Query 000891
Match_columns 1236
No_of_seqs 314 out of 1253
Neff 3.9
Searched_HMMs 46136
Date Tue Apr 2 00:40:15 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000891hhsearch_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 2E-124 4E-129 1111.0 25.0 968 1-1146 1-1052(1414)
2 KOG1473 Nucleosome remodeling 98.9 4.5E-10 9.6E-15 138.3 3.8 124 369-500 339-470 (1414)
3 COG5141 PHD zinc finger-contai 98.5 1.1E-08 2.3E-13 118.3 -1.6 123 278-422 114-244 (669)
4 KOG1244 Predicted transcriptio 98.5 4.2E-08 9.1E-13 107.4 1.2 48 373-420 280-330 (336)
5 KOG0955 PHD finger protein BR1 98.4 3.3E-08 7.2E-13 124.4 -0.1 55 369-425 214-273 (1051)
6 KOG4299 PHD Zn-finger protein 98.4 5E-08 1.1E-12 116.3 1.2 49 374-422 253-306 (613)
7 PF00628 PHD: PHD-finger; Int 98.1 8.7E-07 1.9E-11 74.3 0.2 45 376-420 1-50 (51)
8 cd04718 BAH_plant_2 BAH, or Br 98.0 2E-06 4.3E-11 88.3 2.4 78 395-474 1-79 (148)
9 KOG0383 Predicted helicase [Ge 98.0 2.2E-06 4.7E-11 105.1 2.7 54 369-422 42-95 (696)
10 KOG0825 PHD Zn-finger protein 98.0 3.1E-06 6.7E-11 102.5 2.1 46 375-420 216-265 (1134)
11 smart00249 PHD PHD zinc finger 97.9 7.2E-06 1.6E-10 65.7 2.4 43 376-418 1-47 (47)
12 COG5034 TNG2 Chromatin remodel 97.6 4.2E-05 9E-10 84.1 3.3 47 371-420 218-269 (271)
13 KOG4323 Polycomb-like PHD Zn-f 97.6 4.9E-05 1.1E-09 89.7 3.9 132 375-508 84-273 (464)
14 KOG1973 Chromatin remodeling p 97.5 4.3E-05 9.4E-10 85.3 2.8 43 375-420 222-267 (274)
15 KOG1512 PHD Zn-finger protein 97.4 4.7E-05 1E-09 84.6 1.5 46 373-420 313-362 (381)
16 KOG0956 PHD finger protein AF1 97.4 4.2E-05 9.2E-10 92.2 0.8 44 375-420 6-56 (900)
17 KOG4443 Putative transcription 97.2 0.00015 3.4E-09 87.6 2.1 46 374-419 68-116 (694)
18 KOG0954 PHD finger protein [Ge 97.0 0.00025 5.5E-09 86.4 1.2 46 373-420 270-320 (893)
19 KOG1245 Chromatin remodeling c 96.8 0.00027 5.9E-09 93.0 -0.2 49 373-421 1107-1158(1404)
20 PF09465 LBR_tudor: Lamin-B re 96.6 0.0022 4.7E-08 56.6 3.7 42 41-82 5-50 (55)
21 PF13831 PHD_2: PHD-finger; PD 96.1 0.0014 2.9E-08 53.2 -0.4 34 384-419 2-36 (36)
22 KOG4323 Polycomb-like PHD Zn-f 95.8 0.0031 6.8E-08 75.0 1.1 47 376-422 170-225 (464)
23 KOG4443 Putative transcription 95.6 0.0042 9.2E-08 75.7 1.0 94 373-472 17-117 (694)
24 KOG0957 PHD finger protein [Ge 95.5 0.0058 1.2E-07 72.5 1.4 45 375-419 545-596 (707)
25 KOG1512 PHD Zn-finger protein 95.4 0.0045 9.7E-08 69.4 0.4 90 375-472 259-361 (381)
26 KOG0383 Predicted helicase [Ge 95.1 0.018 4E-07 71.8 4.0 70 391-460 1-81 (696)
27 PF15612 WHIM1: WSTF, HB1, Itc 94.8 0.024 5.3E-07 48.1 2.9 44 258-301 5-48 (50)
28 KOG1244 Predicted transcriptio 94.0 0.016 3.4E-07 65.0 0.2 88 374-467 224-325 (336)
29 smart00333 TUDOR Tudor domain. 93.0 0.099 2.1E-06 44.6 3.3 48 42-89 3-53 (57)
30 KOG1246 DNA-binding protein ju 91.4 0.14 3.1E-06 66.0 3.4 145 374-525 155-322 (904)
31 KOG0957 PHD finger protein [Ge 90.5 0.18 4E-06 60.4 3.0 47 375-421 120-179 (707)
32 KOG4299 PHD Zn-finger protein 86.4 0.38 8.2E-06 59.3 2.0 47 374-420 47-94 (613)
33 smart00743 Agenet Tudor-like d 85.4 1.1 2.3E-05 39.3 3.8 49 42-90 3-57 (61)
34 cd04508 TUDOR Tudor domains ar 81.7 1.7 3.8E-05 35.9 3.5 41 47-87 3-47 (48)
35 PF09038 53-BP1_Tudor: Tumour 81.6 1.8 3.8E-05 44.3 4.1 38 42-79 3-43 (122)
36 PLN00163 histone H4; Provision 80.1 1.3 2.8E-05 40.1 2.2 24 958-981 30-53 (59)
37 PF14446 Prok-RING_1: Prokaryo 73.4 1.4 3.1E-05 39.3 0.7 30 375-404 6-39 (54)
38 PF15446 zf-PHD-like: PHD/FYVE 72.9 1.4 3E-05 47.2 0.6 44 376-419 1-58 (175)
39 PF00130 C1_1: Phorbol esters/ 72.1 2.6 5.6E-05 35.9 2.0 31 1151-1181 10-42 (53)
40 KOG4628 Predicted E3 ubiquitin 65.0 3.8 8.3E-05 48.3 2.1 45 375-422 230-277 (348)
41 KOG3467 Histone H4 [Chromatin 57.7 5.7 0.00012 38.6 1.5 40 958-997 30-72 (103)
42 PF11793 FANCL_C: FANCL C-term 57.0 1.9 4.1E-05 39.7 -1.7 46 375-420 3-63 (70)
43 PF02178 AT_hook: AT hook moti 53.4 5.8 0.00013 26.4 0.5 10 6-15 1-10 (13)
44 KOG1081 Transcription factor N 53.4 7.7 0.00017 47.3 2.0 49 371-422 86-134 (463)
45 PF13639 zf-RING_2: Ring finge 53.1 2 4.4E-05 35.4 -2.0 41 375-419 1-44 (44)
46 KOG3612 PHD Zn-finger protein 52.0 11 0.00024 46.5 3.0 50 371-421 57-108 (588)
47 smart00417 H4 Histone H4. 50.9 8.1 0.00018 36.5 1.3 24 958-981 14-37 (74)
48 smart00384 AT_hook DNA binding 46.8 12 0.00026 29.2 1.4 16 6-21 1-16 (26)
49 KOG1973 Chromatin remodeling p 46.4 10 0.00022 43.2 1.5 47 399-458 206-255 (274)
50 PF13901 DUF4206: Domain of un 46.2 8.8 0.00019 41.9 0.9 37 1153-1189 153-196 (202)
51 smart00109 C1 Protein kinase C 42.2 9.9 0.00021 31.1 0.4 31 1152-1182 11-42 (49)
52 cd00029 C1 Protein kinase C co 39.4 12 0.00027 30.9 0.6 31 1153-1183 12-44 (50)
53 cd00076 H4 Histone H4, one of 39.3 16 0.00034 35.5 1.3 24 958-981 14-37 (85)
54 PF12861 zf-Apc11: Anaphase-pr 38.9 12 0.00025 36.4 0.4 29 391-420 51-79 (85)
55 PF12678 zf-rbx1: RING-H2 zinc 36.5 11 0.00024 34.9 -0.1 25 391-419 49-73 (73)
56 PF09337 zf-H2C2: His(2)-Cys(2 35.8 8.5 0.00018 32.2 -0.9 31 750-784 9-39 (39)
57 PTZ00015 histone H4; Provision 35.7 24 0.00052 35.4 2.0 35 947-981 18-54 (102)
58 PF13901 DUF4206: Domain of un 35.7 21 0.00045 39.0 1.8 36 375-419 153-196 (202)
59 PF13771 zf-HC5HC2H: PHD-like 34.6 16 0.00034 34.2 0.5 32 373-404 35-69 (90)
60 PF13832 zf-HC5HC2H_2: PHD-zin 33.7 18 0.00038 35.2 0.7 31 373-403 54-87 (110)
61 KOG3532 Predicted protein kina 33.3 13 0.00029 47.0 -0.2 45 1152-1196 757-801 (1051)
62 smart00659 RPOLCX RNA polymera 30.9 26 0.00057 30.1 1.2 24 1152-1175 2-27 (44)
63 PF14446 Prok-RING_1: Prokaryo 30.7 31 0.00068 31.1 1.7 43 1150-1192 3-51 (54)
64 PF00301 Rubredoxin: Rubredoxi 29.8 31 0.00068 30.1 1.5 33 389-422 4-44 (47)
65 smart00249 PHD PHD zinc finger 27.8 37 0.0008 27.0 1.5 27 1155-1181 2-28 (47)
66 cd04476 RPA1_DBD_C RPA1_DBD_C: 27.4 87 0.0019 32.7 4.6 49 1154-1215 36-84 (166)
67 cd00162 RING RING-finger (Real 27.3 18 0.00038 28.3 -0.4 41 377-420 2-43 (45)
68 smart00184 RING Ring finger. E 26.9 16 0.00035 27.4 -0.7 39 377-418 1-39 (39)
69 PF00628 PHD: PHD-finger; Int 26.4 24 0.00052 29.7 0.2 27 1155-1181 2-28 (51)
70 PF03604 DNA_RNApol_7kD: DNA d 26.4 35 0.00075 27.7 1.1 22 1153-1174 1-24 (32)
71 COG1773 Rubredoxin [Energy pro 26.1 40 0.00087 30.6 1.6 19 403-422 28-46 (55)
72 PHA02929 N1R/p28-like protein; 24.7 31 0.00068 39.0 0.8 44 373-420 173-224 (238)
73 PLN00035 histone H4; Provision 22.6 45 0.00098 33.6 1.3 24 958-981 30-53 (103)
74 cd00730 rubredoxin Rubredoxin; 22.3 51 0.0011 29.1 1.5 33 388-421 3-43 (50)
75 KOG4218 Nuclear hormone recept 21.7 31 0.00067 40.9 0.1 24 373-396 14-42 (475)
76 KOG4236 Serine/threonine prote 21.5 18 0.0004 45.1 -1.8 29 375-403 157-190 (888)
No 1
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=1.7e-124 Score=1111.01 Aligned_cols=968 Identities=35% Similarity=0.484 Sum_probs=789.5
Q ss_pred CCCCCCCCCCCCcCCCCCCccccCCCCCCccceeecc-cccceeecceehhccCC-ceEEEEEEEEecceEEEEecCCCc
Q 000891 1 MEAKVKRPRGRPRKRKRPEDEDVTDGAGGKKRVVAVE-AKPIALVGRYVLKEFES-GIFLGKIVYYESGLYRVDYEDGDC 78 (1236)
Q Consensus 1 me~~~~~~~~r~r~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~LvGr~V~k~f~~-~~~~GkV~~yd~g~Y~V~yEDGd~ 78 (1236)
||.+++|||||||||.|+|+.+. +.+++|+|+..++ +.|+.|.|+|+.|.+.+ ++|+||+++||+|+|||.|||||+
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 9999999943332 34569999999999999 999999999999999999999999
Q ss_pred cccChhHHHhhhccCCCcchHHHHHHhhhhhhhcccccccccccccccCCCCcccccccccccccccccccccccCCccc
Q 000891 79 EDLDSSELRQFLLNENDFDADLTRRRKKLDDWLVKRSLKNEKSNLEKKDGDAKSEVDRIEASTLSEVSCGLTVEDVGEQV 158 (1236)
Q Consensus 79 Edl~~~el~~~l~~~~~~~~~~~~Rr~kld~~~~~~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 158 (1236)
|+++-..+++.++.++.++..+..||.+||+.....+....-...+.+..|.++... ..+.+-..+
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 999999999999999999999999999999998887755111111222222222211 011122334
Q ss_pred cCCCCCCCCcccccccCCCCCCCCCCCCCCCCCCCCCCch-----------hHHHHHH--HHhhhcCCCCch---hhh--
Q 000891 159 EGDMDSSSDSCEHVRETDAGLEAETPLLPPPQLPPSSGTI-----------ALMRVLR--RHLETLSSDGSE---LAS-- 220 (1236)
Q Consensus 159 ~~d~~sss~s~~~~~~~~~~~~~~~p~~ppleLP~SS~di-----------Sl~rvLR--rhle~LSs~g~e---~As-- 220 (1236)
+++..++........+.++..+.+.|.+||||||+||||| |||++|| +|..||+||+|| +|+
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 4555666666777777777788999999999999999999 9999999 899999999998 565
Q ss_pred ----------------------------------hhhhccccccccccchHHHHHHHhhhcccccCCCcccccccccccc
Q 000891 221 ----------------------------------NCLRCIDWSLLDTLTWPVYVVQYLTSMGYIKGTQWTGFYDEVSVRE 266 (1236)
Q Consensus 221 ----------------------------------~CLRni~w~lLD~lTWP~~L~eYl~s~G~~~~~e~k~f~~~ll~~E 266 (1236)
+|++||+|+|||+||||+|||+|+++||+..++-|..|...+..+|
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 3455999999999999999999999999999999988887777899
Q ss_pred ccccchhhHHHHHHHHHhhhcchHHHHHHHhhccccccC----CCcccc-ccccccccccc------CCCccCCCcccch
Q 000891 267 YYSLSAGRKLMILQILCDDVLDSEELRAEIDAREESEVG----LDPDAA-SYGSEIARRRV------HPRFSKTPDCKNR 335 (1236)
Q Consensus 267 Yy~~pV~~KL~ILq~LcD~~l~s~efRsE~dmrEese~~----Ld~~n~-~l~~e~G~rr~------~pR~sktSa~k~k 335 (1236)
||+.|++.||+|||+|||+|++++.+|.||+.+++.+.+ ++.+.. .+.+|+++|++ ||++.++++....
