Query 000290
Match_columns 1717
No_of_seqs 496 out of 1780
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:02:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1473 Nucleosome remodeling 100.0 3E-186 6E-191 1679.6 39.4 1380 1-1716 1-1413(1414)
2 PF02791 DDT: DDT domain; Int 99.6 2.9E-15 6.2E-20 136.2 5.2 60 202-261 1-60 (61)
3 smart00571 DDT domain in diffe 99.5 2.4E-14 5.3E-19 131.1 5.1 60 202-261 1-62 (63)
4 KOG1473 Nucleosome remodeling 98.8 2.5E-09 5.4E-14 135.6 2.6 201 316-537 251-459 (1414)
5 KOG1973 Chromatin remodeling p 98.5 3.9E-08 8.5E-13 113.5 3.1 54 1357-1415 213-269 (274)
6 COG5034 TNG2 Chromatin remodel 98.4 1.7E-07 3.7E-12 105.3 3.6 56 1354-1414 212-270 (271)
7 KOG4299 PHD Zn-finger protein 98.4 1E-07 2.3E-12 117.2 1.3 50 426-475 253-307 (613)
8 PF00628 PHD: PHD-finger; Int 98.3 1.6E-07 3.4E-12 82.1 1.0 48 1365-1413 1-50 (51)
9 KOG1244 Predicted transcriptio 98.2 3.2E-07 6.9E-12 103.5 1.3 47 426-472 281-330 (336)
10 cd04718 BAH_plant_2 BAH, or Br 98.2 5.5E-07 1.2E-11 95.4 2.0 91 447-539 1-98 (148)
11 COG5141 PHD zinc finger-contai 98.1 5.1E-07 1.1E-11 107.8 -1.0 135 318-474 104-244 (669)
12 smart00249 PHD PHD zinc finger 98.1 2.8E-06 6.1E-11 71.2 3.7 45 1366-1411 3-47 (47)
13 KOG0955 PHD finger protein BR1 98.0 1.1E-06 2.4E-11 114.9 0.7 54 422-477 215-273 (1051)
14 KOG0825 PHD Zn-finger protein 97.9 3.6E-06 7.8E-11 104.7 2.1 47 426-472 215-265 (1134)
15 PF00628 PHD: PHD-finger; Int 97.9 3.1E-06 6.8E-11 74.0 0.2 45 428-472 1-50 (51)
16 KOG0383 Predicted helicase [Ge 97.7 1.6E-05 3.4E-10 101.2 2.1 54 422-475 43-96 (696)
17 smart00249 PHD PHD zinc finger 97.7 2.4E-05 5.3E-10 65.5 2.6 43 428-470 1-47 (47)
18 KOG1632 Uncharacterized PHD Zn 97.3 8.5E-05 1.8E-09 88.8 1.5 57 1358-1414 234-295 (345)
19 KOG1973 Chromatin remodeling p 97.3 0.00012 2.6E-09 85.1 2.7 44 426-472 221-267 (274)
20 KOG1512 PHD Zn-finger protein 97.2 0.00011 2.4E-09 84.0 1.6 44 427-472 315-362 (381)
21 KOG1632 Uncharacterized PHD Zn 97.2 0.0001 2.2E-09 88.2 1.3 51 1363-1413 60-112 (345)
22 COG5034 TNG2 Chromatin remodel 97.2 0.0002 4.2E-09 81.4 3.4 47 423-472 218-269 (271)
23 KOG0957 PHD finger protein [Ge 97.2 0.0015 3.2E-08 79.4 9.8 45 427-471 545-596 (707)
24 PF15612 WHIM1: WSTF, HB1, Itc 97.2 0.00033 7.2E-09 61.7 3.4 46 309-354 4-49 (50)
25 KOG0956 PHD finger protein AF1 97.0 0.0002 4.4E-09 89.1 0.2 44 427-472 6-56 (900)
26 KOG4443 Putative transcription 96.9 0.00031 6.8E-09 87.7 1.4 45 427-471 69-116 (694)
27 KOG0954 PHD finger protein [Ge 96.6 0.00075 1.6E-08 85.0 1.2 47 425-473 270-321 (893)
28 KOG1245 Chromatin remodeling c 96.5 0.00068 1.5E-08 92.7 -0.3 50 425-474 1107-1159(1404)
29 PF09465 LBR_tudor: Lamin-B re 96.4 0.0043 9.4E-08 56.5 4.2 41 41-81 5-49 (55)
30 KOG4323 Polycomb-like PHD Zn-f 96.3 0.0016 3.5E-08 79.9 2.0 50 1364-1414 172-224 (464)
31 KOG0383 Predicted helicase [Ge 96.0 0.0052 1.1E-07 79.1 4.2 83 443-525 1-94 (696)
32 KOG1246 DNA-binding protein ju 95.4 0.01 2.2E-07 79.4 3.4 151 426-577 155-322 (904)
33 PF13831 PHD_2: PHD-finger; PD 95.0 0.0055 1.2E-07 51.4 -0.4 34 436-471 2-36 (36)
34 KOG4443 Putative transcription 94.9 0.0087 1.9E-07 75.4 0.7 94 425-524 17-117 (694)
35 KOG1512 PHD Zn-finger protein 94.7 0.0079 1.7E-07 69.4 -0.4 88 427-523 259-360 (381)
36 KOG4323 Polycomb-like PHD Zn-f 94.3 0.013 2.7E-07 72.4 0.3 47 428-474 170-225 (464)
37 KOG2752 Uncharacterized conser 94.2 0.021 4.6E-07 67.0 1.7 27 1363-1389 128-159 (345)
38 KOG1244 Predicted transcriptio 93.8 0.015 3.3E-07 66.9 -0.4 79 436-519 244-325 (336)
39 KOG1844 PHD Zn-finger proteins 92.6 0.067 1.5E-06 67.0 2.5 57 1361-1419 84-140 (508)
40 smart00333 TUDOR Tudor domain. 91.5 0.22 4.7E-06 44.5 3.8 48 42-89 3-53 (57)
41 PF13831 PHD_2: PHD-finger; PD 89.0 0.1 2.3E-06 43.9 -0.3 34 1377-1412 3-36 (36)
42 KOG0825 PHD Zn-finger protein 87.6 0.3 6.4E-06 63.0 2.2 53 1360-1414 213-266 (1134)
43 KOG0957 PHD finger protein [Ge 83.9 0.86 1.9E-05 56.6 3.5 53 1201-1253 541-595 (707)
44 PF15446 zf-PHD-like: PHD/FYVE 83.5 1.7 3.7E-05 48.1 5.2 50 1207-1256 2-60 (175)
45 KOG4299 PHD Zn-finger protein 82.6 0.69 1.5E-05 59.1 2.0 47 426-472 47-94 (613)
46 smart00743 Agenet Tudor-like d 80.5 2.5 5.3E-05 38.6 4.4 49 42-90 3-57 (61)
47 PF07227 DUF1423: Protein of u 80.4 1.3 2.8E-05 55.1 3.2 51 1364-1415 130-193 (446)
48 KOG1245 Chromatin remodeling c 79.3 0.88 1.9E-05 63.7 1.5 56 1359-1416 1105-1160(1404)
49 PF09038 53-BP1_Tudor: Tumour 78.9 2.8 6.1E-05 44.3 4.6 40 42-81 3-45 (122)
50 KOG0955 PHD finger protein BR1 77.5 2.2 4.7E-05 58.2 4.3 55 1357-1414 214-269 (1051)
51 PLN00163 histone H4; Provision 77.4 1.7 3.7E-05 40.6 2.3 35 999-1033 17-53 (59)
52 KOG0954 PHD finger protein [Ge 77.0 1.6 3.5E-05 56.6 2.7 56 1361-1419 270-326 (893)
53 cd04508 TUDOR Tudor domains ar 76.3 3.6 7.8E-05 35.5 3.9 41 47-87 3-47 (48)
54 PF15446 zf-PHD-like: PHD/FYVE 68.0 2.1 4.5E-05 47.4 0.7 44 428-471 1-58 (175)
55 KOG0956 PHD finger protein AF1 66.3 2.9 6.4E-05 54.0 1.6 63 1362-1427 5-76 (900)
56 PF13901 DUF4206: Domain of un 64.8 5.2 0.00011 45.4 3.0 58 1187-1258 138-200 (202)
57 cd00029 C1 Protein kinase C co 56.4 4.2 9.1E-05 35.2 0.4 28 1668-1695 14-44 (50)
58 PF13639 zf-RING_2: Ring finge 55.6 2.1 4.5E-05 36.8 -1.6 43 1364-1412 2-44 (44)
59 PF14446 Prok-RING_1: Prokaryo 55.5 5.7 0.00012 36.9 1.0 35 1203-1237 4-39 (54)
60 PF00130 C1_1: Phorbol esters/ 55.3 6.7 0.00014 34.9 1.5 33 1204-1236 11-45 (53)
61 PF06003 SMN: Survival motor n 54.9 8.1 0.00018 45.7 2.5 50 41-90 68-122 (264)
62 KOG3467 Histone H4 [Chromatin 54.0 7.1 0.00015 39.1 1.5 40 1010-1049 30-72 (103)
63 PF14446 Prok-RING_1: Prokaryo 53.6 5.7 0.00012 36.8 0.7 31 426-456 5-39 (54)
64 smart00109 C1 Protein kinase C 51.2 5.2 0.00011 34.2 0.1 28 1668-1695 14-43 (49)
65 PF00130 C1_1: Phorbol esters/ 49.4 7.5 0.00016 34.6 0.8 28 1668-1695 14-44 (53)
66 KOG1081 Transcription factor N 46.6 11 0.00024 47.9 2.0 48 424-474 87-134 (463)
67 PF02178 AT_hook: AT hook moti 45.8 9 0.0002 26.4 0.5 10 6-15 1-10 (13)
68 smart00417 H4 Histone H4. 44.5 12 0.00025 36.8 1.3 24 1010-1033 14-37 (74)
69 KOG4628 Predicted E3 ubiquitin 42.0 15 0.00032 45.2 2.0 45 427-474 230-277 (348)
70 smart00384 AT_hook DNA binding 40.4 17 0.00037 29.3 1.4 16 6-21 1-16 (26)
71 PF11793 FANCL_C: FANCL C-term 40.1 5 0.00011 38.5 -1.8 45 426-470 2-61 (70)
72 cd04714 BAH_BAHCC1 BAH, or Bro 39.2 16 0.00035 38.3 1.5 22 1360-1381 100-121 (121)
73 PF12898 Stc1: Stc1 domain; I 39.2 18 0.0004 36.0 1.8 45 1664-1716 36-84 (84)
74 PF13832 zf-HC5HC2H_2: PHD-zin 38.2 17 0.00037 36.9 1.5 31 1361-1394 54-86 (110)
75 KOG1886 BAH domain proteins [T 35.5 32 0.0007 43.7 3.5 51 1360-1414 168-218 (464)
76 KOG3612 PHD Zn-finger protein 35.1 30 0.00065 44.5 3.1 50 424-474 58-109 (588)
77 cd00076 H4 Histone H4, one of 33.2 22 0.00048 35.8 1.3 24 1010-1033 14-37 (85)
78 COG2956 Predicted N-acetylgluc 32.9 19 0.00042 43.9 1.0 23 318-340 97-119 (389)
79 cd04718 BAH_plant_2 BAH, or Br 32.0 29 0.00062 38.3 2.0 27 1388-1415 2-28 (148)
80 PF13341 RAG2_PHD: RAG2 PHD do 31.2 18 0.00038 35.3 0.3 34 1377-1410 29-67 (78)
81 PF12678 zf-rbx1: RING-H2 zinc 30.7 27 0.00059 33.7 1.5 42 1364-1412 21-73 (73)
82 smart00109 C1 Protein kinase C 30.7 17 0.00038 31.0 0.1 32 1205-1236 12-44 (49)
83 PF07496 zf-CW: CW-type Zinc F 30.5 30 0.00065 31.3 1.6 40 1377-1419 2-43 (50)
84 PTZ00015 histone H4; Provision 30.2 33 0.00071 35.7 2.0 35 999-1033 18-54 (102)
85 PF09337 zf-H2C2: His(2)-Cys(2 28.9 13 0.00028 32.3 -0.9 31 802-836 9-39 (39)
86 PF07649 C1_3: C1-like domain; 28.2 21 0.00046 28.8 0.2 29 1364-1393 2-30 (30)
87 cd00029 C1 Protein kinase C co 28.1 24 0.00051 30.6 0.5 32 1205-1236 12-45 (50)
88 PF13639 zf-RING_2: Ring finge 27.6 8.6 0.00019 33.1 -2.3 41 427-471 1-44 (44)
89 PF12861 zf-Apc11: Anaphase-pr 26.1 24 0.00053 35.6 0.3 29 443-472 51-79 (85)
90 KOG4198 RNA-binding Ran Zn-fin 25.8 53 0.0011 39.6 2.9 24 1609-1633 35-58 (280)
91 KOG2626 Histone H3 (Lys4) meth 25.8 56 0.0012 42.2 3.2 56 1359-1414 16-76 (544)
92 PF13832 zf-HC5HC2H_2: PHD-zin 24.0 33 0.00072 34.9 0.8 31 426-456 55-88 (110)
93 PF13771 zf-HC5HC2H: PHD-like 22.5 48 0.001 32.4 1.5 32 1362-1396 36-69 (90)
94 PF03107 C1_2: C1 domain; Int 22.5 63 0.0014 26.4 1.9 28 1667-1694 2-30 (30)
95 KOG1829 Uncharacterized conser 22.2 33 0.00071 44.9 0.4 62 1185-1258 495-561 (580)
96 PF13771 zf-HC5HC2H: PHD-like 21.9 36 0.00079 33.2 0.6 31 426-456 36-69 (90)
97 PF13901 DUF4206: Domain of un 21.8 52 0.0011 37.6 1.8 37 427-472 153-197 (202)
98 PF07649 C1_3: C1-like domain; 20.9 23 0.00051 28.6 -0.8 27 1667-1693 2-29 (30)
No 1
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=2.8e-186 Score=1679.59 Aligned_cols=1380 Identities=38% Similarity=0.578 Sum_probs=1144.4
Q ss_pred CCCCCCCCCCCCcCCCCCCccccCCCCCCccccccc-ccccceeecceeeeecCC-ceeEeEEEEEecceEEEEccCCCc
Q 000290 1 MEAKVKRPRGRPRKRKRPEDEDVTDGAGGKKRVVAV-EAKPIALVGRYVLKEFES-GIFLGKIVYYESGLYRVDYEDGDC 78 (1717)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~lvGR~V~k~f~~-~~~~GkV~~yd~g~y~VvYEDGd~ 78 (1717)
||.+++|||||||||.|+|+.+. +.+++|+|+-.. .+.|+.|.|+|+.|.+.+ ++|+||+++||+|+|||.|||||.
