1.4 44 467-512 8-55 (900)
81 KOG1701 Focal adhesion adaptor 91.8 0.027 5.9E-07 60.4 -1.9 95 411-513 332-460 (468)
82 KOG1473 Nucleosome remodeling 91.3 0.1 2.2E-06 61.8 1.9 44 466-512 346-389 (1414)
83 KOG1246 DNA-binding protein ju 90.0 0.22 4.7E-06 59.8 3.2 51 295-346 154-204 (904)
84 PF15446 zf-PHD-like: PHD/FYVE 87.0 0.33 7.1E-06 46.4 1.6 31 467-497 2-35 (175)
85 PF13832 zf-HC5HC2H_2: PHD-zin 86.2 0.61 1.3E-05 41.2 2.8 72 415-496 2-87 (110)
86 PF14446 Prok-RING_1: Prokaryo 84.5 0.56 1.2E-05 36.6 1.5 32 297-328 6-38 (54)
87 KOG1246 DNA-binding protein ju 83.6 0.85 1.9E-05 54.8 3.3 47 466-513 157-203 (904)
88 PF14446 Prok-RING_1: Prokaryo 81.4 0.87 1.9E-05 35.6 1.5 31 466-496 7-38 (54)
89 KOG1632 Uncharacterized PHD Zn 67.3 3.2 6.9E-05 44.5 1.9 38 310-347 74-114 (345)
90 PF12861 zf-Apc11: Anaphase-pr 66.7 1.6 3.4E-05 37.3 -0.4 45 467-513 35-79 (85)
91 PF07649 C1_3: C1-like domain; 64.7 1.9 4.1E-05 29.2 -0.2 28 466-493 2-29 (30)
92 PF11793 FANCL_C: FANCL C-term 64.1 2 4.3E-05 35.3 -0.3 49 467-515 5-65 (70)
93 cd05494 Bromodomain_1 Bromodom 63.3 2.8 6E-05 37.7 0.5 47 168-215 8-60 (114)
94 PF11793 FANCL_C: FANCL C-term 62.4 0.94 2E-05 37.1 -2.5 47 298-344 4-62 (70)
95 PF13901 DUF4206: Domain of un 61.9 5.2 0.00011 39.6 2.1 38 466-512 154-196 (202)
96 PF07649 C1_3: C1-like domain; 58.5 3.6 7.8E-05 27.9 0.2 29 298-326 2-30 (30)
97 PF00641 zf-RanBP: Zn-finger i 56.4 4.7 0.0001 27.3 0.5 27 335-362 2-28 (30)
98 PF13639 zf-RING_2: Ring finge 55.1 0.93 2E-05 33.3 -3.4 42 298-343 2-43 (44)
99 PF13901 DUF4206: Domain of un 54.6 10 0.00022 37.6 2.7 41 296-345 152-197 (202)
100 PF07227 DUF1423: Protein of u 53.4 28 0.00061 38.4 6.1 53 461-513 125-191 (446)
101 smart00547 ZnF_RBZ Zinc finger 50.0 9.6 0.00021 24.7 1.2 24 336-360 1-24 (26)
102 PF12861 zf-Apc11: Anaphase-pr 49.5 6.7 0.00015 33.6 0.5 34 310-345 46-79 (85)
103 KOG4628 Predicted E3 ubiquitin 48.8 9.3 0.0002 40.9 1.5 46 297-345 230-275 (348)
104 PF10497 zf-4CXXC_R1: Zinc-fin 48.2 9.1 0.0002 34.0 1.2 62 295-363 6-81 (105)
105 PF13771 zf-HC5HC2H: PHD-like 45.1 10 0.00022 32.0 0.9 28 298-327 38-67 (90)
106 KOG1080 Histone H3 (Lys4) meth 44.7 40 0.00087 41.1 6.1 85 293-381 570-656 (1005)
107 PF13771 zf-HC5HC2H: PHD-like 44.6 11 0.00023 31.8 1.0 35 411-450 34-68 (90)
108 KOG2932 E3 ubiquitin ligase in 43.9 18 0.0004 37.9 2.7 43 476-521 87-139 (389)
109 PF03107 C1_2: C1 domain; Int 39.3 24 0.00053 23.9 1.9 29 466-494 2-30 (30)
110 PF05191 ADK_lid: Adenylate ki 39.0 17 0.00036 26.1 1.1 27 481-513 3-29 (36)
111 KOG1734 Predicted RING-contain 38.1 9.7 0.00021 39.2 -0.3 60 466-527 226-292 (328)
112 KOG3612 PHD Zn-finger protein 37.9 31 0.00067 38.9 3.5 47 457-512 58-106 (588)
113 PRK14559 putative protein seri 37.0 29 0.00062 40.4 3.2 46 298-345 3-49 (645)
114 KOG2114 Vacuolar assembly/sort 36.8 23 0.00051 41.8 2.4 54 466-528 842-895 (933)
115 KOG0804 Cytoplasmic Zn-finger 36.4 21 0.00045 39.3 1.8 87 411-527 173-265 (493)
116 KOG1472 Histone acetyltransfer 34.3 20 0.00044 41.9 1.5 41 196-237 642-682 (720)
117 cd00162 RING RING-finger (Real 34.1 12 0.00026 26.2 -0.3 41 299-344 2-42 (45)
118 KOG1632 Uncharacterized PHD Zn 34.0 25 0.00055 37.7 2.0 38 478-515 74-114 (345)
119 KOG1701 Focal adhesion adaptor 33.6 7.6 0.00017 42.3 -1.9 75 411-494 272-361 (468)
120 PF15227 zf-C3HC4_4: zinc fing 33.4 11 0.00023 27.7 -0.6 42 416-465 1-42 (42)
121 KOG2879 Predicted E3 ubiquitin 32.0 2E+02 0.0043 30.1 7.9 44 298-346 241-285 (298)
122 KOG1952 Transcription factor N 30.7 21 0.00045 42.2 0.8 49 298-347 193-246 (950)
123 cd05493 Bromo_ALL-1 Bromodomai 30.6 42 0.00092 31.1 2.6 36 199-235 58-93 (131)
124 KOG0804 Cytoplasmic Zn-finger 29.1 34 0.00073 37.7 2.0 48 291-344 170-218 (493)
125 cd00730 rubredoxin Rubredoxin; 28.5 60 0.0013 25.0 2.7 33 481-514 3-43 (50)
126 COG1773 Rubredoxin [Energy pro 28.4 47 0.001 26.2 2.1 10 504-513 35-44 (55)
127 PF07227 DUF1423: Protein of u 28.3 37 0.00081 37.5 2.2 55 292-346 124-192 (446)
128 PF05502 Dynactin_p62: Dynacti 26.6 37 0.0008 38.2 1.8 32 310-346 4-35 (483)
129 KOG1734 Predicted RING-contain 26.4 20 0.00043 37.0 -0.3 48 296-345 224-278 (328)
130 KOG3612 PHD Zn-finger protein 25.8 55 0.0012 37.0 2.9 47 296-346 60-108 (588)
131 PF00130 C1_1: Phorbol esters/ 25.8 38 0.00082 25.5 1.2 31 466-496 13-45 (53)
132 PF10497 zf-4CXXC_R1: Zinc-fin 25.0 24 0.00051 31.4 -0.0 13 501-513 57-69 (105)
133 PF00301 Rubredoxin: Rubredoxi 23.7 35 0.00075 26.0 0.7 32 481-513 3-42 (47)
134 PF00130 C1_1: Phorbol esters/ 22.9 54 0.0012 24.6 1.6 31 297-327 12-44 (53)
135 COG1645 Uncharacterized Zn-fin 22.2 31 0.00068 31.9 0.2 15 497-512 37-51 (131)
136 smart00744 RINGv The RING-vari 22.2 29 0.00063 26.4 -0.0 33 415-450 1-35 (49)
137 KOG1844 PHD Zn-finger proteins 22.1 49 0.0011 37.0 1.7 43 470-513 91-134 (508)
138 TIGR01562 FdhE formate dehydro 20.8 1.9E+02 0.004 30.7 5.6 29 191-219 122-150 (305)
139 PRK14873 primosome assembly pr 20.8 68 0.0015 37.6 2.6 41 459-513 383-430 (665)
140 PF12773 DZR: Double zinc ribb 20.6 86 0.0019 23.3 2.3 10 336-345 28-37 (50)
141 cd00350 rubredoxin_like Rubred 20.2 69 0.0015 22.2 1.5 10 504-513 16-25 (33)
No 1
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.52 E-value=1.9e-15 Score=149.40 Aligned_cols=100 Identities=32% Similarity=0.892 Sum_probs=83.5
Q ss_pred cccccccccCcccccC-----CCcccccCCccCCCccccccCCCccc--c-ccCCCCccCCCc-ccccccccCCCCceee
Q 008421 411 ESANLCKICGRKVEES-----SDKFRSCEHAFCYSKFYHERCLTPKQ--L-KRYGPCWFCPSC-LCRACLTDKDDEKIVM 481 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~-----~~~Ll~C~~~~C~~k~yH~~CL~~~~--~-~~~~~~w~Cp~C-~C~~C~~~~~~~~ll~ 481 (566)
.+.++|.+|......+ .+.|+.|+. | ++..|++||.-+. + ......|+|.+| .|.+|+.+..+++||+
T Consensus 222 ~Pn~YCDFclgdsr~nkkt~~peelvscsd--c-grsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllf 298 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSRENKKTGMPEELVSCSD--C-GRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLF 298 (336)
T ss_pred cCCcccceeccccccccccCCchhhcchhh--c-CCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEe
Confidence 4667888887543221 567999986 8 8999999996532 2 223458999999 7999999999999999
Q ss_pred ccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 482 CDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 482 Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
||.|++.|||+||.||+..+|.|.|.|..|..
T Consensus 299 cddcdrgyhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 299 CDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred ecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence 99999999999999999999999999999964
No 2
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=99.07 E-value=7.3e-11 Score=137.50 Aligned_cols=144 Identities=17% Similarity=0.360 Sum_probs=107.8
Q ss_pred CcCcccccccccccC--CCCceeeccCCCCCcccccCCCCCCCCCCCccCccccccCCCCCCcccccccccCCCCccccc
Q 008421 293 VYKVHTCRQCEEKAG--EKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAKGFGSPHENCIVCERMNANAPRIQI 370 (566)
Q Consensus 293 ~~~~~~C~~C~~~~~--~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R~~~ 370 (566)
...+.+|.+|.+.+- .+.+|+||+|+.++|+.|+ +++.+|+|.|+|..|..... ...+|.+|+..+++..++..
T Consensus 216 ~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cy--gi~~ipeg~WlCr~Cl~s~~--~~v~c~~cp~~~gAFkqt~d 291 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECY--GIPFIPEGQWLCRRCLQSPQ--RPVRCLLCPSKGGAFKQTDD 291 (1051)
T ss_pred cCCCccceeecccccCCCceEEEcCCCcchhhhhcc--CCCCCCCCcEeehhhccCcC--cccceEeccCCCCcceeccC
Confidence 344568999988544 4789999999999999999 57889999999999986663 23689999999999999999
Q ss_pred cccCCCCCCCCCCCCccccccccccccCcCCCCCCCCCCccccccccccCcccccCCCcccccCCccCCCccccccCCC
Q 008421 371 NQAGDEICPANGETSTEFEENSNCTTANVDKPTDNGVDSRESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLT 449 (566)
Q Consensus 371 ~~~~~~~~~~~~e~~~e~E~~s~~~~~~~~~~~~e~~~s~~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~ 449 (566)
++|.|..|+.+.+...-.-. ...+.. ...+.++..+....|.+|.... .+..++|....| ..+||..|-.
T Consensus 292 grw~Hv~caiwipev~F~nt---~~~E~I--~~i~~i~~aRwkL~cy~cK~~~---~gaciqcs~~~c-~~a~hvtca~ 361 (1051)
T KOG0955|consen 292 GRWAHVVCAIWIPEVSFANT---VFLEPI--DSIENIPPARWKLTCYICKQKG---LGACIQCSKANC-YTAFHVTCAR 361 (1051)
T ss_pred Cceeeeehhhcccccccccc---hhhccc--cchhcCcHhhhhceeeeeccCC---CCcceecchhhh-hhhhhhhhHh
Confidence 99999999999754322111 111110 1112222224667999999874 267899988788 7889999963
No 3
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.04 E-value=4.5e-11 Score=119.33 Aligned_cols=94 Identities=32% Similarity=0.762 Sum_probs=75.0
Q ss_pred ccccccccCcccccC----CCcccccCCccCCCccccccCCCcc-----ccccCCCCccCCCc-ccccccccCCCCceee
Q 008421 412 SANLCKICGRKVEES----SDKFRSCEHAFCYSKFYHERCLTPK-----QLKRYGPCWFCPSC-LCRACLTDKDDEKIVM 481 (566)
Q Consensus 412 ~~~~C~~Cgs~~~~~----~~~Ll~C~~~~C~~k~yH~~CL~~~-----~~~~~~~~w~Cp~C-~C~~C~~~~~~~~ll~ 481 (566)
+...|.+|..-.... ...++.|.. | ...||+.|+.+. +++.| .|.|.+| .|.+|+....++.+++
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~~--C-~~~~HP~Ci~M~~elv~~~KTY--~W~C~~C~lC~IC~~P~~E~E~~F 331 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCKP--C-ATRPHPYCVAMIPELVGQYKTY--FWKCSSCELCRICLGPVIESEHLF 331 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeecc--c-ccCCCCcchhcCHHHHhHHhhc--chhhcccHhhhccCCcccchheec
Confidence 445778886542221 356899976 8 567999999873 33444 7999999 8999999999999999
Q ss_pred ccCCCCCCcCCCCCCCCCCCCCCCcccC-CCc
Q 008421 482 CDGCDQGYHLYCMDPPRTSVPKGNWFCR-KCD 512 (566)
Q Consensus 482 Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~-~C~ 512 (566)
||.||+.||.+|++ |..+|.|.|+|. .|.
T Consensus 332 CD~CDRG~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 332 CDVCDRGPHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred cccccCCCCccccc--cccccCccchhhhHHH
Confidence 99999999999997 489999999997 453
No 4
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=99.03 E-value=6.8e-11 Score=129.61 Aligned_cols=100 Identities=36% Similarity=0.959 Sum_probs=85.4
Q ss_pred cccccccccCcccccCCCcccccCCccCCCccccccCCCcccccc-CCCCccCCCc-ccccccccCCCCceeeccCCCCC
Q 008421 411 ESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTPKQLKR-YGPCWFCPSC-LCRACLTDKDDEKIVMCDGCDQG 488 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~~~~~~-~~~~w~Cp~C-~C~~C~~~~~~~~ll~Cd~C~~~ 488 (566)
....+|.+|+.......+.|+.|.. | ++.||+.|+++-.... -...|.||.| +|..|+..++..+.++|+.|+-+
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~~--c-~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvs 92 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACSD--C-GQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVS 92 (694)
T ss_pred hhhhhhhhhccccccccCcchhhhh--h-cccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCccccccccccccc
Confidence 4667899998877666778999986 7 8899999999633222 1234999999 79999999999999999999999
Q ss_pred CcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 489 YHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 489 ~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
||.||+.|++..+|.+.|+|+.|..
T Consensus 93 yh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 93 YHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred ccccccCCccccccCcccccHHHHh
Confidence 9999999999999999999999864
No 5
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=99.03 E-value=6.1e-11 Score=130.76 Aligned_cols=139 Identities=16% Similarity=0.412 Sum_probs=105.3
Q ss_pred Ccccccccccc--cCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccccCCCCCCcccccccccCCCCccccc-c
Q 008421 295 KVHTCRQCEEK--AGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAKGFGSPHENCIVCERMNANAPRIQI-N 371 (566)
Q Consensus 295 ~~~~C~~C~~~--~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R~~~-~ 371 (566)
++.+|.+|... ++.++|++||.|+...|+.|+ ++.++|+|.|.|..|... +.+.|++|++.++....+.. .
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCy--GIle~p~gpWlCr~Calg----~~ppCvLCPkkGGamK~~~sgT 343 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACY--GILEVPEGPWLCRTCALG----IEPPCVLCPKKGGAMKPTKSGT 343 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhh--ceeecCCCCeeehhcccc----CCCCeeeccccCCcccccCCCC
Confidence 44589999874 457799999999999999999 999999999999999843 56689999999999665543 4
Q ss_pred ccCCCCCCCCCCCCccccccccccccC-cCCCCCCCCCCccccccccccCcccccCCCcccccCCccCCCccccccCCCc
Q 008421 372 QAGDEICPANGETSTEFEENSNCTTAN-VDKPTDNGVDSRESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTP 450 (566)
Q Consensus 372 ~~~~~~~~~~~e~~~e~E~~s~~~~~~-~~~~~~e~~~s~~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~ 450 (566)
+|.|..|+.|+..-. ...++- ++-+..+.++..+...+|.+|..+ .+..+.|....| -..||+.|-..