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 999999999999999999999999999999998887766 555444 58899999999 9999999888766
Q ss_pred hhhhhhhccccc----CCCcCCCCCCCCCCCCCC-CCCcccccccccccccccCcccccCC-CCccccc-cccc--cccC
Q 000891 336 EAVEFNAENDRM----KTSCKAKPLGFKGTEMDA-PGVDVDGNGDECRICGMDGTLLCCDG-CPSAYHT-RCIG--VSKM 406 (1236)
Q Consensus 336 ea~E~~ees~~~----sps~~s~~sr~~~~e~~~-~~~~~d~ndD~C~VCgdgGeLLcCD~-CprafHl-~CL~--PpL~ 406 (1236)
+...+.. .++. -+..+..++.+..+-+.+ ....-.-+.+.|.+|+..+.+|||++ |+..||+ .|++ -.-+
T Consensus 386 evc~~hk-vngvvd~vl~~~K~~~~iR~~~iG~dr~gr~ywfi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~ 464 (1414)
T KOG1473|consen 386 EVCNIHK-VNGVVDCVLPPSKNVDSIRHTPIGRDRYGRKYWFISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEM 464 (1414)
T ss_pred hhhhhhc-cCcccccccChhhcccceeccCCCcCccccchhceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHH
Confidence 6665422 1111 011111112122222221 12223456678999999999999998 9999999 9999 4557
Q ss_pred CCCCCCccccccccccCCCcccccccccccccccccchhhhhhhh-cccceeeccCCCchhcccccccCchhHHHHhhhc
Q 000891 407 YVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFLGT-CNHLLVLNASSNTEQYIRYYNPIDIPKVLQALLS 485 (1236)
Q Consensus 407 ~iPeGdW~Cp~C~~~k~gpe~E~g~s~rg~e~LGcD~cgQ~Yh~k-C~rlLve~~s~D~e~c~rYYs~vDl~evLevL~~ 485 (1236)
.+|+|-|+|+.|...+.+++.+.+...+++--||.|+++|.|.+. |.-+|+.......+.-..|+...++..++.++..
T Consensus 465 ~L~d~i~~~~ee~~rqM~lT~~ltne~R~~~~f~~~~h~r~~l~~~c~~~lv~~iq~~~da~l~e~~l~~i~k~v~~~~S 544 (1414)
T KOG1473|consen 465 YLCDGIWERREEIIRQMGLTEELTNELRGAVDFGEDPHGRLFLGRDCAVLLVLCIQVVEDAILKEENLGDIDKVVLVLIS 544 (1414)
T ss_pred hhccchhhhHHHHHHhccchhhhhhhhhcccccccCCCcceeeecchhhHHhhhhhhhhhhhhhHhhhcchHhhhhhhhh
Confidence 899999999999999999988888888888889999999999885 4433332222222344778888888899999999
Q ss_pred cccchhhhhhHHHHHHHhhcCCCCCCCC-CCccccccccccccccccCCCCCCCccccccccccccCCCCCCCCCCCCcc
Q 000891 486 SVQHVSLYLGICKAILHYWDIPESVVPF-MGMETNTINAKADEKFCSQSHHPPIKESQRITDMVEAGNASSNNGSNVDNV 564 (1236)
Q Consensus 486 SDih~~~Y~eIc~~I~e~Wdi~~nl~~~-~~~e~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 (1236)
+..|...|.++|.+|.++|+.+....-+ -......+.++. ..++|-...+...+-.-
T Consensus 545 ~s~~~eE~~e~ck~is~~~d~p~~n~~~~~e~~~dqtf~~y----------------------~ys~n~vse~~~~d~e~ 602 (1414)
T KOG1473|consen 545 ASAHQEEYVEICKAISQYWDLPEGNLWRLREEGNDQTFMKY----------------------YYSGNEVSEIFLTDSEN 602 (1414)
T ss_pred cccchHHHHHHHHHHhhcccccccchhhhhhcccccchhhh----------------------cccCCchhhccCCchhh
Confidence 9999999999999999999999876642 112222221210 11122222221111100
Q ss_pred cccccccccccccCCCCccccccccchhhcccccccccCCCCCccccccccccCCccccCCCCccccccccccccccccc
Q 000891 565 AVSSLHTFMNTMSQTGVPFVQSNDITVTEKLQDCLVLNGKLPGHVKMESAMSTGSVSQQADPSDVTYQSLVDRSSAIDFM 644 (1236)
Q Consensus 565 ~~~~~~~~~~~~~q~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 644 (1236)
...+.+ ...+|+... ++.+-+.++.|.
T Consensus 603 ~dkk~~------------------------------~~tkf~l~~--nsd~~~~g~~~t--------------------- 629 (1414)
T KOG1473|consen 603 ADKKSH------------------------------MQTKFALIT--NSDGVTAGNVTT--------------------- 629 (1414)
T ss_pred hccccc------------------------------ccceecccc--cccceecccccc---------------------
Confidence 001111 111121100 000000011000
Q ss_pred cccccCcCCCCCCCCCcCCCCCcccccccccCCCccccccccCCcccccccccCccchhh----ccchh-hhHHHHHHHH
Q 000891 645 TCTSQISNDGNSGHASSCLSPNISFLSKERNHGGLLGVGTNYANKCAFMGSVFKPHSYIN----QYMHG-EFAAAAAAKL 719 (1236)
Q Consensus 645 ~~~~g~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~n~~~~~~~~~~~~~p~~YiN----~Y~~g-~~aasaAa~L 719 (1236)
.+|.+ ...+.+.--...|-+++|.+||| +|..| +.|+|||+.+
T Consensus 630 ----------~gt~~----------------------~~~~~~~~t~~~~lSniP~s~~n~~w~~~tkg~~lavs~A~~~ 677 (1414)
T KOG1473|consen 630 ----------YGTGS----------------------QHKKLIARTLQQGLSNIPISYNNRKWPVYTKGFELAVSAAADL 677 (1414)
T ss_pred ----------ccchh----------------------hcchHHHhhhhhhhccCchHhhhccchhhccchhhhhhccchH
Confidence 00001 12233444466678999999999 99999 9999999999
Q ss_pred hhhccccccccccccccCcccccchhhHHHHHHhhhccccccccccccccccccCccccccccccCCCCCCCCceeehhh
Q 000891 720 AVLSSEESQASEMHKSGNTRKAMSGSISLQAKAFSSTASRFFWPCSERKLWEVPRERCSWCYSCKSPPSNRRGCMLNSAM 799 (1236)
Q Consensus 720 a~~ssee~~~~~~~~s~n~~k~~~~~~~~Q~Kafs~~~~~F~Wps~ekk~~ev~rerCGWC~sCk~s~~~~~~C~ln~a~ 799 (1236)
|.+++ |..+++.++-.|..|+.+.++..|+|+||.+|++||||+..+| +..|||||||++|+....+.++||+|.+.
