Query 000462
Match_columns 1482
No_of_seqs 453 out of 1297
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:36:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000462.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000462hhsearch_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-127 4E-132 1150.1 32.3 962 104-1326 158-1184(1414)
2 smart00571 DDT domain in diffe 99.6 7E-16 1.5E-20 138.7 5.5 60 136-195 1-62 (63)
3 PF02791 DDT: DDT domain; Int 99.6 1.1E-15 2.4E-20 136.4 5.6 60 136-195 1-60 (61)
4 PF00628 PHD: PHD-finger; Int 98.4 7.8E-08 1.7E-12 82.3 0.5 48 1267-1316 2-50 (51)
5 KOG4299 PHD Zn-finger protein 98.2 2.6E-07 5.7E-12 112.1 1.1 48 332-379 253-307 (613)
6 KOG1973 Chromatin remodeling p 98.2 4.8E-07 1E-11 102.5 2.1 53 1259-1317 213-268 (274)
7 smart00249 PHD PHD zinc finger 98.2 8.9E-07 1.9E-11 72.4 3.1 46 1267-1314 2-47 (47)
8 KOG1244 Predicted transcriptio 98.0 2E-06 4.3E-11 96.0 1.8 45 333-377 282-331 (336)
9 KOG1473 Nucleosome remodeling 98.0 1.4E-06 3.1E-11 110.0 0.5 132 330-461 426-568 (1414)
10 PF00628 PHD: PHD-finger; Int 98.0 2.6E-06 5.5E-11 73.0 1.1 43 334-376 1-50 (51)
11 KOG1973 Chromatin remodeling p 97.9 4.8E-06 1E-10 94.5 2.4 41 338-378 226-269 (274)
12 COG5034 TNG2 Chromatin remodel 97.8 1.3E-05 2.8E-10 89.4 3.1 43 334-376 222-269 (271)
13 KOG0825 PHD Zn-finger protein 97.7 1.1E-05 2.5E-10 99.2 2.0 43 334-376 217-265 (1134)
14 smart00249 PHD PHD zinc finger 97.7 2.5E-05 5.5E-10 63.9 2.9 40 335-374 2-47 (47)
15 KOG1632 Uncharacterized PHD Zn 97.6 2.1E-05 4.6E-10 92.0 1.2 48 1267-1315 62-111 (345)
16 KOG0383 Predicted helicase [Ge 97.6 2.2E-05 4.8E-10 98.1 1.0 49 329-377 44-94 (696)
17 KOG1512 PHD Zn-finger protein 97.5 4.7E-05 1E-09 85.8 1.7 44 334-377 316-363 (381)
18 COG5034 TNG2 Chromatin remodel 97.4 7E-05 1.5E-09 83.7 2.6 53 1259-1317 215-270 (271)
19 KOG1632 Uncharacterized PHD Zn 97.4 1.5E-05 3.3E-10 93.2 -2.8 56 1260-1316 235-294 (345)
20 cd04718 BAH_plant_2 BAH, or Br 97.3 0.0002 4.4E-09 75.1 3.7 28 353-380 1-30 (148)
21 KOG0955 PHD finger protein BR1 97.1 0.00046 1E-08 89.7 5.0 50 331-380 218-272 (1051)
22 KOG0956 PHD finger protein AF1 96.6 0.001 2.3E-08 82.0 2.6 44 333-376 6-56 (900)
23 KOG4443 Putative transcription 96.5 0.0015 3.3E-08 80.7 3.0 44 334-377 70-118 (694)
24 KOG1245 Chromatin remodeling c 96.3 0.00087 1.9E-08 89.9 -0.8 53 327-379 1103-1160(1404)
25 COG5141 PHD zinc finger-contai 95.9 0.0031 6.8E-08 75.6 1.3 48 330-377 191-243 (669)
26 PF15612 WHIM1: WSTF, HB1, Itc 95.4 0.0082 1.8E-07 52.0 1.7 38 248-285 9-46 (50)
27 KOG4323 Polycomb-like PHD Zn-f 95.3 0.009 1.9E-07 72.4 2.5 52 1265-1318 171-225 (464)
28 KOG4323 Polycomb-like PHD Zn-f 95.1 0.0099 2.1E-07 72.1 1.9 46 333-378 169-225 (464)
29 KOG0383 Predicted helicase [Ge 95.1 0.0057 1.2E-07 77.3 -0.2 100 349-462 1-114 (696)
30 KOG0954 PHD finger protein [Ge 94.9 0.012 2.6E-07 73.6 1.8 49 331-379 270-323 (893)
31 PF13831 PHD_2: PHD-finger; PD 94.3 0.013 2.8E-07 48.5 0.2 34 342-375 2-36 (36)
32 PF07227 DUF1423: Protein of u 93.9 0.04 8.6E-07 66.6 3.1 50 1266-1318 130-193 (446)
33 KOG1844 PHD Zn-finger proteins 93.8 0.028 6E-07 68.6 1.7 55 1264-1321 85-140 (508)
34 KOG0957 PHD finger protein [Ge 93.6 0.026 5.6E-07 68.2 1.1 43 334-376 546-597 (707)
35 KOG2752 Uncharacterized conser 93.5 0.047 1E-06 63.4 2.8 34 1055-1090 53-86 (345)
36 KOG4443 Putative transcription 92.1 0.043 9.3E-07 68.5 -0.0 88 332-446 18-113 (694)