T Consensus 344 ~wAHvsCALwIPEVs------ie~~ekmePItkfs~IpesRwslvC~LCk~k----~GACIqCs~k~C-~t~fHv~CA~~ 412 (893)
T KOG0954|consen 344 KWAHVSCALWIPEVS------IECPEKMEPITKFSHIPESRWSLVCNLCKVK----SGACIQCSNKTC-RTAFHVTCAFE 412 (893)
T ss_pred eeeEeeeeeccceee------ccCHhhcCcccccCCCcHHHHHHHHHHhccc----CcceEEecccch-hhhccchhhhh
Confidence 899999998865321 111111 111223344445677899999988 567899998889 56799999753
No 6
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=99.00 E-value=2.6e-10 Score=124.87 Aligned_cols=188 Identities=17% Similarity=0.442 Sum_probs=123.7
Q ss_pred ccccccccc--CCCCceeec--cCCCCCcccccCCCCCCCCCCCccCccccccCCCCCCcccccccccCCCCcccccccc
Q 008421 298 TCRQCEEKA--GEKDGLVCD--SCEEMYHLSCIEPAFKDIPPKSWYCARCTAKGFGSPHENCIVCERMNANAPRIQINQA 373 (566)
Q Consensus 298 ~C~~C~~~~--~~~~ll~Cd--~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R~~~~~~ 373 (566)
-|-+|-+.. .+.-|++|| .|.-+.|..|+ ++-++|.|.|||..|+.... ....+|-+|+.-.++.+|+-...|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCY--GIvqVPtGpWfCrKCesqer-aarvrCeLCP~kdGALKkTDn~GW 83 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACY--GIVQVPTGPWFCRKCESQER-AARVRCELCPHKDGALKKTDNGGW 83 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcc--eeEecCCCchhhhhhhhhhh-hccceeecccCcccceecccCCCc
Confidence 488997633 366799999 59999999999 99999999999999986552 223689999999999999999999
Q ss_pred CCCCCCCCCCCCccccccccccccCcCCCCCCCCCCccccccccccCccccc---CCCcccccCCccCCCccccccCCCc
Q 008421 374 GDEICPANGETSTEFEENSNCTTANVDKPTDNGVDSRESANLCKICGRKVEE---SSDKFRSCEHAFCYSKFYHERCLTP 450 (566)
Q Consensus 374 ~~~~~~~~~e~~~e~E~~s~~~~~~~~~~~~e~~~s~~~~~~C~~Cgs~~~~---~~~~Ll~C~~~~C~~k~yH~~CL~~ 450 (566)
.|..|+.-+... .|-.. ..++.+ ...-++..+....|+||...... ..+..+.|....| .+.||..|-..
T Consensus 84 AHVVCALYIPEV-rFgNV--~TMEPI---iLq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~C-kqaFHVTCAQ~ 156 (900)
T KOG0956|consen 84 AHVVCALYIPEV-RFGNV--HTMEPI---ILQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGC-KQAFHVTCAQR 156 (900)
T ss_pred eEEEEEeeccce-eeccc--ccccce---eeccCchhhhcceeeeecccCCccccccccceecccccc-hhhhhhhHhhh
Confidence 999987654321 11111 111111 11223333677799999765332 2567888988888 67899998763
Q ss_pred cccccCCCCccCCCccccccccc-CCCCceeeccCCCCCCcCCCCC--CCCCCCCCCCcccCCCc
Q 008421 451 KQLKRYGPCWFCPSCLCRACLTD-KDDEKIVMCDGCDQGYHLYCMD--PPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 451 ~~~~~~~~~w~Cp~C~C~~C~~~-~~~~~ll~Cd~C~~~~H~~Cl~--Ppl~~~p~~~W~C~~C~ 512 (566)
.- -.|-+. ..-+.+-.|.+|. ||+.=|. +....+|.++-.-..|.
T Consensus 157 ~G---------------LLCEE~gn~~dNVKYCGYCk--~HfsKlkk~~~~k~ipsy~~s~s~s~ 204 (900)
T KOG0956|consen 157 AG---------------LLCEEEGNISDNVKYCGYCK--YHFSKLKKSPAIKVIPSYKPSQSASP 204 (900)
T ss_pred hc---------------cceeccccccccceechhHH--HHHHHhhcCCCcccCCCCccccccCC
Confidence 21 122222 1245566677774 5555443 34455665554444443
No 7
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.95 E-value=1.5e-10 Score=122.62 Aligned_cols=141 Identities=21% Similarity=0.422 Sum_probs=104.1
Q ss_pred ccccccccccc--CCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccccCCCCCCcccccccccCCCCcccccccc
Q 008421 296 VHTCRQCEEKA--GEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAKGFGSPHENCIVCERMNANAPRIQINQA 373 (566)
Q Consensus 296 ~~~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R~~~~~~ 373 (566)
++.|.+|...+ +.+.+++||+|+-+.|..|+ ++..+|+|.|+|..|.-..+ .-..|.+|+.-.|+.+.+..++|
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CY--GI~f~peG~WlCrkCi~~~~--~i~~C~fCps~dGaFkqT~dgrW 268 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCY--GIQFLPEGFWLCRKCIYGEY--QIRCCSFCPSSDGAFKQTSDGRW 268 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhcc--cceecCcchhhhhhhccccc--ceeEEEeccCCCCceeeccCCch
Confidence 34799998744 45679999999999999999 88999999999999985441 12348999999999999999999
Q ss_pred CCCCCCCCCCCCccccccccccccCcCCCCCCCCCCccccccccccCcccccCCCcccccCCccCCCccccccCCCc
Q 008421 374 GDEICPANGETSTEFEENSNCTTANVDKPTDNGVDSRESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTP 450 (566)
Q Consensus 374 ~~~~~~~~~e~~~e~E~~s~~~~~~~~~~~~e~~~s~~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~ 450 (566)
.|.+|+++...-+-..-.+....++. ..++..+....|.+|... +|..++|....| ...||..|..-
T Consensus 269 ~H~iCA~~~pelsF~~l~~~dpI~~i-----~sVs~srwkl~C~iCk~~----~GtcIqCs~~nC-~~aYHVtCArr 335 (669)
T COG5141 269 GHVICAMFNPELSFGHLLSKDPIDNI-----ASVSSSRWKLGCLICKEF----GGTCIQCSYFNC-TRAYHVTCARR 335 (669)
T ss_pred HhHhHHHhcchhccccccccchhhhh-----cccchhhHhheeeEEccc----Ccceeeecccch-hhhhhhhhhhh
Confidence 99999888543221111111111111 112223566789999988 677999999899 67899999753
No 8
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=98.93 E-value=3e-10 Score=120.67 Aligned_cols=142 Identities=20% Similarity=0.418 Sum_probs=96.5
Q ss_pred ccccccc--ccCCCCceeeccCCCCCcccccCCC-CCCCCCC-------CccCccccccCCCCCCcccccccccCCCCcc
Q 008421 298 TCRQCEE--KAGEKDGLVCDSCEEMYHLSCIEPA-FKDIPPK-------SWYCARCTAKGFGSPHENCIVCERMNANAPR 367 (566)
Q Consensus 298 ~C~~C~~--~~~~~~ll~Cd~C~~~~H~~Cl~P~-l~~~P~g-------~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R 367 (566)
+|-+|.. ..+.+++|.||.|.-..|-.|+... -..||.| .|||..|.-. ...+.|-+|+...+..++
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G---vs~P~CElCPn~~GifKe 197 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG---VSLPHCELCPNRFGIFKE 197 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcC---CCCCccccCCCcCCcccc
Confidence 8999965 5678899999999999999999532 1245554 5999999843 333689999999999999
Q ss_pred ccccccCCCCCCCCCCCCccccccccccccCcCCCCCCCCCCccccccccccCcccccCCCcccccCCccCCCccccccC
Q 008421 368 IQINQAGDEICPANGETSTEFEENSNCTTANVDKPTDNGVDSRESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERC 447 (566)
Q Consensus 368 ~~~~~~~~~~~~~~~e~~~e~E~~s~~~~~~~~~~~~e~~~s~~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~C 447 (566)
+-+.+|.|.+|+.-.....-.+..... .+...... .+.-....|..|-.+.....+..+.|+.+-| ..|||..|
T Consensus 198 tDigrWvH~iCALYvpGVafg~~~~l~----~Vtl~em~-ysk~Gak~Cs~Ced~~fARtGvci~CdaGMC-k~YfHVTC 271 (707)
T KOG0957|consen 198 TDIGRWVHAICALYVPGVAFGQTHTLC----GVTLEEMD-YSKFGAKTCSACEDKIFARTGVCIRCDAGMC-KEYFHVTC 271 (707)
T ss_pred cchhhHHHHHHHhhcCccccccccccc----cccHHHhh-hhhhccchhccccchhhhhcceeeeccchhh-hhhhhhhH
Confidence 999999999885432221111100000 00000000 1112345788888776666778889988888 67899999
Q ss_pred C
Q 008421 448 L 448 (566)
Q Consensus 448 L 448 (566)
.
T Consensus 272 A 272 (707)
T KOG0957|consen 272 A 272 (707)
T ss_pred H
Confidence 5
No 9
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.89 E-value=7.4e-10 Score=121.44 Aligned_cols=51 Identities=35% Similarity=0.978 Sum_probs=45.1
Q ss_pred cccccccccccCCCCceeeccCCCCCcccccCCCC--CCCCCCCccCcccccc
Q 008421 296 VHTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAF--KDIPPKSWYCARCTAK 346 (566)
Q Consensus 296 ~~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l--~~~P~g~W~C~~C~~~ 346 (566)
.++|..|+....-.++++||+|+++||+.||+||+ ..+|.|.|||++|.-+
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 34899999976667779999999999999999995 6899999999999744
No 10
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.85 E-value=2.5e-09 Score=117.29 Aligned_cols=48 Identities=38% Similarity=1.100 Sum_probs=42.1
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCC--CCCCCCCCcccCCCcc
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPP--RTSVPKGNWFCRKCDA 513 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Pp--l~~~p~~~W~C~~C~~ 513 (566)
.|..|+..+.-..+++||.|+++||++||+|| ...+|.|.|+|+.|..
T Consensus 255 fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~ 304 (613)
T KOG4299|consen 255 FCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKI 304 (613)
T ss_pred HHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCee
Confidence 46777777666778999999999999999999 5779999999999964
No 11
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.67 E-value=7.6e-09 Score=103.09 Aligned_cols=48 Identities=31% Similarity=0.878 Sum_probs=45.6
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
.|.+||..++.+.||+||-|++.||+|||.||+.+.|+|.|-|.-|..
T Consensus 283 ~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 283 YCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred eeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence 588999999999999999999999999999999999999999999963
No 12
>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=98.60 E-value=8.5e-09 Score=78.91 Aligned_cols=48 Identities=38% Similarity=1.020 Sum_probs=42.5
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCC--CCCCCCccCccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFK--DIPPKSWYCARCTA 345 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~--~~P~g~W~C~~C~~ 345 (566)
+|.+|+...+.+.+|.|+.|..+||+.|+.|+.. .++.+.|+|+.|..
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 4889999888999999999999999999999886 55666899999974
No 13
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.56 E-value=2.1e-08 Score=111.42 Aligned_cols=52 Identities=33% Similarity=0.903 Sum_probs=48.1
Q ss_pred cccccccccccCCCCceeeccCCCC-CcccccCCCCCCCCCCCccCccccccC
Q 008421 296 VHTCRQCEEKAGEKDGLVCDSCEEM-YHLSCIEPAFKDIPPKSWYCARCTAKG 347 (566)
Q Consensus 296 ~~~C~~C~~~~~~~~ll~Cd~C~~~-~H~~Cl~P~l~~~P~g~W~C~~C~~~~ 347 (566)
...|.+|+..+..+.||+||+|+.. ||+|||+|+|.++|.+.|||++|....
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE 267 (1134)
T ss_pred cccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhhh
Confidence 4479999999999999999999999 999999999999999999999997653
No 14
>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=98.47 E-value=2.4e-08 Score=76.42 Aligned_cols=47 Identities=36% Similarity=1.138 Sum_probs=40.6
Q ss_pred cccccccCCCCceeeccCCCCCCcCCCCCCCCC--CCCCCCcccCCCcc
Q 008421 467 CRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRT--SVPKGNWFCRKCDA 513 (566)
Q Consensus 467 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~--~~p~~~W~C~~C~~ 513 (566)
|.+|++..+++.||.|+.|+.+||+.|++|+.. ..+...|+|+.|..
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 678888888999999999999999999999876 44556899999963
No 15
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.42 E-value=1.1e-07 Score=104.95 Aligned_cols=48 Identities=31% Similarity=0.890 Sum_probs=43.9
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
+|..|+...+...+++|++|+.+||.||..|+++.+|.|.|+|+.|..
T Consensus 70 vCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 70 VCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred eeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHh
Confidence 566677777888999999999999999999999999999999999983
No 16
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.38 E-value=1.8e-07 Score=104.18 Aligned_cols=49 Identities=31% Similarity=1.057 Sum_probs=46.3
Q ss_pred cccccccccCCCCceeeccCCCCC-CcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 465 CLCRACLTDKDDEKIVMCDGCDQG-YHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 465 C~C~~C~~~~~~~~ll~Cd~C~~~-~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
|.|.+|......+.||.||.|+.+ ||+|||+|+|..+|.+.|||++|..
T Consensus 216 ~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 216 VKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred ccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 579999999889999999999998 9999999999999999999999974
No 17
>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 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=98.33 E-value=9.1e-07 Score=78.74 Aligned_cols=93 Identities=23% Similarity=0.383 Sum_probs=73.8
Q ss_pred hHHHHHHHHHHHhhhhHHHHHHh----hhccCCCCccCCccchhhhhhhhccc--cccCcchhhhhhHHHHHHHHHHH--
Q 008421 165 TDMCQRAFLEIITSEKFTLLCKV----LLGNFQGIKVDRVFNLSAINSRMKQG--AYENSPMQFMADVQQVWKKFQEI-- 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~~----l~~~~~~~~~~~~~Dl~~Id~rl~~g--~Y~~~p~~f~~DV~~vW~kl~~~-- 236 (566)
...|..+|..++.. .++.++.. ....|... |.+||||++|..||..+ .+|.++.+|..|+++||.|...|
T Consensus 6 ~~~c~~il~~l~~~-~~s~~F~~pv~~~~p~Y~~i-I~~PmdL~tI~~kL~~~~~~~Y~s~~~f~~D~~li~~Na~~yN~ 83 (109)
T cd05502 6 QRKCERLLLELYCH-ELSLPFHEPVSPSVPNYYKI-IKTPMDLSLIRKKLQPKSPQHYSSPEEFVADVRLMFKNCYKFNE 83 (109)
T ss_pred HHHHHHHHHHHHhC-CCChhhcCCCCCCCCCHHHH-CCCCccHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Confidence 45699888888875 34444443 23344455 89999999999999996 56689999999999999998887
Q ss_pred -hHHHHHHHHHhhhhhhhhHhhhc
Q 008421 237 -GAEIITLAKKLSELSQASYIEHV 259 (566)
Q Consensus 237 -g~ev~~LA~~Ls~i~~~~~~~~~ 259 (566)
+..+..+|..|...|...+.+++
T Consensus 84 ~~s~i~~~a~~l~~~f~~~~~~~~ 107 (109)
T cd05502 84 EDSEVAQAGKELELFFEEQLKEIL 107 (109)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHC
Confidence 57899999999999888777765
No 19
>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=98.32 E-value=7.4e-07 Score=77.82 Aligned_cols=85 Identities=14% Similarity=0.404 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHhhhhHHHHHHhhh-----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---h
Q 008421 166 DMCQRAFLEIITSEKFTLLCKVLL-----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---G 237 (566)
Q Consensus 166 ~~c~~~l~~~l~se~f~~~~~~l~-----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g 237 (566)
+.|..+|..++..+ ++.++.... ..|-.. |.+||||+||..||..|.| .++.+|..|+++||.|...| +
T Consensus 3 ~~c~~il~~l~~~~-~s~~F~~pv~~~~~pdY~~i-Ik~PmDL~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~~yN~~~ 79 (97)
T cd05505 3 QKCEEILSKILKYR-FSWPFREPVTADEAEDYKKV-ITNPMDLQTMQTKCSCGSY-SSVQEFLDDMKLVFSNAEKYYENG 79 (97)
T ss_pred HHHHHHHHHHHhCC-CcccccCCCChhhcccHHHH-cCCcCCHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHHHCCCC
Confidence 46888888887643 344443322 234455 8999999999999999988 78899999999999998887 5
Q ss_pred HHHHHHHHHhhhhhhh
Q 008421 238 AEIITLAKKLSELSQA 253 (566)
Q Consensus 238 ~ev~~LA~~Ls~i~~~ 253 (566)
..+..+|..|...|..
T Consensus 80 s~i~~~a~~le~~f~~ 95 (97)
T cd05505 80 SYVLSCMRKTEQCCVN 95 (97)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 7899999999887653
No 20
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.32 E-value=3.5e-07 Score=103.65 Aligned_cols=47 Identities=32% Similarity=0.863 Sum_probs=43.5
Q ss_pred CcccccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCcccc
Q 008421 295 KVHTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCT 344 (566)
Q Consensus 295 ~~~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~ 344 (566)
+...|++|+. ++.+|+||+|..+||.+|+.||+..+|.++|.|+.|.
T Consensus 46 ~~e~c~ic~~---~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 46 EQEACRICAD---GGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred hhhhhhhhcC---CCcEEEeccccHHHHHHccCCCCCcCCccceeeeeec
Confidence 4558999986 8999999999999999999999999999999999994
No 21
>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 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=98.21 E-value=1.7e-06 Score=75.40 Aligned_cols=86 Identities=15% Similarity=0.352 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHhhhhHHHHHHhhh----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hH
Q 008421 166 DMCQRAFLEIITSEKFTLLCKVLL----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GA 238 (566)
Q Consensus 166 ~~c~~~l~~~l~se~f~~~~~~l~----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ 238 (566)
..|+.+|-.++..+....+...+- ..|... |.+||||++|..||.+|.| .++.+|..|+.+||.|...| +.
T Consensus 3 ~~c~~il~~l~~~~~~~~F~~pv~~~~~p~Y~~i-Ik~PmdL~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~~yN~~~s 80 (97)
T cd05503 3 ALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKI-IKKPMDFSTIREKLESGQY-KTLEEFAEDVRLVFDNCETFNEDDS 80 (97)
T ss_pred HHHHHHHHHHHcCCCchhhcCCCCccccCCHHHH-hCCCCCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 458888877777664443333221 223344 8999999999999999987 89999999999999998887 46
Q ss_pred HHHHHHHHhhhhhhh
Q 008421 239 EIITLAKKLSELSQA 253 (566)
Q Consensus 239 ev~~LA~~Ls~i~~~ 253 (566)
.+..+|..|...|+.
T Consensus 81 ~i~~~a~~l~~~f~~ 95 (97)
T cd05503 81 EVGRAGHNMRKFFEK 95 (97)
T ss_pred HHHHHHHHHHHHHHH
Confidence 788889988887654
No 23
>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=98.19 E-value=1.9e-06 Score=76.50 Aligned_cols=61 Identities=18% Similarity=0.394 Sum_probs=52.4
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQAS 254 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~ 254 (566)
|-.. +.+||||+||..||.+|.| .++.+|..|+.+||.|...| +..+..+|..|..++...