T Consensus 678 ~el~s-~t~~~d~s~~~~~~~~~ssn~L~qtklesitaa~f~~~~~~~K--ri~rer~~~~~~~~l~~~s~k~~~~~~~~ 754 (1414)
T KOG1473|consen 678 AELSS-ETLEPDLSKRSNAFKAASSNILGQTKLESITAAQFFWPSPDKK--RITRERCGWCESCRLTFASRKGTMLLAAV 754 (1414)
T ss_pred HHHHH-hhcccchhhhhhhhccchhhhhcchhheeeehhhhccCCcccc--cccccccchhhhcceeeehhccccchhhc
Confidence 99999 8889999999999999999999999999999999999999999 99999999999999988899999999999
Q ss_pred hhhhhhhHHHhcCcccccCCCCChHHHHHHHHhhhhhccccccccCCChhhHHHHHHHHHhhcchhhHHHHHHHhhhccc
Q 000891 800 TVATKSAMKILNGLLAPKTGEGNLPTIVTYIMYMEESLCGLISGPFRSVSYRKKWRKQVAEACTLNSIKALLLELEENIC 879 (1236)
Q Consensus 800 ~~a~kg~~~~~~gl~~~k~~~~hl~si~~yil~mEe~L~GLl~Gp~~~~~~r~~Wrk~v~~As~~~~ik~lLL~LEsnir 879 (1236)
+.|+||+|++.+||.|.||+++.|.+|++|++++||+++|++|||++..+-|++||+.|+. .+.++++||+||+
T Consensus 755 ~gaqKGa~~r~~G~~~l~n~~~vlS~~~~~~~~~~es~~~v~v~~~~~Esnr~~~r~~L~~------r~~~~~q~ee~i~ 828 (1414)
T KOG1473|consen 755 IGAQKGAMYRNSGLFPLKNWEWVLSSIAAYWLALEESPRGVIVGEFKSESNRKQERKELLV------RRSGGKQLEENIC 828 (1414)
T ss_pred cccccccceeeeccccccChhHHHHHHHHHHHhhhccccceeecccccccchhhHHHHhhh------hhhhhhhhccccc
Confidence 9999999999999999999999999999999999999999999999999999999999988 4999999999999
Q ss_pred ceeeccchhhhhhccc-ccccccccccccccccccccCCCCCCCccccccccccCCCCCCceeeecCCcchhhhhhcccC
Q 000891 880 HIALSGDWVKLMDDWL-GDSSVIQSASCNFVTTQKRGLSGKRGRKHSVISEVTADDCNDQSFSWWQGGKSTKLISKKAIL 958 (1236)
Q Consensus 880 ~iA~s~dW~K~~D~~~-v~~s~~~~~~~~~~~~qk~g~~gkr~rk~~~~~e~~~~~~~~~~~~WwrGG~lsr~if~~~~L 958 (1236)
-+|++-+|.|.||+|. ++.|..++..-+.++.|+|++|+++ +. ..-|.++.+....+|.|||||+ |+.|+|+|+|
T Consensus 829 ~~~~~~y~~~~~~n~~rie~s~~~~ng~~v~akQ~r~pgr~~-~s--~~~ek~A~~s~ld~f~~~Rggk-s~vvl~kavL 904 (1414)
T KOG1473|consen 829 SGALSCYWPKQMDNWLRIEHSIFQSNGVTVGAKQARDPGRTK-QS--LQAEKTAPKSDLDSFTWWRGGK-SKVVLQKAVL 904 (1414)
T ss_pred cccccccchhhccCceeeeechhccCceeechhhhcCCcchh-hh--cchhhccccccccchhhhhcCc-ceeeehhhhc
Confidence 9999999999999999 9999999999999999999995544 33 3338899999999999999999 9999999999
Q ss_pred hHHHHHHHHHhcCcccccccccC--CCccccchhhhhhhhhhcccchhHHHHHHhhhcccccccccCCCcccccCCCCch
Q 000891 959 PHTIIRNAARRGGLRKISGVNYT--AEMPKRSRQLVWRAAVERSKTVSQLALQVRYIDLHVRWSELVRPEQNLQDGKGPE 1036 (1236)
Q Consensus 959 p~s~v~kAaRQgG~rki~gi~Y~--se~~rRsr~~~WraaVe~s~~~sqLaLQvR~Ld~~iRW~el~~~~~~~~~~K~~~ 1036 (1236)
-++.++|+|.|+|.+++|+..|. +.+|+|+++..|.+||+-++|++|||||+ .|+.+|+|+++
T Consensus 905 ~~~~mk~~v~~~g~ta~~k~nfl~~~y~p~~s~~s~wk~av~n~enlh~LAlQ~---------------~q~v~d~~s~~ 969 (1414)
T KOG1473|consen 905 SQSIMKKLVWQQGFTAGPKSNFLDWSYIPRRSRRSCWKAAVENSENLHQLALQL---------------RQNVQDVKSPE 969 (1414)
T ss_pred chHHHHHHhhccccccCCcccccccccccchhhhhhhhhhhcChhhHHHHHHHH---------------HHHHhccCCch
Confidence 99999999999999999999999 88999999999999999999999999998 68999999999
Q ss_pred hhhhhcccceeeeccccccceEEEEecCCcccCChhhhhhhhhhhcccCCCCccccccCCchhHhHHHHHhhccccccCC
Q 000891 1037 TEAFAFRNAIICDKKIVENKIRYGVAFGIHRHLPSRVMKNIIDIELSQDGKEKYWFPETCLPLFLIKEYEERVDMVIAPS 1116 (1236)
Q Consensus 1037 ~~a~~fr~~ii~~k~~~~~~~~Y~~~fg~~~~lp~~v~kn~~~~e~~~~~~~k~W~~E~~vPL~LlkefE~~~~~~~~~s 1116 (1236)
+.++.||||-||.|++-+++.+|+.-|++ +.+||.|.+ ||+.|.-|+| .||+.+
T Consensus 970 ~r~ai~r~~~ic~~~l~d~~~~~~~~~~s------~~~~~~~~~---------~~~~~~~~sl----~~~~fr------- 1023 (1414)
T KOG1473|consen 970 TRRAIFRNAEICIKKLYDNKEEEGESWLS------SEFSHVISS---------RPQRHEFVSL----GYEKFR------- 1023 (1414)
T ss_pred hhHHHhhhhhhhccccccCCcccccchhh------hhhhhhhhc---------ccccCceeec----cchhhh-------
Confidence 99999999999999999999999999999 889999887 9999999999 388853
Q ss_pred CCCCCchhhHHHHHhhcccccCcceeeeec
Q 000891 1117 SKKPSNELSEFQKKQLKASRKDLFSYLVCR 1146 (1236)
Q Consensus 1117 ~k~~s~~~~~~~~~~~k~~~~~~FsYL~~k 1146 (1236)
.++.-..+++++.++|.+...+|.|+-.+
T Consensus 1024 -~~~~~r~~~~q~~~~~~~~~~v~~~~~~~ 1052 (1414)
T KOG1473|consen 1024 -SLDNRRATAIQREWLKGSTANVFEIKDYW 1052 (1414)
T ss_pred -cchhhhhHHHHhhhhcccccceeeeeccC
Confidence 24455678999999999999999999877
No 2
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=98.93 E-value=4.5e-10 Score=138.26 Aligned_cols=124 Identities=28% Similarity=0.554 Sum_probs=100.0
Q ss_pred cccccccccccccccCcccccCCCCccccccccccccCCCCCCCccccccccccCCCcc-------cccccccccccccc
Q 000891 369 DVDGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGPIV-------TIGTSLRGAELFGI 441 (1236)
Q Consensus 369 ~~d~ndD~C~VCgdgGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k~gpe~-------E~g~s~rg~e~LGc 441 (1236)
+....+|+|++|++.|.++||..||+.||++|..+|+..+|+..|.|-.|...+..... +...+. +.+.+|.
T Consensus 339 ~~~~~ddhcrf~~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvngvvd~vl~~~K~~~~i-R~~~iG~ 417 (1414)
T KOG1473|consen 339 GEIEYDDHCRFCHDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNGVVDCVLPPSKNVDSI-RHTPIGR 417 (1414)
T ss_pred cceeecccccccCcccceeecccCCceEEeeecCCccccCCCccchhhhhhhhccCcccccccChhhcccce-eccCCCc
Confidence 44456789999999999999999999999999999999999999999999876654221 222222 4678999
Q ss_pred cchhhhhhhhcccceeeccCCCchhcccccc-cCchhHHHHhhhccccchhhhhhHHHHH
Q 000891 442 DLYERVFLGTCNHLLVLNASSNTEQYIRYYN-PIDIPKVLQALLSSVQHVSLYLGICKAI 500 (1236)
Q Consensus 442 D~cgQ~Yh~kC~rlLve~~s~D~e~c~rYYs-~vDl~evLevL~~SDih~~~Y~eIc~~I 500 (1236)
|.+++.||+.-+++.++.+ | ++..+||+ +.++..++++|+... ...+||..|
T Consensus 418 dr~gr~ywfi~rrl~Ie~~--d-et~l~yysT~pqly~ll~cLd~~~----~e~~L~d~i 470 (1414)
T KOG1473|consen 418 DRYGRKYWFISRRLRIEGM--D-ETLLWYYSTCPQLYHLLRCLDRTY----VEMYLCDGI 470 (1414)
T ss_pred CccccchhceeeeeEEecC--C-CcEEEEecCcHHHHHHHHHhchHH----HHHhhccch
Confidence 9999999999999999864 3 78899999 558999999999765 333555544
No 3
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.52 E-value=1.1e-08 Score=118.35 Aligned_cols=123 Identities=23% Similarity=0.309 Sum_probs=83.8
Q ss_pred HHHHHHhhhc-chHHHHHHHhhccccccCCCcccccccccccccccCCCccCCCcccchhhhhhhhcccccCCC--cCCC
Q 000891 278 ILQILCDDVL-DSEELRAEIDAREESEVGLDPDAASYGSEIARRRVHPRFSKTPDCKNREAVEFNAENDRMKTS--CKAK 354 (1236)
Q Consensus 278 ILq~LcD~~l-~s~efRsE~dmrEese~~Ld~~n~~l~~e~G~rr~~pR~sktSa~k~kea~E~~ees~~~sps--~~s~ 354 (1236)
-.+...++.+ .-..|...|||||.|++|+.|+|+..+.++- ..+.+|++...-++.+. ....
T Consensus 114 e~~Kfi~i~p~~~~~f~v~YdlDe~D~m~l~Ylne~~~~e~v---------------S~e~fEii~t~lE~EWf~~e~~l 178 (669)
T COG5141 114 EGKKFIDIEPPRGLFFSVIYDLDEYDTMWLRYLNESAIDENV---------------SEEAFEIIVTRLEKEWFFFEHGL 178 (669)
T ss_pred hhhhceeccCCcCccCceeecccchhHHHHHHHHHHHhhhhh---------------hHHHHHHHHHHHHHHHHhhhccC
Confidence 3455666666 7778999999999999999999984333321 23444443322223332 1111
Q ss_pred CCCCCCCCCCCCCCccccccccccccccc-----CcccccCCCCccccccccccccCCCCCCCcccccccccc
Q 000891 355 PLGFKGTEMDAPGVDVDGNGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 355 ~sr~~~~e~~~~~~~~d~ndD~C~VCgdg-----GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k 422 (1236)
+++ ..+..+.+|.-++.|.+|... ..+++||+|+.+.|+.|+|++ .+|+|.|+|..|...+
T Consensus 179 p~k-----~vepi~~~d~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~--f~peG~WlCrkCi~~~ 244 (669)
T COG5141 179 PDK-----HVEPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQ--FLPEGFWLCRKCIYGE 244 (669)
T ss_pred ccc-----cccccCCchhhhhhhHhccccccCCcceEEEecCcchhhhhhcccce--ecCcchhhhhhhcccc
Confidence 111 112222344567899999874 479999999999999999999 8999999999998643
No 4
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.47 E-value=4.2e-08 Score=107.39 Aligned_cols=48 Identities=42% Similarity=0.949 Sum_probs=43.2
Q ss_pred cccccccccc---cCcccccCCCCccccccccccccCCCCCCCcccccccc
Q 000891 373 NGDECRICGM---DGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 373 ndD~C~VCgd---gGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
+-..|.+|+. +++||+||.|+++||++||.||+.+.|+|.|.|..|..