37 KOG1244 Predicted transcriptio 90.1 0.15 3.2E-06 58.5 1.7 86 341-453 243-333 (336)
38 KOG0825 PHD Zn-finger protein 89.9 0.16 3.5E-06 64.4 2.0 50 1263-1315 214-264 (1134)
39 KOG1512 PHD Zn-finger protein 88.7 0.15 3.3E-06 58.6 0.5 46 333-378 259-318 (381)
40 KOG4299 PHD Zn-finger protein 86.8 0.33 7.2E-06 60.8 1.9 46 332-377 47-95 (613)
41 PF13831 PHD_2: PHD-finger; PD 81.3 0.34 7.4E-06 40.3 -0.8 34 1280-1315 3-36 (36)
42 PLN00163 histone H4; Provision 81.1 0.85 1.8E-05 42.0 1.5 26 863-888 30-55 (59)
43 KOG0957 PHD finger protein [Ge 80.4 1.1 2.3E-05 55.2 2.4 43 334-376 121-178 (707)
44 PF00130 C1_1: Phorbol esters/ 79.0 1.3 2.7E-05 38.6 1.9 35 1056-1090 10-46 (53)
45 PF13639 zf-RING_2: Ring finge 75.6 0.51 1.1E-05 39.7 -1.4 43 1266-1315 2-44 (44)
46 KOG0955 PHD finger protein BR1 69.4 3.7 8E-05 55.1 3.4 69 1244-1317 201-269 (1051)
47 KOG3467 Histone H4 [Chromatin 63.9 3.6 7.8E-05 40.6 1.3 42 863-904 30-72 (103)
48 KOG1081 Transcription factor N 61.0 6.4 0.00014 48.9 3.1 48 329-377 86-133 (463)
49 KOG0954 PHD finger protein [Ge 60.5 4.5 9.8E-05 52.0 1.7 56 1263-1321 270-326 (893)
50 PF13901 DUF4206: Domain of un 59.1 5.5 0.00012 44.3 1.9 42 1057-1108 152-198 (202)
51 PF10497 zf-4CXXC_R1: Zinc-fin 58.1 10 0.00022 38.6 3.4 53 1263-1317 6-70 (105)
52 KOG3612 PHD Zn-finger protein 57.0 13 0.00028 46.9 4.6 49 330-378 58-109 (588)
53 smart00109 C1 Protein kinase C 56.0 4.2 9.1E-05 34.0 0.3 33 1058-1090 12-45 (49)
54 KOG1245 Chromatin remodeling c 55.6 3 6.4E-05 57.7 -1.0 58 1263-1323 1107-1167(1404)
55 PF15446 zf-PHD-like: PHD/FYVE 55.5 5.5 0.00012 43.7 1.1 41 335-375 2-58 (175)
56 cd00029 C1 Protein kinase C co 53.4 5.8 0.00013 33.6 0.7 33 1058-1090 12-46 (50)
57 PF12678 zf-rbx1: RING-H2 zinc 52.2 5.8 0.00012 37.5 0.6 43 1266-1315 21-73 (73)
58 smart00417 H4 Histone H4. 48.4 6.4 0.00014 37.9 0.3 30 863-892 14-43 (74)
59 KOG1246 DNA-binding protein ju 47.9 12 0.00026 50.0 2.6 45 333-377 156-204 (904)
60 PF14446 Prok-RING_1: Prokaryo 46.7 10 0.00022 34.8 1.3 29 333-361 6-38 (54)
61 PF07496 zf-CW: CW-type Zinc F 38.9 14 0.00031 32.7 0.9 35 1280-1315 2-36 (50)
62 PF03604 DNA_RNApol_7kD: DNA d 38.7 17 0.00036 30.1 1.2 23 1058-1080 1-25 (32)
63 cd00076 H4 Histone H4, one of 38.0 13 0.00028 36.8 0.5 28 863-890 14-41 (85)
64 KOG4628 Predicted E3 ubiquitin 35.9 25 0.00053 42.6 2.5 45 333-378 230-277 (348)
65 PF09337 zf-H2C2: His(2)-Cys(2 35.3 10 0.00022 32.5 -0.6 31 658-692 9-39 (39)
66 smart00659 RPOLCX RNA polymera 33.6 22 0.00047 31.2 1.2 24 1057-1080 2-27 (44)
67 KOG4236 Serine/threonine prote 33.4 8.8 0.00019 48.4 -1.7 42 1047-1090 270-313 (888)
68 PF07649 C1_3: C1-like domain; 33.3 16 0.00034 29.1 0.3 29 1266-1296 2-30 (30)
69 KOG1886 BAH domain proteins [T 33.0 38 0.00082 42.4 3.5 46 1265-1315 171-216 (464)
70 KOG1829 Uncharacterized conser 31.8 11 0.00023 48.2 -1.3 28 1282-1317 532-559 (580)
71 PF14446 Prok-RING_1: Prokaryo 31.5 25 0.00054 32.4 1.3 35 1056-1090 4-39 (54)
72 PF13832 zf-HC5HC2H_2: PHD-zin 31.5 27 0.00059 34.7 1.7 30 1263-1296 54-85 (110)
73 cd04714 BAH_BAHCC1 BAH, or Bro 29.9 30 0.00065 35.6 1.7 21 1263-1284 101-121 (121)
74 PF13771 zf-HC5HC2H: PHD-like 29.6 26 0.00057 33.4 1.2 30 332-361 36-68 (90)
75 PF13832 zf-HC5HC2H_2: PHD-zin 29.6 27 0.00059 34.7 1.3 30 332-361 55-87 (110)
76 PTZ00015 histone H4; Provision 28.8 26 0.00056 35.9 1.0 40 852-891 18-59 (102)
77 PF12861 zf-Apc11: Anaphase-pr 28.5 24 0.00052 35.1 0.7 30 348-377 50-80 (85)