T Consensus 40 Y~~i-Ik~PmDL~tI~~kL~~~~Y-~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~l~~~f~~~ 103 (107)
T cd05497 40 YHKI-IKTPMDLGTIKKRLENNYY-WSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQK 103 (107)
T ss_pred HHHH-HcCcccHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Confidence 4445 8999999999999999866 78999999999999998887 567888999998876543
No 24
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=98.19 E-value=2.5e-06 Score=74.72 Aligned_cols=90 Identities=12% Similarity=0.232 Sum_probs=68.6
Q ss_pred hHHHHHHHHHHHhhhhHHHHHHhhh----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---h
Q 008421 165 TDMCQRAFLEIITSEKFTLLCKVLL----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---G 237 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~~l~----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g 237 (566)
+..|+.+|-.++..+.+..+...+- ..|-.. |.+||||++|..||..|.| .++.+|..|+++||.|...| +
T Consensus 3 ~~~~~~il~~l~~~~~a~~F~~pv~~~~~p~Y~~~-I~~PmdL~tI~~kl~~~~Y-~s~~~f~~Dv~li~~Na~~yN~~~ 80 (101)
T cd05509 3 YTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDV-IKKPMDLSTMEEKLENGYY-VTLEEFVADLKLIFDNCRLYNGPD 80 (101)
T ss_pred HHHHHHHHHHHHhCCCchhhcCCCChhhcCCHHHH-hcCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCCCC
Confidence 4568877777777654444443222 223444 8999999999999999987 79999999999999998887 5
Q ss_pred HHHHHHHHHhhhhhhhhHh
Q 008421 238 AEIITLAKKLSELSQASYI 256 (566)
Q Consensus 238 ~ev~~LA~~Ls~i~~~~~~ 256 (566)
..+...|..|...+.....
T Consensus 81 s~~~~~a~~l~~~f~~~~~ 99 (101)
T cd05509 81 TEYYKCANKLEKFFWKKLK 99 (101)
T ss_pred CHHHHHHHHHHHHHHHHHh
Confidence 6788899999888665443
No 25
>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=98.15 E-value=3.1e-06 Score=76.65 Aligned_cols=93 Identities=17% Similarity=0.354 Sum_probs=70.8
Q ss_pred hHHHHHHHHHHHhhhhHHHHHHhhh-----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHh--
Q 008421 165 TDMCQRAFLEIITSEKFTLLCKVLL-----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIG-- 237 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~~l~-----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g-- 237 (566)
...|..+|..++..+ .+.++.... ..|... |.+||||+||..||.+|.| .++.+|..|+.+||.|...|.
T Consensus 7 ~~~c~~il~~l~~~~-~s~~F~~PVd~~~~pdY~~i-Ik~PmDL~tIk~kL~~~~Y-~~~~ef~~D~~lif~Na~~yN~~ 83 (119)
T cd05496 7 KKQCKELVNLMWDCE-DSEPFRQPVDLLKYPDYRDI-IDTPMDLGTVKETLFGGNY-DDPMEFAKDVRLIFSNSKSYTPN 83 (119)
T ss_pred HHHHHHHHHHHHhCC-ccccccCCCChhhcCcHHHH-hCCcccHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHHHHHCCC
Confidence 466887777776653 333333222 234445 8999999999999999988 689999999999999988873
Q ss_pred --HHHHHHHHHhhhhhhhhHhhhcC
Q 008421 238 --AEIITLAKKLSELSQASYIEHVG 260 (566)
Q Consensus 238 --~ev~~LA~~Ls~i~~~~~~~~~~ 260 (566)
..|..+|..|...|...+.+...
T Consensus 84 ~~s~i~~~a~~L~~~F~~~~~~l~~ 108 (119)
T cd05496 84 KRSRIYSMTLRLSALFEEHIKKIIS 108 (119)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888999999998877766654
No 26
>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=98.14 E-value=2.7e-06 Score=74.18 Aligned_cols=86 Identities=19% Similarity=0.475 Sum_probs=66.6
Q ss_pred hHHHHHHHHHHHhhhhHHHHHHhhhc-------cCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH-
Q 008421 165 TDMCQRAFLEIITSEKFTLLCKVLLG-------NFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI- 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~~l~~-------~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~- 236 (566)
+..|..+|..++..+ ++.++....+ .|... +.+||||++|..||.+|.| .++.+|..|+.+||.|...|
T Consensus 2 ~~~c~~il~~l~~~~-~~~~F~~pv~~~~~~~p~Y~~~-I~~P~dl~tI~~kL~~~~Y-~s~~ef~~D~~li~~Na~~yn 78 (99)
T cd05506 2 MKQCGTLLRKLMKHK-WGWVFNAPVDVVALGLPDYFDI-IKKPMDLGTVKKKLEKGEY-SSPEEFAADVRLTFANAMRYN 78 (99)
T ss_pred HHHHHHHHHHHHhCC-CCccccCCCCccccCCCCHHHH-HcCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHC
Confidence 567888888887765 4444443322 23334 8999999999999999997 68999999999999998887
Q ss_pred --hHHHHHHHHHhhhhhhh
Q 008421 237 --GAEIITLAKKLSELSQA 253 (566)
Q Consensus 237 --g~ev~~LA~~Ls~i~~~ 253 (566)
+..+..+|..|...|+.
T Consensus 79 ~~~s~i~~~a~~l~~~fe~ 97 (99)
T cd05506 79 PPGNDVHTMAKELLKIFET 97 (99)
T ss_pred CCCCHHHHHHHHHHHHHHH
Confidence 56788888888877653
No 27
>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=98.13 E-value=4.4e-06 Score=73.54 Aligned_cols=89 Identities=10% Similarity=0.213 Sum_probs=65.4
Q ss_pred HHHHHHHHHHhhhhHHHHHHh---hhccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHhH--HHH
Q 008421 167 MCQRAFLEIITSEKFTLLCKV---LLGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIGA--EII 241 (566)
Q Consensus 167 ~c~~~l~~~l~se~f~~~~~~---l~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g~--ev~ 241 (566)
.|...|..+..-+ .+.++-. -..+|... +.+||||+||..+|.+|.| .++.+|..|+++||.|...|.. .+.
T Consensus 6 ~ce~il~~l~~~~-~s~~f~~~p~~~pdY~~i-Ik~PMDL~tI~~kL~~~~Y-~s~~ef~~D~~Lif~N~~~yN~~~~~~ 82 (102)
T cd05501 6 KCEFLLLKVYCMS-KSGFFISKPYYIRDYCQG-IKEPMWLNKVKERLNERVY-HTVEGFVRDMRLIFHNHKLFYKDDDFG 82 (102)
T ss_pred HHHHHHHHHHhCc-ccccccCCCCCCCchHHH-cCCCCCHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 3776666555443 3333321 12334455 8999999999999999998 6899999999999999888732 677
Q ss_pred HHHHHhhhhhhhhHhhh
Q 008421 242 TLAKKLSELSQASYIEH 258 (566)
Q Consensus 242 ~LA~~Ls~i~~~~~~~~ 258 (566)
.+|..|+..|...+.+.
T Consensus 83 ~~a~~L~~~Fek~~~~~ 99 (102)
T cd05501 83 QVGITLEKKFEKNFKEV 99 (102)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88999998877666554
No 28
>KOG1474 consensus Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription]
Probab=98.10 E-value=3e-06 Score=96.81 Aligned_cols=93 Identities=19% Similarity=0.409 Sum_probs=75.1
Q ss_pred hHHHHHHHHHHHhhhhHHHHHH-------hhhccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH-
Q 008421 165 TDMCQRAFLEIITSEKFTLLCK-------VLLGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI- 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~-------~l~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~- 236 (566)
...|..+|.+++... ++=+|. |-+..||.. |.+||||+||..+|..|.| .++..|..||+++|.|+..|
T Consensus 224 lk~C~~iLk~l~~~k-~awpF~~PVD~v~LgLpDY~~I-IK~PMDLgTIK~kL~~~~Y-~~~~eF~~DVRL~F~Ncm~YN 300 (640)
T KOG1474|consen 224 LKQCLSILKRLMKHK-HAWPFNEPVDVVKLGLPDYHDI-IKHPMDLGTIKKKLEKGEY-KSAEEFAADVRLTFDNCMTYN 300 (640)
T ss_pred HHHHHHHHHHHHhcc-CCCCcCCCcCHHhcCCcchhhh-cCCCccHHHHHhhhccccc-CCHHHHHHHHHHHHHHHHhcC
Confidence 345887777777654 334444 222458888 9999999999999999997 88999999999999999998
Q ss_pred --hHHHHHHHHHhhhhhhhhHhhhcC
Q 008421 237 --GAEIITLAKKLSELSQASYIEHVG 260 (566)
Q Consensus 237 --g~ev~~LA~~Ls~i~~~~~~~~~~ 260 (566)
|.+|..+|..|..+|+.-+...-.
T Consensus 301 p~g~dV~~Ma~~L~~~Fe~rw~~~~~ 326 (640)
T KOG1474|consen 301 PEGSDVYAMAKKLQEVFEERWASMPL 326 (640)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhhccc
Confidence 678999999999999887766443
No 29
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.09 E-value=1.6e-06 Score=98.25 Aligned_cols=44 Identities=36% Similarity=1.043 Sum_probs=39.4
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
.|++| .+++.+++|+.|+.+||++|++||+...|.+.|.|+.|.
T Consensus 49 ~c~ic---~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 49 ACRIC---ADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred hhhhh---cCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeec
Confidence 35666 567889999999999999999999999999999999994
No 30
>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=98.08 E-value=4.1e-06 Score=74.53 Aligned_cols=90 Identities=17% Similarity=0.283 Sum_probs=69.4
Q ss_pred hHHHHHHHHHHHhhhhHHHHHHhhh-------ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH-
Q 008421 165 TDMCQRAFLEIITSEKFTLLCKVLL-------GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI- 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~f~~~~~~l~-------~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~- 236 (566)
...|..+|-.++..+.++.++.-.. ..|-.. +.+||||+||..+|.+|.| .++.+|..|+.+||.|...|
T Consensus 5 ~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~i-Ik~PmDL~tI~~kL~~~~Y-~s~~ef~~D~~li~~Na~~yN 82 (108)
T cd05495 5 RQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDI-VKNPMDLSTIRRKLDTGQY-QDPWQYVDDVWLMFDNAWLYN 82 (108)
T ss_pred HHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHH-hCCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHC
Confidence 4457777777777745555555322 234444 8999999999999999987 67999999999999998887
Q ss_pred --hHHHHHHHHHhhhhhhhhHh
Q 008421 237 --GAEIITLAKKLSELSQASYI 256 (566)
Q Consensus 237 --g~ev~~LA~~Ls~i~~~~~~ 256 (566)
+..+..+|..|..+|.....
T Consensus 83 ~~~s~i~~~a~~l~~~F~~~~~ 104 (108)
T cd05495 83 RKTSRVYKYCTKLAEVFEQEID 104 (108)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 56788999999988776443
No 31
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.07 E-value=1.4e-06 Score=87.72 Aligned_cols=46 Identities=35% Similarity=0.894 Sum_probs=41.5
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCc-cccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCA-RCTA 345 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~-~C~~ 345 (566)
.|.+|+....++++++||.|++.||++|+ +|..+|.|.|.|. .|..
T Consensus 316 lC~IC~~P~~E~E~~FCD~CDRG~HT~CV--GL~~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDVCDRGPHTLCV--GLQDLPRGEWICDMRCRE 362 (381)
T ss_pred hhhccCCcccchheeccccccCCCCcccc--ccccccCccchhhhHHHH
Confidence 68888888889999999999999999999 9999999999998 4643
No 32
>cd05499 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. 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=98.07 E-value=4.4e-06 Score=73.45 Aligned_cols=86 Identities=20% Similarity=0.472 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHhh------hhHHHHHHhh---hccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH
Q 008421 166 DMCQRAFLEIITS------EKFTLLCKVL---LGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI 236 (566)
Q Consensus 166 ~~c~~~l~~~l~s------e~f~~~~~~l---~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~ 236 (566)
..|..+|..++.. ..|..+.+-. ...|... |.+||||++|..||.+|.| .++++|..|+++||.|...|
T Consensus 3 ~~c~~Il~~l~~~~~~~~s~~F~~pvd~~~~~~pdY~~~-I~~P~dL~~I~~kl~~~~Y-~s~~ef~~D~~li~~N~~~y 80 (102)
T cd05499 3 KFCEEVLKELMKPKHSAYNWPFLDPVDPVALNIPNYFSI-IKKPMDLGTISKKLQNGQY-QSAKEFERDVRLIFKNCYTF 80 (102)
T ss_pred HHHHHHHHHHHcccCCcccchhcCCCCccccCCCCHHHH-hcCCCCHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHHH
Confidence 3577777777763 3333333221 2234445 8999999999999999987 78999999999999998887
Q ss_pred ---hHHHHHHHHHhhhhhhh
Q 008421 237 ---GAEIITLAKKLSELSQA 253 (566)
Q Consensus 237 ---g~ev~~LA~~Ls~i~~~ 253 (566)
+..+..+|..|..+|+.
T Consensus 81 n~~~s~~~~~a~~l~~~fe~ 100 (102)
T cd05499 81 NPEGTDVYMMGHQLEEVFND 100 (102)
T ss_pred CCCCCHHHHHHHHHHHHHHH
Confidence 57788899999888654
No 33
>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=98.06 E-value=6.6e-06 Score=74.07 Aligned_cols=92 Identities=14% Similarity=0.280 Sum_probs=70.8
Q ss_pred cchHHHHHHHHHHHhhhhHHHHHHhhhc-----cCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH-
Q 008421 163 TNTDMCQRAFLEIITSEKFTLLCKVLLG-----NFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI- 236 (566)
Q Consensus 163 ~~~~~c~~~l~~~l~se~f~~~~~~l~~-----~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~- 236 (566)
-....|..+|-.|+.-+ .+.++....+ .|... |.+||||++|..+|..|.| .++.+|..|+.+||.|...|
T Consensus 12 ~~~~~c~~il~~l~~~~-~s~~F~~pvd~~~~pdY~~v-I~~PmDL~tI~~kL~~~~Y-~s~~~f~~Dv~LI~~Na~~yN 88 (115)
T cd05504 12 LNLSALEQLLVEIVKHK-DSWPFLRPVSKIEVPDYYDI-IKKPMDLGTIKEKLNMGEY-KLAEEFLSDIQLVFSNCFLYN 88 (115)
T ss_pred HHHHHHHHHHHHHHhCC-CchhhcCCCCccccccHHHH-hcCcccHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHC
Confidence 34556887777777644 5555543332 24445 8999999999999999977 78999999999999998887
Q ss_pred --hHHHHHHHHHhhhhhhhhHhh
Q 008421 237 --GAEIITLAKKLSELSQASYIE 257 (566)
Q Consensus 237 --g~ev~~LA~~Ls~i~~~~~~~ 257 (566)
+..+..+|..|..+|...+.+
T Consensus 89 ~~~s~i~~~A~~l~~~f~~~~~~ 111 (115)
T cd05504 89 PEHTSVYKAGTRLQRFFIKRCRK 111 (115)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Confidence 577889999999887665543
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=98.02 E-value=4.9e-06 Score=89.23 Aligned_cols=50 Identities=30% Similarity=0.895 Sum_probs=46.0
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCC----ccCccccccC
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKS----WYCARCTAKG 347 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~----W~C~~C~~~~ 347 (566)
.|.+|.+..+...++.||.|...||+.||+|||+.+|+.. |+|.+|....
T Consensus 546 sCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~e 599 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNE 599 (707)
T ss_pred eeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccccccc
Confidence 7999999999999999999999999999999999999965 9999995443
No 35
>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=97.98 E-value=3.3e-06 Score=78.55 Aligned_cols=28 Identities=32% Similarity=1.017 Sum_probs=26.2
Q ss_pred CCcccccCCCCCCCCCCCccCccccccC
Q 008421 320 MYHLSCIEPAFKDIPPKSWYCARCTAKG 347 (566)
Q Consensus 320 ~~H~~Cl~P~l~~~P~g~W~C~~C~~~~ 347 (566)
.||++||+|||+.+|+|+|+||.|....
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~ 28 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEK 28 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCC
Confidence 4999999999999999999999998765
No 36
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []. Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
Probab=97.98 E-value=9.3e-06 Score=68.06 Aligned_cols=76 Identities=21% Similarity=0.419 Sum_probs=55.9
Q ss_pred HHHHHHHHHhhhhHHHHHHhh----hccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHH
Q 008421 168 CQRAFLEIITSEKFTLLCKVL----LGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEI 240 (566)
Q Consensus 168 c~~~l~~~l~se~f~~~~~~l----~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev 240 (566)
|+.+|..++..+....+-+.+ ...|... +..||||++|..||.+|.| +++.+|..||.+||.|...+ +..+
T Consensus 1 C~~il~~l~~~~~~~~F~~~~~~~~~p~y~~~-i~~P~dL~~I~~kl~~~~Y-~s~~~f~~Dv~~i~~Na~~yn~~~s~~ 78 (84)
T PF00439_consen 1 CREILEELMKHPISSPFSKPVDPKEYPDYYEI-IKNPMDLSTIRKKLENGKY-KSIEEFEADVRLIFQNARRYNPPDSPI 78 (84)
T ss_dssp HHHHHHHHHTSTTGGGGSSSTHTTTSTTHHHH-SSSS--HHHHHHHHHTTSS-SSHHHHHHHHHHHHHHHHHHSCTTSHH
T ss_pred CHHHHHHHHcCCCchhhcCCCChhhCCCHHHH-HhhccchhhhhHHhhccch-hhHHHHHHHHHHHHHHHHHHCCCcCHH
Confidence 788888888777555444332 2334445 8999999999999999999 58999999999999998876 4455
Q ss_pred HHHHH
Q 008421 241 ITLAK 245 (566)
Q Consensus 241 ~~LA~ 245 (566)
...|.