T Consensus 280 eck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred ecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence 4457888987 46999999999999999999999999999999999973
No 5
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.45 E-value=3.3e-08 Score=124.40 Aligned_cols=55 Identities=33% Similarity=0.862 Sum_probs=46.8
Q ss_pred ccccccccccccccc-----CcccccCCCCccccccccccccCCCCCCCccccccccccCCC
Q 000891 369 DVDGNGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGP 425 (1236)
Q Consensus 369 ~~d~ndD~C~VCgdg-----GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k~gp 425 (1236)
.....|..|.||.++ ..+|+||+|+.++|+.|++.+ .+|+|.|.|..|...+.++
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~--~ipeg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIP--FIPEGQWLCRRCLQSPQRP 273 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCC--CCCCCcEeehhhccCcCcc
Confidence 344567899999985 479999999999999999977 8999999999999766543
No 6
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.45 E-value=5e-08 Score=116.29 Aligned_cols=49 Identities=43% Similarity=1.221 Sum_probs=45.0
Q ss_pred ccccccccccCcc---cccCCCCccccccccccc--cCCCCCCCcccccccccc
Q 000891 374 GDECRICGMDGTL---LCCDGCPSAYHTRCIGVS--KMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 374 dD~C~VCgdgGeL---LcCD~CprafHl~CL~Pp--L~~iPeGdW~Cp~C~~~k 422 (1236)
.++|..|++.|.. +|||+||++||+.|+.|| .+.+|.|.|+|+.|.++-
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKS 306 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeee
Confidence 6799999998866 999999999999999999 689999999999998754
No 7
>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=98.06 E-value=8.7e-07 Score=74.35 Aligned_cols=45 Identities=42% Similarity=1.224 Sum_probs=38.5
Q ss_pred ccccccc---cCcccccCCCCccccccccccccC--CCCCCCcccccccc
Q 000891 376 ECRICGM---DGTLLCCDGCPSAYHTRCIGVSKM--YVPEGSWYCPECAI 420 (1236)
Q Consensus 376 ~C~VCgd---gGeLLcCD~CprafHl~CL~PpL~--~iPeGdW~Cp~C~~ 420 (1236)
+|.+|+. ++.+|.||.|...||..|++|+.. .++.+.|+|+.|..
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 4788887 579999999999999999999865 55567999999973
No 8
>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=98.04 E-value=2e-06 Score=88.27 Aligned_cols=78 Identities=23% Similarity=0.340 Sum_probs=47.4
Q ss_pred cccccccccccCCCCCCCccccccccccCCCcccccccccccccccccchhhhhhhhcccceeeccCCCchhc-cccccc
Q 000891 395 AYHTRCIGVSKMYVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDLYERVFLGTCNHLLVLNASSNTEQY-IRYYNP 473 (1236)
Q Consensus 395 afHl~CL~PpL~~iPeGdW~Cp~C~~~k~gpe~E~g~s~rg~e~LGcD~cgQ~Yh~kC~rlLve~~s~D~e~c-~rYYs~ 473 (1236)
+||+.||.|||..+|+|+|+||.|.....+..........+...-+-...+..|-.+.++++..+ .. .++. .|||.+
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~vArIekiW~~~-G~-~~~~grWy~rP 78 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQLPPTSRSACEKLLSGDLWLARIEKLWEEN-GT-YWYAARWYTLP 78 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCcccccCCCcchhhhhhhccCchHHHHHHHHHhcc-Cc-eEEEEEEEeCc
Confidence 69999999999999999999999997665433322111111111112244566767777777653 11 2333 555654
Q ss_pred C
Q 000891 474 I 474 (1236)
Q Consensus 474 v 474 (1236)
-
T Consensus 79 E 79 (148)
T cd04718 79 E 79 (148)
T ss_pred h
Confidence 3
No 9
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.03 E-value=2.2e-06 Score=105.10 Aligned_cols=54 Identities=39% Similarity=0.930 Sum_probs=49.2
Q ss_pred cccccccccccccccCcccccCCCCccccccccccccCCCCCCCcccccccccc
Q 000891 369 DVDGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 369 ~~d~ndD~C~VCgdgGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k 422 (1236)
.++.+...|++|+++|.+|+||.|+.+||.+|+++|+..+|.++|.|+.|.++.
T Consensus 42 ~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 42 WDDAEQEACRICADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPK 95 (696)
T ss_pred cchhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCC
Confidence 556677899999999999999999999999999999999999999999996543
No 10
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.95 E-value=3.1e-06 Score=102.47 Aligned_cols=46 Identities=35% Similarity=0.970 Sum_probs=41.2
Q ss_pred ccccccccc---CcccccCCCCcc-ccccccccccCCCCCCCcccccccc
Q 000891 375 DECRICGMD---GTLLCCDGCPSA-YHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 375 D~C~VCgdg---GeLLcCD~Cpra-fHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
..|.+|... ..||+||.|+.+ ||++||+|++-++|-+.|||+.|.-
T Consensus 216 ~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 216 VKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred ccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 458888874 489999999999 9999999999999999999999963
No 11
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.58 E-value=4.2e-05 Score=84.08 Aligned_cols=47 Identities=38% Similarity=1.070 Sum_probs=39.2
Q ss_pred ccccccccccccc--CcccccCC--CCc-cccccccccccCCCCCCCcccccccc
Q 000891 371 DGNGDECRICGMD--GTLLCCDG--CPS-AYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 371 d~ndD~C~VCgdg--GeLLcCD~--Cpr-afHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
.++.-+|. |+++ |+|+-||+ |.+ .||+.|++.. ..|.|.|||+.|..
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 44555676 8875 89999995 986 6999999987 88999999999974
No 13
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.56 E-value=4.9e-05 Score=89.65 Aligned_cols=132 Identities=15% Similarity=0.223 Sum_probs=90.4
Q ss_pred cccccccc-----cCcccccCCCCccccccccccccCCCCCCCccccccccccC---------CCcc-----------cc
Q 000891 375 DECRICGM-----DGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKV---------GPIV-----------TI 429 (1236)
Q Consensus 375 D~C~VCgd-----gGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k~---------gpe~-----------E~ 429 (1236)
-.|.+|.. +.++..|+.|..+||+.|..|. ..-.+.|.|..|..... ++-. ..
T Consensus 84 ~~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~--~~~~~~~~~~~c~~~~~~~~g~a~K~g~~a~~~l~y~~~~l~w 161 (464)
T KOG4323|consen 84 LNPNVLTSETVLPENEKVICGRCKSGYHQGCNIPR--FPSLDIGESTECVFPIFSQEGGALKKGRLARPSLPYPEASLDW 161 (464)
T ss_pred cCCcccccccccCchhhhhhhhhccCcccccCccC--cCcCCccccccccccccccccccccccccccccccCccccccc
Confidence 44666765 3468899999999999999997 34457899999964321 1000 10
Q ss_pred c----------ccc-----cccccccccchhhhhhhhcccceeeccCCCchhcccccc-cCchhHHHHhhhc--------
Q 000891 430 G----------TSL-----RGAELFGIDLYERVFLGTCNHLLVLNASSNTEQYIRYYN-PIDIPKVLQALLS-------- 485 (1236)
Q Consensus 430 g----------~s~-----rg~e~LGcD~cgQ~Yh~kC~rlLve~~s~D~e~c~rYYs-~vDl~evLevL~~-------- 485 (1236)
+ +|. ...+|+.|+.|.++||..|+++++.++..++.+..|||. |....+.+.++.+
T Consensus 162 D~~~~~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~t~~~~dv~~l 241 (464)
T KOG4323|consen 162 DSGHKVNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRLTLRWADVLHL 241 (464)
T ss_pred CccccccceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccccccccccccch
Confidence 0 111 223689999999999999999999988887788899998 4444444333333
Q ss_pred -----cccchhhhh----hHHHHHHHhhcCCC
Q 000891 486 -----SVQHVSLYL----GICKAILHYWDIPE 508 (1236)
Q Consensus 486 -----SDih~~~Y~----eIc~~I~e~Wdi~~ 508 (1236)
..++..+|+ +|..|+.+.|.-+.
T Consensus 242 al~~~~~~~~~k~~~~~~ei~~f~e~~~~slp 273 (464)
T KOG4323|consen 242 ALYNLKPMLKKKYFKSLVEILLFCEESWPSLP 273 (464)
T ss_pred hhhhhhhhhccCCcccHHHHHHHHhhcccccc
Confidence 333444555 78888888887654
No 14
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.54 E-value=4.3e-05 Score=85.30 Aligned_cols=43 Identities=37% Similarity=1.039 Sum_probs=37.3
Q ss_pred cccccccccCcccccCC--CC-ccccccccccccCCCCCCCcccccccc
Q 000891 375 DECRICGMDGTLLCCDG--CP-SAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 375 D~C~VCgdgGeLLcCD~--Cp-rafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
.+|. |...|+|+-||+ |+ ..||+.|+|.. ..|.|.|||+.|..
T Consensus 222 C~Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVGL~--~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 222 CICN-QVSYGKMIGCDNPGCPIEWFHFTCVGLK--TKPKGKWYCPRCKA 267 (274)
T ss_pred EEec-ccccccccccCCCCCCcceEEEeccccc--cCCCCcccchhhhh
Confidence 3455 556899999998 99 89999999997 78999999999985
No 15
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.44 E-value=4.7e-05 Score=84.56 Aligned_cols=46 Identities=37% Similarity=0.873 Sum_probs=39.3
Q ss_pred ccccccccccc---CcccccCCCCccccccccccccCCCCCCCcccc-cccc
Q 000891 373 NGDECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCP-ECAI 420 (1236)
Q Consensus 373 ndD~C~VCgdg---GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp-~C~~ 420 (1236)
....|.+|+++ .++++||.|+++||.+|++.. .+|.|.|.|. .|..
T Consensus 313 ~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~--~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 313 SCELCRICLGPVIESEHLFCDVCDRGPHTLCVGLQ--DLPRGEWICDMRCRE 362 (381)
T ss_pred ccHhhhccCCcccchheeccccccCCCCccccccc--cccCccchhhhHHHH
Confidence 44568889885 589999999999999999987 8999999998 4653
No 16
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.41 E-value=4.2e-05 Score=92.24 Aligned_cols=44 Identities=39% Similarity=1.105 Sum_probs=39.4
Q ss_pred ccccccccc-----CcccccCC--CCccccccccccccCCCCCCCcccccccc
Q 000891 375 DECRICGMD-----GTLLCCDG--CPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 375 D~C~VCgdg-----GeLLcCD~--CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
.-|.||-|. .-|+.||+ |.-+.|+.|+++. .+|.|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv--qVPtGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV--QVPTGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeE--ecCCCchhhhhhhh
Confidence 459999983 37999995 9999999999998 89999999999974
No 17
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.19 E-value=0.00015 Score=87.63 Aligned_cols=46 Identities=35% Similarity=0.930 Sum_probs=40.5
Q ss_pred ccccccccccC---cccccCCCCccccccccccccCCCCCCCccccccc
Q 000891 374 GDECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 419 (1236)
Q Consensus 374 dD~C~VCgdgG---eLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~ 419 (1236)
.-.|..|+.+| .+++|+.|+.+||.+|..|+...+|.|.|+|+.|.
T Consensus 68 crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~ 116 (694)
T KOG4443|consen 68 CRVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCT 116 (694)
T ss_pred ceeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHH
Confidence 34677777544 79999999999999999999999999999999995
No 18
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.97 E-value=0.00025 Score=86.44 Aligned_cols=46 Identities=35% Similarity=0.938 Sum_probs=40.9
Q ss_pred ccccccccccc-----CcccccCCCCccccccccccccCCCCCCCcccccccc
Q 000891 373 NGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 373 ndD~C~VCgdg-----GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
++-.|.||..+ .+|++||.|..-.|+.|+++. .+|+|.|.|..|..