T Consensus 1 m~g~~arpRGRp~k~p~~e~~nr-~~~~~kkp~~~~e~~~p~s~l~~r~~~d~~d~~~~~~k~~s~d~~~~rv~~e~~~~ 79 (1414)
T KOG1473|consen 1 MEGKVARPRGRPRKRPRSEDGNR-SINRGKKPVEEVESAVPRSLLGKRYLKDGDDKKVFLGKIVSYDTGLYRVKYEDGDV 79 (1414)
T ss_pred CCCCCCCCCCCCCCCCCcccccc-hhhhccCccccccccCccccccccccCCccchhhhhcccccccCcceeEEeecccc
Confidence 99999999999999999999999 999999994322 345679999999999999 999999999999999999999999
Q ss_pred cccChHHHHHHhcCCCCCchHHHHHHhhcchhhhcccccccccccccccCCCcccccccccccccccccCcccccccccc
Q 000290 79 EDLDSSELRQFLLNENDFDADLTRRRKKLDDWLVKRSLKNEKSNLEKKDGDAKSEVDRIEASTLSEVSCGLTVEDVGEQV 158 (1717)
Q Consensus 79 Edl~~~el~~~l~~~~~~~~~~~~Rr~~ld~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 158 (1717)
|+++...+++.++.+++++++...||.+||.++++.+..-..+..+.+.++.+..-. +.+.+...+
T Consensus 80 ~~~~~s~v~~~~~s~s~~~eet~~rr~dl~d~~edk~d~~dd~e~~e~~~ed~~~~N--------------~~~~v~~se 145 (1414)
T KOG1473|consen 80 ESLEASTVRPLIISDSGKDEETRPRRKDLDDQEEDKDDKKDDSEEEEKDDEDPFMCN--------------EDSSVQESE 145 (1414)
T ss_pred cccccccccccccccccccccccccccchhhhhhhhhhcccccccccccccchhhcC--------------chhhhhhhh
Confidence 999999999999999999999999999999999887755111111111111111100 111122333
Q ss_pred cCCCCCCCCccccccccccCccccCCCCCCCCCCCCCCCCCCChhhHHhHHHHHHHHHhcccceecCCcCHHHHHhhhcc
Q 000290 159 EGDMDSSSDSCEHVRETDAGLEAETPLLPPPQLPPSSGTIGMPEEYVSHLFSVYGFLRSFGIHLFLSPIGLDDFVGSLNC 238 (1717)
Q Consensus 159 ~~~~~sss~~~~~~~~~~~~~~~~~~~~P~l~LP~SS~dl~VP~e~VgdLL~VWeFLrsF~~vL~LSPFTLDDF~aAL~~ 238 (1717)
+++..+....+....+.++..+.+.+.+|||+||+||+||.||+++|+++|+||+|||+|+.+|+|+||+|||||+||.+
T Consensus 146 ~~~n~t~~~~~~~~d~~~p~~~~e~~~vPpleLP~SSedi~IPne~Vm~alsIYevLRsF~~~LrisPF~feDFcaAL~~ 225 (1414)
T KOG1473|consen 146 SGLNYTDIGRPPRLDEPNPDLEEEPPLVPPLELPESSEDIGIPNEHVMDALSIYEVLRSFSRQLRISPFRFEDFCAALIS 225 (1414)
T ss_pred cccccCCCCCCCCCCCCCCChhhccccCCCccCCCcccccCCcHHHHHHHHHHHHHHHhhcceEEeCCccHHHHHHHHHh
Confidence 44445555555666666666788999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccHHHHHHHHHHHHHhhhhcccCCCchhccccccccccchhccCChHHHHHHHHHHcCCcCCCcchhhhhhhcccc
Q 000290 239 CVPNTLLDAIHVALMRVLRRHLETLSSDGSELASNCLRCIDWSLLDTLTWPVYVVQYLTSMGYIKGTQWTGFYDEVSVRE 318 (1717)
Q Consensus 239 ~e~s~LL~EIH~aLLkaLlr~~e~lsse~se~a~~~lr~i~W~lLD~lTWpeiLr~yL~s~G~~~~p~~k~il~~Llr~e 318 (1717)
.++|.||+|+|++|||+|++|++++++..++.++++++||+|++||.+|||||||+|+++++.-..+-|..+-.-+...+
T Consensus 226 ~~~ssLlaeVHvaLLrA~lr~eD~~~Thfs~~d~KdsvnI~l~liD~lTWPevLrqY~ea~~~ad~~v~~~~n~fv~~~e 305 (1414)
T KOG1473|consen 226 HEQSSLLAEVHVALLRALLREEDRLSTHFSPLDSKDSVNIDLYLIDTLTWPEVLRQYFEADKHADGPVWDIFNPFVVEDE 305 (1414)
T ss_pred cCchhHHHHHHHHHHHHHhhhhhhcccccCccccccceeeeeehhccccHHHHHHHHHHhccccCcchhhhhcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999998866654444444455799
Q ss_pred ccccChhhHHHHHHHHHHhccCcHHHHHHHHhhhhcccc----CCcCcc-ccchhhccccc------CCCCCCCCcccch
Q 000290 319 YYSLSAGRKLMILQILCDDVLDSEELRAEIDAREESEVG----LDPDAA-SYGSEIARRRV------HPRFSKTPDCKNR 387 (1717)
Q Consensus 319 Y~~LpVn~KLkILq~LcDl~L~s~~fRsemD~ReEse~~----le~~n~-~~~~e~G~Rr~------~~R~sk~sa~k~~ 387 (1717)
|+..||..||+|||||||+++++..+|.+|+.+.+.+.+ +..+.. .+.-|+++|++ ||+..++++....
T Consensus 306 Y~~~pv~~klkILQ~L~Dq~l~~~s~R~e~~se~~~~~ddhcrf~~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~ 385 (1414)
T KOG1473|consen 306 YPYRPVSNKLKILQFLCDQFLTVNSLRDEIDSEGEIEYDDHCRFCHDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWEC 385 (1414)
T ss_pred ccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccceeecccccccCcccceeecccCCceEEeeecCCccccCCCccchh
Confidence 999999999999999999999999999999988887766 555544 67799999999 8999988877654
Q ss_pred hhhhhhccccccccC-CCCC--CC-CCCCCCCCCCCCccccccccccccccCCcccccCC-CCccccc-cccC--cccCC
Q 000290 388 EAVEFNAENDRMKTS-CKAK--PL-GFKGTEMDAPGVDVDGNGDECRICGMDGTLLCCDG-CPSAYHT-RCIG--VSKMY 459 (1717)
Q Consensus 388 ~~~E~~~e~~~~s~~-~~s~--~s-r~~~~e~~e~~~~~d~ndd~C~VC~~gG~LLcCD~-Cp~afHl-~CL~--PpL~~ 459 (1717)
+.-.+..=....... ..++ .+ |...-..+..+..-..+.+.|.+|+..+.+|||++ |+..||+ .||+ -.-+.
T Consensus 386 evc~~hkvngvvd~vl~~~K~~~~iR~~~iG~dr~gr~ywfi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~~ 465 (1414)
T KOG1473|consen 386 EVCNIHKVNGVVDCVLPPSKNVDSIRHTPIGRDRYGRKYWFISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEMY 465 (1414)
T ss_pred hhhhhhccCcccccccChhhcccceeccCCCcCccccchhceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHHh
Confidence 444321101111010 1111 12 22222222233334456678999999999999998 9999999 9999 55578
Q ss_pred CCCCCcccccCcccccCCccccccccccccccccchhhhHHHh-hcccceeeccCCCchhcccccccCchhhHHHHhccc
Q 000290 460 VPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFLG-TCNHLLVLNASSNTEQYIRYYNPIDIPKVLQALLSS 538 (1717)
Q Consensus 460 vPeGdW~Cp~C~~~~~~p~~E~g~~~rg~EllgcD~c~r~Yh~-kCerLlLe~~s~D~~~c~rYYs~~Dl~~v~~vLygs 538 (1717)
+++|-|+|+.|...+++++.+..+..+++--||.|++++.|.. .|.-+++.....-...-..||...++.++..++-.+
T Consensus 466 L~d~i~~~~ee~~rqM~lT~~ltne~R~~~~f~~~~h~r~~l~~~c~~~lv~~iq~~~da~l~e~~l~~i~k~v~~~~S~ 545 (1414)
T KOG1473|consen 466 LCDGIWERREEIIRQMGLTEELTNELRGAVDFGEDPHGRLFLGRDCAVLLVLCIQVVEDAILKEENLGDIDKVVLVLISA 545 (1414)
T ss_pred hccchhhhHHHHHHhccchhhhhhhhhcccccccCCCcceeeecchhhHHhhhhhhhhhhhhhHhhhcchHhhhhhhhhc
Confidence 9999999999999999999999988999999999999999887 455444443332223457888888888999999999
Q ss_pred cccccchhhHHHHHHHHhcCCcCcC-CcccccccccccccccccccCCCCCCCccccccccceecCCCCCCCCCCCcccc
Q 000290 539 VQHVSLYLGICKAILHYWDIPESVV-PFMGMETNTINAKADEKFCSQSHHPPIKESQRITDMVEAGNASSNNGSNVDNVA 617 (1717)
Q Consensus 539 DiH~~~y~~I~kAI~~YW~hplNl~-~l~~~E~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 617 (1717)
.+|.+.|.+||++|.+||+.|..-. .+..-+..+..|+ ...++|-...+.+.+-...
T Consensus 546 s~~~eE~~e~ck~is~~~d~p~~n~~~~~e~~~dqtf~~----------------------y~ys~n~vse~~~~d~e~~ 603 (1414)
T KOG1473|consen 546 SAHQEEYVEICKAISQYWDLPEGNLWRLREEGNDQTFMK----------------------YYYSGNEVSEIFLTDSENA 603 (1414)
T ss_pred ccchHHHHHHHHHHhhcccccccchhhhhhcccccchhh----------------------hcccCCchhhccCCchhhh
Confidence 9999999999999999999998443 2111111112211 0112222222222210000
Q ss_pred ccccccccccccCCCCcccccccchhhhhhcchhhccCCCCCccccccccccCCccccCCCCCccccccccccccccccc
Q 000290 618 VSSLHTFMNTMSQTGVPFVQSNDITVTEKLQDCLVLNGKLPGHVKMESAMSTGSVSQQADPSDVTYQSLVDRSSAIDFMT 697 (1717)
Q Consensus 618 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 697 (1717)
..+. +...+|+...++ ..-..+|.|- .+
T Consensus 604 dkk~------------------------------~~~tkf~l~~ns--d~~~~g~~~t-------------~g------- 631 (1414)
T KOG1473|consen 604 DKKS------------------------------HMQTKFALITNS--DGVTAGNVTT-------------YG------- 631 (1414)
T ss_pred cccc------------------------------cccceecccccc--cceecccccc-------------cc-------
Confidence 0011 112223221100 0000011000 00
Q ss_pred ccccccCCCCCCCCccCCCCCcccccccccCCCccccccccCCcccccccccCccchhh----ccchh-hHHHHHHHHHh
Q 000290 698 CTSQISNDGNSGHASSCLSPNISFLSKERNHGGLLGVGTNYANKCAFMGSVFKPHSYIN----QYMHG-EFAAAAAAKLA 772 (1717)
Q Consensus 698 ~~~g~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~n~~~~~~~~~~~~~p~~Y~N----~Y~~g-~~aasaA~~l~ 772 (1717)
++ -...+....-.+.+.+|+|.+||| +|..| +.|+|||+.+|
T Consensus 632 -----------t~----------------------~~~~~~~~~t~~~~lSniP~s~~n~~w~~~tkg~~lavs~A~~~~ 678 (1414)
T KOG1473|consen 632 -----------TG----------------------SQHKKLIARTLQQGLSNIPISYNNRKWPVYTKGFELAVSAAADLA 678 (1414)
T ss_pred -----------ch----------------------hhcchHHHhhhhhhhccCchHhhhccchhhccchhhhhhccchHH
Confidence 00 011334444567789999999999 99999 99999999999
Q ss_pred hhccccccccccccccCcccccchhhHHHHHHhhhccccccccccccccccccCccccccccccCCCCCCCCceeehhhh
Q 000290 773 VLSSEESQASEMHKSGNTRKAMSGSISLQAKAFSSTASRFFWPCSERKLWEVPRERCSWCYSCKSPPSNRRGCMLNSAMT 852 (1717)
Q Consensus 773 ~~ss~e~~~~~~~~~~n~~k~~~~~~~~q~Kafs~~~~~f~wps~~kk~~ev~rerCGWC~sCk~~~~~~~~C~ln~a~~ 852 (1717)
.+++ |..+.+.++-.|..|+.+.++..|+|+||.+|++||||+..+| +..|||||||++|+....+.++||+|.+.+
T Consensus 679 el~s-~t~~~d~s~~~~~~~~~ssn~L~qtklesitaa~f~~~~~~~K--ri~rer~~~~~~~~l~~~s~k~~~~~~~~~ 755 (1414)
T KOG1473|consen 679 ELSS-ETLEPDLSKRSNAFKAASSNILGQTKLESITAAQFFWPSPDKK--RITRERCGWCESCRLTFASRKGTMLLAAVI 755 (1414)
T ss_pred HHHH-hhcccchhhhhhhhccchhhhhcchhheeeehhhhccCCcccc--cccccccchhhhcceeeehhccccchhhcc
Confidence 9999 9999999999999999999999999999999999999999999 999999999999999888999999999999
Q ss_pred hhhhhhHHHhcCcccccCCCCChhHHHHHHHhhhhhccccccccCCChhHHHHHHHHHHhhcchhhHHHHHHHhhhcccc
Q 000290 853 VATKSAMKILNGLLAPKTGEGNLPTIVTYIMYMEESLCGLISGPFRSVSYRKKWRKQVAEACTLNSIKALLLELEENICH 932 (1717)
Q Consensus 853 ~~~k~~~~~~~gl~~~k~~~~~l~~i~~yil~mEe~L~GLl~Gp~~~~~~~~~Wrk~~~~as~~~~ik~lLL~LEsnir~ 932 (1717)
.|+||+|++.+||.|.||+++.|.+|++|++++||+++|++||||+..+-|++||+.|+. .+.++++||+||+-
T Consensus 756 gaqKGa~~r~~G~~~l~n~~~vlS~~~~~~~~~~es~~~v~v~~~~~Esnr~~~r~~L~~------r~~~~~q~ee~i~~ 829 (1414)
T KOG1473|consen 756 GAQKGAMYRNSGLFPLKNWEWVLSSIAAYWLALEESPRGVIVGEFKSESNRKQERKELLV------RRSGGKQLEENICS 829 (1414)
T ss_pred ccccccceeeeccccccChhHHHHHHHHHHHhhhccccceeecccccccchhhHHHHhhh------hhhhhhhhcccccc
Confidence 999999999999999999999999999999999999999999999999999999999988 49999999999999
Q ss_pred eeeccchhhhhhccc-ccccccccccccccccccccCCCCCCCcccCccccccCCCCCCceeeccCCcchhhhhhcccCh
Q 000290 933 IALSGDWVKLMDDWL-GDSSVIQSASCNFVTTQKRGLSGKRGRKHSVISEVTADDCNDQSFSWWQGGKSTKLISKKAILP 1011 (1717)
Q Consensus 933 iA~s~~W~k~~D~~~-v~~s~~~~~~~~~~~~~k~g~~~rr~r~~~~~~e~~~~~~~~~~~~WwrGG~lsr~i~~~~~Lp 1011 (1717)
+|++-+|.|+||+|. ++.|..++..-+.++.|+|++|+++ +..++ |.++.+....+|.|||||+ |+.|+++|||-
T Consensus 830 ~~~~~y~~~~~~n~~rie~s~~~~ng~~v~akQ~r~pgr~~-~s~~~--ek~A~~s~ld~f~~~Rggk-s~vvl~kavL~ 905 (1414)
T KOG1473|consen 830 GALSCYWPKQMDNWLRIEHSIFQSNGVTVGAKQARDPGRTK-QSLQA--EKTAPKSDLDSFTWWRGGK-SKVVLQKAVLS 905 (1414)
T ss_pred ccccccchhhccCceeeeechhccCceeechhhhcCCcchh-hhcch--hhccccccccchhhhhcCc-ceeeehhhhcc
Confidence 999999999999999 9999999999999999999995544 33333 8899998899999999999 99999999999
Q ss_pred HHHHHHHHHhcCcccccccccC--CCcccchhhhhhhhhhhcccchhHHHHHHhhhcccccccccCCCcccccCCCCchh
Q 000290 1012 HTIIRNAARRGGLRKISGVNYT--AEMPKRSRQLVWRAAVERSKTVSQLALQVRYIDLHVRWSELVRPEQNLQDGKGPET 1089 (1717)
Q Consensus 1012 ~s~v~kaarqgG~~ki~gi~y~--s~~~rRsr~~~WraaVe~s~~~sqLalqvr~Ld~~irW~e~~~~~~~~~~~k~~~~ 1089 (1717)
++.++|+|.|+|.+++|+..|. +.+|||+++..|.+||+-++|++|||||| .|+.+|+|++++
T Consensus 906 ~~~mk~~v~~~g~ta~~k~nfl~~~y~p~~s~~s~wk~av~n~enlh~LAlQ~---------------~q~v~d~~s~~~ 970 (1414)
T KOG1473|consen 906 QSIMKKLVWQQGFTAGPKSNFLDWSYIPRRSRRSCWKAAVENSENLHQLALQL---------------RQNVQDVKSPET 970 (1414)
T ss_pred hHHHHHHhhccccccCCcccccccccccchhhhhhhhhhhcChhhHHHHHHHH---------------HHHHhccCCchh
Confidence 9999999999999999999999 88999999999999999999999999998 689999999999
Q ss_pred hhhhcccceeeeccccccceEEEEecCCcccCChhhhhhhhhhccccCCCCccccccCCchhHHHHHHHhhccccccCCC
Q 000290 1090 EAFAFRNAIICDKKIVENKIRYGVAFGIHRHLPSRVMKNIIDIELSQDGKEKYWFPETCLPLFLIKEYEERVDMVIAPSS 1169 (1717)
Q Consensus 1090 ~~~~fr~~~i~~k~~~~~~~~y~~~fg~~~~lp~~v~k~~~~~e~~~~~~~k~w~~e~~vPL~L~kefE~~~~~~~~~s~ 1169 (1717)
.++.||||-||.|++.+++.+|+.-|++ +++||.|.+ ||+.|.-|+| .||..+
T Consensus 971 r~ai~r~~~ic~~~l~d~~~~~~~~~~s------~~~~~~~~~---------~~~~~~~~sl----~~~~fr-------- 1023 (1414)
T KOG1473|consen 971 RRAIFRNAEICIKKLYDNKEEEGESWLS------SEFSHVISS---------RPQRHEFVSL----GYEKFR-------- 1023 (1414)
T ss_pred hHHHhhhhhhhccccccCCcccccchhh------hhhhhhhhc---------ccccCceeec----cchhhh--------
Confidence 9999999999999999999999999999 889999887 9999999999 388853
Q ss_pred CCCCchhhHHHHHhhcccccchhhhhhhcccccccccccccccccccccccccccccccccccccccCCcCCCCCcccee
Q 000290 1170 KKPSNELSEFQKKQLKASRKDLFSYLVCRRDKIEKCACASCQIDVLLGNAVKCGTCQGYCHEGCTSSSMHMNSGVEPMIV 1249 (1717)
Q Consensus 1170 ~~~~~~~~~~~~~~~k~~~~~~f~yL~~k~~~le~~~C~~C~kdV~~~~aVtC~~Cqg~fHk~C~~~S~~~~~~~~~~y~ 1249 (1717)
.++.-..+++++.++|.+...+|.|+-.+- . +
T Consensus 1024 ~~~~~r~~~~q~~~~~~~~~~v~~~~~~~~----------------------------------~--~------------ 1055 (1414)
T KOG1473|consen 1024 SLDNRRATAIQREWLKGSTANVFEIKDYWP----------------------------------P--S------------ 1055 (1414)
T ss_pred cchhhhhHHHHhhhhcccccceeeeeccCC----------------------------------c--h------------
Confidence 244556789999999999999999987440 0 0
Q ss_pred cccccCcccccccccccCCCCCCCCcccccccceecccccCCCCCCCcccccc-cccCCcccccccCCCccccccccccc
Q 000290 1250 CNRCYLPRALATSEIRSESPTSPLPLHRQEYHTAVKVSKGTRPKGFNQALASI-RTQESSESKQTVSDSSTVTKTRNRTL 1328 (1717)
Q Consensus 1250 C~rCl~~k~~~i~~~~~~~~~spl~~~~~~~~~avtapK~~r~K~~kqpl~s~-~tk~~sg~Kk~s~~k~~~~Kkk~k~~ 1328 (1717)
+.+++- .+-+.+|+|+-++..... +.+.++.