T Consensus 79 ~~~A~ 83 (84)
T PF00439_consen 79 YKAAE 83 (84)
T ss_dssp HHHHH
T ss_pred HHHhc
Confidence 55553
No 37
>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=97.97 E-value=9.8e-06 Score=71.12 Aligned_cols=86 Identities=16% Similarity=0.399 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHhhh--hHHHHHHhhh-------ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH
Q 008421 166 DMCQRAFLEIITSE--KFTLLCKVLL-------GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI 236 (566)
Q Consensus 166 ~~c~~~l~~~l~se--~f~~~~~~l~-------~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~ 236 (566)
+.|..+|..++..+ .++.++.-.. ..|-.. +.+||||++|..+|..|.| .++.+|..|+++||.|...|
T Consensus 3 ~~c~~il~~l~~~~~~~~a~~F~~pv~~~~~~~p~Y~~~-I~~Pmdl~~I~~kl~~~~Y-~s~~ef~~D~~li~~Na~~y 80 (102)
T cd05498 3 KFCSGILKELFSKKHKAYAWPFYKPVDPEALGLHDYHDI-IKHPMDLSTIKKKLDNREY-ADAQEFAADVRLMFSNCYKY 80 (102)
T ss_pred hHHHHHHHHHHhCCCccccCcccCcCCccccCCCcHHHH-ccCCCcHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHH
Confidence 45888888777773 3444444222 223334 8999999999999999987 68999999999999998887
Q ss_pred ---hHHHHHHHHHhhhhhhh
Q 008421 237 ---GAEIITLAKKLSELSQA 253 (566)
Q Consensus 237 ---g~ev~~LA~~Ls~i~~~ 253 (566)
+..+..+|..|...|+.
T Consensus 81 n~~~s~i~~~a~~l~~~fe~ 100 (102)
T cd05498 81 NPPDHPVHAMARKLQDVFED 100 (102)
T ss_pred CCCCCHHHHHHHHHHHHHHH
Confidence 46788889988877653
No 38
>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=97.96 E-value=1.5e-05 Score=71.62 Aligned_cols=64 Identities=22% Similarity=0.220 Sum_probs=57.8
Q ss_pred cCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhhHhhhcCC
Q 008421 197 VDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQASYIEHVGG 261 (566)
Q Consensus 197 ~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~~~~~~~~ 261 (566)
+.+||||++|..||..|.| .++.+|..|+.++|.|...| +..+...|..|...|.....++..+
T Consensus 45 I~~Pmdl~tI~~kl~~~~Y-~s~~~f~~D~~lm~~Na~~yN~~~s~~~~~A~~L~~~f~~~~~~~~~~ 111 (113)
T cd05524 45 VSNPIDLLKIQQKLKTEEY-DDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEVLSG 111 (113)
T ss_pred hCCccCHHHHHHHhCcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence 8999999999999999987 78999999999999998887 5788999999999988888777654
No 39
>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=97.94 E-value=1.4e-05 Score=70.60 Aligned_cols=87 Identities=13% Similarity=0.239 Sum_probs=63.4
Q ss_pred chHHHHHHHHHHHhhhhHHHHHHhhh-----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH--
Q 008421 164 NTDMCQRAFLEIITSEKFTLLCKVLL-----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI-- 236 (566)
Q Consensus 164 ~~~~c~~~l~~~l~se~f~~~~~~l~-----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~-- 236 (566)
-.+.|..+|-.+.. .+.+.++.... ..|... |.+||||+||..||..|.| .++.+|..|+.+||.|...|
T Consensus 4 ~~~~~~~il~~l~~-~~~a~~F~~pV~~~~~p~Y~~i-Ik~PmDL~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~~yN~ 80 (104)
T cd05507 4 WKKAILLVYRTLAS-HRYASVFLKPVTEDIAPGYHSV-VYRPMDLSTIKKNIENGTI-RSTAEFQRDVLLMFQNAIMYNS 80 (104)
T ss_pred HHHHHHHHHHHHHc-CCCCHhhcCCCCccccCCHHHH-hCCCcCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCC
Confidence 34556655555544 33455554333 235555 9999999999999999987 68999999999999998887
Q ss_pred -hHHHHHHHHHhhhhhhh
Q 008421 237 -GAEIITLAKKLSELSQA 253 (566)
Q Consensus 237 -g~ev~~LA~~Ls~i~~~ 253 (566)
+..+..+|..|...+..
T Consensus 81 ~~s~v~~~A~~l~~~~~~ 98 (104)
T cd05507 81 SDHDVYLMAVEMQREVMS 98 (104)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 35677788887766443
No 40
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.94 E-value=3.9e-06 Score=86.49 Aligned_cols=45 Identities=33% Similarity=0.894 Sum_probs=38.6
Q ss_pred cccccccccccCCCCceeecc--CC-CCCcccccCCCCCCCCCCCccCcccccc
Q 008421 296 VHTCRQCEEKAGEKDGLVCDS--CE-EMYHLSCIEPAFKDIPPKSWYCARCTAK 346 (566)
Q Consensus 296 ~~~C~~C~~~~~~~~ll~Cd~--C~-~~~H~~Cl~P~l~~~P~g~W~C~~C~~~ 346 (566)
.++|. |. ..+.|+-||. |+ .+||+.|+ +|...|+|.|||+.|...
T Consensus 221 yC~Cn-qv---syg~Mi~CDn~~C~~eWFH~~CV--GL~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 221 YCICN-QV---SYGKMIGCDNPGCPIEWFHFTCV--GLKTKPKGKWYCPRCKAE 268 (274)
T ss_pred EEEec-cc---ccccccccCCCCCCcceEEEecc--ccccCCCCcccchhhhhh
Confidence 44565 43 4889999996 99 99999999 999999999999999853
No 41
>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=97.93 E-value=1.5e-05 Score=70.19 Aligned_cols=87 Identities=14% Similarity=0.272 Sum_probs=65.9
Q ss_pred hHHHHHHHHHHHhhh---hHHHHHHhh---hccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH--
Q 008421 165 TDMCQRAFLEIITSE---KFTLLCKVL---LGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI-- 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~se---~f~~~~~~l---~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~-- 236 (566)
...|..++..++..+ .|..+.+-. ...|-.. +.+||||++|..||.+|.| .++.+|..|+++||.|...|
T Consensus 6 ~~~~~~ii~~l~~~~~a~~F~~pv~~~~~~~p~Y~~~-I~~P~dL~tI~~kl~~~~Y-~s~~~f~~D~~li~~Na~~yN~ 83 (103)
T cd05500 6 HKFLLSSIRSLKRLKDARPFLVPVDPVKLNIPHYPTI-IKKPMDLGTIERKLKSNVY-TSVEEFTADFNLMVDNCLTFNG 83 (103)
T ss_pred HHHHHHHHHHHHcCCCChhhcCCCCcccccCCCHHHH-hcCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCC
Confidence 456887777777654 333333322 2234455 9999999999999999987 78999999999999998887
Q ss_pred -hHHHHHHHHHhhhhhhh
Q 008421 237 -GAEIITLAKKLSELSQA 253 (566)
Q Consensus 237 -g~ev~~LA~~Ls~i~~~ 253 (566)
+..+...|..|...|+.
T Consensus 84 ~~s~~~~~A~~l~~~fe~ 101 (103)
T cd05500 84 PEHPVSQMGKRLQAAFEK 101 (103)
T ss_pred CCCHHHHHHHHHHHHHHH
Confidence 56788888888877653
No 42
>cd05516 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.93 E-value=2.2e-05 Score=69.79 Aligned_cols=89 Identities=15% Similarity=0.199 Sum_probs=65.1
Q ss_pred hHHHHHHHHHHHhhhh-----HHHHHHhhh-----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHH
Q 008421 165 TDMCQRAFLEIITSEK-----FTLLCKVLL-----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQ 234 (566)
Q Consensus 165 ~~~c~~~l~~~l~se~-----f~~~~~~l~-----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~ 234 (566)
+..|+.+|-.++.-+. ++.++.-+. ..|-.. +.+||||++|..+|..|.| .++.+|..|+.+||.|..
T Consensus 3 ~~~~~~il~~v~~~~d~~g~~~s~~F~~~p~~~~~pdYy~i-I~~Pmdl~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~ 80 (107)
T cd05516 3 TKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYEL-IRKPVDFKKIKERIRNHKY-RSLEDLEKDVMLLCQNAQ 80 (107)
T ss_pred HHHHHHHHHHHHhhhCcCCCEeeHHhhcCCCcccCCCHHHH-cCCCCCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHH
Confidence 4556666555555432 133333222 223344 8999999999999999998 689999999999999988
Q ss_pred HH---hHHHHHHHHHhhhhhhhhH
Q 008421 235 EI---GAEIITLAKKLSELSQASY 255 (566)
Q Consensus 235 ~~---g~ev~~LA~~Ls~i~~~~~ 255 (566)
.| +..+...|..|...|....
T Consensus 81 ~yN~~~s~i~~~a~~l~~~f~~~~ 104 (107)
T cd05516 81 TFNLEGSLIYEDSIVLQSVFKSAR 104 (107)
T ss_pred HHCCCCCHHHHHHHHHHHHHHHHH
Confidence 87 6789999999998876544
No 43
>cd05508 Bromo_RACK7 Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.89 E-value=1.7e-05 Score=69.62 Aligned_cols=59 Identities=19% Similarity=0.331 Sum_probs=50.2
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
|... +.+||||+||..||.+|.| .++++|..|+++||.|...| +..+..+|..|...+.
T Consensus 35 Y~~i-Ik~PmDL~tI~~kl~~~~Y-~s~~ef~~Dv~LI~~Na~~YN~~~s~i~~~A~~l~~~~~ 96 (99)
T cd05508 35 YAQY-VFKPMDLSTLEKNVRKKAY-GSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICE 96 (99)
T ss_pred HHHH-cCCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 4444 8999999999999999987 78999999999999998877 4678888888876644
No 44
>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=97.85 E-value=3.1e-05 Score=68.53 Aligned_cols=57 Identities=14% Similarity=0.244 Sum_probs=50.0
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQA 253 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~ 253 (566)
.+.+||||++|..+|..|.| .++.+|..|+.+||.|...| +..+...|..|..++..
T Consensus 42 iIk~PmdL~tI~~kl~~~~Y-~s~~ef~~D~~l~~~Na~~yN~~~s~i~~~A~~L~~~~~~ 101 (105)
T cd05515 42 VIKKPIDMEKIRSKIEGNQY-QSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLLE 101 (105)
T ss_pred HcCCCcCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence 38999999999999999987 78999999999999998887 57788888888877543
No 45
>cd05510 Bromo_SPT7_like Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.81 E-value=3.5e-05 Score=69.09 Aligned_cols=91 Identities=13% Similarity=0.241 Sum_probs=66.1
Q ss_pred cchHHHHHHHHHHHhhhhHHHHHHhhh-----ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHh
Q 008421 163 TNTDMCQRAFLEIITSEKFTLLCKVLL-----GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIG 237 (566)
Q Consensus 163 ~~~~~c~~~l~~~l~se~f~~~~~~l~-----~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g 237 (566)
.....|..+|..+..-..++.++.... ..|... +.+||||++|..+|.+|.| .++.+|..|+.+||.|...|.
T Consensus 7 ~~~~~~~~il~~l~~~~~~s~~F~~pv~~~~~pdY~~i-Ik~PmdL~tI~~kl~~~~Y-~s~~ef~~D~~Li~~N~~~yN 84 (112)
T cd05510 7 EFYESLDKVLNELKTYTEHSTPFLTKVSKREAPDYYDI-IKKPMDLGTMLKKLKNLQY-KSKAEFVDDLNLIWKNCLLYN 84 (112)
T ss_pred HHHHHHHHHHHHHHhcCccccchhcCCChhhcCCHHHH-hcCccCHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHHHHHC
Confidence 345668877777766533444444333 224455 8999999999999999977 689999999999999988873
Q ss_pred H----HHHHHHHHhhhhhhhhH
Q 008421 238 A----EIITLAKKLSELSQASY 255 (566)
Q Consensus 238 ~----ev~~LA~~Ls~i~~~~~ 255 (566)
. .+...|..|...+....
T Consensus 85 ~~~s~~~~~~A~~l~~~~~~~~ 106 (112)
T cd05510 85 SDPSHPLRRHANFMKKKAEHLL 106 (112)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 2 24567888887765443
No 46
>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=97.80 E-value=3.5e-05 Score=67.87 Aligned_cols=56 Identities=20% Similarity=0.335 Sum_probs=49.1
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
.+.+||||++|..||..|.| .++.+|..|+++||.|...| +..+...|..|...|.
T Consensus 42 iIk~Pmdl~~I~~kl~~~~Y-~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~ 100 (103)
T cd05519 42 IIKRPIALDQIKRRIEGRAY-KSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKAFK 100 (103)
T ss_pred HcCCCcCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 38999999999999999987 78999999999999998887 4678888888877654
No 47
>smart00297 BROMO bromo domain.
Probab=97.79 E-value=3.7e-05 Score=67.44 Aligned_cols=63 Identities=27% Similarity=0.479 Sum_probs=53.4
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhhHh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQASYI 256 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~~~ 256 (566)
|... +.+||||++|..||.+|.| .++.+|..|+++||.|...| +.++...|..|...+.....
T Consensus 40 Y~~~-i~~P~dl~~I~~kl~~~~Y-~s~~ef~~D~~li~~Na~~~n~~~s~~~~~a~~l~~~f~~~~~ 105 (107)
T smart00297 40 YYDI-IKKPMDLSTIKKKLENGKY-SSVEEFVADVQLMFSNAKTYNGPDSEVYKDAKKLEKFFEKKLR 105 (107)
T ss_pred HHHH-hcCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Confidence 4444 8999999999999999988 78999999999999998876 46788889988887665543
No 48
>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=97.76 E-value=3e-05 Score=67.84 Aligned_cols=83 Identities=14% Similarity=0.248 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHhhh---hHHHHHHh-hhccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hH
Q 008421 166 DMCQRAFLEIITSE---KFTLLCKV-LLGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GA 238 (566)
Q Consensus 166 ~~c~~~l~~~l~se---~f~~~~~~-l~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ 238 (566)
..|..+|..+...+ .|..+.+. ....|... +.+||||+||..||..|.| .++.+|..|+.+||.|...| +.
T Consensus 4 ~~l~~il~~l~~~~~~~~F~~PV~~~~~pdY~~v-Ik~PmDL~tI~~kl~~~~Y-~s~~~f~~D~~li~~Na~~yN~~~s 81 (98)
T cd05513 4 KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSI-IKHPMDFSTMKEKIKNNDY-QSIEEFKDDFKLMCENAMKYNKPDT 81 (98)
T ss_pred HHHHHHHHHHHcCCccccccCcCCccccccHHHH-HcCccCHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 34555555555443 33333331 22344555 8999999999999999987 68999999999999998887 45
Q ss_pred HHHHHHHHhhhh
Q 008421 239 EIITLAKKLSEL 250 (566)
Q Consensus 239 ev~~LA~~Ls~i 250 (566)
.+...|..|.+.
T Consensus 82 ~~~~~A~~L~~~ 93 (98)
T cd05513 82 IYYKAAKKLLHS 93 (98)
T ss_pred HHHHHHHHHHHh
Confidence 677777777653
No 49
>cd04369 Bromodomain Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=97.75 E-value=4.7e-05 Score=64.69 Aligned_cols=85 Identities=21% Similarity=0.329 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHhhh-hHHHHHHh-h----hccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---
Q 008421 166 DMCQRAFLEIITSE-KFTLLCKV-L----LGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI--- 236 (566)
Q Consensus 166 ~~c~~~l~~~l~se-~f~~~~~~-l----~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~--- 236 (566)
..|..++..+.... .++.++.. + ...|... +.+||||++|..|+..|.| .++.+|..|+++||.|...+
T Consensus 3 ~~~~~i~~~l~~~~~~~~~~F~~~~~~~~~~~Y~~~-i~~P~~l~~I~~kl~~~~Y-~s~~~f~~D~~li~~Na~~~n~~ 80 (99)
T cd04369 3 KKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEV-IKNPMDLSTIKKKLKNGEY-KSLEEFEADVRLIFSNAKTYNGP 80 (99)
T ss_pred HHHHHHHHHHHhhcccccHHHhcCCChhcCCCHHHH-HhCcccHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCCC
Confidence 34665555554430 23333332 2 2334455 8999999999999999966 79999999999999998876
Q ss_pred hHHHHHHHHHhhhhhh
Q 008421 237 GAEIITLAKKLSELSQ 252 (566)
Q Consensus 237 g~ev~~LA~~Ls~i~~ 252 (566)
+..+...|..|...+.
T Consensus 81 ~~~~~~~a~~l~~~~~ 96 (99)
T cd04369 81 GSPIYKDAKKLEKLFE 96 (99)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 4578888888876644
No 50
>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=97.73 E-value=1.6e-05 Score=74.04 Aligned_cols=26 Identities=46% Similarity=1.361 Sum_probs=24.6
Q ss_pred CCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 488 GYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 488 ~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
.||++||+|||..+|.|+|+||.|..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~ 26 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEV 26 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcC
Confidence 59999999999999999999999974
No 51
>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_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=97.73 E-value=4.6e-05 Score=69.89 Aligned_cols=88 Identities=18% Similarity=0.202 Sum_probs=63.0
Q ss_pred hHHHHHHHHHHHh------hhhHHHHHHhh--hccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH
Q 008421 165 TDMCQRAFLEIIT------SEKFTLLCKVL--LGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI 236 (566)
Q Consensus 165 ~~~c~~~l~~~l~------se~f~~~~~~l--~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~ 236 (566)
.+.|-.+|..++. +..|..+.+.. ...|-.. +..||||++|..||.+|. |.+.++|..|+++||.|...|
T Consensus 26 ~~~i~~~l~~l~~~~~~~~~~~F~~pv~~~~~~p~Y~~i-I~~PmdL~tI~~kl~~~~-Y~s~~~f~~Dv~Li~~Na~~y 103 (128)
T cd05529 26 RERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNR-VPVPMDLETIRSRLENRY-YRSLEALRHDVRLILSNAETF 103 (128)
T ss_pred HHHHHHHHHHHHhcccCcccccccCCCCccccCCcHHHH-cCCCCCHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHHHHH
Confidence 3445555666663 23333333322 2234445 899999999999999995 577999999999999998887
Q ss_pred ---hHHHHHHHHHhhhhhhhh
Q 008421 237 ---GAEIITLAKKLSELSQAS 254 (566)
Q Consensus 237 ---g~ev~~LA~~Ls~i~~~~ 254 (566)
+..+..+|..|...+...