78 PRK04023 DNA polymerase II lar 26.3 47 0.001 45.0 2.9 42 1263-1323 625-668 (1121)
79 PF13771 zf-HC5HC2H: PHD-like 25.8 38 0.00082 32.4 1.5 33 1263-1299 35-69 (90)
80 cd00162 RING RING-finger (Real 25.5 20 0.00043 28.7 -0.4 42 1267-1316 2-43 (45)
81 PF12861 zf-Apc11: Anaphase-pr 24.2 23 0.00049 35.2 -0.3 50 1265-1317 22-80 (85)
82 KOG1829 Uncharacterized conser 23.1 22 0.00049 45.5 -0.8 46 1056-1109 510-560 (580)
83 PLN00035 histone H4; Provision 22.5 38 0.00082 34.8 0.8 29 863-891 30-58 (103)
84 PF13901 DUF4206: Domain of un 22.2 54 0.0012 36.7 2.0 43 1264-1318 152-199 (202)
85 PF11793 FANCL_C: FANCL C-term 22.1 42 0.00091 31.7 1.0 29 331-359 1-37 (70)
86 KOG1734 Predicted RING-contain 20.2 33 0.00072 40.3 -0.1 46 332-377 224-279 (328)
87 KOG4628 Predicted E3 ubiquitin 20.0 2.5E+02 0.0053 34.6 6.9 46 1265-1318 230-277 (348)
No 1
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=2.1e-127 Score=1150.15 Aligned_cols=962 Identities=24% Similarity=0.336 Sum_probs=733.1
Q ss_pred ccCCCCCCcccCCCCCCCCCCCCCCCCCCCCCchhHHhHHHHHHHhHhccccccccCCCHHHHHHHhcCCCCCchHHHHH
Q 000462 104 LPATLDAGRIEEPVVNPPKLLLPPSSRNLDLDGIPVLDLFSIYACLRSFSTLLFLSPFELEDFVAALKCSSPNLLFDSVH 183 (1482)
Q Consensus 104 ~~~~~~~~~~e~~~~~~P~l~LPpSS~DL~VP~e~V~~lLmVy~FLrSFs~~L~LSPFTLDDF~aAL~hde~s~LL~EIH 183 (1482)
++-..+ ||+|+-..+.|||+||+||+||.||+++|+++|+||+|||+|+++|+||||+||||||||.+.++|.||+|||
T Consensus 158 ~~d~~~-p~~~~e~~~vPpleLP~SSedi~IPne~Vm~alsIYevLRsF~~~LrisPF~feDFcaAL~~~~~ssLlaeVH 236 (1414)
T KOG1473|consen 158 RLDEPN-PDLEEEPPLVPPLELPESSEDIGIPNEHVMDALSIYEVLRSFSRQLRISPFRFEDFCAALISHEQSSLLAEVH 236 (1414)
T ss_pred CCCCCC-CChhhccccCCCccCCCcccccCCcHHHHHHHHHHHHHHHhhcceEEeCCccHHHHHHHHHhcCchhHHHHHH
Confidence 333444 5666555555999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhhhccCccchhhhhhcccccCCCCCChHHHHHHHHHhcCCCCCCccccccceeccCCccccchhhHHH
Q 000462 184 VSILRILRKHLEHLSKEGCESASDCLRSLNWGLLDLITWPIFMAEYFLIHNSGLKPGFELTRLKLFSSEYCKQPVSVKIE 263 (1482)
Q Consensus 184 vALLr~Lrkd~E~ls~~G~~~a~~~lr~i~w~~LD~lTWPE~LrqYLes~G~~~~Pele~~~L~ils~EYp~lpV~~KLe 263 (1482)
+||||+|++|++.+++.++..++++.+||+|++||.+|||||||+|+++++.-..+-|...+-.+...+||+.|+.+||+
T Consensus 237 vaLLrA~lr~eD~~~Thfs~~d~KdsvnI~l~liD~lTWPevLrqY~ea~~~ad~~v~~~~n~fv~~~eY~~~pv~~klk 316 (1414)
T KOG1473|consen 237 VALLRALLREEDRLSTHFSPLDSKDSVNIDLYLIDTLTWPEVLRQYFEADKHADGPVWDIFNPFVVEDEYPYRPVSNKLK 316 (1414)
T ss_pred HHHHHHHhhhhhhcccccCccccccceeeeeehhccccHHHHHHHHHHhccccCcchhhhhccccccccccccchhhhHH
Confidence 99999999999988888888888999999999999999999999999998876666565443334568999999999999
Q ss_pred HHHHhhhhhhhhHHHHHHHhcccccCCCCccccccccccccccccccccccCCCcCcccccccCCCCCCccccccccCCc
Q 000462 264 ILRCLCDDMIEVEAIRMELNRRSSVAEPEMDFDRNINNEIGKRRRVAMDISAGSCLTEEVVDDANDWNSDECCLCKMDGS 343 (1482)
Q Consensus 264 ILqfLcD~~LeSeaIRdELd~R~~~~E~~~~~d~~~~~es~RKr~~~~~~s~g~sl~e~~vd~~~d~ndD~C~VC~~gG~ 343 (1482)
|||||||+||.+..+|+||+.| ..+. .+|.|.+|++.|+
T Consensus 317 ILQ~L~Dq~l~~~s~R~e~~se-----~~~~------------------------------------~ddhcrf~~d~~~ 355 (1414)
T KOG1473|consen 317 ILQFLCDQFLTVNSLRDEIDSE-----GEIE------------------------------------YDDHCRFCHDLGD 355 (1414)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc-----ccee------------------------------------ecccccccCcccc
Confidence 9999999999999999999754 2111 2679999999999
Q ss_pred eeecCCCCCcccccccCCC--CCCCCCccCccccccCCCCCc-------CCCCccccccccccCCCCcEEEEecCeEEEe