T Consensus 1056 -----------------------------------------------s~~~s~~~~~~~~gvkq~tpd~n~~-~~~~~~~ 1087 (1414)
T KOG1473|consen 1056 -----------------------------------------------QQLPSEKNNVNYSGVKQRTPDGNER-KSKKKTL 1087 (1414)
T ss_pred -----------------------------------------------hhCcccccCCCccceeeecCCcchh-hhccCCc
Confidence 001111 122446778888887777 7888899
Q ss_pred ceeeeeeccCcccccchhhhcccCCCCCCC-CCCCCeeeccCCCCCCCcceEecCCCCccccccccccCccccCCccceE
Q 000290 1329 SWGIIWRKKNIEDAGADFRRANVLPRGKSV-AHLEPVCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVGFK 1407 (1717)
Q Consensus 1329 ~~Gl~wkKk~~dd~g~~fr~e~v~~~s~~~-~~~~~vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~ 1407 (1717)
+||++|++++-.+.+..||..|+++.+.++ +...++|-+|..||+++..+|.|-.|.-|||++.|.+..........|.
T Consensus 1088 s~~v~~~~~~~a~t~~~~~~qnii~ag~~~kp~~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k 1167 (1414)
T KOG1473|consen 1088 SSGVIWRKKNYADTGVPFRHQNIILAGRSDKPTLSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFK 1167 (1414)
T ss_pred cccccccccccccCCCCcchhhHHhccCCCCCCCCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhh
Confidence 999999999999999999999999888766 8999999999999999999999999999999999999999999999999
Q ss_pred ecCccccCCCCCCCCCchhhHHhhhhHHHHHHHHHHhhhccCCCCCCCCCCCccCCCCCccccccccccCCCCCCcccCC
Q 000290 1408 CCRCRRIGGPECPYMDPELKEQKRKKDQKRKKDQKRKKQQLNAPKQGQGSMRVDSDDGTISESKEFKLTTPMYPMEEMFV 1487 (1717)
Q Consensus 1408 Cp~C~r~~~P~cp~~~~~~k~q~e~k~q~~~~~~~~~~~q~na~~~~~~~~g~~s~~~~~~~~~~~~~~~~~~~~~~~~~ 1487 (1717)
|.+|++++.|.|||++++++.|.++++.--+. . ...|++.|.++|+..+.|++++++++|-++++++|+
T Consensus 1168 ~~~~~ri~~P~~~~~~~~~~~~~~~kr~~~~~---q--------~~~q~~~~~~s~s~~~~e~~~~~~a~p~~~~d~~~i 1236 (1414)
T KOG1473|consen 1168 CCQCRRIRSPDCPYMDPKLKEQKQTKRGGFRN---Q--------KHQQGNQGRDSDSERMSESKDSLPATPDNDGDDPFI 1236 (1414)
T ss_pred HHhhhccCCCCCCcCCchhhHHHhhhhhhhHH---H--------HHhhhccccccccccccccccccccCCCCCCCCccc
Confidence 99999999999999999999998888754433 1 334566799999999999999999999999999999
Q ss_pred CCCCCcceeccceeecCCCCCccccccccCCCCCCCccccccccccCCCCCCCCCCCCCCcccccCcCcCCCCCCCcCCC
Q 000290 1488 PEDDPLLFSLSTVELITEPNSEVDCGWNNSAPGPQKLPVRRQTKCEGDVGSGSVGNNVPNVDLSMSFDANNVMNPKEELS 1567 (1717)
Q Consensus 1488 ~~~dpll~s~~~ve~~~~~~~~~~~~~~~~~pg~~kl~vrr~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1567 (1717)
+++||+|++.++|++||+...++||......||||||+|||++|+++.+.+ ++.+-..|.|+.+-+
T Consensus 1237 p~~dp~l~~~~k~~q~~p~sr~v~~~~~~~~~~~q~~~v~~~i~~~~sd~~--------------~p~~~~iv~p~~~~a 1302 (1414)
T KOG1473|consen 1237 PEDDPLLVSVSKVQQITPQSRDVEWTPAQMIPGPQKLGVRRVVKREDSDGQ--------------FPEGTPIVKPEREPA 1302 (1414)
T ss_pred cCCCchhhhHHHHHHhCccccchhccccCccCCCcccccccceeehhcccc--------------CCCCccccCccccch
Confidence 999999999999999999988888877777999999999999999988732 233333478875559
Q ss_pred ccccccccCCCCCcccccccCCCCCccCCccccccceecccccccCCCCCCcccccCCccccccCCcccccccCCCcccc
Q 000290 1568 VPCVEWDASGNGLEGEMLFDYDGLNYEDMEFEPQTYFSFSELLASDDGGQSDGVDASGVVFGNREDLSCSIQQDGAPQQC 1647 (1717)
Q Consensus 1568 ~~~~~~d~~~~~~~~~~~~d~~~~~~~~~~~ep~tyfs~~ell~~dd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1647 (1717)
+|+++||++ ++++|| |+||||||||||++||||..||.| +|+.+++++.-++++ -..-++|
T Consensus 1303 ~~~~~~~~s-----~~~v~~-----~~~~e~~pq~~~~~~~~~~~~~sg--a~y~dd~~~~~pg~q-------~~~~~q~ 1363 (1414)
T KOG1473|consen 1303 VPVREWDAS-----GELVFD-----YEDMEFEPQTYFSLTELLTVDDSG--AGYMDDQDTPNPGQQ-------VRYVEQC 1363 (1414)
T ss_pred hhhhhhhcC-----cceeec-----hhccCcchHHHHHHHhhhhhhccC--ccccccCCCCCCCCC-------cchHhhc
Confidence 999999999 699999 999999999999999999999998 779888887744443 2234777
Q ss_pred CCCCCCCCCCCcccccccccccccCCCCCCCCccceeccceEeccCCCCCcccccCCCCCccccccccC
Q 000290 1648 GLGTSKDPSNCTVSTVNKMQCRICPDIEPAPNLSCQICGLVIHSQCSPWPWVESSYMEGSWKCGNCRDW 1716 (1717)
Q Consensus 1648 ~~~~~~~~~~~~~~~~~~~~c~~c~~~~p~p~l~c~~c~~~ih~~csp~~w~e~~~~~~~w~cg~cr~w 1716 (1717)
|... .+|+.|++++|+|||.|++|+..||+| +| | +...+++|+||.||.|
T Consensus 1364 g~n~--------------~P~~~~~~~~p~~~l~~~~~~~q~h~~-s~--~--s~~~g~~~~~g~~rv~ 1413 (1414)
T KOG1473|consen 1364 GPNV--------------NPCQVCSRGGPGPDLMCMVCQQQIHSH-SP--W--SDATGFSWSCGTCRVP 1413 (1414)
T ss_pred CCCc--------------CcchhhhccCccchhHHHHHHHHhcCC-CC--c--ccCcccceeeeeeecc
Confidence 7433 449999999999999999999999999 99 7 7789999999999998
No 2
>PF02791 DDT: DDT domain; InterPro: IPR004022 This domain is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is found in foetal Alzheimer antigen and several hypothetical and uncharacterised proteins.
Probab=99.56 E-value=2.9e-15 Score=136.22 Aligned_cols=60 Identities=43% Similarity=0.628 Sum_probs=56.9
Q ss_pred hhhHHhHHHHHHHHHhcccceecCCcCHHHHHhhhccCCCCccHHHHHHHHHHHHHhhhh
Q 000290 202 EEYVSHLFSVYGFLRSFGIHLFLSPIGLDDFVGSLNCCVPNTLLDAIHVALMRVLRRHLE 261 (1717)
Q Consensus 202 ~e~VgdLL~VWeFLrsF~~vL~LSPFTLDDF~aAL~~~e~s~LL~EIH~aLLkaLlr~~e 261 (1717)
+++|+++||||+||++|+++|+|+|||||||++||.+++++.||+|||++||++|+++.+
T Consensus 1 ~~~~~~~L~v~~Fl~~F~~~L~L~~ftlddf~~AL~~~~~~~ll~ei~~~LL~~l~~~~~ 60 (61)
T PF02791_consen 1 GEAFGDLLMVWEFLNTFGEVLGLSPFTLDDFEQALLCNDPSGLLAEIHCALLKALLADEE 60 (61)
T ss_pred CcHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHcCCCcchhHHHHHHHHHHHHHhccC
Confidence 368999999999999999999999999999999999999989999999999999987764
No 3
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=99.48 E-value=2.4e-14 Score=131.10 Aligned_cols=60 Identities=43% Similarity=0.707 Sum_probs=56.9
Q ss_pred hhhHHhHHHHHHHHHhcccceecCCcC--HHHHHhhhccCCCCccHHHHHHHHHHHHHhhhh
Q 000290 202 EEYVSHLFSVYGFLRSFGIHLFLSPIG--LDDFVGSLNCCVPNTLLDAIHVALMRVLRRHLE 261 (1717)
Q Consensus 202 ~e~VgdLL~VWeFLrsF~~vL~LSPFT--LDDF~aAL~~~e~s~LL~EIH~aLLkaLlr~~e 261 (1717)
++.|+++||||+||++|+++|.|+||+ ||||++||++.+++.||+|||++||++|+++.+
T Consensus 1 ~~~~~d~l~V~eFl~~F~~~L~L~~f~~~l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~ 62 (63)
T smart00571 1 NEAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62 (63)
T ss_pred CcHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCC
Confidence 468999999999999999999999999 999999999999999999999999999988654
No 4
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=98.76 E-value=2.5e-09 Score=135.57 Aligned_cols=201 Identities=22% Similarity=0.352 Sum_probs=128.8
Q ss_pred cccccccChhhHHHHHHHHHHhccCcHHHHHHHHhhhhcccc-CCcCccccchhhcccccCCCCCCCCcccchhhhhhhc
Q 000290 316 VREYYSLSAGRKLMILQILCDDVLDSEELRAEIDAREESEVG-LDPDAASYGSEIARRRVHPRFSKTPDCKNREAVEFNA 394 (1717)
Q Consensus 316 r~eY~~LpVn~KLkILq~LcDl~L~s~~fRsemD~ReEse~~-le~~n~~~~~e~G~Rr~~~R~sk~sa~k~~~~~E~~~ 394 (1717)
..+|.-++...-++|--.|+|-+.+.+.+|.|++..-.-... .+..|+ |. ++.-|=-....-+..+.++|.
T Consensus 251 ~Thfs~~d~KdsvnI~l~liD~lTWPevLrqY~ea~~~ad~~v~~~~n~--fv------~~~eY~~~pv~~klkILQ~L~ 322 (1414)
T KOG1473|consen 251 STHFSPLDSKDSVNIDLYLIDTLTWPEVLRQYFEADKHADGPVWDIFNP--FV------VEDEYPYRPVSNKLKILQFLC 322 (1414)
T ss_pred ccccCccccccceeeeeehhccccHHHHHHHHHHhccccCcchhhhhcc--cc------ccccccccchhhhHHHHHHHH
Confidence 356777777777999999999999999999999754432111 111111 00 000000000011233344443
Q ss_pred cccccccCCCCCCCCCCCCCCCCCCCccccccccccccccCCcccccCCCCccccccccCcccCCCCCCCcccccCcccc
Q 000290 395 ENDRMKTSCKAKPLGFKGTEMDAPGVDVDGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 474 (1717)
Q Consensus 395 e~~~~s~~~~s~~sr~~~~e~~e~~~~~d~ndd~C~VC~~gG~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~ 474 (1717)
+-....- .-+..-..++....+|.|.+|++.|.++||.+|++.||++|..+|...+|+..|.|-.|...+
T Consensus 323 Dq~l~~~----------s~R~e~~se~~~~~ddhcrf~~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hk 392 (1414)
T KOG1473|consen 323 DQFLTVN----------SLRDEIDSEGEIEYDDHCRFCHDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHK 392 (1414)
T ss_pred HHHHHHH----------HHHHHHhcccceeecccccccCcccceeecccCCceEEeeecCCccccCCCccchhhhhhhhc
Confidence 2111000 000000111233466899999999999999999999999999999999999999999998766
Q ss_pred cCCcc------ccccccccccccccchhhhHHHhhcccceeeccCCCchhcccccccC-chhhHHHHhcc
Q 000290 475 VGPIV------TIGTSLRGAELFGIDLYERVFLGTCNHLLVLNASSNTEQYIRYYNPI-DIPKVLQALLS 537 (1717)
Q Consensus 475 ~~p~~------E~g~~~rg~EllgcD~c~r~Yh~kCerLlLe~~s~D~~~c~rYYs~~-Dl~~v~~vLyg 537 (1717)
..... .........+.+|.|.++++||+.-+++.++. .| +...+||++. ++-.+++.|..