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIl--e~p~gpWlCr~Cal 320 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGIL--EVPEGPWLCRTCAL 320 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhcee--ecCCCCeeehhccc
Confidence 66678888875 499999999999999999997 89999999999964
No 19
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.82 E-value=0.00027 Score=93.02 Aligned_cols=49 Identities=33% Similarity=0.868 Sum_probs=44.0
Q ss_pred cccccccccccC---cccccCCCCccccccccccccCCCCCCCccccccccc
Q 000891 373 NGDECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAIN 421 (1236)
Q Consensus 373 ndD~C~VCgdgG---eLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~ 421 (1236)
....|.+|...+ .+++||.|..+||++|+.|.+..+|.|+|+||.|+..
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchh
Confidence 446799999743 7999999999999999999999999999999999853
No 20
>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=96.59 E-value=0.0022 Score=56.63 Aligned_cols=42 Identities=31% Similarity=0.505 Sum_probs=32.3
Q ss_pred ceeecceehhccCC--ceEEEEEEEEe--cceEEEEecCCCccccC
Q 000891 41 IALVGRYVLKEFES--GIFLGKIVYYE--SGLYRVDYEDGDCEDLD 82 (1236)
Q Consensus 41 ~~LvGr~V~k~f~~--~~~~GkV~~yd--~g~Y~V~yEDGd~Edl~ 82 (1236)
++=+|+.|.-..++ -+|-|||++|| ...|.|.|+||+..+|-
T Consensus 5 k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~lk 50 (55)
T PF09465_consen 5 KFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELELK 50 (55)
T ss_dssp SS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEEE
T ss_pred cccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEec
Confidence 35689999988888 78899999999 99999999999986553
No 21
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.05 E-value=0.0014 Score=53.17 Aligned_cols=34 Identities=50% Similarity=1.165 Sum_probs=20.2
Q ss_pred CcccccCCCCccccccccccccCCCCCC-Cccccccc
Q 000891 384 GTLLCCDGCPSAYHTRCIGVSKMYVPEG-SWYCPECA 419 (1236)
Q Consensus 384 GeLLcCD~CprafHl~CL~PpL~~iPeG-dW~Cp~C~ 419 (1236)
+.||.|++|....|..|++.. .+|++ +|+|..|.
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 468999999999999999998 66776 79999884
No 22
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.85 E-value=0.0031 Score=74.98 Aligned_cols=47 Identities=30% Similarity=0.708 Sum_probs=38.0
Q ss_pred ccccccccC-----cccccCCCCccccccccccccC----CCCCCCcccccccccc
Q 000891 376 ECRICGMDG-----TLLCCDGCPSAYHTRCIGVSKM----YVPEGSWYCPECAINK 422 (1236)
Q Consensus 376 ~C~VCgdgG-----eLLcCD~CprafHl~CL~PpL~----~iPeGdW~Cp~C~~~k 422 (1236)
.|.||+.++ +||.|++|...||+.|+.|+.. .-|...|||..|...+
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 499998643 8999999999999999999642 2255689999998543
No 23
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=95.59 E-value=0.0042 Score=75.73 Aligned_cols=94 Identities=20% Similarity=0.432 Sum_probs=67.9
Q ss_pred ccccccccccc-----CcccccCCCCccccccccccccCCCC-CCCcccccccc-ccCCCcccccccccccccccccchh
Q 000891 373 NGDECRICGMD-----GTLLCCDGCPSAYHTRCIGVSKMYVP-EGSWYCPECAI-NKVGPIVTIGTSLRGAELFGIDLYE 445 (1236)
Q Consensus 373 ndD~C~VCgdg-----GeLLcCD~CprafHl~CL~PpL~~iP-eGdW~Cp~C~~-~k~gpe~E~g~s~rg~e~LGcD~cg 445 (1236)
....|.+|+.. |.|+-|..|..-||.+|+...+...- .+-|.|+.|+. ..|+... .-...+-|+.|.
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~g------D~~kf~~Ck~cD 90 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTG------DPKKFLLCKRCD 90 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccC------Cccccccccccc
Confidence 34568888764 47999999999999999996543321 23499999984 3343111 113345689999
Q ss_pred hhhhhhcccceeeccCCCchhcccccc
Q 000891 446 RVFLGTCNHLLVLNASSNTEQYIRYYN 472 (1236)
Q Consensus 446 Q~Yh~kC~rlLve~~s~D~e~c~rYYs 472 (1236)
-.||.-|.++.....+.++++|.+...
T Consensus 91 vsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 91 VSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred ccccccccCCccccccCcccccHHHHh
Confidence 999999999998888888777766555
No 24
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.46 E-value=0.0058 Score=72.50 Aligned_cols=45 Identities=33% Similarity=0.824 Sum_probs=39.2
Q ss_pred cccccccccC---cccccCCCCccccccccccccCCCCCC----Cccccccc
Q 000891 375 DECRICGMDG---TLLCCDGCPSAYHTRCIGVSKMYVPEG----SWYCPECA 419 (1236)
Q Consensus 375 D~C~VCgdgG---eLLcCD~CprafHl~CL~PpL~~iPeG----dW~Cp~C~ 419 (1236)
-.|.+|...- -++.||.|...||+-||.|||..+|.- .|+|..|.
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 4699999843 578899999999999999999999974 49999995
No 25
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.44 E-value=0.0045 Score=69.40 Aligned_cols=90 Identities=14% Similarity=0.158 Sum_probs=63.9
Q ss_pred ccccccccc---------CcccccCCCCcccccccccccc---CCCCCCCccccccc-cccCCCcccccccccccccccc
Q 000891 375 DECRICGMD---------GTLLCCDGCPSAYHTRCIGVSK---MYVPEGSWYCPECA-INKVGPIVTIGTSLRGAELFGI 441 (1236)
Q Consensus 375 D~C~VCgdg---------GeLLcCD~CprafHl~CL~PpL---~~iPeGdW~Cp~C~-~~k~gpe~E~g~s~rg~e~LGc 441 (1236)
..|.+|-++ ..+++|..|..++|..|+..+. ..+-.-.|.|..|. |..|+.. ....+++-|
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P------~~E~E~~FC 332 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGP------VIESEHLFC 332 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCc------ccchheecc
Confidence 468888774 3699999999999999998653 23334589999996 4444321 223567779
Q ss_pred cchhhhhhhhcccceeeccCCCchhcccccc
Q 000891 442 DLYERVFLGTCNHLLVLNASSNTEQYIRYYN 472 (1236)
Q Consensus 442 D~cgQ~Yh~kC~rlLve~~s~D~e~c~rYYs 472 (1236)
|.|+|.||..|.-+- ....+.|.|--|+.
T Consensus 333 D~CDRG~HT~CVGL~--~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 333 DVCDRGPHTLCVGLQ--DLPRGEWICDMRCR 361 (381)
T ss_pred ccccCCCCccccccc--cccCccchhhhHHH
Confidence 999999999997663 33455566665554
No 26
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.06 E-value=0.018 Score=71.76 Aligned_cols=70 Identities=24% Similarity=0.363 Sum_probs=53.1
Q ss_pred CCCccccccccccccCCCCCCCccccccccccCCCcccc-----------cccccccccccccchhhhhhhhcccceeec
Q 000891 391 GCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGPIVTI-----------GTSLRGAELFGIDLYERVFLGTCNHLLVLN 459 (1236)
Q Consensus 391 ~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k~gpe~E~-----------g~s~rg~e~LGcD~cgQ~Yh~kC~rlLve~ 459 (1236)
.|+++||..|+.|.+..-|+++|.||.|.....+-+... +.+..+++++.|+.|..+||..|...-+..
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 499999999999998888899999999975433321111 134667888999999999999998554333
Q ss_pred c
Q 000891 460 A 460 (1236)
Q Consensus 460 ~ 460 (1236)
.
T Consensus 81 ~ 81 (696)
T KOG0383|consen 81 Q 81 (696)
T ss_pred C
Confidence 3
No 27
>PF15612 WHIM1: WSTF, HB1, Itc1p, MBD9 motif 1; PDB: 2Y9Z_B 2Y9Y_B.
Probab=94.79 E-value=0.024 Score=48.09 Aligned_cols=44 Identities=45% Similarity=0.738 Sum_probs=36.2
Q ss_pred cccccccccccccchhhHHHHHHHHHhhhcchHHHHHHHhhccc
Q 000891 258 FYDEVSVREYYSLSAGRKLMILQILCDDVLDSEELRAEIDAREE 301 (1236)
Q Consensus 258 f~~~ll~~EYy~~pV~~KL~ILq~LcD~~l~s~efRsE~dmrEe 301 (1236)
....+.+.+|+.+++..|+.||++|||..+++..+|.+++..++
T Consensus 5 ~~~~l~~~~y~~L~~~~kl~iL~~L~~~~l~s~~vr~~i~~~~e 48 (50)
T PF15612_consen 5 LAPPLETGEYYELSPEEKLEILRALCDQLLSSSSVRNEIEEREE 48 (50)
T ss_dssp G-CCCCCSTCCCS-HHHHHHHHHHHHHHHCC-CCHHHHHHHHHT
T ss_pred hhHHHHcCCcccCCHHHHHHHHHHHHHHHcCcHHHHHHHHHhhc
Confidence 34456678999999999999999999999999999999986654
No 28
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=94.03 E-value=0.016 Score=64.95 Aligned_cols=88 Identities=19% Similarity=0.375 Sum_probs=63.2
Q ss_pred ccccccccc----------cCcccccCCCCcccccccccccc---CCCCCCCccccccc-cccCCCcccccccccccccc
Q 000891 374 GDECRICGM----------DGTLLCCDGCPSAYHTRCIGVSK---MYVPEGSWYCPECA-INKVGPIVTIGTSLRGAELF 439 (1236)
Q Consensus 374 dD~C~VCgd----------gGeLLcCD~CprafHl~CL~PpL---~~iPeGdW~Cp~C~-~~k~gpe~E~g~s~rg~e~L 439 (1236)
..+|.-|.+ +.+|+-|..|+++=|..||.-.. ..+-...|+|-.|. +..|+... -..+++
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtse------nddqll 297 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSE------NDDQLL 297 (336)
T ss_pred CcccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcC------CCceeE
Confidence 356777765 34899999999999999998532 24455689999998 34443222 225678
Q ss_pred cccchhhhhhhhcccceeeccCCCchhc
Q 000891 440 GIDLYERVFLGTCNHLLVLNASSNTEQY 467 (1236)
Q Consensus 440 GcD~cgQ~Yh~kC~rlLve~~s~D~e~c 467 (1236)
-||.|+|.||--|..+-+..-..++|.|
T Consensus 298 fcddcdrgyhmyclsppm~eppegswsc 325 (336)
T KOG1244|consen 298 FCDDCDRGYHMYCLSPPMVEPPEGSWSC 325 (336)
T ss_pred eecccCCceeeEecCCCcCCCCCCchhH
Confidence 8999999999999887655445555554
No 29
>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=92.97 E-value=0.099 Score=44.65 Aligned_cols=48 Identities=27% Similarity=0.440 Sum_probs=41.9
Q ss_pred eeecceehhcc-CCceEEEEEEEEec-ceEEEEecC-CCccccChhHHHhh
Q 000891 42 ALVGRYVLKEF-ESGIFLGKIVYYES-GLYRVDYED-GDCEDLDSSELRQF 89 (1236)
Q Consensus 42 ~LvGr~V~k~f-~~~~~~GkV~~yd~-g~Y~V~yED-Gd~Edl~~~el~~~ 89 (1236)
+-+|-.|.-.| .+..|=|+|++++. +.|.|.|.| |+.|.+...+|+.+
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 44677777778 67999999999995 999999999 99999999998765
No 30
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=91.36 E-value=0.14 Score=66.04 Aligned_cols=145 Identities=17% Similarity=0.375 Sum_probs=89.3
Q ss_pred ccccccccccC--cccccCCCCccccccccccccCCCCCCCccccccccccCCCc-cccccccccccccc-------ccc
Q 000891 374 GDECRICGMDG--TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINKVGPI-VTIGTSLRGAELFG-------IDL 443 (1236)
Q Consensus 374 dD~C~VCgdgG--eLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k~gpe-~E~g~s~rg~e~LG-------cD~ 443 (1236)
...|..|..+. .++.|++|...||..|..+++..+|+|+|.|+.|........ ...|.. .+..-+. .+.