Q 000462 344 LLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALDRHKPWM-------KPRKSLRGAELLGVDPHGRLYFCSCGYLLVS 414 (1482)
Q Consensus 344 LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~~~~~~~-------k~r~~lrgaEilg~D~~gRkY~~~CgrLLvc 414 (1482)
++||.+||+.||+.|+.+| .+|+..|.|-.|...++.... +.. ..-..+.+|.|++||+||+..++|++|
T Consensus 356 ~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvngvvd~vl~~~K~~-~~iR~~~iG~dr~gr~ywfi~rrl~Ie 434 (1414)
T KOG1473|consen 356 LLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNGVVDCVLPPSKNV-DSIRHTPIGRDRYGRKYWFISRRLRIE 434 (1414)
T ss_pred eeecccCCceEEeeecCCccccCCCccchhhhhhhhccCcccccccChhhcc-cceeccCCCcCccccchhceeeeeEEe
Confidence 9999999999999999987 599999999999877665432 221 223467889999999999999999999
Q ss_pred ecCCCCccccccc-cCchhHHHHhhccCc--h----hHHHHHHHHHHHhccCCCCCCc-ccccc----cchhhhccc---
Q 000462 415 DSCDTELILNYYC-RDDLNFVIDVLKSSD--T----FYGGIINAICKQWDITVSSNGV-RSNLA----LNTVSLSRH--- 479 (1482)
Q Consensus 415 dsC~ses~l~YY~-~~dL~~vL~~L~s~e--~----~y~~I~~~I~~~w~ip~~l~~~-~s~l~----~n~~~~~~~--- 479 (1482)
+-- +..++||+ ..+|..+|+.|+... + ......++|++||++|+++++. |-..+ .-..+|+..
T Consensus 435 ~~d--et~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rqM~lT~~ltne~R~~~~f~~~~h~r~~l~~~c~ 512 (1414)
T KOG1473|consen 435 GMD--ETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQMGLTEELTNELRGAVDFGEDPHGRLFLGRDCA 512 (1414)
T ss_pred cCC--CcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHhccchhhhhhhhhcccccccCCCcceeeecchh
Confidence 854 45789999 689999999999643 2 2335569999999999998665 31111 011222211
Q ss_pred ---ccc-------CCCcccccchhhhhhhhhcccccCCCCcccccc----cccccccccc----cCCccCCCCccchhc-
Q 000462 480 ---MKA-------EVPTISEIDNEQKLEENFLAGYSNRPDNALSKS----ANLLDSVTAM----ELPNISSEGSAETTQ- 540 (1482)
Q Consensus 480 ---~~~-------~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~----~~~~~~~~~~----~~~~~~s~~s~~~~q- 540 (1482)
+.. ..+..+..+.. .+.+.++..+++.. +..+. .++-|....+ ..-. -++|...-+
T Consensus 513 ~~lv~~iq~~~da~l~e~~l~~i~--k~v~~~~S~s~~~e-E~~e~ck~is~~~d~p~~n~~~~~e~~--~dqtf~~y~y 587 (1414)
T KOG1473|consen 513 VLLVLCIQVVEDAILKEENLGDID--KVVLVLISASAHQE-EYVEICKAISQYWDLPEGNLWRLREEG--NDQTFMKYYY 587 (1414)
T ss_pred hHHhhhhhhhhhhhhhHhhhcchH--hhhhhhhhcccchH-HHHHHHHHHhhcccccccchhhhhhcc--cccchhhhcc
Confidence 000 01111110010 11222222222221 00000 0000000000 0000 000000000
Q ss_pred ccCCCcCcccCCCCC----ccchhcccccccccCCCCCCCCCCCCccchhhhccccCCC---CCCCCCCCCCCCcccccc
Q 000462 541 MNSGFDNFQKEGPDN----SIRAAEFSNQSEIAGKLPAPGHNSMTSSTSDIKQKFASSG---CNSSPTNSRKGDALQLQP 613 (1482)
Q Consensus 541 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~ 613 (1482)
.++.++.+..--+.. +.+.-.|+-.. +--.+.+.|-...++.+-....+.-+ +.|+.
T Consensus 588 s~n~vse~~~~d~e~~dkk~~~~tkf~l~~---nsd~~~~g~~~t~gt~~~~~~~~~~t~~~~lSni------------- 651 (1414)
T KOG1473|consen 588 SGNEVSEIFLTDSENADKKSHMQTKFALIT---NSDGVTAGNVTTYGTGSQHKKLIARTLQQGLSNI------------- 651 (1414)
T ss_pred cCCchhhccCCchhhhcccccccceecccc---cccceeccccccccchhhcchHHHhhhhhhhccC-------------
Confidence 000010000000000 00000000000 00000000100001111111111110 23444
Q ss_pred chhhhh----cccch-hhhHHHHHHhhhccccccccCC---CCchHH----HHHHHHHHHhhccceeeecCCcccccccc
Q 000462 614 EIAYMN----RYSFA-QTASSVAEELMHKSSNEISKEP---INSNEE----IISKQMKAILKKWDKFYWPNTQKLNADTQ 681 (1482)
Q Consensus 614 ~~~Y~N----~Y~~g-~~AasaA~~La~~ssee~~~~~---~~~~~~----~~~~Q~Kafs~~~~~F~Wps~ekk~~ev~ 681 (1482)
|++||| +|..| +.|+|||+.++.+++ ++.+.. .++..+ ++..|+|+||.+|++||||+..+| +..