T Consensus 393 vngvvd~vl~~~K~~~~iR~~~iG~dr~gr~ywfi~rrl~Ie~--~d-et~l~yysT~pqly~ll~cLd~ 459 (1414)
T KOG1473|consen 393 VNGVVDCVLPPSKNVDSIRHTPIGRDRYGRKYWFISRRLRIEG--MD-ETLLWYYSTCPQLYHLLRCLDR 459 (1414)
T ss_pred cCcccccccChhhcccceeccCCCcCccccchhceeeeeEEec--CC-CcEEEEecCcHHHHHHHHHhch
Confidence 54322 11112335678999999999999999999874 34 6778999954 55555555543
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.53 E-value=3.9e-08 Score=113.47 Aligned_cols=54 Identities=30% Similarity=0.583 Sum_probs=44.2
Q ss_pred CCCCCCCeeeccCCCCCCCcceEecCC--CC-ccccccccccCccccCCccceEecCccccC
Q 000290 1357 SVAHLEPVCDLCKQPYNSNLMYIHCET--CQ-RWFHADAVELEESKLSDVVGFKCCRCRRIG 1415 (1717)
Q Consensus 1357 ~~~~~~~vcClC~kPy~~d~~MI~CD~--C~-~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~~ 1415 (1717)
..+.+++.||+|.+... ..||.||. |. +|||+.||||+...- ++|+|+.|+...
T Consensus 213 ~~d~~e~~yC~Cnqvsy--g~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~ 269 (274)
T KOG1973|consen 213 AVDPDEPTYCICNQVSY--GKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAEN 269 (274)
T ss_pred ccCCCCCEEEEeccccc--ccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhh
Confidence 33778999999996443 37999998 99 999999999996543 469999997654
No 6
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.39 E-value=1.7e-07 Score=105.32 Aligned_cols=56 Identities=23% Similarity=0.601 Sum_probs=44.9
Q ss_pred CCCCCCCCCCeeeccCCCCCCCcceEecCC--CC-ccccccccccCccccCCccceEecCcccc
Q 000290 1354 RGKSVAHLEPVCDLCKQPYNSNLMYIHCET--CQ-RWFHADAVELEESKLSDVVGFKCCRCRRI 1414 (1717)
Q Consensus 1354 ~s~~~~~~~~vcClC~kPy~~d~~MI~CD~--C~-~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~ 1414 (1717)
.+.+.++++.+||.|+++.-+ -||.||. |+ +|||..||||.+-. -.+|+|+.|+..
T Consensus 212 ss~d~se~e~lYCfCqqvSyG--qMVaCDn~nCkrEWFH~~CVGLk~pP---KG~WYC~eCk~~ 270 (271)
T COG5034 212 SSEDNSEGEELYCFCQQVSYG--QMVACDNANCKREWFHLECVGLKEPP---KGKWYCPECKKA 270 (271)
T ss_pred CccccccCceeEEEecccccc--cceecCCCCCchhheeccccccCCCC---CCcEeCHHhHhc
Confidence 334447889999999997654 6999996 87 89999999997543 357999999754
No 7
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.36 E-value=1e-07 Score=117.21 Aligned_cols=50 Identities=44% Similarity=1.220 Sum_probs=45.6
Q ss_pred cccccccccCCcc---cccCCCCccccccccCcc--cCCCCCCCcccccCccccc
Q 000290 426 GDECRICGMDGTL---LCCDGCPSAYHTRCIGVS--KMYVPEGSWYCPECAINKV 475 (1717)
Q Consensus 426 dd~C~VC~~gG~L---LcCD~Cp~afHl~CL~Pp--L~~vPeGdW~Cp~C~~~~~ 475 (1717)
.++|..|++.|.. ||||+||++||+.||.|| .+.+|.|.|+|++|.++..
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 5799999999855 999999999999999999 5899999999999987654
No 8
>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=98.32 E-value=1.6e-07 Score=82.06 Aligned_cols=48 Identities=27% Similarity=0.625 Sum_probs=38.9
Q ss_pred ee-ccCCCCCCCcceEecCCCCccccccccccCccccCCc-cceEecCccc
Q 000290 1365 CD-LCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDV-VGFKCCRCRR 1413 (1717)
Q Consensus 1365 cC-lC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i-~~Y~Cp~C~r 1413 (1717)
+| +|++ .+.+..||+|+.|+.|||..|++++....... ..|+|+.|.+
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 35 8998 44567899999999999999999997744332 2899999975
No 9
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.23 E-value=3.2e-07 Score=103.49 Aligned_cols=47 Identities=40% Similarity=0.933 Sum_probs=42.4
Q ss_pred cccccccccC---CcccccCCCCccccccccCcccCCCCCCCcccccCcc
Q 000290 426 GDECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 426 dd~C~VC~~g---G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
.-.|.+|+.. ++||+||.|+++||+|||.||+-..|+|.|.|-.|+-
T Consensus 281 ck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred cceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence 3568889873 5999999999999999999999999999999999974
No 10
>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=98.20 E-value=5.5e-07 Score=95.36 Aligned_cols=91 Identities=21% Similarity=0.289 Sum_probs=57.5
Q ss_pred cccccccCcccCCCCCCCcccccCcccccCCccccccccccccccccchhhhHHHhhcccceeeccCCCchhc-cccccc
Q 000290 447 AYHTRCIGVSKMYVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFLGTCNHLLVLNASSNTEQY-IRYYNP 525 (1717)
Q Consensus 447 afHl~CL~PpL~~vPeGdW~Cp~C~~~~~~p~~E~g~~~rg~EllgcD~c~r~Yh~kCerLlLe~~s~D~~~c-~rYYs~ 525 (1717)
+||++||.|||+.+|+|+|+||.|..+..+..........+...-.-...++.|-...++|+... ...++. .+||.+
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~vArIekiW~~~--G~~~~~grWy~rP 78 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQLPPTSRSACEKLLSGDLWLARIEKLWEEN--GTYWYAARWYTLP 78 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCcccccCCCcchhhhhhhccCchHHHHHHHHHhcc--CceEEEEEEEeCc
Confidence 59999999999999999999999997765433322111111111122345667778888888754 223554 555654
Q ss_pred C------chhhHHHHhcccc
Q 000290 526 I------DIPKVLQALLSSV 539 (1717)
Q Consensus 526 ~------Dl~~v~~vLygsD 539 (1717)
. +.....+.|+-+|
T Consensus 79 EET~~gr~~~~~~kEvFlS~ 98 (148)
T cd04718 79 EETHMGRQPHNLRRELYLTN 98 (148)
T ss_pred hhccCccccccccceeeecc
Confidence 3 3344466777777
No 11
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.09 E-value=5.1e-07 Score=107.75 Aligned_cols=135 Identities=20% Similarity=0.237 Sum_probs=85.9
Q ss_pred cccccChhhHHHHHHHHHHhcc-CcHHHHHHHHhhhhccccCCcCccccchhhcccccCCCCCCCCcccchhhhhhhccc
Q 000290 318 EYYSLSAGRKLMILQILCDDVL-DSEELRAEIDAREESEVGLDPDAASYGSEIARRRVHPRFSKTPDCKNREAVEFNAEN 396 (1717)
Q Consensus 318 eY~~LpVn~KLkILq~LcDl~L-~s~~fRsemD~ReEse~~le~~n~~~~~e~G~Rr~~~R~sk~sa~k~~~~~E~~~e~ 396 (1717)
+-+.++...+ ..+.+.++.. ....|...||+++.+++|+.|+|+..+.+. ...+++|++...
T Consensus 104 ~ap~~~~s~~--e~~Kfi~i~p~~~~~f~v~YdlDe~D~m~l~Ylne~~~~e~---------------vS~e~fEii~t~ 166 (669)
T COG5141 104 HAPMSEESHD--EGKKFIDIEPPRGLFFSVIYDLDEYDTMWLRYLNESAIDEN---------------VSEEAFEIIVTR 166 (669)
T ss_pred cCcccccChh--hhhhceeccCCcCccCceeecccchhHHHHHHHHHHHhhhh---------------hhHHHHHHHHHH
Confidence 3344444443 4444555555 667788899999999999999999444331 224455544421
Q ss_pred cccccCCCCCCCCCCCCCCCCCCCccccccccccccccC-----CcccccCCCCccccccccCcccCCCCCCCcccccCc
Q 000290 397 DRMKTSCKAKPLGFKGTEMDAPGVDVDGNGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 471 (1717)
Q Consensus 397 ~~~s~~~~s~~sr~~~~e~~e~~~~~d~ndd~C~VC~~g-----G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~ 471 (1717)
.+.+=.--.+ .-.....+..+.+|.-++.|.+|... ..+++||+|+.+.|..|++.+ .+|+|.|+|..|.
T Consensus 167 lE~EWf~~e~---~lp~k~vepi~~~d~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~--f~peG~WlCrkCi 241 (669)
T COG5141 167 LEKEWFFFEH---GLPDKHVEPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQ--FLPEGFWLCRKCI 241 (669)
T ss_pred HHHHHHhhhc---cCccccccccCCchhhhhhhHhccccccCCcceEEEecCcchhhhhhcccce--ecCcchhhhhhhc
Confidence 1100000000 00011112222334567899999874 379999999999999999999 8999999999998
Q ss_pred ccc
Q 000290 472 INK 474 (1717)
Q Consensus 472 ~~~ 474 (1717)
...
T Consensus 242 ~~~ 244 (669)
T COG5141 242 YGE 244 (669)
T ss_pred ccc
Confidence 754
No 12
>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 KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.05 E-value=1.1e-06 Score=114.93 Aligned_cols=54 Identities=33% Similarity=0.872 Sum_probs=46.3
Q ss_pred cccccccccccccCC-----cccccCCCCccccccccCcccCCCCCCCcccccCcccccCC
Q 000290 422 VDGNGDECRICGMDG-----TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGP 477 (1717)
Q Consensus 422 ~d~ndd~C~VC~~gG-----~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~~~p 477 (1717)
....+..|.||.++. .+|+||+|+.++|++|++.+ .+|+|.|.|..|...+.++
T Consensus 215 ~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~--~ipeg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 215 LLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIP--FIPEGQWLCRRCLQSPQRP 273 (1051)
T ss_pred ccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCC--CCCCCcEeehhhccCcCcc
Confidence 345678899999864 79999999999999999976 8999999999999866544
No 14
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.93 E-value=3.6e-06 Score=104.70 Aligned_cols=47 Identities=34% Similarity=0.944 Sum_probs=41.7
Q ss_pred cccccccccC---CcccccCCCCcc-ccccccCcccCCCCCCCcccccCcc
Q 000290 426 GDECRICGMD---GTLLCCDGCPSA-YHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 426 dd~C~VC~~g---G~LLcCD~Cp~a-fHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
...|.+|... ..||+||+|+.+ ||++||+|++-++|-+.|||+.|..
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 3458888775 489999999999 9999999999999999999999964
No 15
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.87 E-value=3.1e-06 Score=73.96 Aligned_cols=45 Identities=42% Similarity=1.224 Sum_probs=38.7
Q ss_pred ccccccc---CCcccccCCCCccccccccCcccC--CCCCCCcccccCcc
Q 000290 428 ECRICGM---DGTLLCCDGCPSAYHTRCIGVSKM--YVPEGSWYCPECAI 472 (1717)
Q Consensus 428 ~C~VC~~---gG~LLcCD~Cp~afHl~CL~PpL~--~vPeGdW~Cp~C~~ 472 (1717)
+|.+|+. .+.+|.||.|...||..|++|+.. .++.+.|+|+.|..
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 4788888 569999999999999999999976 55567999999963
No 16
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.68 E-value=1.6e-05 Score=101.22 Aligned_cols=54 Identities=39% Similarity=0.948 Sum_probs=48.8
Q ss_pred cccccccccccccCCcccccCCCCccccccccCcccCCCCCCCcccccCccccc
Q 000290 422 VDGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKV 475 (1717)
Q Consensus 422 ~d~ndd~C~VC~~gG~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~~ 475 (1717)
++.+...|++|+++|.+|+||.|+.+||.+|+++|+..+|.|+|.|+.|.++..
T Consensus 43 ~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 43 DDAEQEACRICADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPKN 96 (696)
T ss_pred chhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence 356678899999999999999999999999999999999999999999965544
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 KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.30 E-value=8.5e-05 Score=88.83 Aligned_cols=57 Identities=23% Similarity=0.503 Sum_probs=47.2
Q ss_pred CCCCCCeeec-cCCCCCCCcceEecCCCCccccccccccCccccCCccc----eEecCcccc
Q 000290 1358 VAHLEPVCDL-CKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVG----FKCCRCRRI 1414 (1717)
Q Consensus 1358 ~~~~~~vcCl-C~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~----Y~Cp~C~r~ 1414 (1717)
.++-...+|. |+..+..+.|||+|+.|+.|||+.||.+++.....+.. |+|+.|...
T Consensus 234 ~~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~ 295 (345)
T KOG1632|consen 234 APDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL 295 (345)
T ss_pred ccccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeec
Confidence 3555566674 88777666899999999999999999999998877777 999999653
No 19
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.30 E-value=0.00012 Score=85.12 Aligned_cols=44 Identities=36% Similarity=0.985 Sum_probs=38.4
Q ss_pred cccccccccCCcccccCC--CC-ccccccccCcccCCCCCCCcccccCcc
Q 000290 426 GDECRICGMDGTLLCCDG--CP-SAYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 426 dd~C~VC~~gG~LLcCD~--Cp-~afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
..+|. |...|.|+-||+ |+ ..||+.|++.. ..|.|.|||+.|..
T Consensus 221 yC~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~--~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 221 YCICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLK--TKPKGKWYCPRCKA 267 (274)
T ss_pred EEEec-ccccccccccCCCCCCcceEEEeccccc--cCCCCcccchhhhh
Confidence 34566 677899999998 99 99999999987 78999999999975
No 20
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.25 E-value=0.00011 Score=83.96 Aligned_cols=44 Identities=39% Similarity=0.921 Sum_probs=38.2
Q ss_pred ccccccccC---CcccccCCCCccccccccCcccCCCCCCCcccc-cCcc
Q 000290 427 DECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCP-ECAI 472 (1717)
Q Consensus 427 d~C~VC~~g---G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp-~C~~ 472 (1717)
..|.+|+++ .++++||.|+++||++|++.. .+|.|.|.|. .|..
T Consensus 315 ~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~--~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 315 ELCRICLGPVIESEHLFCDVCDRGPHTLCVGLQ--DLPRGEWICDMRCRE 362 (381)
T ss_pred HhhhccCCcccchheeccccccCCCCccccccc--cccCccchhhhHHHH
Confidence 468888886 489999999999999999976 9999999998 4654
No 21
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.24 E-value=0.0001 Score=88.24 Aligned_cols=51 Identities=20% Similarity=0.553 Sum_probs=47.6
Q ss_pred CeeeccCCCCCCCcceEecCCCCccccccc--cccCccccCCccceEecCccc
Q 000290 1363 PVCDLCKQPYNSNLMYIHCETCQRWFHADA--VELEESKLSDVVGFKCCRCRR 1413 (1717)
Q Consensus 1363 ~vcClC~kPy~~d~~MI~CD~C~~WFHg~C--VgLte~~a~~i~~Y~Cp~C~r 1413 (1717)
..+|.|.++++++.+||+|+.|.+|||++| ||+++.++..++.|+|..|..
T Consensus 60 ~~~~~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~ 112 (345)
T KOG1632|consen 60 QRYCKCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKE 112 (345)
T ss_pred hchhhcccccCchhhhhccccccccccccccccCchhhcCCccccccccccch
Confidence 358999999999889999999999999999 999999999999999999943
No 22
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.23 E-value=0.0002 Score=81.39 Aligned_cols=47 Identities=38% Similarity=1.070 Sum_probs=39.8
Q ss_pred ccccccccccccC--CcccccCC--CCc-cccccccCcccCCCCCCCcccccCcc
Q 000290 423 DGNGDECRICGMD--GTLLCCDG--CPS-AYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 423 d~ndd~C~VC~~g--G~LLcCD~--Cp~-afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
.++.-+|. |.++ |+|+-||+ |.+ .||+.|++.. ..|.|.|||+.|..