T Consensus 104 N~~~s~i~~~A~~l~~~~~~~ 124 (128)
T cd05529 104 NEPNSEIAKKAKRLSDWLLRI 124 (128)
T ss_pred CCCCCHHHHHHHHHHHHHHHH
Confidence 467888888888875543
No 52
>cd05512 Bromo_brd1_like Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.71 E-value=3.2e-05 Score=67.66 Aligned_cols=58 Identities=12% Similarity=0.257 Sum_probs=49.2
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELS 251 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~ 251 (566)
|... |.+||||+||..||.+|.| .++.+|..|+.+||.|...| +..+...|..|....
T Consensus 34 Y~~i-Ik~PmDL~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~~yN~~~s~~~~~A~~l~~~~ 94 (98)
T cd05512 34 YLDH-IKQPMDFSTMRKKLESQRY-RTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQG 94 (98)
T ss_pred HHHH-hcCCcCHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhh
Confidence 4555 8999999999999999987 68999999999999998887 466777787777653
No 53
>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.71 E-value=4.7e-05 Score=67.61 Aligned_cols=56 Identities=20% Similarity=0.336 Sum_probs=50.1
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
.+.+||||++|..+|..|.| .++.+|.+|+.+||.|...| +..+...|..|..+|.
T Consensus 44 ~I~~P~dL~tI~~kl~~~~Y-~s~~ef~~D~~l~f~Na~~yn~~~S~i~~~A~~L~~~f~ 102 (106)
T cd05525 44 RITDPVDLSTIEKQILTGYY-KTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRKAYY 102 (106)
T ss_pred hCCCCcCHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 38999999999999999987 78999999999999998887 5788999999988754
No 54
>cd05528 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver
Probab=97.70 E-value=4.9e-05 Score=68.12 Aligned_cols=64 Identities=17% Similarity=0.249 Sum_probs=52.3
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHh-------HHHHHHHHHhhhhhhhhHhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIG-------AEIITLAKKLSELSQASYIE 257 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g-------~ev~~LA~~Ls~i~~~~~~~ 257 (566)
|-.. +.+||||+||..||.+|.| .++.+|..|+++||.|...|. ..+...|..|.+.+...+.+
T Consensus 36 Y~~v-I~~PmdL~tI~~kl~~~~Y-~s~~ef~~Dv~li~~Na~~yN~~~s~~~s~i~~~A~~L~~~~~~~~~~ 106 (112)
T cd05528 36 YYEI-IKQPMDLQTILQKLDTHQY-LTAKDFLKDIDLIVTNALEYNPDRDPADKLIRSRACELRDEVHAMIEA 106 (112)
T ss_pred HHHH-HcCCCCHHHHHHHHcCCCc-CCHHHHHHHHHHHHHHHHHHCCCCCccccHHHHHHHHHHHHHHHHHHh
Confidence 3444 8999999999999999987 789999999999999988872 36788888888775554443
No 55
>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=97.69 E-value=5.4e-05 Score=66.84 Aligned_cols=55 Identities=24% Similarity=0.427 Sum_probs=49.5
Q ss_pred cCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 197 VDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 197 ~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
|.+||||++|..||..|.| .++.+|..|+.+||.|...| +..+...|..|..+|+
T Consensus 43 I~~PmdL~tI~~kl~~~~Y-~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~L~~~f~ 100 (103)
T cd05520 43 IKNPISLQQIRTKLKNGEY-ETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKLMQ 100 (103)
T ss_pred cCCCcCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 8999999999999999987 78999999999999998887 5678888888888754
No 56
>cd05518 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. 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=97.68 E-value=5.4e-05 Score=66.86 Aligned_cols=55 Identities=15% Similarity=0.332 Sum_probs=48.9
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELS 251 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~ 251 (566)
.+.+||||++|..+|..|.| .++.+|..|+.+||.|...| +..+...|..|...+
T Consensus 42 iIk~Pmdl~tI~~kl~~~~Y-~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~ 99 (103)
T cd05518 42 IILEPIDLKTIEHNIRNDKY-ATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVL 99 (103)
T ss_pred HcCCCcCHHHHHHHHCCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 38899999999999999987 78999999999999998887 578888888887664
No 57
>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=97.56 E-value=0.0001 Score=65.14 Aligned_cols=56 Identities=18% Similarity=0.332 Sum_probs=49.5
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
.+.+||||++|..||..|.| .++..|..|+++||.|...| +..+...|..|..+|.
T Consensus 42 vI~~PmdL~tI~~kl~~~~Y-~s~~~f~~D~~lm~~Na~~yN~~~s~i~~~A~~l~~~f~ 100 (103)
T cd05517 42 VIKEPIDLKTIAQRIQSGYY-KSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFT 100 (103)
T ss_pred HcCCCcCHHHHHHHHCcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Confidence 48999999999999999965 79999999999999998887 5778888888887654
No 58
>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.54 E-value=0.00013 Score=65.33 Aligned_cols=65 Identities=20% Similarity=0.346 Sum_probs=53.8
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhhHhhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQASYIEH 258 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~~~~~ 258 (566)
|... +.+||||++|..+|.+|.| .+.++|..|+++||.|...| +..+...|..|...+...+.+.
T Consensus 33 Y~~~-I~~PmdL~tI~~kl~~~~Y-~s~~ef~~Dv~li~~Na~~yN~~~s~i~~~A~~l~~~~~~~~~~~ 100 (112)
T cd05511 33 YYKI-IKRPMDLQTIRKKISKHKY-QSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAER 100 (112)
T ss_pred HHHH-hcCCCCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3444 9999999999999999977 68999999999999998887 4567888888888766655443
No 59
>cd05492 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=97.53 E-value=0.00014 Score=64.95 Aligned_cols=56 Identities=16% Similarity=0.235 Sum_probs=46.4
Q ss_pred CCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhh
Q 008421 192 FQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSE 249 (566)
Q Consensus 192 ~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~ 249 (566)
|... +.+||||+||..|+.+|.| .+.++|..|+++||.|...| +..+..+|..|-+
T Consensus 39 Y~~i-Ik~PmDL~tI~~kl~~~~Y-~s~~ef~~Dv~LI~~N~~~yNg~~s~~~~~A~~l~~ 97 (109)
T cd05492 39 RRRL-IHTHLDVADIQEKINSEKY-TSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYR 97 (109)
T ss_pred HHHH-hCCCCcHHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Confidence 3344 8999999999999999998 67999999999999998887 3456666666654
No 60
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=97.52 E-value=2.4e-05 Score=90.68 Aligned_cols=47 Identities=30% Similarity=0.757 Sum_probs=43.4
Q ss_pred cccccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 296 VHTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 296 ~~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
++.|++|.+ .+.+++|..|++.||+.|+.||.-.+|+..|.|.-|..
T Consensus 344 ddhcrf~~d---~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~ 390 (1414)
T KOG1473|consen 344 DDHCRFCHD---LGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNI 390 (1414)
T ss_pred cccccccCc---ccceeecccCCceEEeeecCCccccCCCccchhhhhhh
Confidence 348999987 88999999999999999999999999999999999973
No 61
>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=97.43 E-value=0.0002 Score=63.34 Aligned_cols=56 Identities=18% Similarity=0.261 Sum_probs=49.7
Q ss_pred cCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhh
Q 008421 197 VDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQA 253 (566)
Q Consensus 197 ~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~ 253 (566)
|.+||||++|..||..|.| .++.+|..|+.+||.|...| +..+...|..|...|..
T Consensus 44 I~~Pmdl~tI~~kl~~~~Y-~s~~~f~~D~~li~~Na~~yn~~~s~i~~~A~~l~~~f~~ 102 (104)
T cd05522 44 ISNPISLDDIKKKVKRRKY-KSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEARL 102 (104)
T ss_pred hCCCcCHHHHHHHHccCCC-CCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence 8999999999999999987 78999999999999998887 56788888888877553
No 62
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.42 E-value=6.1e-05 Score=75.23 Aligned_cols=41 Identities=34% Similarity=1.045 Sum_probs=34.8
Q ss_pred cccccCCCCceeecc--CC-CCCcccccCCCCCCCCCCCccCccccc
Q 008421 302 CEEKAGEKDGLVCDS--CE-EMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 302 C~~~~~~~~ll~Cd~--C~-~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
|... ..|.|+-||+ |. .+||+-|+ +|...|+|.|||+.|..
T Consensus 226 Cqqv-SyGqMVaCDn~nCkrEWFH~~CV--GLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 226 CQQV-SYGQMVACDNANCKREWFHLECV--GLKEPPKGKWYCPECKK 269 (271)
T ss_pred eccc-ccccceecCCCCCchhheecccc--ccCCCCCCcEeCHHhHh
Confidence 5442 3789999994 86 79999999 99999999999999974
No 63
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.40 E-value=0.00019 Score=77.97 Aligned_cols=47 Identities=30% Similarity=0.694 Sum_probs=36.9
Q ss_pred cccCCCCceeeccCCCCCCcCCCCCCCCCC----CCCCCcccCCCcchhHH
Q 008421 471 LTDKDDEKIVMCDGCDQGYHLYCMDPPRTS----VPKGNWFCRKCDAGIQE 517 (566)
Q Consensus 471 ~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~----~p~~~W~C~~C~~~~~~ 517 (566)
+..+...+||+|+.|..+||..|+.|+... -|...|+|..|......
T Consensus 177 g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 177 GGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKK 227 (464)
T ss_pred CCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhh
Confidence 344556799999999999999999997643 35667999999764433
No 64
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=97.36 E-value=0.00022 Score=67.43 Aligned_cols=66 Identities=21% Similarity=0.617 Sum_probs=47.1
Q ss_pred cccc---ccccCCCCceeeccCCCCCcccccCCCC------CCCCCCC--ccCccccccC-----CCCCCcccccccccC
Q 008421 299 CRQC---EEKAGEKDGLVCDSCEEMYHLSCIEPAF------KDIPPKS--WYCARCTAKG-----FGSPHENCIVCERMN 362 (566)
Q Consensus 299 C~~C---~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l------~~~P~g~--W~C~~C~~~~-----~~~~~~~C~~C~~l~ 362 (566)
|..| +...+-|.|++|-+|-.+||..||.|-. ++|-.+. -+|..|...- ....+..|-.|...+
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~C~~~G 81 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMCQQCKKPG 81 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcccccCCCC
Confidence 6777 5566788999999999999999997643 3454444 6799996432 233456688887777
Q ss_pred CC
Q 008421 363 AN 364 (566)
Q Consensus 363 ~~ 364 (566)
..
T Consensus 82 ~~ 83 (175)
T PF15446_consen 82 PS 83 (175)
T ss_pred CC
Confidence 54
No 65
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.34 E-value=6.4e-05 Score=77.53 Aligned_cols=38 Identities=34% Similarity=0.989 Sum_probs=33.5
Q ss_pred CCCCceeeccC--CC-CCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 474 KDDEKIVMCDG--CD-QGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 474 ~~~~~ll~Cd~--C~-~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
...+.|+-||. |+ .|||+.|++. ...|+|.|||+.|..
T Consensus 227 vsyg~Mi~CDn~~C~~eWFH~~CVGL--~~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 227 VSYGKMIGCDNPGCPIEWFHFTCVGL--KTKPKGKWYCPRCKA 267 (274)
T ss_pred cccccccccCCCCCCcceEEEecccc--ccCCCCcccchhhhh
Confidence 34688999998 99 8999999975 789999999999974
No 66
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.26 E-value=5.4e-05 Score=92.50 Aligned_cols=51 Identities=33% Similarity=0.959 Sum_probs=47.9
Q ss_pred ccccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccccC
Q 008421 297 HTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAKG 347 (566)
Q Consensus 297 ~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~ 347 (566)
..|.+|....+...|++|+.|...||++|+.|.+..+|.|+|+||.|....
T Consensus 1109 ~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1109 ALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred hhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 479999998888999999999999999999999999999999999998655
No 67
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.13 E-value=0.00013 Score=89.37 Aligned_cols=50 Identities=44% Similarity=1.181 Sum_probs=46.9
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcchh
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDAGI 515 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~~~ 515 (566)
.|.+|+..++...|+.|+.|..+||++|+.|.+..+|.++|+||.|+...
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 58999999999999999999999999999999999999999999998654
No 68
>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=97.10 E-value=0.00063 Score=60.42 Aligned_cols=54 Identities=17% Similarity=0.250 Sum_probs=46.9
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQ 252 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~ 252 (566)
.+.+||||++|..||.. |.++.+|..|+.+||+|...| +..+...|..|...+.
T Consensus 43 iI~~PmdL~tI~~kl~~---Y~s~~ef~~D~~li~~Na~~yN~~~s~i~~~A~~le~~~~ 99 (106)
T cd05521 43 IIKNPLSLNTVKKRLPH---YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALILEKYIN 99 (106)
T ss_pred HhcCCCCHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 38999999999999998 689999999999999998887 5677888888876643
No 69
>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi. TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=97.08 E-value=0.00072 Score=60.84 Aligned_cols=60 Identities=23% Similarity=0.423 Sum_probs=46.3
Q ss_pred hhhccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHh-HHHHHHHHHhh
Q 008421 187 VLLGNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIG-AEIITLAKKLS 248 (566)
Q Consensus 187 ~l~~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g-~ev~~LA~~Ls 248 (566)
.+.++-+|- .=-+|||+||..||.+|.| ..|..|+.||+.||.|...++ ++..-.|+.|-
T Consensus 52 ~i~e~~tgk-~~y~MDL~tIe~RL~ng~Y-~tp~~F~~DiklI~~Nc~~ynd~dr~~KA~EM~ 112 (119)
T cd05491 52 TILETASGK-KFYNMDLDTIEERLWNGYY-ATPKDFLKDIKRIVRDAKTIGDRERLLKANEMF 112 (119)
T ss_pred ceeeecCCC-eEeccCHHHHHHHHhcCCC-CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 444444444 5568999999999999765 889999999999999999985 55555555554
No 70
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.01 E-value=0.00011 Score=52.52 Aligned_cols=34 Identities=35% Similarity=0.953 Sum_probs=20.5
Q ss_pred CCceeeccCCCCCcccccCCCCCCCCCC-CccCcccc
Q 008421 309 KDGLVCDSCEEMYHLSCIEPAFKDIPPK-SWYCARCT 344 (566)
Q Consensus 309 ~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g-~W~C~~C~ 344 (566)
+.||.|++|...+|..|+ ++..+|.+ +|+|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CY--Gv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCY--GVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHH--T-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhC--CcccCCCCCcEECCcCC
Confidence 468999999999999999 88888887 89999884
No 71
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.63 E-value=0.0008 Score=67.44 Aligned_cols=35 Identities=37% Similarity=1.069 Sum_probs=30.9
Q ss_pred CCceeeccC--CCC-CCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 476 DEKIVMCDG--CDQ-GYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 476 ~~~ll~Cd~--C~~-~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
-++||-||. |.+ |||+.|++ |..+|+|.|||+.|.
T Consensus 231 yGqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk 268 (271)
T COG5034 231 YGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECK 268 (271)
T ss_pred cccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhH
Confidence 478999985 887 99999997 489999999999996
No 72
>cd05526 Bromo_polybromo_VI Bromodomain, polybromo repeat VI. 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=96.61 E-value=0.004 Score=55.66 Aligned_cols=62 Identities=18% Similarity=0.178 Sum_probs=52.7
Q ss_pred CCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhhHh
Q 008421 194 GIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQASYI 256 (566)
Q Consensus 194 ~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~~~ 256 (566)
...+.+||||.+|..|+..|.| ++.+.|.+|+.++|+|...+ +.++..-|..|..+|.....
T Consensus 41 ~~~ik~Pi~l~~Ik~ki~~~~Y-~~ld~~~~D~~lmf~NAr~yN~~~S~iy~dA~eLq~~f~~~rd 105 (110)
T cd05526 41 VGPKKIPLTLDIIKRNVDKGRY-RRLDKFQEDMFEVLERARRLSRTDSEIYEDAVELQQFFIKIRD 105 (110)
T ss_pred hhhhcCCccHHHHHHHHHcCCc-CcHHHHHHHHHHHHHHHHHhCcccCHHHHHHHHHHHHHHHHHH
Confidence 3458999999999999999997 78999999999999998887 67888888888877665443
No 73
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.49 E-value=0.0011 Score=78.68 Aligned_cols=49 Identities=37% Similarity=0.934 Sum_probs=40.7
Q ss_pred ccccccccCCC--CceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcchhH
Q 008421 466 LCRACLTDKDD--EKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDAGIQ 516 (566)
Q Consensus 466 ~C~~C~~~~~~--~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~~~~ 516 (566)
.|.+|....-. +.+|+||.|+.++|++|.+ +.-+|.|.|+|..|....+
T Consensus 221 ~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 221 VCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPFIPEGQWLCRRCLQSPQ 271 (1051)
T ss_pred cceeecccccCCCceEEEcCCCcchhhhhccC--CCCCCCCcEeehhhccCcC
Confidence 57778766544 8999999999999999999 3579999999999975444
No 74
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=95.85 E-value=0.0055 Score=54.28 Aligned_cols=86 Identities=19% Similarity=0.412 Sum_probs=59.1
Q ss_pred ccccccccCCCCccccccccCCCCCCCCCCCCccccccccccccCcCCCCCCCCCCccccccccccCcccccCCCccccc
Q 008421 354 NCIVCERMNANAPRIQINQAGDEICPANGETSTEFEENSNCTTANVDKPTDNGVDSRESANLCKICGRKVEESSDKFRSC 433 (566)
Q Consensus 354 ~C~~C~~l~~~~~R~~~~~~~~~~~~~~~e~~~e~E~~s~~~~~~~~~~~~e~~~s~~~~~~C~~Cgs~~~~~~~~Ll~C 433 (566)
.|++|+..++..+++...+|.|..|+.+.... .+.......+.. ............|.+|++. .+..+.|
T Consensus 2 ~C~lC~~~~Galk~t~~~~WvHv~Cal~~~~~-~~~~~~~~~~v~-----~~~i~~~~~~~~C~iC~~~----~G~~i~C 71 (110)
T PF13832_consen 2 SCVLCPKRGGALKRTSDGQWVHVLCALWIPEV-IFNNGESMEPVD-----ISNIPPSRFKLKCSICGKS----GGACIKC 71 (110)
T ss_pred ccEeCCCCCCcccCccCCcEEEeEccceeCcc-EEeechhcCccc-----ceeecchhcCCcCcCCCCC----CceeEEc
Confidence 58999999998888888999999999885432 111111110000 1112122456799999998 5679999
Q ss_pred CCccCCCccccccCCCc
Q 008421 434 EHAFCYSKFYHERCLTP 450 (566)
Q Consensus 434 ~~~~C~~k~yH~~CL~~ 450 (566)
.++.| ..+||+.|...