T Consensus 652 P~s~~n~~w~~~tkg~~lavs~A~~~~el~s-~t~~~d~s~~~~~~~~~ssn~L~qtklesitaa~f~~~~~~~K--ri~ 728 (1414)
T KOG1473|consen 652 PISYNNRKWPVYTKGFELAVSAAADLAELSS-ETLEPDLSKRSNAFKAASSNILGQTKLESITAAQFFWPSPDKK--RIT 728 (1414)
T ss_pred chHhhhccchhhccchhhhhhccchHHHHHH-hhcccchhhhhhhhccchhhhhcchhheeeehhhhccCCcccc--ccc
Confidence 499999 99999 999999999999999 555551 133333 578999999999999999999999 999
Q ss_pred ccccccccccccCCCC-CCeeeeeccccccCcchhhhccccccccCCCchHHHHHHHHhhHhhhcccccccCCChhhhHH
Q 000462 682 KEKCGWCFSCKSATDD-MDCLFYMNNGRVLGSSESEVAGLLSKRNKKGHLVDVICHILSIEDRLLGLLLGPWLNPHYTKL 760 (1482)
Q Consensus 682 rerCGWC~sCk~s~~~-~~C~ln~a~~~a~k~~~~~~~gl~~~kn~~~hl~si~~yil~mEe~L~GLl~Gp~~~~~~r~~ 760 (1482)
|||||||++|+..... ++||++.+...|+||+|.+.+||.|.+|.++.|.+|++|++++||+++|++|||++...-|++
T Consensus 729 rer~~~~~~~~l~~~s~k~~~~~~~~~gaqKGa~~r~~G~~~l~n~~~vlS~~~~~~~~~~es~~~v~v~~~~~Esnr~~ 808 (1414)
T KOG1473|consen 729 RERCGWCESCRLTFASRKGTMLLAAVIGAQKGAMYRNSGLFPLKNWEWVLSSIAAYWLALEESPRGVIVGEFKSESNRKQ 808 (1414)
T ss_pred ccccchhhhcceeeehhccccchhhccccccccceeeeccccccChhHHHHHHHHHHHhhhccccceeecccccccchhh
Confidence 9999999999998855 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhhhHHHHHHHHHhhhhchhhccccccccCccc-ccccccceeecccccccccCCCCCcCCCCCCCCcccC
Q 000462 761 WRKSALKAADMASVKHLLLTLEANLQHLALSAEWFKHVDPVV-TVGSASHIVIASSRANSKAGAGRKKARDFDGNPSTKA 839 (1482)
Q Consensus 761 Wrk~~~~As~~~~ik~lLL~LEsnir~iA~s~dW~K~~D~~~-~~~S~~~~~~~s~~~~~k~g~g~rr~r~~~~~~~~~~ 839 (1482)
||+.|+. .+.++++||+||.-+|++-+|.|.||+|. ++.|+.++.+.+.++.|.|+.||++...++ ..++-.
T Consensus 809 ~r~~L~~------r~~~~~q~ee~i~~~~~~~y~~~~~~n~~rie~s~~~~ng~~v~akQ~r~pgr~~~s~~~-ek~A~~ 881 (1414)
T KOG1473|consen 809 ERKELLV------RRSGGKQLEENICSGALSCYWPKQMDNWLRIEHSIFQSNGVTVGAKQARDPGRTKQSLQA-EKTAPK 881 (1414)
T ss_pred HHHHhhh------hhhhhhhhccccccccccccchhhccCceeeeechhccCceeechhhhcCCcchhhhcch-hhcccc
Confidence 9999987 49999999999999999999999999998 899999999999999999999999988555 455556
Q ss_pred CCCcceEEccCCcchhhhhccccCcHHHHHHHHHhcCccccCccccCCCchhhhhhhhhhhhhhhhccccHhHHhHHhhh
Q 000462 840 AGGLSLCWWRGGRLSCQLFSWKRLPRSLVSKAARQAGCMKIPGILYPENSDFARRSRTVAWRAAVESSTSVEQLAIQVRE 919 (1482)
Q Consensus 840 ~~~~~~~WwrGG~lsr~if~~~~Lp~s~v~KAARQgG~~ki~gi~Y~d~se~~rRsr~~aWraaVe~S~n~sQLaLQvR~ 919 (1482)
....+|.|||||+ |+.|+|+|+|-++.++|+|.|+|.+++|+..|.+.+.+|||+++..|.+||+.++|++|||||||
T Consensus 882 s~ld~f~~~Rggk-s~vvl~kavL~~~~mk~~v~~~g~ta~~k~nfl~~~y~p~~s~~s~wk~av~n~enlh~LAlQ~~- 959 (1414)
T KOG1473|consen 882 SDLDSFTWWRGGK-SKVVLQKAVLSQSIMKKLVWQQGFTAGPKSNFLDWSYIPRRSRRSCWKAAVENSENLHQLALQLR- 959 (1414)
T ss_pred ccccchhhhhcCc-ceeeehhhhcchHHHHHHhhccccccCCcccccccccccchhhhhhhhhhhcChhhHHHHHHHHH-
Confidence 6677899999999 99999999999999999999999999999999999999999999999999999999999999982
Q ss_pred ccccccccccccCCCCCcCchhhhHHHhhcccceeeccccccCceEEEEecCCcccCchhhhccccccccccCCCcceee
Q 000462 920 FDSNVRWDDIENTHPLCTMDKEFRKSVRLFKKAIIRRKCLKEEGVKYLVDFGKRRSVPDIVIRHGSMAEESSSGRKKYWL 999 (1482)
Q Consensus 920 Ld~~IrW~el~~~~~~~~~~K~~~~~a~~fr~aii~~K~~~~~~~~Y~~~fg~~k~lP~~v~k~~~~~E~~~~~~~kyW~ 999 (1482)