T Consensus 218 e~e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~CVGLk--~pPKG~WYC~eCk~ 269 (271)
T COG5034 218 EGEELYCF-CQQVSYGQMVACDNANCKREWFHLECVGLK--EPPKGKWYCPECKK 269 (271)
T ss_pred cCceeEEE-ecccccccceecCCCCCchhheeccccccC--CCCCCcEeCHHhHh
Confidence 45556776 7775 79999996 988 8999999976 89999999999974
No 23
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.16 E-value=0.0015 Score=79.36 Aligned_cols=45 Identities=33% Similarity=0.824 Sum_probs=39.5
Q ss_pred ccccccccCC---cccccCCCCccccccccCcccCCCCCC----CcccccCc
Q 000290 427 DECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEG----SWYCPECA 471 (1717)
Q Consensus 427 d~C~VC~~gG---~LLcCD~Cp~afHl~CL~PpL~~vPeG----dW~Cp~C~ 471 (1717)
--|.||.+.. .|+.||.|...||+-||.|||+.+|.- -|+|.+|-
T Consensus 545 ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 545 YSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred eeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 4599998853 678899999999999999999999985 49999994
No 24
>PF15612 WHIM1: WSTF, HB1, Itc1p, MBD9 motif 1; PDB: 2Y9Z_B 2Y9Y_B.
Probab=97.16 E-value=0.00033 Score=61.68 Aligned_cols=46 Identities=46% Similarity=0.755 Sum_probs=38.0
Q ss_pred hhhhhhccccccccChhhHHHHHHHHHHhccCcHHHHHHHHhhhhc
Q 000290 309 GFYDEVSVREYYSLSAGRKLMILQILCDDVLDSEELRAEIDAREES 354 (1717)
Q Consensus 309 ~il~~Llr~eY~~LpVn~KLkILq~LcDl~L~s~~fRsemD~ReEs 354 (1717)
.....+...+|+.|++..|+.||++|||.++++..||++|+.++|+
T Consensus 4 ~~~~~l~~~~y~~L~~~~kl~iL~~L~~~~l~s~~vr~~i~~~~e~ 49 (50)
T PF15612_consen 4 GLAPPLETGEYYELSPEEKLEILRALCDQLLSSSSVRNEIEEREEE 49 (50)
T ss_dssp GG-CCCCCSTCCCS-HHHHHHHHHHHHHHHCC-CCHHHHHHHHHT-
T ss_pred hhhHHHHcCCcccCCHHHHHHHHHHHHHHHcCcHHHHHHHHHhhcc
Confidence 3455567889999999999999999999999999999999988764
No 25
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.95 E-value=0.0002 Score=89.05 Aligned_cols=44 Identities=39% Similarity=1.105 Sum_probs=39.5
Q ss_pred ccccccccC-----CcccccCC--CCccccccccCcccCCCCCCCcccccCcc
Q 000290 427 DECRICGMD-----GTLLCCDG--CPSAYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 427 d~C~VC~~g-----G~LLcCD~--Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
.-|.||-|. .-|+.||+ |.-+.|+.|+++. .||.|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv--qVPtGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV--QVPTGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeE--ecCCCchhhhhhhh
Confidence 469999984 37999996 9999999999998 99999999999974
No 26
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=96.92 E-value=0.00031 Score=87.71 Aligned_cols=45 Identities=36% Similarity=0.965 Sum_probs=39.7
Q ss_pred ccccccccCC---cccccCCCCccccccccCcccCCCCCCCcccccCc
Q 000290 427 DECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 471 (1717)
Q Consensus 427 d~C~VC~~gG---~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~ 471 (1717)
-.|..|+.+| .+++|+.|+.+||.+|..|+++.||.|.|+|+.|.
T Consensus 69 rvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~ 116 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCT 116 (694)
T ss_pred eeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHH
Confidence 3566677544 89999999999999999999999999999999994
No 27
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.59 E-value=0.00075 Score=84.96 Aligned_cols=47 Identities=34% Similarity=0.921 Sum_probs=41.0
Q ss_pred ccccccccccC-----CcccccCCCCccccccccCcccCCCCCCCcccccCccc
Q 000290 425 NGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAIN 473 (1717)
Q Consensus 425 ndd~C~VC~~g-----G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~ 473 (1717)
++-.|.||..+ .+|++||.|....|+.|+++- .+|+|.|.|..|...
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIl--e~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGIL--EVPEGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhcee--ecCCCCeeehhcccc
Confidence 55678888775 499999999999999999987 899999999999653
No 28
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.46 E-value=0.00068 Score=92.65 Aligned_cols=50 Identities=32% Similarity=0.855 Sum_probs=44.6
Q ss_pred ccccccccccCC---cccccCCCCccccccccCcccCCCCCCCcccccCcccc
Q 000290 425 NGDECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 474 (1717)
Q Consensus 425 ndd~C~VC~~gG---~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~ 474 (1717)
....|.+|...+ .+++||.|..+||++|+.|.+..+|.|+|+||.|+...
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 446799998854 78999999999999999999999999999999998644
No 29
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=96.35 E-value=0.0043 Score=56.49 Aligned_cols=41 Identities=32% Similarity=0.513 Sum_probs=32.4
Q ss_pred ceeecceeeeecCC--ceeEeEEEEEe--cceEEEEccCCCcccc
Q 000290 41 IALVGRYVLKEFES--GIFLGKIVYYE--SGLYRVDYEDGDCEDL 81 (1717)
Q Consensus 41 ~~lvGR~V~k~f~~--~~~~GkV~~yd--~g~y~VvYEDGd~Edl 81 (1717)
++-+|+.|.=..+| -+|-|+|.+|| ...|.|.|+||+..+|
T Consensus 5 k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 5 KFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp SS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred cccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEe
Confidence 35689999999999 77899999999 8999999999998666
No 30
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=96.34 E-value=0.0016 Score=79.88 Aligned_cols=50 Identities=22% Similarity=0.594 Sum_probs=36.5
Q ss_pred eeeccCCCCCCCcceEecCCCCcccccccccc--CccccCC-ccceEecCcccc
Q 000290 1364 VCDLCKQPYNSNLMYIHCETCQRWFHADAVEL--EESKLSD-VVGFKCCRCRRI 1414 (1717)
Q Consensus 1364 vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgL--te~~a~~-i~~Y~Cp~C~r~ 1414 (1717)
.||-|++|...+ -||+|+.|..|||-.|..- +.+.+.+ --.|+|..|.+.
T Consensus 172 ~vC~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 172 SVCYCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred eeeecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 444455666556 7999999999999999974 4444433 347999999765
No 31
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=96.01 E-value=0.0052 Score=79.08 Aligned_cols=83 Identities=23% Similarity=0.345 Sum_probs=64.6
Q ss_pred CCCccccccccCcccCCCCCCCcccccCcccccCCcc----------ccc-cccccccccccchhhhHHHhhcccceeec
Q 000290 443 GCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGPIV----------TIG-TSLRGAELFGIDLYERVFLGTCNHLLVLN 511 (1717)
Q Consensus 443 ~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~~~p~~----------E~g-~~~rg~EllgcD~c~r~Yh~kCerLlLe~ 511 (1717)
.|+++||..|+.|.+..-|+++|.|+.|.....+.+. +.. -+..+++++.||.|...||..|....+..
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~ 80 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGELLWCDTCPASFHASCLGPPLTP 80 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCc
Confidence 4999999999999999889999999999754433211 111 15677889999999999999999888877
Q ss_pred cCCCchhccccccc
Q 000290 512 ASSNTEQYIRYYNP 525 (1717)
Q Consensus 512 ~s~D~~~c~rYYs~ 525 (1717)
.++..|.|.+...+
T Consensus 81 ~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 81 QPNGEFICPRCFCP 94 (696)
T ss_pred CCccceeeeeeccC
Confidence 76655778777443
No 32
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=95.36 E-value=0.01 Score=79.36 Aligned_cols=151 Identities=16% Similarity=0.287 Sum_probs=96.5
Q ss_pred cccccccccCC--cccccCCCCccccccccCcccCCCCCCCcccccCcccccCCccccccccccccccccchhhhHHH--
Q 000290 426 GDECRICGMDG--TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFL-- 501 (1717)
Q Consensus 426 dd~C~VC~~gG--~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~~~p~~E~g~~~rg~EllgcD~c~r~Yh-- 501 (1717)
...|..|..+. .++.|++|...||.+|..+++..+|+|+|.|+.|.........+.-+-..+..-+.....+ .|+
T Consensus 155 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gf~~~~~~yt~~~f~-~~~~~ 233 (904)
T KOG1246|consen 155 YPQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTPESKPNYKFGFEQGSREYTLPKFE-EYADN 233 (904)
T ss_pred chhhhccccCCCccceecccccCcccccccCCCCCcCCcCcccCCcccccccCCcccccCcCCCCCccccchhh-hHhhh
Confidence 35689999876 2339999999999999999999999999999999865332111110000001011111111 111
Q ss_pred hhcccceeeccCCCc--hhcccccccCch-hhHHHHhccccccccchhhHH-----H-----HHHHHhcCCcCcCCcccc
Q 000290 502 GTCNHLLVLNASSNT--EQYIRYYNPIDI-PKVLQALLSSVQHVSLYLGIC-----K-----AILHYWDIPESVVPFMGM 568 (1717)
Q Consensus 502 ~kCerLlLe~~s~D~--~~c~rYYs~~Dl-~~v~~vLygsDiH~~~y~~I~-----k-----AI~~YW~hplNl~~l~~~ 568 (1717)
++..+........+. .++..||..+.- ..-..++|++|++...++... + .-.+|-+.++|+++.+..
T Consensus 234 ~~~~~~~~~~~~~~~~~~vE~e~w~~v~~~~~~~~~~~g~d~~~~~~~s~~~~~~~~~~~~~~~~~y~~s~wnL~~i~~~ 313 (904)
T KOG1246|consen 234 FKKDYFPKSKNSPDSTEDVEKEFWRLVASNLESVEVLYGADLSTKEFGSGFPKSASGPLLGSEAEKYSNSGWNLNNIPRL 313 (904)
T ss_pred hhccccccccCCCCchHHHHHHHHHhhcccccceeeeeccchhhccccccccccCCCCCCCcchhhhccCcccccccccC
Confidence 122222222222222 578899996533 333667999999988777665 2 225999999999999999
Q ss_pred ccccccccc
Q 000290 569 ETNTINAKA 577 (1717)
Q Consensus 569 E~sl~~~~~ 577 (1717)
++|+...++
T Consensus 314 ~~svl~~~~ 322 (904)
T KOG1246|consen 314 EGSVLSHID 322 (904)
T ss_pred Ccccccccc
Confidence 999977654
No 33
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=94.99 E-value=0.0055 Score=51.42 Aligned_cols=34 Identities=50% Similarity=1.165 Sum_probs=20.1
Q ss_pred CcccccCCCCccccccccCcccCCCCCC-CcccccCc
Q 000290 436 GTLLCCDGCPSAYHTRCIGVSKMYVPEG-SWYCPECA 471 (1717)
Q Consensus 436 G~LLcCD~Cp~afHl~CL~PpL~~vPeG-dW~Cp~C~ 471 (1717)
..||.|++|...+|..|++.. .+|++ +|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~--~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVS--EVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-S--S--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcc--cCCCCCcEECCcCC
Confidence 358999999999999999998 66776 89999884
No 34
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=94.91 E-value=0.0087 Score=75.44 Aligned_cols=94 Identities=20% Similarity=0.428 Sum_probs=69.2
Q ss_pred ccccccccccCC-----cccccCCCCccccccccCcccCCCC-CCCcccccCcc-cccCCccccccccccccccccchhh
Q 000290 425 NGDECRICGMDG-----TLLCCDGCPSAYHTRCIGVSKMYVP-EGSWYCPECAI-NKVGPIVTIGTSLRGAELFGIDLYE 497 (1717)
Q Consensus 425 ndd~C~VC~~gG-----~LLcCD~Cp~afHl~CL~PpL~~vP-eGdW~Cp~C~~-~~~~p~~E~g~~~rg~EllgcD~c~ 497 (1717)
....|.+|+..| .|+-|..|..-||-+|+...+...- .+-|.|+.|+. +.++.. -.-..++-|+.|+
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~------gD~~kf~~Ck~cD 90 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTT------GDPKKFLLCKRCD 90 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeecccc------CCccccccccccc
Confidence 456788888754 7999999999999999996553331 23499999964 222211 1123456799999
Q ss_pred hHHHhhcccceeeccCCCchhcccccc
Q 000290 498 RVFLGTCNHLLVLNASSNTEQYIRYYN 524 (1717)
Q Consensus 498 r~Yh~kCerLlLe~~s~D~~~c~rYYs 524 (1717)
-.||..|.++...+.+...|+|.+...