T Consensus 72 ~~~~C-~~~fH~~CA~~ 87 (110)
T PF13832_consen 72 SHPGC-STAFHPTCARK 87 (110)
T ss_pred CCCCC-CcCCCHHHHHH
Confidence 99999 68899999764
No 75
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.45 E-value=0.0048 Score=67.33 Aligned_cols=49 Identities=33% Similarity=0.824 Sum_probs=39.5
Q ss_pred ccccccc--ccCCCCceeeccCCCCCcccccCCCCCCC----CCCCccCcccccc
Q 008421 298 TCRQCEE--KAGEKDGLVCDSCEEMYHLSCIEPAFKDI----PPKSWYCARCTAK 346 (566)
Q Consensus 298 ~C~~C~~--~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~----P~g~W~C~~C~~~ 346 (566)
.|.+|.. ....+.||.|++|..+||..|..|.++.. |...|||..|...
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred eeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 4888754 55566999999999999999999887543 4457999999754
No 76
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=93.98 E-value=0.039 Score=59.44 Aligned_cols=73 Identities=18% Similarity=0.265 Sum_probs=59.8
Q ss_pred ccCCCCccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHH---hHHHHHHHHHhhhhhhhhHhhhcCCCCC
Q 008421 190 GNFQGIKVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEI---GAEIITLAKKLSELSQASYIEHVGGSAP 264 (566)
Q Consensus 190 ~~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~---g~ev~~LA~~Ls~i~~~~~~~~~~~~~~ 264 (566)
.+|.-+ +..||||.+|..+|..|.| ++..+|.+|..++|.|...| +..+..-|..|..++...+..+......
T Consensus 179 PdYy~i-Ik~Pm~L~~i~kkl~~~~Y-~s~eef~~D~~lM~~N~~~yN~~~s~v~~~a~~l~~~~~~~i~~~~~~~~~ 254 (371)
T COG5076 179 PDYYEI-IKSPMDLLTIQKKLKNGRY-KSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLE 254 (371)
T ss_pred CChhee-ecchhhHHHHHHHHHhhhh-hhHHHHHHHHHHHHHhhhhccCCCcchhhhhHHHHHHHHHHHHhccccchh
Confidence 345566 8899999999999999999 78999999999999998887 3556778888988877777766654433
No 77
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=93.75 E-value=0.023 Score=64.44 Aligned_cols=45 Identities=33% Similarity=0.977 Sum_probs=39.3
Q ss_pred ccccccccC--CCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 466 LCRACLTDK--DDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 466 ~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
.|.||.... ...+||+||.|....|.-|.+. ..+|.+.|+|..|.
T Consensus 273 iCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGI--le~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 273 ICDVCRSPDSEEANEMVFCDKCNICVHQACYGI--LEVPEGPWLCRTCA 319 (893)
T ss_pred eeceecCCCccccceeEEeccchhHHHHhhhce--eecCCCCeeehhcc
Confidence 588887653 3789999999999999999975 78999999999995
No 78
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=92.65 E-value=0.012 Score=42.02 Aligned_cols=33 Identities=33% Similarity=1.114 Sum_probs=19.0
Q ss_pred CceeeccCCCCCCcCCCCCCCCCCCCCC-CcccCCC
Q 008421 477 EKIVMCDGCDQGYHLYCMDPPRTSVPKG-NWFCRKC 511 (566)
Q Consensus 477 ~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~-~W~C~~C 511 (566)
++||.|+.|.-..|..|-+. ..+|.+ .|+|..|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv--~~~~~~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGV--SEVPDGDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT---SS--SS-----HHH
T ss_pred CceEEeCCCCCcCChhhCCc--ccCCCCCcEECCcC
Confidence 57999999999999999986 345555 6999877
No 79
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=92.57 E-value=0.05 Score=59.20 Aligned_cols=46 Identities=37% Similarity=0.970 Sum_probs=37.7
Q ss_pred ccccccccC--CCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 466 LCRACLTDK--DDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 466 ~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
.|.+|.... ..+.+++||.|+.+.|..|.+. .-+|.|.|+|..|.-
T Consensus 195 ~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI--~f~peG~WlCrkCi~ 242 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDGCEICVHQSCYGI--QFLPEGFWLCRKCIY 242 (669)
T ss_pred hhHhccccccCCcceEEEecCcchhhhhhcccc--eecCcchhhhhhhcc
Confidence 456665433 3578999999999999999987 579999999999963
No 80
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=92.45 E-value=0.055 Score=61.01 Aligned_cols=44 Identities=41% Similarity=1.123 Sum_probs=35.7
Q ss_pred cccccccC--CCCceeeccC--CCCCCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 467 CRACLTDK--DDEKIVMCDG--CDQGYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 467 C~~C~~~~--~~~~ll~Cd~--C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
|-||.... .+..||.||. |.-+.|.-|... ..+|.|.|||..|.
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGI--vqVPtGpWfCrKCe 55 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGI--VQVPTGPWFCRKCE 55 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhccee--EecCCCchhhhhhh
Confidence 44554322 2789999985 999999999986 78999999999995
No 81
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=91.81 E-value=0.027 Score=60.42 Aligned_cols=95 Identities=20% Similarity=0.484 Sum_probs=57.7
Q ss_pred cccccccccCcccccCCCcccccCCccCCCccccccCCCc----------cccccCCCCccCCCc-------cccccccc
Q 008421 411 ESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTP----------KQLKRYGPCWFCPSC-------LCRACLTD 473 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~----------~~~~~~~~~w~Cp~C-------~C~~C~~~ 473 (566)
.....|..|+..+.. ++|.- + ++.||+.|.+- .......++.+|..+ +|.+|...
T Consensus 332 ~tlekC~~Cg~~I~d---~iLrA----~-GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~P 403 (468)
T KOG1701|consen 332 DTLEKCNKCGEPIMD---RILRA----L-GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNP 403 (468)
T ss_pred HHHHHHhhhhhHHHH---HHHHh----c-ccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCC
Confidence 456678888876532 44433 2 67788877642 122234567888877 49999753
Q ss_pred ---C-CCCceeeccCCCCCCcCCCCC-----CCCCCCC--------CCCcccCCCcc
Q 008421 474 ---K-DDEKIVMCDGCDQGYHLYCMD-----PPRTSVP--------KGNWFCRKCDA 513 (566)
Q Consensus 474 ---~-~~~~ll~Cd~C~~~~H~~Cl~-----Ppl~~~p--------~~~W~C~~C~~ 513 (566)
. ..+..+.-..=|+-||+.|.. ..|+.-. .+..+|..|..
T Consensus 404 I~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~ 460 (468)
T KOG1701|consen 404 ILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHL 460 (468)
T ss_pred ccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhh
Confidence 1 234456666678999999853 2344222 23578888853
No 82
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=91.34 E-value=0.1 Score=61.84 Aligned_cols=44 Identities=36% Similarity=0.893 Sum_probs=40.2
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
+|++| .+.+.+++|..|++.||+.|..||+..+|...|-|--|.
T Consensus 346 hcrf~---~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 346 HCRFC---HDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCN 389 (1414)
T ss_pred ccccc---CcccceeecccCCceEEeeecCCccccCCCccchhhhhh
Confidence 57777 566789999999999999999999999999999999996
No 83
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=89.98 E-value=0.22 Score=59.83 Aligned_cols=51 Identities=31% Similarity=0.932 Sum_probs=44.7
Q ss_pred CcccccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCcccccc
Q 008421 295 KVHTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAK 346 (566)
Q Consensus 295 ~~~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~ 346 (566)
+...|..|.+.... .++.|++|...||.+|..|+++.+|+|+|.|+.|...
T Consensus 154 ~~~~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cchhhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCccccc
Confidence 34579999987666 5559999999999999999999999999999999865
No 84
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=87.04 E-value=0.33 Score=46.37 Aligned_cols=31 Identities=35% Similarity=1.029 Sum_probs=25.4
Q ss_pred ccccc---ccCCCCceeeccCCCCCCcCCCCCCC
Q 008421 467 CRACL---TDKDDEKIVMCDGCDQGYHLYCMDPP 497 (566)
Q Consensus 467 C~~C~---~~~~~~~ll~Cd~C~~~~H~~Cl~Pp 497 (566)
|.+|+ .....+.||.|-.|..+||-.||+|.
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 66774 33447899999999999999999983
No 85
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.18 E-value=0.61 Score=41.15 Aligned_cols=72 Identities=15% Similarity=0.395 Sum_probs=43.9
Q ss_pred cccccCcccccCCCcccccCCccCCCccccccCCCcccc-------ccC--CCCccCC---CcccccccccCCCCceeec
Q 008421 415 LCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTPKQL-------KRY--GPCWFCP---SCLCRACLTDKDDEKIVMC 482 (566)
Q Consensus 415 ~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~~~~-------~~~--~~~w~Cp---~C~C~~C~~~~~~~~ll~C 482 (566)
.|.+|... ++.|..-.. +.+.|..|...... ... ....+=+ .=.|.+|++. .+..+.|
T Consensus 2 ~C~lC~~~----~Galk~t~~----~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~~~C~iC~~~--~G~~i~C 71 (110)
T PF13832_consen 2 SCVLCPKR----GGALKRTSD----GQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFKLKCSICGKS--GGACIKC 71 (110)
T ss_pred ccEeCCCC----CCcccCccC----CcEEEeEccceeCccEEeechhcCcccceeecchhcCCcCcCCCCC--CceeEEc
Confidence 47788876 444544432 67889999754110 000 0000000 1257888765 5779999
Q ss_pred cC--CCCCCcCCCCCC
Q 008421 483 DG--CDQGYHLYCMDP 496 (566)
Q Consensus 483 d~--C~~~~H~~Cl~P 496 (566)
.. |..+||+.|..-
T Consensus 72 ~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 72 SHPGCSTAFHPTCARK 87 (110)
T ss_pred CCCCCCcCCCHHHHHH
Confidence 88 999999999653
No 86
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=84.54 E-value=0.56 Score=36.64 Aligned_cols=32 Identities=34% Similarity=0.729 Sum_probs=27.7
Q ss_pred cccccccccc-CCCCceeeccCCCCCcccccCC
Q 008421 297 HTCRQCEEKA-GEKDGLVCDSCEEMYHLSCIEP 328 (566)
Q Consensus 297 ~~C~~C~~~~-~~~~ll~Cd~C~~~~H~~Cl~P 328 (566)
..|.+|++.- ++++++.|..|...||..|+..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 4799999854 4889999999999999999854
No 87
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=83.57 E-value=0.85 Score=54.85 Aligned_cols=47 Identities=47% Similarity=1.249 Sum_probs=40.8
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
.|..|.+.... .++.|+.|...||..|+.||+..++.+.|.|+.|..
T Consensus 157 ~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (904)
T KOG1246|consen 157 QCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIP 203 (904)
T ss_pred hhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccc
Confidence 46777776666 444999999999999999999999999999999964
No 88
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=81.39 E-value=0.87 Score=35.59 Aligned_cols=31 Identities=32% Similarity=0.766 Sum_probs=25.9
Q ss_pred ccccccccC-CCCceeeccCCCCCCcCCCCCC
Q 008421 466 LCRACLTDK-DDEKIVMCDGCDQGYHLYCMDP 496 (566)
Q Consensus 466 ~C~~C~~~~-~~~~ll~Cd~C~~~~H~~Cl~P 496 (566)
.|.+|+..- +++.+|+|..|...||..|...
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 677887654 3788999999999999999864
No 89
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=67.30 E-value=3.2 Score=44.50 Aligned_cols=38 Identities=32% Similarity=0.626 Sum_probs=31.9
Q ss_pred CceeeccCCCCCcccc--cCCCCCCCCC-CCccCccccccC
Q 008421 310 DGLVCDSCEEMYHLSC--IEPAFKDIPP-KSWYCARCTAKG 347 (566)
Q Consensus 310 ~ll~Cd~C~~~~H~~C--l~P~l~~~P~-g~W~C~~C~~~~ 347 (566)
.++-|+.|..+||..| ++.+....|. ..|+|..|....
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence 7899999999999999 8777766665 579999997654
No 90
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=66.73 E-value=1.6 Score=37.33 Aligned_cols=45 Identities=22% Similarity=0.515 Sum_probs=32.9
Q ss_pred cccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 467 CRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 467 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
|..|...+++-.++.+. |...||+.|+..-+.... ..=.||-|+.
T Consensus 35 Cp~Ck~Pgd~Cplv~g~-C~H~FH~hCI~kWl~~~~-~~~~CPmCR~ 79 (85)
T PF12861_consen 35 CPDCKFPGDDCPLVWGK-CSHNFHMHCILKWLSTQS-SKGQCPMCRQ 79 (85)
T ss_pred CCCccCCCCCCceeecc-CccHHHHHHHHHHHcccc-CCCCCCCcCC
Confidence 45567777777777665 999999999876555432 2349999975
No 91
>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=64.71 E-value=1.9 Score=29.24 Aligned_cols=28 Identities=32% Similarity=0.612 Sum_probs=12.1
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCC
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYC 493 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~C 493 (566)
.|.+|+....++....|..|+-..|+.|
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 3778887776668999999999999877
No 92
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=64.10 E-value=2 Score=35.26 Aligned_cols=49 Identities=24% Similarity=0.513 Sum_probs=18.2
Q ss_pred cccccccC---CCCceeecc--CCCCCCcCCCCCCCC-------CCCCCCCcccCCCcchh
Q 008421 467 CRACLTDK---DDEKIVMCD--GCDQGYHLYCMDPPR-------TSVPKGNWFCRKCDAGI 515 (566)
Q Consensus 467 C~~C~~~~---~~~~ll~Cd--~C~~~~H~~Cl~Ppl-------~~~p~~~W~C~~C~~~~ 515 (566)
|.+|.... +....+.|+ .|...||+.||.--+ .....-.+.||.|...+
T Consensus 5 C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 5 CGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp -SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 55665432 234568898 899999999986421 11222346799997543
No 93
>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=63.31 E-value=2.8 Score=37.73 Aligned_cols=47 Identities=6% Similarity=0.067 Sum_probs=33.9
Q ss_pred HHHHHHHHH---hhhhHHHHHHhhh---ccCCCCccCCccchhhhhhhhccccc
Q 008421 168 CQRAFLEII---TSEKFTLLCKVLL---GNFQGIKVDRVFNLSAINSRMKQGAY 215 (566)
Q Consensus 168 c~~~l~~~l---~se~f~~~~~~l~---~~~~~~~~~~~~Dl~~Id~rl~~g~Y 215 (566)
|-..|.+++ .+..|..+.+-.. ..|... +.+||||+||..+|..+.+
T Consensus 8 ~l~~l~~~~~~~~~~pF~~PVd~~~~~~pdY~~i-IK~PMDL~ti~~kl~~~~~ 60 (114)
T cd05494 8 VLRELKRHRRNEDAWPFLEPVNPPRRGAPDYRDV-IKRPMSFGTKVNNIVETGA 60 (114)
T ss_pred HHHHHHHhhhCCCCCCcCCCCCchhcCCCChhhh-cCCCCChHHHHHHHHcccc
Confidence 555666677 6667777776533 334455 8999999999999999744
No 94
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=62.39 E-value=0.94 Score=37.15 Aligned_cols=47 Identities=28% Similarity=0.612 Sum_probs=17.7
Q ss_pred cccccccccC-CC--Cceeec--cCCCCCcccccCCCCCC-------CCCCCccCcccc
Q 008421 298 TCRQCEEKAG-EK--DGLVCD--SCEEMYHLSCIEPAFKD-------IPPKSWYCARCT 344 (566)
Q Consensus 298 ~C~~C~~~~~-~~--~ll~Cd--~C~~~~H~~Cl~P~l~~-------~P~g~W~C~~C~ 344 (566)
.|.+|-.... .+ ..+.|+ .|...||..||.-=+.. .-.-.+-||.|.
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~ 62 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCS 62 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCC
Confidence 5999976432 33 358898 89999999999422111 111226688886
No 95
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=61.92 E-value=5.2 Score=39.59 Aligned_cols=38 Identities=29% Similarity=0.761 Sum_probs=29.8
Q ss_pred ccccccccC-----CCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCc
Q 008421 466 LCRACLTDK-----DDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCD 512 (566)
Q Consensus 466 ~C~~C~~~~-----~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~ 512 (566)
.|.+|...+ +.+....|..|...||..|... =.||.|.
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---------~~CpkC~ 196 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---------KSCPKCA 196 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---------CCCCCcH
Confidence 478887653 2458899999999999999973 1399996
No 96
>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=58.45 E-value=3.6 Score=27.87 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=12.9
Q ss_pred cccccccccCCCCceeeccCCCCCccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCI 326 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl 326 (566)
.|..|+....++..-.|..|+-..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 48999987666678899999999999884
No 97
>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=56.40 E-value=4.7 Score=27.26 Aligned_cols=27 Identities=22% Similarity=0.683 Sum_probs=16.4
Q ss_pred CCCccCccccccCCCCCCcccccccccC
Q 008421 335 PKSWYCARCTAKGFGSPHENCIVCERMN 362 (566)
Q Consensus 335 ~g~W~C~~C~~~~~~~~~~~C~~C~~l~ 362 (566)
+|+|.|+.|..... .....|+.|..+.