++++ +.|++++.++.||||-||.|++.|++.+|+.-|++ +++||.+++ ||+
T Consensus 960 -------------q~v~-d~~s~~~r~ai~r~~~ic~~~l~d~~~~~~~~~~s------~~~~~~~~~---------~~~ 1010 (1414)
T KOG1473|consen 960 -------------QNVQ-DVKSPETRRAIFRNAEICIKKLYDNKEEEGESWLS------SEFSHVISS---------RPQ 1010 (1414)
T ss_pred -------------HHHh-ccCCchhhHHHhhhhhhhccccccCCcccccchhh------hhhhhhhhc---------ccc
Confidence 3333 77999999999999999999999999999999999 889998876 999
Q ss_pred eccccchhhhHhHHhhhccccCCCCCCCCCCcchhhhhcccccccceeecccccccccccccccccccccccceeccccc
Q 000462 1000 NESYVPLHLLKSFEERRVARKSPKLSSGKLSEPFRVIKKSLRDRGFSYLFSKAARSEYYQCGHCSKDVLIRDAVCCQDCK 1079 (1482)
Q Consensus 1000 ~E~~vPL~LlkefEek~~~~~~~~~~~~~~~~~~~~~~k~~~~~~f~yL~~k~~~~~~~~C~~C~kdV~~rdav~C~~Cq 1079 (1482)
.|..|+| .||..+. .+.-+...+++.++|.+.-.+|.|+-.+-
T Consensus 1011 ~~~~~sl----~~~~fr~------~~~~r~~~~q~~~~~~~~~~v~~~~~~~~--------------------------- 1053 (1414)
T KOG1473|consen 1011 RHEFVSL----GYEKFRS------LDNRRATAIQREWLKGSTANVFEIKDYWP--------------------------- 1053 (1414)
T ss_pred cCceeec----cchhhhc------chhhhhHHHHhhhhcccccceeeeeccCC---------------------------
Confidence 9999999 3887422 22234568889999999999999987630
Q ss_pred cccccccccccCccccceeeeeecccccCcccccccccccCCccCCCCCccccccccccccccccccccccCCCcccccC
Q 000462 1080 GYFHKRHIRKSAGAVTTECKYTCYQCQDGRFKKDTRTAKNGTKKGKMNTRSVKVKSQKSKKTTGRRSVQSKNSKKTVVGG 1159 (1482)
Q Consensus 1080 g~~Hk~c~~~s~g~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~K~~~k~~~~~ 1159 (1482)
++ |+ ++
T Consensus 1054 ----------------------------------~~------s~-------~~--------------------------- 1059 (1414)
T KOG1473|consen 1054 ----------------------------------PS------QQ-------LP--------------------------- 1059 (1414)
T ss_pred ----------------------------------ch------hh-------Cc---------------------------
Confidence 00 00 00
Q ss_pred cccccccCcccccchhhhhhhhhhhhhhccccccccccCCCCCccccCCCCCccchhhhccccccccccccceecccCCC
Q 000462 1160 RSLRSRNDKKVAAIPLRRSARRAKLVSVQNRKHAGRKRGRPKSKKKTSRKPKKTTSLQKKRTQSYYSYWLNGLFLSRKPD 1239 (1482)
Q Consensus 1160 r~~~s~~~k~~~~~pl~~s~~~~k~~~~q~~~~~~~K~~~~k~K~~k~kk~~~~~~~~K~rt~~~~~yWl~Gl~w~k~~n 1239 (1482)
+.+... | --|+ ||.++..+. +|...++.+ | |++|.+++-
T Consensus 1060 ----s~~~~~----~-----------------~~gv-------kq~tpd~n~-----~~~~~~~~s--~--~v~~~~~~~ 1098 (1414)
T KOG1473|consen 1060 ----SEKNNV----N-----------------YSGV-------KQRTPDGNE-----RKSKKKTLS--S--GVIWRKKNY 1098 (1414)
T ss_pred ----ccccCC----C-----------------ccce-------eeecCCcch-----hhhccCCcc--c--ccccccccc
Confidence 000000 0 0000 111111111 011122223 6 999999999
Q ss_pred CcccccccccceeccccccCCCCCCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC-
Q 000462 1240 DDRVMQFTRKNFLAASELLTDTLDQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT- 1318 (1482)
Q Consensus 1240 d~~~~~Fr~~~v~~~g~~~~~~~~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~- 1318 (1482)
.+++..||+.||+..|. .+.....|+|.+|.-|| +|.+.||.|-.|..||||..|.|..+.+-+..+|+|++|+++.