T Consensus 91 vsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 91 VSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred ccccccccCCccccccCcccccHHHHh
Confidence 999999999999888888888876665
No 35
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.66 E-value=0.0079 Score=69.39 Aligned_cols=88 Identities=17% Similarity=0.293 Sum_probs=63.9
Q ss_pred ccccccccC---------CcccccCCCCccccccccCcccC---CCCCCCcccccCcc-ccc-CCccccccccccccccc
Q 000290 427 DECRICGMD---------GTLLCCDGCPSAYHTRCIGVSKM---YVPEGSWYCPECAI-NKV-GPIVTIGTSLRGAELFG 492 (1717)
Q Consensus 427 d~C~VC~~g---------G~LLcCD~Cp~afHl~CL~PpL~---~vPeGdW~Cp~C~~-~~~-~p~~E~g~~~rg~Ellg 492 (1717)
..|.+|-++ ..+++|..|..++|-+|+..+.. .+..-.|.|..|.. ..+ +|.. ..|++=
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~-------E~E~~F 331 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVI-------ESEHLF 331 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCccc-------chheec
Confidence 458888774 27999999999999999997642 23345899999953 222 2332 345677
Q ss_pred cchhhhHHHhhcccceeeccCCCchhccccc
Q 000290 493 IDLYERVFLGTCNHLLVLNASSNTEQYIRYY 523 (1717)
Q Consensus 493 cD~c~r~Yh~kCerLlLe~~s~D~~~c~rYY 523 (1717)
||.|+|-||..|-.| ...+.+.|+|--|-
T Consensus 332 CD~CDRG~HT~CVGL--~~lP~G~WICD~~C 360 (381)
T KOG1512|consen 332 CDVCDRGPHTLCVGL--QDLPRGEWICDMRC 360 (381)
T ss_pred cccccCCCCcccccc--ccccCccchhhhHH
Confidence 999999999999876 34566678886443
No 36
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.34 E-value=0.013 Score=72.42 Aligned_cols=47 Identities=30% Similarity=0.723 Sum_probs=38.5
Q ss_pred cccccccCC-----cccccCCCCccccccccCcccCCC----CCCCcccccCcccc
Q 000290 428 ECRICGMDG-----TLLCCDGCPSAYHTRCIGVSKMYV----PEGSWYCPECAINK 474 (1717)
Q Consensus 428 ~C~VC~~gG-----~LLcCD~Cp~afHl~CL~PpL~~v----PeGdW~Cp~C~~~~ 474 (1717)
.|.||..|+ .||.|++|...||..|+.|+.+.. |...|||..|...+
T Consensus 170 qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 170 QCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred eeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 399998654 999999999999999999986432 45679999997643
No 37
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=94.21 E-value=0.021 Score=67.01 Aligned_cols=27 Identities=30% Similarity=0.845 Sum_probs=24.4
Q ss_pred CeeeccCCCCCC-----CcceEecCCCCcccc
Q 000290 1363 PVCDLCKQPYNS-----NLMYIHCETCQRWFH 1389 (1717)
Q Consensus 1363 ~vcClC~kPy~~-----d~~MI~CD~C~~WFH 1389 (1717)
-.||.|..||++ +..|+||..|++|||
T Consensus 128 G~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFH 159 (345)
T KOG2752|consen 128 GLFCKCDTPYPDPVRTEEGEMLQCVICEDWFH 159 (345)
T ss_pred ceeEEecCCCCCccccccceeeeEEeccchhc
Confidence 489999999975 567999999999999
No 38
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=93.83 E-value=0.015 Score=66.90 Aligned_cols=79 Identities=18% Similarity=0.331 Sum_probs=60.5
Q ss_pred CcccccCCCCccccccccCccc---CCCCCCCcccccCcccccCCccccccccccccccccchhhhHHHhhcccceeecc
Q 000290 436 GTLLCCDGCPSAYHTRCIGVSK---MYVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFLGTCNHLLVLNA 512 (1717)
Q Consensus 436 G~LLcCD~Cp~afHl~CL~PpL---~~vPeGdW~Cp~C~~~~~~p~~E~g~~~rg~EllgcD~c~r~Yh~kCerLlLe~~ 512 (1717)
.+|+-|..|.++=|-.||.-.. ..|-.-.|+|-+|..-..-.+.+. ..+++=||-|+|-||-.|..+.+..-
T Consensus 244 eelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsen-----ddqllfcddcdrgyhmyclsppm~ep 318 (336)
T KOG1244|consen 244 EELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEN-----DDQLLFCDDCDRGYHMYCLSPPMVEP 318 (336)
T ss_pred hhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCC-----CceeEeecccCCceeeEecCCCcCCC
Confidence 4899999999999999998543 234456899999975332222222 25677899999999999999988877
Q ss_pred CCCchhc
Q 000290 513 SSNTEQY 519 (1717)
Q Consensus 513 s~D~~~c 519 (1717)
+.++|.|
T Consensus 319 pegswsc 325 (336)
T KOG1244|consen 319 PEGSWSC 325 (336)
T ss_pred CCCchhH
Confidence 7778876
No 39
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=92.60 E-value=0.067 Score=66.99 Aligned_cols=57 Identities=19% Similarity=0.230 Sum_probs=47.0
Q ss_pred CCCeeeccCCCCCCCcceEecCCCCccccccccccCccccCCccceEecCccccCCCCC
Q 000290 1361 LEPVCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCRRIGGPEC 1419 (1717)
Q Consensus 1361 ~~~vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~~~P~c 1419 (1717)
....-|+|+.-++.+.+||+|+.|..|-|.-|+|+-.... .+.|.|..|.......+
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~~~~ 140 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNKEVE 140 (508)
T ss_pred CcccccccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccccccch
Confidence 3557799998776578999999999999999999976654 56899999988765544
No 40
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=91.50 E-value=0.22 Score=44.47 Aligned_cols=48 Identities=27% Similarity=0.440 Sum_probs=41.6
Q ss_pred eeecceeeeec-CCceeEeEEEEEec-ceEEEEccC-CCccccChHHHHHH
Q 000290 42 ALVGRYVLKEF-ESGIFLGKIVYYES-GLYRVDYED-GDCEDLDSSELRQF 89 (1717)
Q Consensus 42 ~lvGR~V~k~f-~~~~~~GkV~~yd~-g~y~VvYED-Gd~Edl~~~el~~~ 89 (1717)
+-+|-.|.-.| .|..|=|+|.+++. +.|.|.|.| |+.|.+...+|+.+
T Consensus 3 ~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l 53 (57)
T smart00333 3 FKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPL 53 (57)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHeecC
Confidence 34677777777 66999999999996 999999999 99999999888765
No 41
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=89.00 E-value=0.1 Score=43.95 Aligned_cols=34 Identities=21% Similarity=0.497 Sum_probs=19.6
Q ss_pred ceEecCCCCccccccccccCccccCCccceEecCcc
Q 000290 1377 MYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCR 1412 (1717)
Q Consensus 1377 ~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~ 1412 (1717)
.||.|+.|.-.+|..|.|+...... ..|+|-.|+
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred ceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 5899999999999999999877554 249999884
No 42
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.64 E-value=0.3 Score=62.97 Aligned_cols=53 Identities=21% Similarity=0.562 Sum_probs=41.4
Q ss_pred CCCCeeeccCCCCCCCcceEecCCCCcc-ccccccccCccccCCccceEecCcccc
Q 000290 1360 HLEPVCDLCKQPYNSNLMYIHCETCQRW-FHADAVELEESKLSDVVGFKCCRCRRI 1414 (1717)
Q Consensus 1360 ~~~~vcClC~kPy~~d~~MI~CD~C~~W-FHg~CVgLte~~a~~i~~Y~Cp~C~r~ 1414 (1717)
++...|=||..+. +...||.||.|++= ||..|+..+..++. +..|+|+.|.-.
T Consensus 213 ~E~~~C~IC~~~D-pEdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVHD-PEDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccCC-hHHhheeecccccceeeccccCccccccc-ccceecCcchhh
Confidence 3445556899765 45689999999987 99999999877664 457999999654
No 43
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=83.93 E-value=0.86 Score=56.60 Aligned_cols=53 Identities=23% Similarity=0.414 Sum_probs=44.0
Q ss_pred ccccccccccccccccccccccccccccccccccccC-C-cCCCCCccceecccc
Q 000290 1201 KIEKCACASCQIDVLLGNAVKCGTCQGYCHEGCTSSS-M-HMNSGVEPMIVCNRC 1253 (1717)
Q Consensus 1201 ~le~~~C~~C~kdV~~~~aVtC~~Cqg~fHk~C~~~S-~-~~~~~~~~~y~C~rC 1253 (1717)
+-..|+|..|.|.---.-.+.|-.|.-.||-.|+.-- . .+.....+.|.|.-|
T Consensus 541 ~a~~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 541 KAMNYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred cccceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccc
Confidence 3458999999998888889999999999999999444 2 355556899999999
No 44
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=83.48 E-value=1.7 Score=48.05 Aligned_cols=50 Identities=26% Similarity=0.531 Sum_probs=38.3
Q ss_pred cccc---ccccccccccccccccccccccccc-cC-----CcCCCCCccceecccccCc
Q 000290 1207 CASC---QIDVLLGNAVKCGTCQGYCHEGCTS-SS-----MHMNSGVEPMIVCNRCYLP 1256 (1717)
Q Consensus 1207 C~~C---~kdV~~~~aVtC~~Cqg~fHk~C~~-~S-----~~~~~~~~~~y~C~rCl~~ 1256 (1717)
|..| ..+-..+..|.||-|-.-||+.|.. +| ...-+...|.+-|.+|+-.
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~ 60 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI 60 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence 6666 4566688999999999999999992 22 2355677889999999543
No 45
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=82.59 E-value=0.69 Score=59.10 Aligned_cols=47 Identities=32% Similarity=0.822 Sum_probs=40.0
Q ss_pred cccccccccCCcccccCCCCccccccccCcccC-CCCCCCcccccCcc
Q 000290 426 GDECRICGMDGTLLCCDGCPSAYHTRCIGVSKM-YVPEGSWYCPECAI 472 (1717)
Q Consensus 426 dd~C~VC~~gG~LLcCD~Cp~afHl~CL~PpL~-~vPeGdW~Cp~C~~ 472 (1717)
-+.|.+|..+|.++||+.|+.+||+.|.++++. ..+.+.|.|..|..
T Consensus 47 ~ts~~~~~~~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSGGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhcCCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 567999999999999999999999999999875 22335788888865
No 46
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=80.55 E-value=2.5 Score=38.64 Aligned_cols=49 Identities=24% Similarity=0.125 Sum_probs=41.5
Q ss_pred eeecceeeeec--CCceeEeEEEEEec-ceEEEEccC---CCccccChHHHHHHh
Q 000290 42 ALVGRYVLKEF--ESGIFLGKIVYYES-GLYRVDYED---GDCEDLDSSELRQFL 90 (1717)
Q Consensus 42 ~lvGR~V~k~f--~~~~~~GkV~~yd~-g~y~VvYED---Gd~Edl~~~el~~~l 90 (1717)
+-+|..|-=.| .+.-|-|+|++++. +-|.|.|.| |+.|.+++..||.+.
T Consensus 3 ~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 3 FKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred cCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 45788888888 88999999999994 889999998 567888888887654
No 47
>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=80.42 E-value=1.3 Score=55.14 Aligned_cols=51 Identities=22% Similarity=0.671 Sum_probs=35.5
Q ss_pred eeeccCCCCC---CCcceEecCCCCcccccccc--------ccCcccc-C-CccceEecCccccC
Q 000290 1364 VCDLCKQPYN---SNLMYIHCETCQRWFHADAV--------ELEESKL-S-DVVGFKCCRCRRIG 1415 (1717)
Q Consensus 1364 vcClC~kPy~---~d~~MI~CD~C~~WFHg~CV--------gLte~~a-~-~i~~Y~Cp~C~r~~ 1415 (1717)
.||+|.+ |+ +.-.||.||.|.-|-|.+|. |.+.... . ....|+|-.|-...
T Consensus 130 ~C~iC~k-fD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 130 MCCICSK-FDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CccccCC-cccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 6889988 43 34569999999999999995 2222211 1 12369999997664
No 48
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=79.35 E-value=0.88 Score=63.70 Aligned_cols=56 Identities=18% Similarity=0.482 Sum_probs=45.5
Q ss_pred CCCCCeeeccCCCCCCCcceEecCCCCccccccccccCccccCCccceEecCccccCC
Q 000290 1359 AHLEPVCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCRRIGG 1416 (1717)
Q Consensus 1359 ~~~~~vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~~~ 1416 (1717)
......|-+|++-.. +-.|+.|+.|..|||..|+-.....+.. ..|.||.|+..++
T Consensus 1105 s~~~~~c~~cr~k~~-~~~m~lc~~c~~~~h~~C~rp~~~~~~~-~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQ-DEKMLLCDECLSGFHLFCLRPALSSVPP-GDWMCPSCRKEHR 1160 (1404)
T ss_pred ccchhhhhhhhhccc-chhhhhhHhhhhhHHHHhhhhhhccCCc-CCccCCccchhhh
Confidence 445678889997654 3479999999999999999988777754 4599999988775
No 49
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=78.91 E-value=2.8 Score=44.29 Aligned_cols=40 Identities=25% Similarity=0.487 Sum_probs=30.2
Q ss_pred eeecceeeeecCC-ce-eEeEEEEEe-cceEEEEccCCCcccc
Q 000290 42 ALVGRYVLKEFES-GI-FLGKIVYYE-SGLYRVDYEDGDCEDL 81 (1717)
Q Consensus 42 ~lvGR~V~k~f~~-~~-~~GkV~~yd-~g~y~VvYEDGd~Edl 81 (1717)
.|||..|.-...+ ++ |.|+|+..- .+-|+|.||||+.-++
T Consensus 3 ~~iG~rV~AkWS~n~yyY~G~I~~~~~~~kykv~FdDG~~~~v 45 (122)
T PF09038_consen 3 SFIGLRVFAKWSDNGYYYPGKITSDKGKNKYKVLFDDGYECRV 45 (122)
T ss_dssp -STT-EEEEESSTTSEEEEEEEEEEETTTEEEEEETTS-EEEE
T ss_pred cccccEEEEEEccCCcccCceEeecCCCCeEEEEecCCcccee
Confidence 5899998877776 67 579999965 9999999999986433
No 50
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=77.53 E-value=2.2 Score=58.15 Aligned_cols=55 Identities=16% Similarity=0.388 Sum_probs=41.5
Q ss_pred CCCCCCCeeeccCCCCCC-CcceEecCCCCccccccccccCccccCCccceEecCcccc
Q 000290 1357 SVAHLEPVCDLCKQPYNS-NLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCRRI 1414 (1717)
Q Consensus 1357 ~~~~~~~vcClC~kPy~~-d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~ 1414 (1717)
...++..+||+|...... .-+.++||.|+-=+|.+|+|+..- ....|.|-+|-..
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~i---peg~WlCr~Cl~s 269 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFI---PEGQWLCRRCLQS 269 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCC---CCCcEeehhhccC
Confidence 336777899999975421 236899999999999999996533 2347999999554
No 51
>PLN00163 histone H4; Provisional
Probab=77.42 E-value=1.7 Score=40.56 Aligned_cols=35 Identities=34% Similarity=0.619 Sum_probs=27.1
Q ss_pred cchhhhhhcc--cChHHHHHHHHHhcCcccccccccC
Q 000290 999 KSTKLISKKA--ILPHTIIRNAARRGGLRKISGVNYT 1033 (1717)
Q Consensus 999 ~lsr~i~~~~--~Lp~s~v~kaarqgG~~ki~gi~y~ 1033 (1717)
|--|+++.-. =+.+.+|++-||.||+++|+|.+|.
T Consensus 17 KRhrk~lrd~i~gItKpaIrRLARRgGVKRIs~~iY~ 53 (59)
T PLN00163 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYE 53 (59)
T ss_pred hhHHHHHHHhhcccchHHHHHHHHhcCceeecchhhH
Confidence 3444554422 2789999999999999999999996
No 52
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=76.99 E-value=1.6 Score=56.61 Aligned_cols=56 Identities=21% Similarity=0.517 Sum_probs=42.8
Q ss_pred CCCeeeccCCCCCC-CcceEecCCCCccccccccccCccccCCccceEecCccccCCCCC
Q 000290 1361 LEPVCDLCKQPYNS-NLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCRRIGGPEC 1419 (1717)
Q Consensus 1361 ~~~vcClC~kPy~~-d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~~~P~c 1419 (1717)
+..+|=+|+-|... .--||.||.|+-=.|-.|.||.+..- .-|.|-.|.-..-|.|
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~~ppC 326 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGIEPPC 326 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccCCCCe
Confidence 33456689988542 22499999999999999999987654 4699999977655655
No 53
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=76.29 E-value=3.6 Score=35.53 Aligned_cols=41 Identities=27% Similarity=0.371 Sum_probs=34.3
Q ss_pred eeeeecC--CceeEeEEEEEe-cceEEEEccC-CCccccChHHHH
Q 000290 47 YVLKEFE--SGIFLGKIVYYE-SGLYRVDYED-GDCEDLDSSELR 87 (1717)
Q Consensus 47 ~V~k~f~--~~~~~GkV~~yd-~g~y~VvYED-Gd~Edl~~~el~ 87 (1717)
.+.-.|. +..|=|+|.+.+ .+.|.|.|.| |..|.+...+|+
T Consensus 3 ~c~a~~~~d~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l~ 47 (48)
T cd04508 3 LCLAKYSDDGKWYRAKITSILSDGKVEVFFVDYGNTEVVPLSDLR 47 (48)
T ss_pred EEEEEECCCCeEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHHcC
Confidence 3444454 589999999999 9999999999 999999888765
No 54
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=68.02 E-value=2.1 Score=47.43 Aligned_cols=44 Identities=36% Similarity=0.977 Sum_probs=32.8
Q ss_pred ccccccc------CCcccccCCCCccccccccCccc------CCCCCCC--cccccCc
Q 000290 428 ECRICGM------DGTLLCCDGCPSAYHTRCIGVSK------MYVPEGS--WYCPECA 471 (1717)
Q Consensus 428 ~C~VC~~------gG~LLcCD~Cp~afHl~CL~PpL------~~vPeGd--W~Cp~C~ 471 (1717)
.|.+|+. -|.|+.|-+|..+||..||++-. +.|-+++ -+|..|.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Ci 58 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCI 58 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhc
Confidence 3778853 36999999999999999999864 2333333 4688885
No 55
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=66.31 E-value=2.9 Score=53.96 Aligned_cols=63 Identities=19% Similarity=0.378 Sum_probs=46.2
Q ss_pred CCeeeccCCCCC-CCcceEecCC--CCccccccccccCccccCCccceEecCcccc------CCCCCCCCCchhh
Q 000290 1362 EPVCDLCKQPYN-SNLMYIHCET--CQRWFHADAVELEESKLSDVVGFKCCRCRRI------GGPECPYMDPELK 1427 (1717)
Q Consensus 1362 ~~vcClC~kPy~-~d~~MI~CD~--C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~------~~P~cp~~~~~~k 1427 (1717)
.--||+|-.--. .+-..|-||. |.-=+|-.|.||-.... .-|+|-+|... +=..|||.|.-+|
T Consensus 5 VGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCesqeraarvrCeLCP~kdGALK 76 (900)
T KOG0956|consen 5 VGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCESQERAARVRCELCPHKDGALK 76 (900)
T ss_pred ccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---CchhhhhhhhhhhhccceeecccCccccee
Confidence 346999964110 1224789995 99999999999975543 46999999655 3367899998888
No 56
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=64.77 E-value=5.2 Score=45.40 Aligned_cols=58 Identities=22% Similarity=0.712 Sum_probs=42.0
Q ss_pred cccchhhhhhhccccccccccccccc-ccc----cccccccccccccccccccccCCcCCCCCccceecccccCccc
Q 000290 1187 SRKDLFSYLVCRRDKIEKCACASCQI-DVL----LGNAVKCGTCQGYCHEGCTSSSMHMNSGVEPMIVCNRCYLPRA 1258 (1717)
Q Consensus 1187 ~~~~~f~yL~~k~~~le~~~C~~C~k-dV~----~~~aVtC~~Cqg~fHk~C~~~S~~~~~~~~~~y~C~rCl~~k~ 1258 (1717)
...-|.+=-.+++. ...|..|+. +++ ...+++|..|...||+.|.... .|++|.+-+.