T Consensus 2 ~g~W~C~~C~~~N~-~~~~~C~~C~~~r 28 (30)
T PF00641_consen 2 EGDWKCPSCTFMNP-ASRSKCVACGAPR 28 (30)
T ss_dssp SSSEEETTTTEEEE-SSSSB-TTT--BT
T ss_pred CcCccCCCCcCCch-HHhhhhhCcCCCC
Confidence 57899999986542 2334688886554
No 98
>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=55.13 E-value=0.93 Score=33.26 Aligned_cols=42 Identities=29% Similarity=0.598 Sum_probs=26.5
Q ss_pred cccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARC 343 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C 343 (566)
.|.+|...-..++.+.--.|...||..|+..-+..- ..||.|
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~----~~CP~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN----NSCPVC 43 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS----SB-TTT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC----CcCCcc
Confidence 699998855433333333499999999996544331 367766
No 99
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=54.65 E-value=10 Score=37.56 Aligned_cols=41 Identities=22% Similarity=0.682 Sum_probs=31.0
Q ss_pred ccccccccccc-----CCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 296 VHTCRQCEEKA-----GEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 296 ~~~C~~C~~~~-----~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
..+|.+|...+ +.+....|..|...||..|... =.||.|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---------~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---------KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---------CCCCCcHh
Confidence 45788997643 2457889999999999999952 22999973
No 100
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=53.37 E-value=28 Score=38.38 Aligned_cols=53 Identities=28% Similarity=0.628 Sum_probs=36.3
Q ss_pred cCCCccccccccc---CCCCceeeccCCCCCCcCCCCCC-CC------CCC----CCCCcccCCCcc
Q 008421 461 FCPSCLCRACLTD---KDDEKIVMCDGCDQGYHLYCMDP-PR------TSV----PKGNWFCRKCDA 513 (566)
Q Consensus 461 ~Cp~C~C~~C~~~---~~~~~ll~Cd~C~~~~H~~Cl~P-pl------~~~----p~~~W~C~~C~~ 513 (566)
+|..|-|-+|.+- .++-.-|.||.|+.+-|+.|--- -+ ..- ....++|..|..
T Consensus 125 FC~~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~ 191 (446)
T PF07227_consen 125 FCRRCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGK 191 (446)
T ss_pred ccccCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCC
Confidence 4667788888753 24667789999999999999422 11 111 233599999964
No 101
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=50.03 E-value=9.6 Score=24.66 Aligned_cols=24 Identities=29% Similarity=0.901 Sum_probs=15.2
Q ss_pred CCccCccccccCCCCCCcccccccc
Q 008421 336 KSWYCARCTAKGFGSPHENCIVCER 360 (566)
Q Consensus 336 g~W~C~~C~~~~~~~~~~~C~~C~~ 360 (566)
|+|.|+.|..... .....|+.|+.
T Consensus 1 g~W~C~~C~~~N~-~~~~~C~~C~~ 24 (26)
T smart00547 1 GDWECPACTFLNF-ASRSKCFACGA 24 (26)
T ss_pred CcccCCCCCCcCh-hhhccccccCC
Confidence 6799999975442 22345666653
No 102
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=49.51 E-value=6.7 Score=33.58 Aligned_cols=34 Identities=18% Similarity=0.403 Sum_probs=23.2
Q ss_pred CceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 310 DGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 310 ~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
.++++. |...||+.|+.-=+.+- ...-.||-|..
T Consensus 46 plv~g~-C~H~FH~hCI~kWl~~~-~~~~~CPmCR~ 79 (85)
T PF12861_consen 46 PLVWGK-CSHNFHMHCILKWLSTQ-SSKGQCPMCRQ 79 (85)
T ss_pred ceeecc-CccHHHHHHHHHHHccc-cCCCCCCCcCC
Confidence 445444 99999999996555442 23458888874
No 103
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.80 E-value=9.3 Score=40.91 Aligned_cols=46 Identities=28% Similarity=0.681 Sum_probs=36.2
Q ss_pred ccccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 297 HTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 297 ~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
+.|.+|-+.-..|+.|.==-|...||..|++|=|.+- .=+||-|..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCCCCCC
Confidence 4799999977777766557899999999999876443 257999974
No 104
>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=48.22 E-value=9.1 Score=33.99 Aligned_cols=62 Identities=26% Similarity=0.717 Sum_probs=38.3
Q ss_pred CcccccccccccCCCCceee------ccC---CCCCcccccCCCC-----CCCCCCCccCccccccCCCCCCcccccccc
Q 008421 295 KVHTCRQCEEKAGEKDGLVC------DSC---EEMYHLSCIEPAF-----KDIPPKSWYCARCTAKGFGSPHENCIVCER 360 (566)
Q Consensus 295 ~~~~C~~C~~~~~~~~ll~C------d~C---~~~~H~~Cl~P~l-----~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~ 360 (566)
....|..|.....+ ....| ..| ...|=-.||.-.. +-+.+++|.||.|...= +|.+|.+
T Consensus 6 ~g~~CHqCrqKt~~-~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiC------nCs~Crr 78 (105)
T PF10497_consen 6 NGKTCHQCRQKTLD-FKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGIC------NCSFCRR 78 (105)
T ss_pred CCCCchhhcCCCCC-CceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCee------CCHhhhc
Confidence 34478888875543 33456 566 6666666654222 23456789999998543 5677765
Q ss_pred cCC
Q 008421 361 MNA 363 (566)
Q Consensus 361 l~~ 363 (566)
-.+
T Consensus 79 k~g 81 (105)
T PF10497_consen 79 KRG 81 (105)
T ss_pred cCC
Confidence 543
No 105
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=45.15 E-value=10 Score=31.96 Aligned_cols=28 Identities=25% Similarity=0.826 Sum_probs=23.8
Q ss_pred cccccccccCCCCceeec--cCCCCCcccccC
Q 008421 298 TCRQCEEKAGEKDGLVCD--SCEEMYHLSCIE 327 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd--~C~~~~H~~Cl~ 327 (566)
.|.+|++. .|..+-|. +|.+.||+.|..
T Consensus 38 ~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 38 KCSICKKK--GGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred CCcCCCCC--CCeEEEEeCCCCCcEEChHHHc
Confidence 79999973 37888897 699999999974
No 106
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=44.73 E-value=40 Score=41.10 Aligned_cols=85 Identities=18% Similarity=0.477 Sum_probs=60.3
Q ss_pred CcCcccccccccccC--CCCceeeccCCCCCcccccCCCCCCCCCCCccCccccccCCCCCCcccccccccCCCCccccc
Q 008421 293 VYKVHTCRQCEEKAG--EKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAKGFGSPHENCIVCERMNANAPRIQI 370 (566)
Q Consensus 293 ~~~~~~C~~C~~~~~--~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~~~~~~~C~~C~~l~~~~~R~~~ 370 (566)
.|..+.|.+|+...+ ....+.|+.|..+.|..|+. .++..+.-.|.|..|.... -.-.|..|...+++...+..
T Consensus 570 ~~~t~~c~~~~~~~~~~~n~~~~~~~~~~~~~s~~~g-~~~~~~~~~~~~~~~~~~~---~~r~~~l~~~~g~al~p~d~ 645 (1005)
T KOG1080|consen 570 KWTTERCAVCRDDEDWEKNVSIICDRCTRSVHSECYG-NLKSYDGTSWVCDSCETLD---IKRSCCLCPVKGGALKPTDE 645 (1005)
T ss_pred CCCcccccccccccccccceeeeeccccccCCCcccc-cCCCCCCCcchhhcccccc---CCchhhhccccCcccCCCCc
Confidence 455678999998543 44568899999999999993 2333333469999998521 12368888888887555557
Q ss_pred cccCCCCCCCC
Q 008421 371 NQAGDEICPAN 381 (566)
Q Consensus 371 ~~~~~~~~~~~ 381 (566)
.+|.|..+...
T Consensus 646 gr~~~~e~a~~ 656 (1005)
T KOG1080|consen 646 GRWVHVECAWF 656 (1005)
T ss_pred cchhhhhchhc
Confidence 77888777653
No 107
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=44.56 E-value=11 Score=31.78 Aligned_cols=35 Identities=29% Similarity=0.649 Sum_probs=29.1
Q ss_pred cccccccccCcccccCCCcccccCCccCCCccccccCCCc
Q 008421 411 ESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTP 450 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~ 450 (566)
.....|.+|++. .|..+.|..+.| ..+||+.|...
T Consensus 34 ~~~~~C~~C~~~----~Ga~i~C~~~~C-~~~fH~~CA~~ 68 (90)
T PF13771_consen 34 RRKLKCSICKKK----GGACIGCSHPGC-SRSFHVPCARK 68 (90)
T ss_pred HhCCCCcCCCCC----CCeEEEEeCCCC-CcEEChHHHcc
Confidence 455699999986 467899999999 68899999865
No 108
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=43.87 E-value=18 Score=37.93 Aligned_cols=43 Identities=28% Similarity=0.784 Sum_probs=28.1
Q ss_pred CCceeeccCCCCC----------CcCCCCCCCCCCCCCCCcccCCCcchhHHHHHH
Q 008421 476 DEKIVMCDGCDQG----------YHLYCMDPPRTSVPKGNWFCRKCDAGIQEIRRV 521 (566)
Q Consensus 476 ~~~ll~Cd~C~~~----------~H~~Cl~Ppl~~~p~~~W~C~~C~~~~~~~~~~ 521 (566)
+..+-+||.|+.- -|.+|++=.+... +-+|+.|...++++.+.
T Consensus 87 ~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~---dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 87 GPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDS---DKICPLCDDRVQRIEQI 139 (389)
T ss_pred CcceEeecccCCcceeeecccccchhhhhhhhhcCc---cccCcCcccHHHHHHHh
Confidence 4446667777753 3777877533222 46899999888877654
No 109
>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=39.26 E-value=24 Score=23.90 Aligned_cols=29 Identities=24% Similarity=0.553 Sum_probs=21.8
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCC
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCM 494 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl 494 (566)
.|.+|++..++...-.|+.|.-..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 47788766544338899999999998883
No 110
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=38.98 E-value=17 Score=26.06 Aligned_cols=27 Identities=30% Similarity=0.743 Sum_probs=20.0
Q ss_pred eccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 481 MCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 481 ~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
.|..|++.||+. ...|+.+..|..|-.
T Consensus 3 ~C~~Cg~~Yh~~------~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIE------FNPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETT------TB--SSTTBCTTTTE
T ss_pred CcCCCCCccccc------cCCCCCCCccCCCCC
Confidence 588999999976 444567789999965
No 111
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.12 E-value=9.7 Score=39.21 Aligned_cols=60 Identities=15% Similarity=0.406 Sum_probs=36.9
Q ss_pred ccccccccCCCCc----ee---eccCCCCCCcCCCCCCCCCCCCCCCcccCCCcchhHHHHHHHHHHhh
Q 008421 466 LCRACLTDKDDEK----IV---MCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDAGIQEIRRVKKAYMH 527 (566)
Q Consensus 466 ~C~~C~~~~~~~~----ll---~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~~~~~~~~~~~~~ek 527 (566)
.|.+|++.-+.+. ++ .==.|...||-+|..- --+-...-.||-|..++.-.+-...++||
T Consensus 226 vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrG--WcivGKkqtCPYCKekVdl~rmfsnpWek 292 (328)
T KOG1734|consen 226 VCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRG--WCIVGKKQTCPYCKEKVDLKRMFSNPWEK 292 (328)
T ss_pred hhHhhcchheeecchhhhhhhheeeecccchHHHhhhh--heeecCCCCCchHHHHhhHhhhccCcccc
Confidence 6888876543211 11 1125899999999864 11222235899998877655555566765
No 112
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.90 E-value=31 Score=38.86 Aligned_cols=47 Identities=17% Similarity=0.254 Sum_probs=36.3
Q ss_pred CCCccCCCcccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCC--CCcccCCCc
Q 008421 457 GPCWFCPSCLCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPK--GNWFCRKCD 512 (566)
Q Consensus 457 ~~~w~Cp~C~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~--~~W~C~~C~ 512 (566)
...|+|..| .-++..+.|+.|-+.||..|+.|. ..++. ..|.|+.|.
T Consensus 58 N~d~~cfec--------hlpg~vl~c~vc~Rs~h~~c~sp~-~q~r~~s~p~~~p~p~ 106 (588)
T KOG3612|consen 58 NIDPFCFEC--------HLPGAVLKCIVCHRSFHENCQSPD-PQKRNYSVPSDKPQPY 106 (588)
T ss_pred CCCcccccc--------cCCcceeeeehhhccccccccCcc-hhhccccccccCCccc
Confidence 356888777 356789999999999999999974 33333 359999885
No 113
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.00 E-value=29 Score=40.41 Aligned_cols=46 Identities=22% Similarity=0.606 Sum_probs=32.4
Q ss_pred cccccccccCCCCceeeccCCCCCc-ccccCCCCCCCCCCCccCccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDSCEEMYH-LSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~C~~~~H-~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
+|..||.. ......+|..|....- ..|-..+ ..+|.+.-||++|-.
T Consensus 3 ~Cp~Cg~~-n~~~akFC~~CG~~l~~~~Cp~CG-~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 3 ICPQCQFE-NPNNNRFCQKCGTSLTHKPCPQCG-TEVPVDEAHCPNCGA 49 (645)
T ss_pred cCCCCCCc-CCCCCccccccCCCCCCCcCCCCC-CCCCcccccccccCC
Confidence 58888873 3556678998877753 5666544 357778889999953
No 114
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.82 E-value=23 Score=41.81 Aligned_cols=54 Identities=22% Similarity=0.455 Sum_probs=37.1
Q ss_pred ccccccccCCCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcchhHHHHHHHHHHhhh
Q 008421 466 LCRACLTDKDDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDAGIQEIRRVKKAYMHK 528 (566)
Q Consensus 466 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~~~~~~~~~~~~~ek~ 528 (566)
.|..|...- +--.+-=.|..+||..|+. .+.-.||.|.......-...++++.+
T Consensus 842 kCs~C~~~L--dlP~VhF~CgHsyHqhC~e-------~~~~~CP~C~~e~~~~m~l~~s~~q~ 895 (933)
T KOG2114|consen 842 KCSACEGTL--DLPFVHFLCGHSYHQHCLE-------DKEDKCPKCLPELRGVMDLKRSQEQK 895 (933)
T ss_pred eecccCCcc--ccceeeeecccHHHHHhhc-------cCcccCCccchhhhhhHHHHHHHHHh
Confidence 466774332 1222234799999999998 45579999998666666666777666
No 115
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=36.35 E-value=21 Score=39.33 Aligned_cols=87 Identities=23% Similarity=0.627 Sum_probs=50.7
Q ss_pred cccccccccCcccccCCC--cccccCCccCCCccccccCCCccccccCCCCccCCCc-ccccccccCCCCceeeccCCCC
Q 008421 411 ESANLCKICGRKVEESSD--KFRSCEHAFCYSKFYHERCLTPKQLKRYGPCWFCPSC-LCRACLTDKDDEKIVMCDGCDQ 487 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~~~--~Ll~C~~~~C~~k~yH~~CL~~~~~~~~~~~w~Cp~C-~C~~C~~~~~~~~ll~Cd~C~~ 487 (566)
--.+.|++|..+.+.+-. .-+.|.| .||-.|+. .|.=..| +|+.|.... ......|-.|..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~H------sfh~~cl~---------~w~~~scpvcR~~q~p~-~ve~~~c~~c~~ 236 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNH------SFHCSCLM---------KWWDSSCPVCRYCQSPS-VVESSLCLACGC 236 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeeccc------ccchHHHh---------hcccCcChhhhhhcCcc-hhhhhhhhhhcc
Confidence 346789999987665322 3344544 58888887 5665566 677776632 233444555533
Q ss_pred CCcCCCCCCCCCCCCCCCcccCCCcc---hhHHHHHHHHHHhh
Q 008421 488 GYHLYCMDPPRTSVPKGNWFCRKCDA---GIQEIRRVKKAYMH 527 (566)
Q Consensus 488 ~~H~~Cl~Ppl~~~p~~~W~C~~C~~---~~~~~~~~~~~~ek 527 (566)
. ..-|.|-.|-. .......+.+.||.
T Consensus 237 ~--------------~~LwicliCg~vgcgrY~eghA~rHwee 265 (493)
T KOG0804|consen 237 T--------------EDLWICLICGNVGCGRYKEGHARRHWEE 265 (493)
T ss_pred c--------------ccEEEEEEccceecccccchhHHHHHHh
Confidence 1 22399999952 22333455566655
No 116
>KOG1472 consensus Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics; Transcription]
Probab=34.31 E-value=20 Score=41.85 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=37.0
Q ss_pred ccCCccchhhhhhhhccccccCcchhhhhhHHHHHHHHHHHh
Q 008421 196 KVDRVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQEIG 237 (566)
Q Consensus 196 ~~~~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~~g 237 (566)
-+.+||||+||.-+|.++.| ....+|+.|+..++.+..-|+
T Consensus 642 ~I~~pmDl~tM~~~l~~~~y-~~~~~f~ad~~~vf~ncr~yn 682 (720)
T KOG1472|consen 642 VIKHPMDLRTMQNRLKDNQY-TEVELFMADVVRVFANCRMYN 682 (720)
T ss_pred HhcccccHHHHhhhccccch-hhHHHHHHHHHHHHhhhhccC
Confidence 48899999999999999988 578899999999999988774
No 117
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=34.12 E-value=12 Score=26.16 Aligned_cols=41 Identities=27% Similarity=0.605 Sum_probs=27.1
Q ss_pred ccccccccCCCCceeeccCCCCCcccccCCCCCCCCCCCccCcccc
Q 008421 299 CRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCT 344 (566)
Q Consensus 299 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~ 344 (566)
|.+|...- ...+.-..|.-.||..|+..-+.. +...||.|.
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~ 42 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCR 42 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCCCCC
Confidence 77787633 234445569999999998644433 456788885
No 118
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=33.95 E-value=25 Score=37.72 Aligned_cols=38 Identities=26% Similarity=0.624 Sum_probs=32.0
Q ss_pred ceeeccCCCCCCcCCC--CCCCCCCCCC-CCcccCCCcchh
Q 008421 478 KIVMCDGCDQGYHLYC--MDPPRTSVPK-GNWFCRKCDAGI 515 (566)
Q Consensus 478 ~ll~Cd~C~~~~H~~C--l~Ppl~~~p~-~~W~C~~C~~~~ 515 (566)
.++.|+.|..+||-.| +.++....|. ..|+|..|....