T Consensus 1099 a~t~~~~~~qnii~ag~-~~kp~~~p~~~i~~~p~-~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~~ 1176 (1414)
T KOG1473|consen 1099 ADTGVPFRHQNIILAGR-SDKPTLSPVCFICTLPY-NPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIRS 1176 (1414)
T ss_pred ccCCCCcchhhHHhccC-CCCCCCCccccceeecc-CCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccCC
Confidence 99999999999999888 78888999999999998 9999999999999999999999999999999999999999999
Q ss_pred Cccccccc
Q 000462 1319 PVCSCMVS 1326 (1482)
Q Consensus 1319 p~Cp~~~~ 1326 (1482)
|.|||+++
T Consensus 1177 P~~~~~~~ 1184 (1414)
T KOG1473|consen 1177 PDCPYMDP 1184 (1414)
T ss_pred CCCCcCCc
Confidence 99999998
No 2
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=99.60 E-value=7e-16 Score=138.72 Aligned_cols=60 Identities=48% Similarity=0.711 Sum_probs=56.9
Q ss_pred chhHHhHHHHHHHhHhccccccccCCC--HHHHHHHhcCCCCCchHHHHHHHHHHHHHHhhh
Q 000462 136 GIPVLDLFSIYACLRSFSTLLFLSPFE--LEDFVAALKCSSPNLLFDSVHVSILRILRKHLE 195 (1482)
Q Consensus 136 ~e~V~~lLmVy~FLrSFs~~L~LSPFT--LDDF~aAL~hde~s~LL~EIHvALLr~Lrkd~E 195 (1482)
++.++++||||+||++||++|+||||+ ||||++||++++++.||+|||++||+++++|.+
T Consensus 1 ~~~~~d~l~V~eFl~~F~~~L~L~~f~~~l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~ 62 (63)
T smart00571 1 NEAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62 (63)
T ss_pred CcHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCC
Confidence 478999999999999999999999999 999999999999999999999999999988753
No 3
>PF02791 DDT: DDT domain; InterPro: IPR004022 This domain is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is found in foetal Alzheimer antigen and several hypothetical and uncharacterised proteins.
Probab=99.59 E-value=1.1e-15 Score=136.38 Aligned_cols=60 Identities=37% Similarity=0.639 Sum_probs=56.9
Q ss_pred chhHHhHHHHHHHhHhccccccccCCCHHHHHHHhcCCCCCchHHHHHHHHHHHHHHhhh
Q 000462 136 GIPVLDLFSIYACLRSFSTLLFLSPFELEDFVAALKCSSPNLLFDSVHVSILRILRKHLE 195 (1482)
Q Consensus 136 ~e~V~~lLmVy~FLrSFs~~L~LSPFTLDDF~aAL~hde~s~LL~EIHvALLr~Lrkd~E 195 (1482)
.++|+++||||+||++||.+|+|+|||||||++||.+.+++.||+|||.+||++|.++.+
T Consensus 1 ~~~~~~~L~v~~Fl~~F~~~L~L~~ftlddf~~AL~~~~~~~ll~ei~~~LL~~l~~~~~ 60 (61)
T PF02791_consen 1 GEAFGDLLMVWEFLNTFGEVLGLSPFTLDDFEQALLCNDPSGLLAEIHCALLKALLADEE 60 (61)
T ss_pred CcHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHcCCCcchhHHHHHHHHHHHHHhccC
Confidence 378999999999999999999999999999999999999999999999999999988765
No 4
>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=98.38 E-value=7.8e-08 Score=82.27 Aligned_cols=48 Identities=25% Similarity=0.726 Sum_probs=41.2
Q ss_pred eeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCc-eEEcCCcCC
Q 000462 1267 CYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLI-GFRCHVCRK 1316 (1482)
Q Consensus 1267 cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~-~y~Cp~Cr~ 1316 (1482)
|.+|++. +.+..||.||.|++|||..|+++++....... .|.|+.|+.
T Consensus 2 C~vC~~~--~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQS--DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSS--CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCc--CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5699995 67788899999999999999999998666544 999999975
No 5
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.25 E-value=2.6e-07 Score=112.05 Aligned_cols=48 Identities=44% Similarity=1.272 Sum_probs=43.2
Q ss_pred CccccccccCCce---eecCCCCCcccccccCCC----CCCCCCccCccccccCC
Q 000462 332 SDECCLCKMDGSL---LCCDGCPAAYHSKCVGVA----NVPEGDWFCPECALDRH 379 (1482)
Q Consensus 332 dD~C~VC~~gG~L---LcCD~CprafHl~CL~Pp----~vPeGdW~Cp~C~~~~~ 379 (1482)
.++|..|++.|.. +|||+||++||+.||.|| .+|.|.|+|++|.++..
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 5699999998876 999999999999999997 49999999999987654
No 6
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.21 E-value=4.8e-07 Score=102.50 Aligned_cols=53 Identities=28% Similarity=0.679 Sum_probs=42.3
Q ss_pred CCCCCCCceeecCCCCCCCCcceEecCC--CC-CccccccccCChhhhccCceEEcCCcCCC
Q 000462 1259 TDTLDQPKCYLCHEAEHTSTSNYIACEI--CG-EWYHGDAFGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1259 ~~~~~~p~cclC~kpy~~~d~fyI~CD~--C~-~WfHG~CVglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
....++|.||+|.+ .+---||+||. |. +|||=.||||++.=- ..|+||+|+..
T Consensus 213 ~~d~~e~~yC~Cnq---vsyg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~ 268 (274)
T KOG1973|consen 213 AVDPDEPTYCICNQ---VSYGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAE 268 (274)
T ss_pred ccCCCCCEEEEecc---cccccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhh
Confidence 34457899999984 44556699999 99 999999999995443 34999999854
No 7
>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 KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.01 E-value=2e-06 Score=96.04 Aligned_cols=45 Identities=38% Similarity=0.964 Sum_probs=38.3
Q ss_pred cccccccc---CCceeecCCCCCcccccccCCC--CCCCCCccCcccccc
Q 000462 333 DECCLCKM---DGSLLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALD 377 (1482)
Q Consensus 333 D~C~VC~~---gG~LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~ 377 (1482)
-+|.+|+. ..+||+||.|+++||+|||.|+ ..|+|.|.|..|...