T Consensus 138 ~~~HV~~C~lC~~k---GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~-----------~CpkC~R~~~ 200 (202)
T PF13901_consen 138 AEKHVYSCELCQQK---GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK-----------SCPKCARRQK 200 (202)
T ss_pred HHHHHHHhHHHHhC---CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC-----------CCCCcHhHhc
Confidence 33344455567776 678999975 444 4589999999999999999431 3999977543
No 57
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=56.39 E-value=4.2 Score=35.17 Aligned_cols=28 Identities=25% Similarity=0.694 Sum_probs=25.4
Q ss_pred ccccCCCCC---CCCccceeccceEeccCCC
Q 000290 1668 CRICPDIEP---APNLSCQICGLVIHSQCSP 1695 (1717)
Q Consensus 1668 c~~c~~~~p---~p~l~c~~c~~~ih~~csp 1695 (1717)
|..|...-+ .+.++|..|++.+|..|..
T Consensus 14 C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~ 44 (50)
T cd00029 14 CDVCRKSIWGLFKQGLRCSWCKVKCHKKCAD 44 (50)
T ss_pred hhhcchhhhccccceeEcCCCCCchhhhhhc
Confidence 999988777 5999999999999999987
No 58
>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=55.58 E-value=2.1 Score=36.80 Aligned_cols=43 Identities=19% Similarity=0.502 Sum_probs=31.1
Q ss_pred eeeccCCCCCCCcceEecCCCCccccccccccCccccCCccceEecCcc
Q 000290 1364 VCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCR 1412 (1717)
Q Consensus 1364 vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~ 1412 (1717)
.|.||...+..+..++... |+-.||.+|+.-=... .+.||.||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence 4779999886666677777 9999999998643322 35888885
No 59
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=55.48 E-value=5.7 Score=36.86 Aligned_cols=35 Identities=26% Similarity=0.602 Sum_probs=30.6
Q ss_pred ccccccccccccc-cccccccccccccccccccccC
Q 000290 1203 EKCACASCQIDVL-LGNAVKCGTCQGYCHEGCTSSS 1237 (1717)
Q Consensus 1203 e~~~C~~C~kdV~-~~~aVtC~~Cqg~fHk~C~~~S 1237 (1717)
+...|..|.+.+. -.++|-|..|...||..|-..-
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 4678999999887 8999999999999999998443
No 60
>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=55.35 E-value=6.7 Score=34.86 Aligned_cols=33 Identities=27% Similarity=0.593 Sum_probs=27.6
Q ss_pred ccccccccccc--cccccccccccccccccccccc
Q 000290 1204 KCACASCQIDV--LLGNAVKCGTCQGYCHEGCTSS 1236 (1717)
Q Consensus 1204 ~~~C~~C~kdV--~~~~aVtC~~Cqg~fHk~C~~~ 1236 (1717)
.-.|.+|.+-+ .....++|..|+-.+|++|...
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 55799999999 6899999999999999999943
No 61
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=54.95 E-value=8.1 Score=45.70 Aligned_cols=50 Identities=18% Similarity=0.258 Sum_probs=37.3
Q ss_pred ceeecceeeeecCC--ceeEeEEEEEe--cceEEEEccC-CCccccChHHHHHHh
Q 000290 41 IALVGRYVLKEFES--GIFLGKIVYYE--SGLYRVDYED-GDCEDLDSSELRQFL 90 (1717)
Q Consensus 41 ~~lvGR~V~k~f~~--~~~~GkV~~yd--~g~y~VvYED-Gd~Edl~~~el~~~l 90 (1717)
.|=||-..+-.+.+ .+|-++|.+-| .|-+.|+|.+ |..|++.+.+|+.+-
T Consensus 68 ~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 68 KWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSE 122 (264)
T ss_dssp ---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT
T ss_pred CCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhcccc
Confidence 49999999999954 89999999999 5788899976 778888777776653
No 62
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=53.98 E-value=7.1 Score=39.09 Aligned_cols=40 Identities=30% Similarity=0.523 Sum_probs=29.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC---CCcccchhhhhhhhhh
Q 000290 1010 LPHTIIRNAARRGGLRKISGVNYT---AEMPKRSRQLVWRAAV 1049 (1717)
Q Consensus 1010 Lp~s~v~kaarqgG~~ki~gi~y~---s~~~rRsr~~~WraaV 1049 (1717)
+-+.+||+-||.||.++|.|++|- .-|--=-+.++|.|+.
T Consensus 30 itKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~ 72 (103)
T KOG3467|consen 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVT 72 (103)
T ss_pred cchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999997 1111113456777764
No 63
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.61 E-value=5.7 Score=36.85 Aligned_cols=31 Identities=29% Similarity=0.889 Sum_probs=26.6
Q ss_pred ccccccccc----CCcccccCCCCccccccccCcc
Q 000290 426 GDECRICGM----DGTLLCCDGCPSAYHTRCIGVS 456 (1717)
Q Consensus 426 dd~C~VC~~----gG~LLcCD~Cp~afHl~CL~Pp 456 (1717)
...|.+|++ +++++.|..|...||-.|....
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 357999998 5799999999999999998654
No 64
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=51.17 E-value=5.2 Score=34.23 Aligned_cols=28 Identities=25% Similarity=0.685 Sum_probs=25.0
Q ss_pred ccccCCCCCC--CCccceeccceEeccCCC
Q 000290 1668 CRICPDIEPA--PNLSCQICGLVIHSQCSP 1695 (1717)
Q Consensus 1668 c~~c~~~~p~--p~l~c~~c~~~ih~~csp 1695 (1717)
|..|.+.-+. +.+.|..|++.+|..|.+
T Consensus 14 C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~ 43 (49)
T smart00109 14 CCVCRKSIWGSFQGLRCSWCKVKCHKKCAE 43 (49)
T ss_pred ccccccccCcCCCCcCCCCCCchHHHHHHh
Confidence 9999887765 589999999999999987
No 65
>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=49.37 E-value=7.5 Score=34.56 Aligned_cols=28 Identities=32% Similarity=0.865 Sum_probs=23.7
Q ss_pred ccccCCCC---CCCCccceeccceEeccCCC
Q 000290 1668 CRICPDIE---PAPNLSCQICGLVIHSQCSP 1695 (1717)
Q Consensus 1668 c~~c~~~~---p~p~l~c~~c~~~ih~~csp 1695 (1717)
|..|...- -...+.|..|++.+|..|.+
T Consensus 14 C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 14 CDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp -TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 99999988 56789999999999999987
No 66
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=46.56 E-value=11 Score=47.86 Aligned_cols=48 Identities=27% Similarity=0.504 Sum_probs=41.3
Q ss_pred cccccccccccCCcccccCCCCccccccccCcccCCCCCCCcccccCcccc
Q 000290 424 GNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 474 (1717)
Q Consensus 424 ~ndd~C~VC~~gG~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~ 474 (1717)
.+.++|.+|.++|.+++|+.|..++|-.|... ..|.+-|.|..|....
T Consensus 87 ~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~---~~~~c~~~~~d~~~~~ 134 (463)
T KOG1081|consen 87 IEPSECFVCFKGGSLVTCKSRIQAPHRKCKPA---QLEKCSKRCTDCRAFK 134 (463)
T ss_pred CCcchhccccCCCccceeccccccccccCcCc---cCcccccCCcceeeec
Confidence 45689999999999999999999999999766 5788899999887643
No 67
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=45.76 E-value=9 Score=26.35 Aligned_cols=10 Identities=80% Similarity=1.301 Sum_probs=3.9
Q ss_pred CCCCCCCcCC
Q 000290 6 KRPRGRPRKR 15 (1717)
Q Consensus 6 ~~~~~~~~~~ 15 (1717)
.|+||||+|-
T Consensus 1 ~r~RGRP~k~ 10 (13)
T PF02178_consen 1 KRKRGRPRKN 10 (13)
T ss_dssp S--SS--TT-
T ss_pred CCcCCCCccc
Confidence 4789999874
No 68
>smart00417 H4 Histone H4.
Probab=44.53 E-value=12 Score=36.83 Aligned_cols=24 Identities=46% Similarity=0.866 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000290 1010 LPHTIIRNAARRGGLRKISGVNYT 1033 (1717)
Q Consensus 1010 Lp~s~v~kaarqgG~~ki~gi~y~ 1033 (1717)
||+..|++-||.||.++|+|-.|.
T Consensus 14 I~k~~IrRLaRr~GvkRIS~~~y~ 37 (74)
T smart00417 14 ITKPAIRRLARRGGVKRISGLIYD 37 (74)
T ss_pred CCHHHHHHHHHHcCcchhhHHHHH
Confidence 999999999999999999999997
No 69
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.97 E-value=15 Score=45.20 Aligned_cols=45 Identities=31% Similarity=0.631 Sum_probs=32.1
Q ss_pred ccccccccC---CcccccCCCCccccccccCcccCCCCCCCcccccCcccc
Q 000290 427 DECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 474 (1717)
Q Consensus 427 d~C~VC~~g---G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~~~ 474 (1717)
+.|.+|.++ |+.|-==-|.-.||..|++|.|..- .=+||.|....
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCCCCCCcC
Confidence 789999983 4333223577899999999987431 22699998743
No 70
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=40.41 E-value=17 Score=29.30 Aligned_cols=16 Identities=50% Similarity=0.856 Sum_probs=11.9
Q ss_pred CCCCCCCcCCCCCCcc
Q 000290 6 KRPRGRPRKRKRPEDE 21 (1717)
Q Consensus 6 ~~~~~~~~~~~~~~~~ 21 (1717)
+|+||||||.......
T Consensus 1 kRkRGRPrK~~~~~~~ 16 (26)
T smart00384 1 KRKRGRPRKAPKDXXX 16 (26)
T ss_pred CCCCCCCCCCCCcccc
Confidence 4889999987765543
No 71
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=40.10 E-value=5 Score=38.47 Aligned_cols=45 Identities=29% Similarity=0.701 Sum_probs=0.0
Q ss_pred ccccccccc----CCcc--cccC--CCCccccccccCcccCCCCCCC-------cccccC
Q 000290 426 GDECRICGM----DGTL--LCCD--GCPSAYHTRCIGVSKMYVPEGS-------WYCPEC 470 (1717)
Q Consensus 426 dd~C~VC~~----gG~L--LcCD--~Cp~afHl~CL~PpL~~vPeGd-------W~Cp~C 470 (1717)
+..|.||.. ++.+ +.|+ .|...||+.||--.+...+.+. +.||.|
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C 61 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYC 61 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCC
No 72
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=39.23 E-value=16 Score=38.33 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=19.7
Q ss_pred CCCCeeeccCCCCCCCcceEec
Q 000290 1360 HLEPVCDLCKQPYNSNLMYIHC 1381 (1717)
Q Consensus 1360 ~~~~vcClC~kPy~~d~~MI~C 1381 (1717)
...+..|+|..+||++..||+|
T Consensus 100 ~~~~d~~~Ce~~yn~~~~~~~c 121 (121)
T cd04714 100 QDGVDFYYCAGTYNPDTGMLKC 121 (121)
T ss_pred CcCCCEEEEeccCCCCcCcccC
Confidence 4567789999999999999999
No 73
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=39.23 E-value=18 Score=35.97 Aligned_cols=45 Identities=27% Similarity=0.683 Sum_probs=33.6
Q ss_pred ccccccccCCCCCCCCccceeccceEeccCCCCCccc---ccCCCCCc-cccccccC
Q 000290 1664 NKMQCRICPDIEPAPNLSCQICGLVIHSQCSPWPWVE---SSYMEGSW-KCGNCRDW 1716 (1717)
Q Consensus 1664 ~~~~c~~c~~~~p~p~l~c~~c~~~ih~~csp~~w~e---~~~~~~~w-~cg~cr~w 1716 (1717)
..+-|+.|... +..+|.|.+||+.. | =++ ..-..++. +|-.|.+|
T Consensus 36 ~~i~C~~ct~~-q~~El~C~~C~~~k-----~--ld~FSK~QR~~~~~a~C~~Cv~~ 84 (84)
T PF12898_consen 36 SGIRCRECTGG-QVVELTCSPCGKTK-----P--LDEFSKNQRRKPDPARCKDCVQW 84 (84)
T ss_pred CCCCCccCCCC-CcCcCEeccCCCCc-----C--HHHHhHHhhcCCCcccchhhhcC
Confidence 44679999977 99999999999864 4 444 22333445 99999988
No 74
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=38.22 E-value=17 Score=36.92 Aligned_cols=31 Identities=23% Similarity=0.591 Sum_probs=25.8
Q ss_pred CCCeeeccCCCCCCCcceEecCC--CCccccccccc
Q 000290 1361 LEPVCDLCKQPYNSNLMYIHCET--CQRWFHADAVE 1394 (1717)
Q Consensus 1361 ~~~vcClC~kPy~~d~~MI~CD~--C~~WFHg~CVg 1394 (1717)
....|.+|++.. ...|+|.. |..+||..|.-
T Consensus 54 ~~~~C~iC~~~~---G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 54 FKLKCSICGKSG---GACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred cCCcCcCCCCCC---ceeEEcCCCCCCcCCCHHHHH
Confidence 356899999873 36999998 99999999974
No 75
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=35.52 E-value=32 Score=43.70 Aligned_cols=51 Identities=6% Similarity=-0.171 Sum_probs=42.8
Q ss_pred CCCCeeeccCCCCCCCcceEecCCCCccccccccccCccccCCccceEecCcccc
Q 000290 1360 HLEPVCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESKLSDVVGFKCCRCRRI 1414 (1717)
Q Consensus 1360 ~~~~vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~a~~i~~Y~Cp~C~r~ 1414 (1717)
.....||.|++.+++...|.+|..|+.|+|..|++.+. ..+.++|..|...
T Consensus 168 ~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~~----~~~~~~~~~~s~~ 218 (464)
T KOG1886|consen 168 LRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTLN----AAASKRSQQKSEI 218 (464)
T ss_pred ccccchhcccccCCccchhhhcccCCCCCCcccccccc----ccccceecccccc
Confidence 34568999999999999999999999999999999886 3456888888443
No 76
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=35.08 E-value=30 Score=44.50 Aligned_cols=50 Identities=20% Similarity=0.290 Sum_probs=40.9
Q ss_pred cccccccccccCCcccccCCCCccccccccCcccCCCCC--CCcccccCcccc
Q 000290 424 GNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPE--GSWYCPECAINK 474 (1717)
Q Consensus 424 ~ndd~C~VC~~gG~LLcCD~Cp~afHl~CL~PpL~~vPe--GdW~Cp~C~~~~ 474 (1717)
..+-+|..|+.+|..|-|+.|-+.||..|+.|.- .++. ..|.|+.|..-+
T Consensus 58 N~d~~cfechlpg~vl~c~vc~Rs~h~~c~sp~~-q~r~~s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 58 NIDPFCFECHLPGAVLKCIVCHRSFHENCQSPDP-QKRNYSVPSDKPQPYSFK 109 (588)
T ss_pred CCCcccccccCCcceeeeehhhccccccccCcch-hhccccccccCCcccccC
Confidence 3456799999999999999999999999999874 3444 369999997533
No 77
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=33.17 E-value=22 Score=35.79 Aligned_cols=24 Identities=46% Similarity=0.804 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000290 1010 LPHTIIRNAARRGGLRKISGVNYT 1033 (1717)
Q Consensus 1010 Lp~s~v~kaarqgG~~ki~gi~y~ 1033 (1717)
||...|++-||.||.++|++-.|.