T Consensus 155 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gf~-~~~~~yt~~~f~~~~~~ 233 (904)
T KOG1246|consen 155 YPQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTPESKPNYKFGFE-QGSREYTLPKFEEYADN 233 (904)
T ss_pred chhhhccccCCCccceecccccCcccccccCCCCCcCCcCcccCCcccccccCCcccccCcC-CCCCccccchhhhHhhh
Confidence 35688999865 234999999999999999999999999999999986533211 111110 1110111 122
Q ss_pred hhhhhhhhcccceeeccCCC--chhcccccccCch-hHHHHhhhccccchhhhhhHHH----------HHHHhhcCCCCC
Q 000891 444 YERVFLGTCNHLLVLNASSN--TEQYIRYYNPIDI-PKVLQALLSSVQHVSLYLGICK----------AILHYWDIPESV 510 (1236)
Q Consensus 444 cgQ~Yh~kC~rlLve~~s~D--~e~c~rYYs~vDl-~evLevL~~SDih~~~Y~eIc~----------~I~e~Wdi~~nl 510 (1236)
....|... .....+ ..++..||..+.. ..-..+++++|.+...++.+.. .-.+|-+...|+
T Consensus 234 ~~~~~~~~------~~~~~~~~~~vE~e~w~~v~~~~~~~~~~~g~d~~~~~~~s~~~~~~~~~~~~~~~~~y~~s~wnL 307 (904)
T KOG1246|consen 234 FKKDYFPK------SKNSPDSTEDVEKEFWRLVASNLESVEVLYGADLSTKEFGSGFPKSASGPLLGSEAEKYSNSGWNL 307 (904)
T ss_pred hhcccccc------ccCCCCchHHHHHHHHHhhcccccceeeeeccchhhccccccccccCCCCCCCcchhhhccCcccc
Confidence 22222111 111111 1567888986533 3446678999988777764432 113677777888
Q ss_pred CCCCCcccccccccc
Q 000891 511 VPFMGMETNTINAKA 525 (1236)
Q Consensus 511 ~~~~~~e~sl~~~~~ 525 (1236)
++.+..+.++...+.
T Consensus 308 ~~i~~~~~svl~~~~ 322 (904)
T KOG1246|consen 308 NNIPRLEGSVLSHID 322 (904)
T ss_pred cccccCCcccccccc
Confidence 887777777765543
No 31
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=90.51 E-value=0.18 Score=60.42 Aligned_cols=47 Identities=34% Similarity=0.887 Sum_probs=37.9
Q ss_pred cccccccc-----cCcccccCCCCccccccccccc-cCCCCCC-------Cccccccccc
Q 000891 375 DECRICGM-----DGTLLCCDGCPSAYHTRCIGVS-KMYVPEG-------SWYCPECAIN 421 (1236)
Q Consensus 375 D~C~VCgd-----gGeLLcCD~CprafHl~CL~Pp-L~~iPeG-------dW~Cp~C~~~ 421 (1236)
-.|.||-+ .|++|-||.|+-..|--|++.. ...||.| .|||.-|+..
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 38999987 4799999999999999999974 2345543 5999999754
No 32
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=86.37 E-value=0.38 Score=59.35 Aligned_cols=47 Identities=32% Similarity=0.822 Sum_probs=39.6
Q ss_pred ccccccccccCcccccCCCCccccccccccccC-CCCCCCcccccccc
Q 000891 374 GDECRICGMDGTLLCCDGCPSAYHTRCIGVSKM-YVPEGSWYCPECAI 420 (1236)
Q Consensus 374 dD~C~VCgdgGeLLcCD~CprafHl~CL~PpL~-~iPeGdW~Cp~C~~ 420 (1236)
-+.|.+|..+|.++||+.|+.+||+.|-++++. ..+.+.|.|..|..
T Consensus 47 ~ts~~~~~~~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSGGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhcCCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 567999999999999999999999999999875 22235788888864
No 33
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=85.42 E-value=1.1 Score=39.30 Aligned_cols=49 Identities=24% Similarity=0.125 Sum_probs=42.0
Q ss_pred eeecceehhcc--CCceEEEEEEEEe-cceEEEEecC---CCccccChhHHHhhh
Q 000891 42 ALVGRYVLKEF--ESGIFLGKIVYYE-SGLYRVDYED---GDCEDLDSSELRQFL 90 (1236)
Q Consensus 42 ~LvGr~V~k~f--~~~~~~GkV~~yd-~g~Y~V~yED---Gd~Edl~~~el~~~l 90 (1236)
+-+|..|.=.| .+.-|-|+|++++ .+-|.|.|.| |+.|.+++..||.+.
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 8899999999999 4889999998 578888888888754
No 34
>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=81.70 E-value=1.7 Score=35.87 Aligned_cols=41 Identities=27% Similarity=0.371 Sum_probs=34.5
Q ss_pred eehhccC--CceEEEEEEEEe-cceEEEEecC-CCccccChhHHH
Q 000891 47 YVLKEFE--SGIFLGKIVYYE-SGLYRVDYED-GDCEDLDSSELR 87 (1236)
Q Consensus 47 ~V~k~f~--~~~~~GkV~~yd-~g~Y~V~yED-Gd~Edl~~~el~ 87 (1236)
.+.-.|. +..|=|+|.+.+ .+.|.|.|.| |..|.+...+|+
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 689999999999 9999999999 999999988775
No 35
>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=81.56 E-value=1.8 Score=44.26 Aligned_cols=38 Identities=26% Similarity=0.500 Sum_probs=29.3
Q ss_pred eeecceehhccCC-ce-EEEEEEEEe-cceEEEEecCCCcc
Q 000891 42 ALVGRYVLKEFES-GI-FLGKIVYYE-SGLYRVDYEDGDCE 79 (1236)
Q Consensus 42 ~LvGr~V~k~f~~-~~-~~GkV~~yd-~g~Y~V~yEDGd~E 79 (1236)
.|||..|.-...+ ++ |-|+|+..- .+-|+|.|+||+.-
T Consensus 3 ~~iG~rV~AkWS~n~yyY~G~I~~~~~~~kykv~FdDG~~~ 43 (122)
T PF09038_consen 3 SFIGLRVFAKWSDNGYYYPGKITSDKGKNKYKVLFDDGYEC 43 (122)
T ss_dssp -STT-EEEEESSTTSEEEEEEEEEEETTTEEEEEETTS-EE
T ss_pred cccccEEEEEEccCCcccCceEeecCCCCeEEEEecCCccc
Confidence 5899998877776 67 579999965 89999999999863
No 36
>PLN00163 histone H4; Provisional
Probab=80.11 E-value=1.3 Score=40.12 Aligned_cols=24 Identities=46% Similarity=0.865 Sum_probs=22.8
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000891 958 LPHTIIRNAARRGGLRKISGVNYT 981 (1236)
Q Consensus 958 Lp~s~v~kAaRQgG~rki~gi~Y~ 981 (1236)
+.+.+|++-||.||.++|+|.+|.
T Consensus 30 ItKpaIrRLARRgGVKRIs~~iY~ 53 (59)
T PLN00163 30 ITKPAIRRLARRGGVKRISGLIYE 53 (59)
T ss_pred cchHHHHHHHHhcCceeecchhhH
Confidence 789999999999999999999996
No 37
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=73.40 E-value=1.4 Score=39.30 Aligned_cols=30 Identities=27% Similarity=0.845 Sum_probs=26.5
Q ss_pred cccccccc----cCcccccCCCCccccccccccc
Q 000891 375 DECRICGM----DGTLLCCDGCPSAYHTRCIGVS 404 (1236)
Q Consensus 375 D~C~VCgd----gGeLLcCD~CprafHl~CL~Pp 404 (1236)
..|.+|++ +++++.|..|...||..|....
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 57999997 5799999999999999999654
No 38
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=72.92 E-value=1.4 Score=47.22 Aligned_cols=44 Identities=36% Similarity=0.977 Sum_probs=33.0
Q ss_pred ccccccc------cCcccccCCCCcccccccccccc------CCCCCCC--ccccccc
Q 000891 376 ECRICGM------DGTLLCCDGCPSAYHTRCIGVSK------MYVPEGS--WYCPECA 419 (1236)
Q Consensus 376 ~C~VCgd------gGeLLcCD~CprafHl~CL~PpL------~~iPeGd--W~Cp~C~ 419 (1236)
.|.+|+. -|.|+.|-+|-.+||..|+++-. ..|-+++ .+|..|+
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 3788853 36899999999999999999842 2333333 6888886
No 39
>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=72.06 E-value=2.6 Score=35.88 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=26.8
Q ss_pred cccccCcccccc--eeccceecccccccccccc
Q 000891 1151 EKCACASCQIDV--LLGNAVKCGTCQGMLITNL 1181 (1236)
Q Consensus 1151 e~~~C~~C~kdV--~~r~av~C~~Cqg~~hk~~ 1181 (1236)
....|.+|++-+ +.+.+.+|..|+-.+|++|
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C 42 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKC 42 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTG
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhh
Confidence 456899999999 8999999999999999998
No 40
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.99 E-value=3.8 Score=48.28 Aligned_cols=45 Identities=31% Similarity=0.631 Sum_probs=32.7
Q ss_pred ccccccccc---CcccccCCCCccccccccccccCCCCCCCcccccccccc
Q 000891 375 DECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 375 D~C~VCgdg---GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k 422 (1236)
+.|.+|.++ |+.|-==-|...||..|.+|.+..- .=+||.|+...
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 5433334578899999999986421 33799998643
No 41
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=57.73 E-value=5.7 Score=38.63 Aligned_cols=40 Identities=30% Similarity=0.523 Sum_probs=29.1
Q ss_pred ChHHHHHHHHHhcCcccccccccC---CCccccchhhhhhhhh
Q 000891 958 LPHTIIRNAARRGGLRKISGVNYT---AEMPKRSRQLVWRAAV 997 (1236)
Q Consensus 958 Lp~s~v~kAaRQgG~rki~gi~Y~---se~~rRsr~~~WraaV 997 (1236)
+.+.+||+-||.||.++|.|+.|- .-+--=-+.++|.|+.
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 457899999999999999999997 1111113456777764
No 42
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=57.01 E-value=1.9 Score=39.66 Aligned_cols=46 Identities=26% Similarity=0.566 Sum_probs=19.2
Q ss_pred ccccccccc----C--cccccC--CCCccccccccccccCCCCCC-------Ccccccccc
Q 000891 375 DECRICGMD----G--TLLCCD--GCPSAYHTRCIGVSKMYVPEG-------SWYCPECAI 420 (1236)
Q Consensus 375 D~C~VCgdg----G--eLLcCD--~CprafHl~CL~PpL~~iPeG-------dW~Cp~C~~ 420 (1236)
..|.+|... + -.+.|+ .|...||..||--.+...+.+ .+.||.|..