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence 7899999999999999 8887777665 569999997543
No 119
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=33.62 E-value=7.6 Score=42.29 Aligned_cols=75 Identities=23% Similarity=0.565 Sum_probs=45.0
Q ss_pred cccccccccCcccccCCCcccccCCccCCCccccccCCCc----ccc-----ccCCCCccCCCc------ccccccccCC
Q 008421 411 ESANLCKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTP----KQL-----KRYGPCWFCPSC------LCRACLTDKD 475 (566)
Q Consensus 411 ~~~~~C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~----~~~-----~~~~~~w~Cp~C------~C~~C~~~~~ 475 (566)
....+|..|++.+...+ ..|.. -++-||..|.+- +++ ......-+|..| .|.+|+.. .
T Consensus 272 ~~~~iC~~C~K~V~g~~---~ac~A---m~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~-I 344 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQG---LAVEA---MDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEP-I 344 (468)
T ss_pred hhhhhhhhcCCcccCcc---hHHHH---hhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhH-H
Confidence 45669999999866421 22221 056789888764 222 222345678777 37888542 1
Q ss_pred CCceeeccCCCCCCcCCCC
Q 008421 476 DEKIVMCDGCDQGYHLYCM 494 (566)
Q Consensus 476 ~~~ll~Cd~C~~~~H~~Cl 494 (566)
-+.|| ..|+++||..|.
T Consensus 345 ~d~iL--rA~GkayHp~CF 361 (468)
T KOG1701|consen 345 MDRIL--RALGKAYHPGCF 361 (468)
T ss_pred HHHHH--HhcccccCCCce
Confidence 23333 478899998874
No 120
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=33.38 E-value=11 Score=27.74 Aligned_cols=42 Identities=31% Similarity=0.725 Sum_probs=19.2
Q ss_pred ccccCcccccCCCcccccCCccCCCccccccCCCccccccCCCCccCCCc
Q 008421 416 CKICGRKVEESSDKFRSCEHAFCYSKFYHERCLTPKQLKRYGPCWFCPSC 465 (566)
Q Consensus 416 C~~Cgs~~~~~~~~Ll~C~~~~C~~k~yH~~CL~~~~~~~~~~~w~Cp~C 465 (566)
|.+|..--. ....+.|+|.||. .|+..-.....+..+.||.|
T Consensus 1 CpiC~~~~~--~Pv~l~CGH~FC~------~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK--DPVSLPCGHSFCR------SCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S--SEEE-SSSSEEEH------HHHHHHHCCSSSST---SSS
T ss_pred CCccchhhC--CccccCCcCHHHH------HHHHHHHHccCCcCCCCcCC
Confidence 455555432 3567888887772 45544222222223677765
No 121
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.04 E-value=2e+02 Score=30.05 Aligned_cols=44 Identities=23% Similarity=0.492 Sum_probs=26.1
Q ss_pred cccccccccCCCCceeecc-CCCCCcccccCCCCCCCCCCCccCcccccc
Q 008421 298 TCRQCEEKAGEKDGLVCDS-CEEMYHLSCIEPAFKDIPPKSWYCARCTAK 346 (566)
Q Consensus 298 ~C~~C~~~~~~~~ll~Cd~-C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~ 346 (566)
.|.+||.. ..+-.--+ |...|-.+|+.- ...-+..+.||.|-..
T Consensus 241 ~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~t--s~~~~asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 241 ECPVCGEP---PTIPHVIGKCGHIYCYYCIAT--SRLWDASFTCPLCGEN 285 (298)
T ss_pred eeeccCCC---CCCCeeeccccceeehhhhhh--hhcchhhcccCccCCC
Confidence 69999983 33333333 555666667632 2333456889999643
No 122
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=30.69 E-value=21 Score=42.19 Aligned_cols=49 Identities=29% Similarity=0.700 Sum_probs=34.4
Q ss_pred cccccccc-cCCCCceeeccCCCCCcccccCCC---C-CCCCCCCccCccccccC
Q 008421 298 TCRQCEEK-AGEKDGLVCDSCEEMYHLSCIEPA---F-KDIPPKSWYCARCTAKG 347 (566)
Q Consensus 298 ~C~~C~~~-~~~~~ll~Cd~C~~~~H~~Cl~P~---l-~~~P~g~W~C~~C~~~~ 347 (566)
.|.||-.. .....+--|.+|...||++|+.-= . .+.+ ..|-||.|....
T Consensus 193 eCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 193 ECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPACQSVS 246 (950)
T ss_pred EEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCcccchh
Confidence 69999763 334567779999999999998411 1 1222 349999998554
No 123
>cd05493 Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=30.63 E-value=42 Score=31.08 Aligned_cols=36 Identities=19% Similarity=0.440 Sum_probs=30.6
Q ss_pred CccchhhhhhhhccccccCcchhhhhhHHHHHHHHHH
Q 008421 199 RVFNLSAINSRMKQGAYENSPMQFMADVQQVWKKFQE 235 (566)
Q Consensus 199 ~~~Dl~~Id~rl~~g~Y~~~p~~f~~DV~~vW~kl~~ 235 (566)
.|.||.-+..+|.+|.| .+...|.+||=.|....-+
T Consensus 58 ~p~dL~~V~kkl~~G~Y-~sv~~F~~DvvkIiqa~l~ 93 (131)
T cd05493 58 PPLDLEAVGKKLEAGFY-TSVLDFSDDIVKIIQAALN 93 (131)
T ss_pred CcccHHHHHHHHhccce-ehHHHHHHHHHHHHHHHHh
Confidence 38999999999999966 7899999999888777443
No 124
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=29.10 E-value=34 Score=37.73 Aligned_cols=48 Identities=23% Similarity=0.524 Sum_probs=31.3
Q ss_pred cCCcCcccccccccccCCC-CceeeccCCCCCcccccCCCCCCCCCCCccCcccc
Q 008421 291 CDVYKVHTCRQCEEKAGEK-DGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCT 344 (566)
Q Consensus 291 ~~~~~~~~C~~C~~~~~~~-~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~ 344 (566)
.+.-+...|.+|...=|.+ ..++=--|..+||-.|+.- -++--||-|.
T Consensus 170 ~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~------w~~~scpvcR 218 (493)
T KOG0804|consen 170 TGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMK------WWDSSCPVCR 218 (493)
T ss_pred CCcccCCCcchhHhhcCccccceeeeecccccchHHHhh------cccCcChhhh
Confidence 3444556899998743333 4566677999999999832 1233566665
No 125
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=28.49 E-value=60 Score=25.01 Aligned_cols=33 Identities=33% Similarity=0.766 Sum_probs=18.8
Q ss_pred eccCCCCCCcCCCCCCCCCCCCC--------CCcccCCCcch
Q 008421 481 MCDGCDQGYHLYCMDPPRTSVPK--------GNWFCRKCDAG 514 (566)
Q Consensus 481 ~Cd~C~~~~H~~Cl~Ppl~~~p~--------~~W~C~~C~~~ 514 (566)
.|..|...|...=-+| ...+|. .+|.||.|...
T Consensus 3 ~C~~CgyiYd~~~Gd~-~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDP-DEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCc-ccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 4666666666543332 122222 27999999753
No 126
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.40 E-value=47 Score=26.19 Aligned_cols=10 Identities=30% Similarity=1.335 Sum_probs=8.2
Q ss_pred CCcccCCCcc
Q 008421 504 GNWFCRKCDA 513 (566)
Q Consensus 504 ~~W~C~~C~~ 513 (566)
.+|.||.|-.
T Consensus 35 d~w~CP~Cg~ 44 (55)
T COG1773 35 DDWVCPECGV 44 (55)
T ss_pred CccCCCCCCC
Confidence 3699999974
No 127
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=28.34 E-value=37 Score=37.48 Aligned_cols=55 Identities=18% Similarity=0.390 Sum_probs=38.1
Q ss_pred CCcCcccccccccccC---CCCceeeccCCCCCcccccC------CCC-CC----CCCCCccCcccccc
Q 008421 292 DVYKVHTCRQCEEKAG---EKDGLVCDSCEEMYHLSCIE------PAF-KD----IPPKSWYCARCTAK 346 (566)
Q Consensus 292 ~~~~~~~C~~C~~~~~---~~~ll~Cd~C~~~~H~~Cl~------P~l-~~----~P~g~W~C~~C~~~ 346 (566)
+..+.+.|.+|.+-++ +-.-+-||.|..+-|+.|.- ++. .. ..++.++|..|-..
T Consensus 124 gFC~~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 124 GFCRRCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred CccccCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 4566888999988443 33458899999999999952 111 11 13457999999754
No 128
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=26.56 E-value=37 Score=38.18 Aligned_cols=32 Identities=25% Similarity=0.797 Sum_probs=19.7
Q ss_pred CceeeccCCCCCcccccCCCCCCCCCCCccCcccccc
Q 008421 310 DGLVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTAK 346 (566)
Q Consensus 310 ~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~ 346 (566)
.|.+|..|...-...|+..- | ..||||+|...
T Consensus 4 ~L~fC~~C~~irc~~c~~~E---i--~~~yCp~CL~~ 35 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRCVSEE---I--DSYYCPNCLFE 35 (483)
T ss_pred cceecccccccCChhhcccc---c--ceeECcccccc
Confidence 45666666666666666332 2 45888888643
No 129
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.43 E-value=20 Score=37.02 Aligned_cols=48 Identities=25% Similarity=0.502 Sum_probs=28.4
Q ss_pred cccccccccccC----CCCc---eeeccCCCCCcccccCCCCCCCCCCCccCccccc
Q 008421 296 VHTCRQCEEKAG----EKDG---LVCDSCEEMYHLSCIEPAFKDIPPKSWYCARCTA 345 (566)
Q Consensus 296 ~~~C~~C~~~~~----~~~l---l~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~ 345 (566)
+.+|.+||..-+ ++.+ ..=-+|+..||-+|+. +.= +=...-.||.|..
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIr-GWc-ivGKkqtCPYCKe 278 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIR-GWC-IVGKKQTCPYCKE 278 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhh-hhe-eecCCCCCchHHH
Confidence 448999998321 1211 2223799999999984 221 1112357888863
No 130
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=25.79 E-value=55 Score=36.98 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=36.9
Q ss_pred cccccccccccCCCCceeeccCCCCCcccccCCCCCCCCC--CCccCcccccc
Q 008421 296 VHTCRQCEEKAGEKDGLVCDSCEEMYHLSCIEPAFKDIPP--KSWYCARCTAK 346 (566)
Q Consensus 296 ~~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~--g~W~C~~C~~~ 346 (566)
+..|..|.. ++..|.|+.|-+.||..|+.|.- +++. -.|.|+.|...
T Consensus 60 d~~cfechl---pg~vl~c~vc~Rs~h~~c~sp~~-q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 60 DPFCFECHL---PGAVLKCIVCHRSFHENCQSPDP-QKRNYSVPSDKPQPYSF 108 (588)
T ss_pred CcccccccC---CcceeeeehhhccccccccCcch-hhccccccccCCccccc
Confidence 347999987 78899999999999999997653 3333 35999998743
No 131
>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=25.78 E-value=38 Score=25.52 Aligned_cols=31 Identities=19% Similarity=0.373 Sum_probs=21.8
Q ss_pred cccccccc--CCCCceeeccCCCCCCcCCCCCC
Q 008421 466 LCRACLTD--KDDEKIVMCDGCDQGYHLYCMDP 496 (566)
Q Consensus 466 ~C~~C~~~--~~~~~ll~Cd~C~~~~H~~Cl~P 496 (566)
.|.+|++. +...+-+.|..|....|..|+.-
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 35555443 25678899999999999999863
No 132
>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=25.02 E-value=24 Score=31.37 Aligned_cols=13 Identities=38% Similarity=1.035 Sum_probs=10.3
Q ss_pred CCCCCcccCCCcc
Q 008421 501 VPKGNWFCRKCDA 513 (566)
Q Consensus 501 ~p~~~W~C~~C~~ 513 (566)
+...+|.||.|+.
T Consensus 57 ~~~~~W~CP~Crg 69 (105)
T PF10497_consen 57 LEDPNWKCPKCRG 69 (105)
T ss_pred hcCCceECCCCCC
Confidence 3456799999985
No 133
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=23.72 E-value=35 Score=25.96 Aligned_cols=32 Identities=31% Similarity=0.762 Sum_probs=16.1
Q ss_pred eccCCCCCCcCCCCCCCCCCCCC--------CCcccCCCcc
Q 008421 481 MCDGCDQGYHLYCMDPPRTSVPK--------GNWFCRKCDA 513 (566)
Q Consensus 481 ~Cd~C~~~~H~~Cl~Ppl~~~p~--------~~W~C~~C~~ 513 (566)
.|..|...|...=-+| ...+|. .+|.||.|..
T Consensus 3 ~C~~CgyvYd~~~Gd~-~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDP-ENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EETTTSBEEETTTBBG-GGTB-TT--GGGS-TT-B-TTTSS
T ss_pred CCCCCCEEEcCCcCCc-ccCcCCCCCHHHCCCCCcCcCCCC
Confidence 4666666665554332 122222 3699999975
No 134
>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=22.88 E-value=54 Score=24.64 Aligned_cols=31 Identities=26% Similarity=0.592 Sum_probs=23.6
Q ss_pred cccccccccc--CCCCceeeccCCCCCcccccC
Q 008421 297 HTCRQCEEKA--GEKDGLVCDSCEEMYHLSCIE 327 (566)
Q Consensus 297 ~~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~ 327 (566)
..|.+|++.= ....-+.|..|...+|..|+.
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 3799998843 456678999999999999984
No 135
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.20 E-value=31 Score=31.92 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=12.7
Q ss_pred CCCCCCCCCcccCCCc
Q 008421 497 PRTSVPKGNWFCRKCD 512 (566)
Q Consensus 497 pl~~~p~~~W~C~~C~ 512 (566)
||+. -.|.-+||.|-
T Consensus 37 PLF~-KdG~v~CPvC~ 51 (131)
T COG1645 37 PLFR-KDGEVFCPVCG 51 (131)
T ss_pred ccee-eCCeEECCCCC
Confidence 6777 67889999996
No 136
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=22.19 E-value=29 Score=26.36 Aligned_cols=33 Identities=30% Similarity=0.857 Sum_probs=19.6
Q ss_pred cccccCcccccCCCcccccCCccCCC--ccccccCCCc
Q 008421 415 LCKICGRKVEESSDKFRSCEHAFCYS--KFYHERCLTP 450 (566)
Q Consensus 415 ~C~~Cgs~~~~~~~~Ll~C~~~~C~~--k~yH~~CL~~ 450 (566)
+|.+|.........-+.+|. |.+ +|+|..||..
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~---C~G~~~~vH~~Cl~~ 35 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCR---CKGSLKYVHQECLER 35 (49)
T ss_pred CccCCCCCCCCCCeeEeccc---cCCchhHHHHHHHHH
Confidence 36777762222133344554 554 6899999985
No 137
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=22.10 E-value=49 Score=36.95 Aligned_cols=43 Identities=21% Similarity=0.607 Sum_probs=34.9
Q ss_pred ccccCC-CCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 470 CLTDKD-DEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 470 C~~~~~-~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
|+...+ ++.++.|+.|+.|=|..|+....... ...+.|..|..
T Consensus 91 c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~-p~~y~c~~c~~ 134 (508)
T KOG1844|consen 91 CGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK-PDKYVCEICTP 134 (508)
T ss_pred cccccCCCceeeCCcccCcccCceeeeecCCCC-chhceeeeecc
Confidence 455566 89999999999999999999754444 56789999975
No 138
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.83 E-value=1.9e+02 Score=30.71 Aligned_cols=29 Identities=10% Similarity=0.185 Sum_probs=21.1
Q ss_pred cCCCCccCCccchhhhhhhhccccccCcc
Q 008421 191 NFQGIKVDRVFNLSAINSRMKQGAYENSP 219 (566)
Q Consensus 191 ~~~~~~~~~~~Dl~~Id~rl~~g~Y~~~p 219 (566)
+++.+.-....+|+.+-..|.+|+|..-+
T Consensus 122 ~l~~l~~~~~~~le~~a~alL~~~~~~~~ 150 (305)
T TIGR01562 122 ALEQLREAEEGQLKAMAIALLAGDFDLLS 150 (305)
T ss_pred HHHHHHhCCHHHHHHHHHHHhcCCccccc
Confidence 34443345688899999999999996644
No 139
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.82 E-value=68 Score=37.59 Aligned_cols=41 Identities=24% Similarity=0.748 Sum_probs=25.3
Q ss_pred CccCCCc----ccccccccC---CCCceeeccCCCCCCcCCCCCCCCCCCCCCCcccCCCcc
Q 008421 459 CWFCPSC----LCRACLTDK---DDEKIVMCDGCDQGYHLYCMDPPRTSVPKGNWFCRKCDA 513 (566)
Q Consensus 459 ~w~Cp~C----~C~~C~~~~---~~~~ll~Cd~C~~~~H~~Cl~Ppl~~~p~~~W~C~~C~~ 513 (566)
...|..| .|..|...- .....+.|..|+.. . . .|.||.|..
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~--~---~---------p~~Cp~Cgs 430 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRA--A---P---------DWRCPRCGS 430 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCC--C---c---------CccCCCCcC
Confidence 3456666 366665322 13567889999741 1 1 399999964
No 140
>PF12773 DZR: Double zinc ribbon
Probab=20.56 E-value=86 Score=23.34 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=5.6
Q ss_pred CCccCccccc
Q 008421 336 KSWYCARCTA 345 (566)
Q Consensus 336 g~W~C~~C~~ 345 (566)
..++|+.|-.
T Consensus 28 ~~~~C~~Cg~ 37 (50)
T PF12773_consen 28 SKKICPNCGA 37 (50)
T ss_pred CCCCCcCCcC
Confidence 3466666643
No 141
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.22 E-value=69 Score=22.19 Aligned_cols=10 Identities=40% Similarity=1.225 Sum_probs=8.2
Q ss_pred CCcccCCCcc
Q 008421 504 GNWFCRKCDA 513 (566)
Q Consensus 504 ~~W~C~~C~~ 513 (566)
.+|.||.|..
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4599999975
Done!