T Consensus 14 i~k~~I~RLarr~GvkRIS~d~y~ 37 (85)
T cd00076 14 ITKPAIRRLARRGGVKRISGGVYD 37 (85)
T ss_pred CCHHHHHHHHHHcCcchhhHHHHH
Confidence 999999999999999999999987
No 78
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=32.89 E-value=19 Score=43.93 Aligned_cols=23 Identities=30% Similarity=0.353 Sum_probs=15.5
Q ss_pred cccccChhhHHHHHHHHHHhccC
Q 000290 318 EYYSLSAGRKLMILQILCDDVLD 340 (1717)
Q Consensus 318 eY~~LpVn~KLkILq~LcDl~L~ 340 (1717)
+-|.++.+.|+.+|+.|...++.
T Consensus 97 ~spdlT~~qr~lAl~qL~~Dym~ 119 (389)
T COG2956 97 ESPDLTFEQRLLALQQLGRDYMA 119 (389)
T ss_pred cCCCCchHHHHHHHHHHHHHHHH
Confidence 45667777777777777765543
No 79
>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=31.98 E-value=29 Score=38.26 Aligned_cols=27 Identities=15% Similarity=0.267 Sum_probs=23.2
Q ss_pred ccccccccCccccCCccceEecCccccC
Q 000290 1388 FHADAVELEESKLSDVVGFKCCRCRRIG 1415 (1717)
Q Consensus 1388 FHg~CVgLte~~a~~i~~Y~Cp~C~r~~ 1415 (1717)
||..|+.-+...+++ ..|+||.|....
T Consensus 2 ~H~~CL~Ppl~~~P~-g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPPLKEVPE-GDWICPFCEVEK 28 (148)
T ss_pred cccccCCCCCCCCCC-CCcCCCCCcCCC
Confidence 899999998888877 569999997664
No 80
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=31.17 E-value=18 Score=35.25 Aligned_cols=34 Identities=26% Similarity=0.600 Sum_probs=20.3
Q ss_pred ceEecCC-CCccccccccccCccccC----CccceEecC
Q 000290 1377 MYIHCET-CQRWFHADAVELEESKLS----DVVGFKCCR 1410 (1717)
Q Consensus 1377 ~MI~CD~-C~~WFHg~CVgLte~~a~----~i~~Y~Cp~ 1410 (1717)
-||.|.. =+.|.|..|++|++..+- .-.+|+|..
T Consensus 29 AMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 29 AMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp -EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred eEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 3999986 668999999999987542 335799975
No 81
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=30.71 E-value=27 Score=33.69 Aligned_cols=42 Identities=26% Similarity=0.665 Sum_probs=27.4
Q ss_pred eeeccCCCCCC---------CcceEecCCCCccccccccc--cCccccCCccceEecCcc
Q 000290 1364 VCDLCKQPYNS---------NLMYIHCETCQRWFHADAVE--LEESKLSDVVGFKCCRCR 1412 (1717)
Q Consensus 1364 vcClC~kPy~~---------d~~MI~CD~C~~WFHg~CVg--Lte~~a~~i~~Y~Cp~C~ 1412 (1717)
.|.||+.++.. +...|.=..|+--||..|+. +... -.||.||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCCCC
Confidence 58899988721 23455556699999999986 3211 2888886
No 82
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=30.71 E-value=17 Score=31.01 Aligned_cols=32 Identities=22% Similarity=0.746 Sum_probs=26.5
Q ss_pred ccccccccccccc-ccccccccccccccccccc
Q 000290 1205 CACASCQIDVLLG-NAVKCGTCQGYCHEGCTSS 1236 (1717)
Q Consensus 1205 ~~C~~C~kdV~~~-~aVtC~~Cqg~fHk~C~~~ 1236 (1717)
..|.+|++-+... ..++|..|+-.+|++|...
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 4599998887743 4899999999999999843
No 83
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=30.54 E-value=30 Score=31.29 Aligned_cols=40 Identities=18% Similarity=0.526 Sum_probs=19.5
Q ss_pred ceEecCCCCccccccccccCc--cccCCccceEecCccccCCCCC
Q 000290 1377 MYIHCETCQRWFHADAVELEE--SKLSDVVGFKCCRCRRIGGPEC 1419 (1717)
Q Consensus 1377 ~MI~CD~C~~WFHg~CVgLte--~~a~~i~~Y~Cp~C~r~~~P~c 1419 (1717)
.||||+.|.+|=..- .++.. +.+. +.|+|..-.-...-.|
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~--d~W~C~~n~~~~~~sC 43 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELP--DPWYCSMNPDPPFNSC 43 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSS--TT--GGGSS-CCC-ST
T ss_pred eEEECCCCCceeeCC-hhhCcccccCC--CeEEcCCCCCCCCCCC
Confidence 589999999998775 33333 3333 3899987553333444
No 84
>PTZ00015 histone H4; Provisional
Probab=30.20 E-value=33 Score=35.70 Aligned_cols=35 Identities=40% Similarity=0.652 Sum_probs=28.5
Q ss_pred cchhhhhhccc--ChHHHHHHHHHhcCcccccccccC
Q 000290 999 KSTKLISKKAI--LPHTIIRNAARRGGLRKISGVNYT 1033 (1717)
Q Consensus 999 ~lsr~i~~~~~--Lp~s~v~kaarqgG~~ki~gi~y~ 1033 (1717)
+=.|+++.-.+ ||...|++-||.||.++|++-.|.
T Consensus 18 kr~rk~~r~~i~gI~k~~IrRLarr~GvkRIS~d~y~ 54 (102)
T PTZ00015 18 KRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYE 54 (102)
T ss_pred hhHHHHHhhcccCCCHHHHHHHHHHcCCccchHHHHH
Confidence 44555554333 899999999999999999999997
No 85
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 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 an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.91 E-value=13 Score=32.28 Aligned_cols=31 Identities=26% Similarity=0.647 Sum_probs=23.5
Q ss_pred HHHhhhccccccccccccccccccCcccccccccc
Q 000290 802 AKAFSSTASRFFWPCSERKLWEVPRERCSWCYSCK 836 (1717)
Q Consensus 802 ~Kafs~~~~~f~wps~~kk~~ev~rerCGWC~sCk 836 (1717)
-|++++-+.+|+||...+-+.++-| -|..||
T Consensus 9 ~kT~~~i~~~y~W~gm~~~V~~~ir----~C~~Cq 39 (39)
T PF09337_consen 9 NKTTAKISQRYHWPGMKKDVRRVIR----SCPQCQ 39 (39)
T ss_pred HHHHHHHHHhheecCHHHHHHHHHh----cCcccC
Confidence 4788999999999999887666544 355554
No 86
>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=28.20 E-value=21 Score=28.82 Aligned_cols=29 Identities=24% Similarity=0.700 Sum_probs=11.9
Q ss_pred eeeccCCCCCCCcceEecCCCCcccccccc
Q 000290 1364 VCDLCKQPYNSNLMYIHCETCQRWFHADAV 1393 (1717)
Q Consensus 1364 vcClC~kPy~~d~~MI~CD~C~~WFHg~CV 1393 (1717)
.|-+|+++-+. .++-.|..|+-.+|..|+
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S---EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCC-CceEECccCCCccChhcC
Confidence 35579988765 356679999999999885
No 87
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=28.06 E-value=24 Score=30.56 Aligned_cols=32 Identities=22% Similarity=0.705 Sum_probs=27.2
Q ss_pred cccccccccccc--cccccccccccccccccccc
Q 000290 1205 CACASCQIDVLL--GNAVKCGTCQGYCHEGCTSS 1236 (1717)
Q Consensus 1205 ~~C~~C~kdV~~--~~aVtC~~Cqg~fHk~C~~~ 1236 (1717)
..|.+|++-+.. ....+|..|+-.+|++|...
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 459999887764 69999999999999999943
No 88
>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=27.57 E-value=8.6 Score=33.07 Aligned_cols=41 Identities=32% Similarity=0.596 Sum_probs=26.3
Q ss_pred ccccccccC---CcccccCCCCccccccccCcccCCCCCCCcccccCc
Q 000290 427 DECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 471 (1717)
Q Consensus 427 d~C~VC~~g---G~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~ 471 (1717)
|.|.+|.+. ++.+.--.|.-.||..|+...+..- -.||.|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC----CcCCccC
Confidence 468888773 3222223399999999998876442 3888884
No 89
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=26.14 E-value=24 Score=35.59 Aligned_cols=29 Identities=24% Similarity=0.480 Sum_probs=22.2
Q ss_pred CCCccccccccCcccCCCCCCCcccccCcc
Q 000290 443 GCPSAYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 443 ~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
.|.-.||+.|+.--+..- ...=.||.|+.
T Consensus 51 ~C~H~FH~hCI~kWl~~~-~~~~~CPmCR~ 79 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQ-SSKGQCPMCRQ 79 (85)
T ss_pred cCccHHHHHHHHHHHccc-cCCCCCCCcCC
Confidence 499999999998876542 33348999985
No 90
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=25.82 E-value=53 Score=39.58 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=17.3
Q ss_pred ccccCCCCCCcccccCCccccccCC
Q 000290 1609 LLASDDGGQSDGVDASGVVFGNRED 1633 (1717)
Q Consensus 1609 ll~~dd~~~~~~~~~~~~~~~~~~~ 1633 (1717)
++.+||++ +++++..-..+-+..|
T Consensus 35 ~i~~~~~~-~~tid~~~~~~~~~~~ 58 (280)
T KOG4198|consen 35 YIQPDDDE-ARTIDVMRLLLTNSKD 58 (280)
T ss_pred cccccccc-cCccchhhhcccccCC
Confidence 36677777 9999988666655555
No 91
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=25.79 E-value=56 Score=42.17 Aligned_cols=56 Identities=23% Similarity=0.485 Sum_probs=41.2
Q ss_pred CCCCCeeeccCCCCCCCcceEecCCCCccccccccccCccc---cCC--ccceEecCcccc
Q 000290 1359 AHLEPVCDLCKQPYNSNLMYIHCETCQRWFHADAVELEESK---LSD--VVGFKCCRCRRI 1414 (1717)
Q Consensus 1359 ~~~~~vcClC~kPy~~d~~MI~CD~C~~WFHg~CVgLte~~---a~~--i~~Y~Cp~C~r~ 1414 (1717)
.......|.|....+....-+||..|-+|||.-|...++.- +.. -..|.|..|...
T Consensus 16 ~~~~~~~~y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 16 KMKQATVCYCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred cccCccccccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCc
Confidence 34567899999988888889999999999998665543321 111 236999999665
No 92
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=24.02 E-value=33 Score=34.85 Aligned_cols=31 Identities=32% Similarity=0.864 Sum_probs=26.1
Q ss_pred ccccccccc-CCcccccCC--CCccccccccCcc
Q 000290 426 GDECRICGM-DGTLLCCDG--CPSAYHTRCIGVS 456 (1717)
Q Consensus 426 dd~C~VC~~-gG~LLcCD~--Cp~afHl~CL~Pp 456 (1717)
...|.+|+. .|.++-|.. |...||..|.-..
T Consensus 55 ~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 55 KLKCSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 467999999 578888987 9999999997643
No 93
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.55 E-value=48 Score=32.42 Aligned_cols=32 Identities=28% Similarity=0.638 Sum_probs=25.6
Q ss_pred CCeeeccCCCCCCCcceEecCC--CCccccccccccC
Q 000290 1362 EPVCDLCKQPYNSNLMYIHCET--CQRWFHADAVELE 1396 (1717)
Q Consensus 1362 ~~vcClC~kPy~~d~~MI~CD~--C~~WFHg~CVgLt 1396 (1717)
..+|.+|++++. -.|.|.. |...||..|.-..
T Consensus 36 ~~~C~~C~~~~G---a~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 36 KLKCSICKKKGG---ACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred CCCCcCCCCCCC---eEEEEeCCCCCcEEChHHHccC
Confidence 358889998743 5899986 9999999997643
No 94
>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=22.50 E-value=63 Score=26.36 Aligned_cols=28 Identities=21% Similarity=0.622 Sum_probs=22.8
Q ss_pred cccccCCCCCCC-CccceeccceEeccCC
Q 000290 1667 QCRICPDIEPAP-NLSCQICGLVIHSQCS 1694 (1717)
Q Consensus 1667 ~c~~c~~~~p~p-~l~c~~c~~~ih~~cs 1694 (1717)
.|..|-+.-.+. --.|..|+..+|..|.
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 478886666666 6789999999999994
No 95
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=22.19 E-value=33 Score=44.86 Aligned_cols=62 Identities=26% Similarity=0.519 Sum_probs=41.7
Q ss_pred cccccchhhhhhhcccccccccccccccccc-----cccccccccccccccccccccCCcCCCCCccceecccccCccc
Q 000290 1185 KASRKDLFSYLVCRRDKIEKCACASCQIDVL-----LGNAVKCGTCQGYCHEGCTSSSMHMNSGVEPMIVCNRCYLPRA 1258 (1717)
Q Consensus 1185 k~~~~~~f~yL~~k~~~le~~~C~~C~kdV~-----~~~aVtC~~Cqg~fHk~C~~~S~~~~~~~~~~y~C~rCl~~k~ 1258 (1717)
|.+.+-|-.=..+... ...|-.|+++-. .+.+.+|..|-..||+.|.... .+ .|++|.+-+.
T Consensus 495 k~~~~HV~~C~lC~~~---gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~-s~--------~CPrC~R~q~ 561 (580)
T KOG1829|consen 495 KLSSKHVKECDLCTGK---GFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK-SP--------CCPRCERRQK 561 (580)
T ss_pred HHhhhhhhhchhhccC---eeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc-CC--------CCCchHHHHH
Confidence 3344444444455555 677888877665 4566999999999999999444 11 2999966543
No 96
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=21.89 E-value=36 Score=33.24 Aligned_cols=31 Identities=29% Similarity=0.839 Sum_probs=26.4
Q ss_pred cccccccccC-CcccccC--CCCccccccccCcc
Q 000290 426 GDECRICGMD-GTLLCCD--GCPSAYHTRCIGVS 456 (1717)
Q Consensus 426 dd~C~VC~~g-G~LLcCD--~Cp~afHl~CL~Pp 456 (1717)
...|.+|+.. |..+-|. +|...||..|.--.
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccC
Confidence 3579999998 9888897 49999999998654
No 97
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.77 E-value=52 Score=37.62 Aligned_cols=37 Identities=38% Similarity=0.887 Sum_probs=28.7
Q ss_pred ccccccccCC--------cccccCCCCccccccccCcccCCCCCCCcccccCcc
Q 000290 427 DECRICGMDG--------TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 472 (1717)
Q Consensus 427 d~C~VC~~gG--------~LLcCD~Cp~afHl~CL~PpL~~vPeGdW~Cp~C~~ 472 (1717)
..|.+|..++ ...-|..|...||..|.... .||.|..
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~---------~CpkC~R 197 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK---------SCPKCAR 197 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC---------CCCCcHh
Confidence 4688888753 56779999999999999841 1999963
No 98
>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=20.92 E-value=23 Score=28.59 Aligned_cols=27 Identities=22% Similarity=0.623 Sum_probs=11.9
Q ss_pred cccccCCCCCC-CCccceeccceEeccC
Q 000290 1667 QCRICPDIEPA-PNLSCQICGLVIHSQC 1693 (1717)
Q Consensus 1667 ~c~~c~~~~p~-p~l~c~~c~~~ih~~c 1693 (1717)
.|..|...-.. +-..|.+|+..||-.|
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 48888877777 8899999999999766
Done!