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~ 63 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSS 63 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-S
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCC
Confidence 458888752 2 247798 899999999998643222221 367999974
No 43
>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=53.39 E-value=5.8 Score=26.39 Aligned_cols=10 Identities=80% Similarity=1.301 Sum_probs=3.9
Q ss_pred CCCCCCCcCC
Q 000891 6 KRPRGRPRKR 15 (1236)
Q Consensus 6 ~~~~~r~r~~ 15 (1236)
.|+||||+|-
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 44
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=53.39 E-value=7.7 Score=47.34 Aligned_cols=49 Identities=27% Similarity=0.497 Sum_probs=41.7
Q ss_pred cccccccccccccCcccccCCCCccccccccccccCCCCCCCcccccccccc
Q 000891 371 DGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 371 d~ndD~C~VCgdgGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~~k 422 (1236)
..+.++|.+|.++|.+++|+.|..++|-.|... ..|++.|.|..|....
T Consensus 86 ~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~---~~~~c~~~~~d~~~~~ 134 (463)
T KOG1081|consen 86 KIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPA---QLEKCSKRCTDCRAFK 134 (463)
T ss_pred CCCcchhccccCCCccceeccccccccccCcCc---cCcccccCCcceeeec
Confidence 345689999999999999999999999999865 5788899999988543
No 45
>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=53.13 E-value=2 Score=35.41 Aligned_cols=41 Identities=32% Similarity=0.621 Sum_probs=26.9
Q ss_pred ccccccccc---CcccccCCCCccccccccccccCCCCCCCccccccc
Q 000891 375 DECRICGMD---GTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 419 (1236)
Q Consensus 375 D~C~VCgdg---GeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~ 419 (1236)
|.|.+|.++ ++.+.--.|...||..|+...+.. .-.||.|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~----~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR----NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH----SSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh----CCcCCccC
Confidence 468888872 333333349999999999986543 23899885
No 46
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=52.01 E-value=11 Score=46.54 Aligned_cols=50 Identities=18% Similarity=0.272 Sum_probs=40.7
Q ss_pred cccccccccccccCcccccCCCCccccccccccccCCCCC--CCccccccccc
Q 000891 371 DGNGDECRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPE--GSWYCPECAIN 421 (1236)
Q Consensus 371 d~ndD~C~VCgdgGeLLcCD~CprafHl~CL~PpL~~iPe--GdW~Cp~C~~~ 421 (1236)
...+-+|..|+.+|..|.|+-|-+.||..|..|.- .++. ..|.|+.|..-
T Consensus 57 ~N~d~~cfechlpg~vl~c~vc~Rs~h~~c~sp~~-q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 57 SNIDPFCFECHLPGAVLKCIVCHRSFHENCQSPDP-QKRNYSVPSDKPQPYSF 108 (588)
T ss_pred cCCCcccccccCCcceeeeehhhccccccccCcch-hhccccccccCCccccc
Confidence 34456899999999999999999999999999853 3444 35999999743
No 47
>smart00417 H4 Histone H4.
Probab=50.93 E-value=8.1 Score=36.52 Aligned_cols=24 Identities=46% Similarity=0.866 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000891 958 LPHTIIRNAARRGGLRKISGVNYT 981 (1236)
Q Consensus 958 Lp~s~v~kAaRQgG~rki~gi~Y~ 981 (1236)
||+..|++-||.||.++|+|-.|.
T Consensus 14 I~k~~IrRLaRr~GvkRIS~~~y~ 37 (74)
T smart00417 14 ITKPAIRRLARRGGVKRISGLIYD 37 (74)
T ss_pred CCHHHHHHHHHHcCcchhhHHHHH
Confidence 999999999999999999999987
No 48
>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=46.80 E-value=12 Score=29.21 Aligned_cols=16 Identities=50% Similarity=0.856 Sum_probs=12.0
Q ss_pred CCCCCCCcCCCCCCcc
Q 000891 6 KRPRGRPRKRKRPEDE 21 (1236)
Q Consensus 6 ~~~~~r~r~~~~~~~~ 21 (1236)
+|+||||||.......
T Consensus 1 kRkRGRPrK~~~~~~~ 16 (26)
T smart00384 1 KRKRGRPRKAPKDXXX 16 (26)
T ss_pred CCCCCCCCCCCCcccc
Confidence 4889999988765543
No 49
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=46.35 E-value=10 Score=43.21 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=31.6
Q ss_pred cccccccCCCCCCCccccccccccCCCcccccccccccccccccc--hh-hhhhhhcccceee
Q 000891 399 RCIGVSKMYVPEGSWYCPECAINKVGPIVTIGTSLRGAELFGIDL--YE-RVFLGTCNHLLVL 458 (1236)
Q Consensus 399 ~CL~PpL~~iPeGdW~Cp~C~~~k~gpe~E~g~s~rg~e~LGcD~--cg-Q~Yh~kC~rlLve 458 (1236)
....++...-|+..|||.-+.. ..++|.+||- |+ .|||+.|.-+...
T Consensus 206 ~~~~~~~~~d~~e~~yC~Cnqv-------------syg~Mi~CDn~~C~~eWFH~~CVGL~~~ 255 (274)
T KOG1973|consen 206 ESMESEEAVDPDEPTYCICNQV-------------SYGKMIGCDNPGCPIEWFHFTCVGLKTK 255 (274)
T ss_pred cccccccccCCCCCEEEEeccc-------------ccccccccCCCCCCcceEEEeccccccC
Confidence 3444554455556666654421 2467889987 99 9999999988644
No 50
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=46.17 E-value=8.8 Score=41.88 Aligned_cols=37 Identities=19% Similarity=0.591 Sum_probs=30.3
Q ss_pred cccCcccc-ccee----ccceecccccccccccc--eeeeeecc
Q 000891 1153 CACASCQI-DVLL----GNAVKCGTCQGMLITNL--SVFCFRDV 1189 (1236)
Q Consensus 1153 ~~C~~C~k-dV~~----r~av~C~~Cqg~~hk~~--~~~~~~~~ 1189 (1236)
..|..|+. ||++ ..++.|..|...||++| .-.|.||.
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~~CpkC~ 196 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKKSCPKCA 196 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCCCCCCcH
Confidence 47899996 5654 48999999999999999 55688885
No 51
>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=42.23 E-value=9.9 Score=31.06 Aligned_cols=31 Identities=13% Similarity=0.415 Sum_probs=26.1
Q ss_pred ccccCcccccceec-cceecccccccccccce
Q 000891 1152 KCACASCQIDVLLG-NAVKCGTCQGMLITNLS 1182 (1236)
Q Consensus 1152 ~~~C~~C~kdV~~r-~av~C~~Cqg~~hk~~~ 1182 (1236)
...|..|++-+... .+.+|..|+-.+|++|.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~ 42 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCA 42 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHH
Confidence 34699999988754 49999999999999984
No 52
>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=39.42 E-value=12 Score=30.90 Aligned_cols=31 Identities=13% Similarity=0.345 Sum_probs=26.9
Q ss_pred cccCccccccee--ccceeccccccccccccee
Q 000891 1153 CACASCQIDVLL--GNAVKCGTCQGMLITNLSV 1183 (1236)
Q Consensus 1153 ~~C~~C~kdV~~--r~av~C~~Cqg~~hk~~~~ 1183 (1236)
..|.+|++-+.. ..+.+|..|+-.+|++|..
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~ 44 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCAD 44 (50)
T ss_pred CChhhcchhhhccccceeEcCCCCCchhhhhhc
Confidence 469999998876 6999999999999999853
No 53
>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=39.28 E-value=16 Score=35.49 Aligned_cols=24 Identities=46% Similarity=0.804 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000891 958 LPHTIIRNAARRGGLRKISGVNYT 981 (1236)
Q Consensus 958 Lp~s~v~kAaRQgG~rki~gi~Y~ 981 (1236)
||...|++-||.||.++|++-.|.
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 54
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=38.92 E-value=12 Score=36.45 Aligned_cols=29 Identities=24% Similarity=0.480 Sum_probs=22.3
Q ss_pred CCCccccccccccccCCCCCCCcccccccc
Q 000891 391 GCPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 391 ~CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
.|...||+.|+.--+..- ...=.||.|+.
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 599999999998876542 33458999985
No 55
>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=36.47 E-value=11 Score=34.87 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=18.7
Q ss_pred CCCccccccccccccCCCCCCCccccccc
Q 000891 391 GCPSAYHTRCIGVSKMYVPEGSWYCPECA 419 (1236)
Q Consensus 391 ~CprafHl~CL~PpL~~iPeGdW~Cp~C~ 419 (1236)
.|+-.||..|+..-+.. ...||.|+
T Consensus 49 ~C~H~FH~~Ci~~Wl~~----~~~CP~CR 73 (73)
T PF12678_consen 49 PCGHIFHFHCISQWLKQ----NNTCPLCR 73 (73)
T ss_dssp TTSEEEEHHHHHHHHTT----SSB-TTSS
T ss_pred ccCCCEEHHHHHHHHhc----CCcCCCCC
Confidence 59999999999876543 24899985
No 56
>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=35.85 E-value=8.5 Score=32.22 Aligned_cols=31 Identities=26% Similarity=0.647 Sum_probs=23.6
Q ss_pred HHHhhhccccccccccccccccccCcccccccccc
Q 000891 750 AKAFSSTASRFFWPCSERKLWEVPRERCSWCYSCK 784 (1236)
Q Consensus 750 ~Kafs~~~~~F~Wps~ekk~~ev~rerCGWC~sCk 784 (1236)
-|++++-+.+|+||...+-..++-| -|..||
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 356654
No 57
>PTZ00015 histone H4; Provisional
Probab=35.72 E-value=24 Score=35.39 Aligned_cols=35 Identities=40% Similarity=0.652 Sum_probs=28.2
Q ss_pred cchhhhhhccc--ChHHHHHHHHHhcCcccccccccC
Q 000891 947 KSTKLISKKAI--LPHTIIRNAARRGGLRKISGVNYT 981 (1236)
Q Consensus 947 ~lsr~if~~~~--Lp~s~v~kAaRQgG~rki~gi~Y~ 981 (1236)
+=.|+++.-.+ ||...|++-||.||.++|++-.|.
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 44455554333 899999999999999999999997
No 58
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.71 E-value=21 Score=39.03 Aligned_cols=36 Identities=39% Similarity=0.934 Sum_probs=28.6
Q ss_pred cccccccccC--------cccccCCCCccccccccccccCCCCCCCccccccc
Q 000891 375 DECRICGMDG--------TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECA 419 (1236)
Q Consensus 375 D~C~VCgdgG--------eLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~ 419 (1236)
-.|.+|..++ ...-|..|...||..|.... .||.|.
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~---------~CpkC~ 196 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK---------SCPKCA 196 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC---------CCCCcH
Confidence 4688888643 56789999999999999841 199996
No 59
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=34.62 E-value=16 Score=34.21 Aligned_cols=32 Identities=25% Similarity=0.733 Sum_probs=27.0
Q ss_pred ccccccccccc-CcccccCC--CCccccccccccc
Q 000891 373 NGDECRICGMD-GTLLCCDG--CPSAYHTRCIGVS 404 (1236)
Q Consensus 373 ndD~C~VCgdg-GeLLcCD~--CprafHl~CL~Pp 404 (1236)
....|.+|+.. |..+-|.. |...||..|..-.
T Consensus 35 ~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 35 RKLKCSICKKKGGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred hCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccC
Confidence 34579999998 98888984 9999999998753
No 60
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=33.66 E-value=18 Score=35.22 Aligned_cols=31 Identities=32% Similarity=0.819 Sum_probs=26.3
Q ss_pred cccccccccc-cCcccccCC--CCcccccccccc
Q 000891 373 NGDECRICGM-DGTLLCCDG--CPSAYHTRCIGV 403 (1236)
Q Consensus 373 ndD~C~VCgd-gGeLLcCD~--CprafHl~CL~P 403 (1236)
....|.+|+. .|..+-|.. |...||..|...
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHH
Confidence 3467999998 588888997 999999999865
No 61
>KOG3532 consensus Predicted protein kinase [General function prediction only]
Probab=33.33 E-value=13 Score=47.01 Aligned_cols=45 Identities=9% Similarity=-0.034 Sum_probs=42.1
Q ss_pred ccccCcccccceeccceecccccccccccceeeeeeccCCCeEEE
Q 000891 1152 KCACASCQIDVLLGNAVKCGTCQGMLITNLSVFCFRDVLGFPVVY 1196 (1236)
Q Consensus 1152 ~~~C~~C~kdV~~r~av~C~~Cqg~~hk~~~~~~~~~~~~~~~~~ 1196 (1236)
..+|..|++-+-+-+|.-|+-|--.||+.|..+|.-+..|-||-.
T Consensus 757 ~~~~~~~~~ki~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~i~~ 801 (1051)
T KOG3532|consen 757 KRSASTRKAKIQATFAAGKKKVLDLMPQKRKNTDASDLNGESIEI 801 (1051)
T ss_pred hcccchhccceeehhhhcccHHHHhcchhhhcchhhhccCCceee
Confidence 569999999999999999999999999999999999999999853
No 62
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.93 E-value=26 Score=30.08 Aligned_cols=24 Identities=21% Similarity=0.578 Sum_probs=20.3
Q ss_pred ccccCcccccceec--cceecccccc
Q 000891 1152 KCACASCQIDVLLG--NAVKCGTCQG 1175 (1236)
Q Consensus 1152 ~~~C~~C~kdV~~r--~av~C~~Cqg 1175 (1236)
.|-|+.|..+|.+. +.|+|.+|-.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCc
Confidence 47899999999887 8899998853
No 63
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=30.72 E-value=31 Score=31.13 Aligned_cols=43 Identities=23% Similarity=0.411 Sum_probs=35.3
Q ss_pred ccccccCcccccce-eccceecccccccccccce---eeeee--ccCCC
Q 000891 1150 IEKCACASCQIDVL-LGNAVKCGTCQGMLITNLS---VFCFR--DVLGF 1192 (1236)
Q Consensus 1150 ~e~~~C~~C~kdV~-~r~av~C~~Cqg~~hk~~~---~~~~~--~~~~~ 1192 (1236)
-+...|..|.+.+. -.|+|-|..|...-|++|- -.|.. |..|+
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 34568999999997 7899999999999999994 66766 65554
No 64
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.78 E-value=31 Score=30.10 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=16.3
Q ss_pred cCCCCcccccccccc--------ccCCCCCCCcccccccccc
Q 000891 389 CDGCPSAYHTRCIGV--------SKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 389 CD~CprafHl~CL~P--------pL~~iPeGdW~Cp~C~~~k 422 (1236)
|..|.-.|...=-+| +...+|+ +|.||.|...+
T Consensus 4 C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~-~w~CP~C~a~K 44 (47)
T PF00301_consen 4 CPVCGYVYDPEKGDPENGIPPGTPFEDLPD-DWVCPVCGAPK 44 (47)
T ss_dssp ETTTSBEEETTTBBGGGTB-TT--GGGS-T-T-B-TTTSSBG
T ss_pred CCCCCEEEcCCcCCcccCcCCCCCHHHCCC-CCcCcCCCCcc
Confidence 555655555433322 2344544 79999998643
No 65
>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 cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=27.35 E-value=87 Score=32.68 Aligned_cols=49 Identities=18% Similarity=0.299 Sum_probs=33.6
Q ss_pred ccCcccccceeccceecccccccccccceeeeeeccCCCeEEEEEEEEEEEeeccCCcEEee
Q 000891 1154 ACASCQIDVLLGNAVKCGTCQGMLITNLSVFCFRDVLGFPVVYLRFYVNIYVKNFTDNIIFL 1215 (1236)
Q Consensus 1154 ~C~~C~kdV~~r~av~C~~Cqg~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1215 (1236)
.|..|+|-|.-.+. =+|.|-+|..=.+-.-.||.+++-+...|+.+-+.
T Consensus 36 aC~~C~kkv~~~~~-------------~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~ 84 (166)
T cd04476 36 ACPGCNKKVVEEGN-------------GTYRCEKCNKSVPNPEYRYILSLNVADHTGEAWLT 84 (166)
T ss_pred cccccCcccEeCCC-------------CcEECCCCCCcCCCccEEEEEEEEEEeCCCCEEEE
Confidence 57789988876542 24555555433334456888999999999988665
No 67
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=27.26 E-value=18 Score=28.27 Aligned_cols=41 Identities=24% Similarity=0.454 Sum_probs=28.4
Q ss_pred cccccccC-cccccCCCCccccccccccccCCCCCCCcccccccc
Q 000891 377 CRICGMDG-TLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 377 C~VCgdgG-eLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
|.+|.+.- ..+.-..|...||..|+...+.. +...||.|..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHh---CcCCCCCCCC
Confidence 67777643 33444568889999999875433 5677999874
No 68
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=26.94 E-value=16 Score=27.41 Aligned_cols=39 Identities=26% Similarity=0.479 Sum_probs=25.1
Q ss_pred cccccccCcccccCCCCccccccccccccCCCCCCCcccccc
Q 000891 377 CRICGMDGTLLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPEC 418 (1236)
Q Consensus 377 C~VCgdgGeLLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C 418 (1236)
|.+|.+......-..|...||..|+...+. .+.-.||.|
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~---~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIRKWLK---SGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHHHHHH---hCcCCCCCC
Confidence 566776554444556888899999876533 334457765
No 69
>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=26.44 E-value=24 Score=29.73 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=24.0
Q ss_pred cCcccccceeccceecccccccccccc
Q 000891 1155 CASCQIDVLLGNAVKCGTCQGMLITNL 1181 (1236)
Q Consensus 1155 C~~C~kdV~~r~av~C~~Cqg~~hk~~ 1181 (1236)
|..|...-...+.|.|..|..-+|-.|
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C 28 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQEC 28 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTT
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCccc
Confidence 677777777889999999999999998
No 70
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=26.38 E-value=35 Score=27.73 Aligned_cols=22 Identities=32% Similarity=0.955 Sum_probs=17.4
Q ss_pred cccCccccccee--ccceeccccc
Q 000891 1153 CACASCQIDVLL--GNAVKCGTCQ 1174 (1236)
Q Consensus 1153 ~~C~~C~kdV~~--r~av~C~~Cq 1174 (1236)
|.|+.|..+|.+ +|.|+|.+|-
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 579999998876 5779999985
No 71
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.07 E-value=40 Score=30.58 Aligned_cols=19 Identities=37% Similarity=1.041 Sum_probs=13.8
Q ss_pred cccCCCCCCCcccccccccc
Q 000891 403 VSKMYVPEGSWYCPECAINK 422 (1236)
Q Consensus 403 PpL~~iPeGdW~Cp~C~~~k 422 (1236)
-+.+++|+ +|.||.|-..+
T Consensus 28 T~fedlPd-~w~CP~Cg~~K 46 (55)
T COG1773 28 TPFEDLPD-DWVCPECGVGK 46 (55)
T ss_pred CchhhCCC-ccCCCCCCCCH
Confidence 44566776 89999998643
No 72
>PHA02929 N1R/p28-like protein; Provisional
Probab=24.71 E-value=31 Score=39.02 Aligned_cols=44 Identities=25% Similarity=0.514 Sum_probs=30.5
Q ss_pred cccccccccccC---c-----ccccCCCCccccccccccccCCCCCCCcccccccc
Q 000891 373 NGDECRICGMDG---T-----LLCCDGCPSAYHTRCIGVSKMYVPEGSWYCPECAI 420 (1236)
Q Consensus 373 ndD~C~VCgdgG---e-----LLcCD~CprafHl~CL~PpL~~iPeGdW~Cp~C~~ 420 (1236)
.+..|.+|.+.- . ...=..|...||..|+...+..- =.||.|+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~----~tCPlCR~ 224 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK----NTCPVCRT 224 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC----CCCCCCCC
Confidence 456899999841 1 11223688899999998865433 36999985
No 73
>PLN00035 histone H4; Provisional
Probab=22.59 E-value=45 Score=33.59 Aligned_cols=24 Identities=46% Similarity=0.865 Sum_probs=23.2
Q ss_pred ChHHHHHHHHHhcCcccccccccC
Q 000891 958 LPHTIIRNAARRGGLRKISGVNYT 981 (1236)
Q Consensus 958 Lp~s~v~kAaRQgG~rki~gi~Y~ 981 (1236)
||...|++-||.||.++|++-.|.
T Consensus 30 ipk~~IrRLARr~GvkRIS~~ay~ 53 (103)
T PLN00035 30 ITKPAIRRLARRGGVKRISGLIYE 53 (103)
T ss_pred CCHHHHHHHHHHcCcccchHHHHH
Confidence 999999999999999999999886
No 74
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.31 E-value=51 Score=29.14 Aligned_cols=33 Identities=24% Similarity=0.568 Sum_probs=19.5
Q ss_pred ccCCCCcccccccccc--------ccCCCCCCCccccccccc
Q 000891 388 CCDGCPSAYHTRCIGV--------SKMYVPEGSWYCPECAIN 421 (1236)
Q Consensus 388 cCD~CprafHl~CL~P--------pL~~iPeGdW~Cp~C~~~ 421 (1236)
.|..|.-.|...==++ +...+|+ +|.||.|...
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~-~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPD-DWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCC-CCCCCCCCCc
Confidence 3666766666432222 2334555 8999999753
No 75
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=21.69 E-value=31 Score=40.90 Aligned_cols=24 Identities=38% Similarity=1.034 Sum_probs=18.8
Q ss_pred cccccccccc--cC---cccccCCCCccc
Q 000891 373 NGDECRICGM--DG---TLLCCDGCPSAY 396 (1236)
Q Consensus 373 ndD~C~VCgd--gG---eLLcCD~Cpraf 396 (1236)
.++.|.|||+ .| .||-|+.|..-|
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCESCKGFF 42 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCESCKGFF 42 (475)
T ss_pred cccccccccCccccceeeeeehhhhhhHH
Confidence 4568999998 33 689999997655
No 76
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=21.53 E-value=18 Score=45.06 Aligned_cols=29 Identities=38% Similarity=0.781 Sum_probs=23.7
Q ss_pred cccccccc-----cCcccccCCCCcccccccccc
Q 000891 375 DECRICGM-----DGTLLCCDGCPSAYHTRCIGV 403 (1236)
Q Consensus 375 D~C~VCgd-----gGeLLcCD~CprafHl~CL~P 403 (1236)
.+|.-|+. -.+-|-|++|+..||..|..-
T Consensus 157 tFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~k 190 (888)
T KOG4236|consen 157 TFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAFK 190 (888)
T ss_pred hHHHHHHHHHHHHHHccccccCCCCcHhhhhhhc
Confidence 57889987 136678999999999999864
Done!