T Consensus 282 k~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 282 KYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred ceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHH
Confidence 35777875 4579999999999999999997 599999999999743
No 9
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=98.00 E-value=1.4e-06 Score=109.95 Aligned_cols=132 Identities=31% Similarity=0.455 Sum_probs=105.6
Q ss_pred CCCccccccccCCceeecCC-CCCcccc-cccCCC----CCCCCCccCccccccCCCCCcCCCCccccccccccCCCCcE
Q 000462 330 WNSDECCLCKMDGSLLCCDG-CPAAYHS-KCVGVA----NVPEGDWFCPECALDRHKPWMKPRKSLRGAELLGVDPHGRL 403 (1482)
Q Consensus 330 ~ndD~C~VC~~gG~LLcCD~-CprafHl-~CL~Pp----~vPeGdW~Cp~C~~~~~~~~~k~r~~lrgaEilg~D~~gRk 403 (1482)
.+.+.|.+|+..+.++||++ ||..||+ .|++-. .+++|-|+|+.|..+...........++++-.|++|+|||.
T Consensus 426 fi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rqM~lT~~ltne~R~~~~f~~~~h~r~ 505 (1414)
T KOG1473|consen 426 FISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQMGLTEELTNELRGAVDFGEDPHGRL 505 (1414)
T ss_pred ceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHhccchhhhhhhhhcccccccCCCcce
Confidence 34578999999999999997 9999998 999942 49999999999998877666555566778888999999999
Q ss_pred EEE-ecCeEEEe-ecCCCCccccccccCchhHHHHhhccCc---hhHHHHHHHHHHHhccCCC
Q 000462 404 YFC-SCGYLLVS-DSCDTELILNYYCRDDLNFVIDVLKSSD---TFYGGIINAICKQWDITVS 461 (1482)
Q Consensus 404 Y~~-~CgrLLvc-dsC~ses~l~YY~~~dL~~vL~~L~s~e---~~y~~I~~~I~~~w~ip~~ 461 (1482)
|.. .|.-||+. ..-.....+.||...++..+...+-+.. .-|.++|+.|.++|+.|+.
T Consensus 506 ~l~~~c~~~lv~~iq~~~da~l~e~~l~~i~k~v~~~~S~s~~~eE~~e~ck~is~~~d~p~~ 568 (1414)
T KOG1473|consen 506 FLGRDCAVLLVLCIQVVEDAILKEENLGDIDKVVLVLISASAHQEEYVEICKAISQYWDLPEG 568 (1414)
T ss_pred eeecchhhHHhhhhhhhhhhhhhHhhhcchHhhhhhhhhcccchHHHHHHHHHHhhccccccc
Confidence 887 47655542 2223346789999998887776666544 3788999999999999884
No 10
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.95 E-value=2.6e-06 Score=73.01 Aligned_cols=43 Identities=44% Similarity=1.247 Sum_probs=36.4
Q ss_pred ccccccc---CCceeecCCCCCcccccccCCC----CCCCCCccCccccc
Q 000462 334 ECCLCKM---DGSLLCCDGCPAAYHSKCVGVA----NVPEGDWFCPECAL 376 (1482)
Q Consensus 334 ~C~VC~~---gG~LLcCD~CprafHl~CL~Pp----~vPeGdW~Cp~C~~ 376 (1482)
+|.+|+. .++||.||.|..+||..|++++ ..+.+.|+|+.|..
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 4788877 6689999999999999999986 34556999999974
No 11
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.90 E-value=4.8e-06 Score=94.49 Aligned_cols=41 Identities=37% Similarity=1.070 Sum_probs=36.9
Q ss_pred cccCCceeecCC--CC-CcccccccCCCCCCCCCccCccccccC
Q 000462 338 CKMDGSLLCCDG--CP-AAYHSKCVGVANVPEGDWFCPECALDR 378 (1482)
Q Consensus 338 C~~gG~LLcCD~--Cp-rafHl~CL~Pp~vPeGdW~Cp~C~~~~ 378 (1482)
|...|+|+-||. |+ .+||+.|+|+...|.|.||||.|....
T Consensus 226 qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 226 QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKAEN 269 (274)
T ss_pred ccccccccccCCCCCCcceEEEeccccccCCCCcccchhhhhhh
Confidence 455899999997 99 799999999999999999999998653
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.78 E-value=1.3e-05 Score=89.40 Aligned_cols=43 Identities=40% Similarity=1.190 Sum_probs=38.1
Q ss_pred ccccccc--CCceeecCC--CCC-cccccccCCCCCCCCCccCccccc
Q 000462 334 ECCLCKM--DGSLLCCDG--CPA-AYHSKCVGVANVPEGDWFCPECAL 376 (1482)
Q Consensus 334 ~C~VC~~--gG~LLcCD~--Cpr-afHl~CL~Pp~vPeGdW~Cp~C~~ 376 (1482)
..+-|++ -|+|+-||+ |.+ +||+.|+|+...|+|.|||+.|..
T Consensus 222 lYCfCqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 222 LYCFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred eEEEecccccccceecCCCCCchhheeccccccCCCCCCcEeCHHhHh
Confidence 3556877 589999995 999 999999999999999999999975
No 13
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.74 E-value=1.1e-05 Score=99.16 Aligned_cols=43 Identities=35% Similarity=1.065 Sum_probs=37.5
Q ss_pred cccccccCC---ceeecCCCCCc-ccccccCCC--CCCCCCccCccccc
Q 000462 334 ECCLCKMDG---SLLCCDGCPAA-YHSKCVGVA--NVPEGDWFCPECAL 376 (1482)
Q Consensus 334 ~C~VC~~gG---~LLcCD~Cpra-fHl~CL~Pp--~vPeGdW~Cp~C~~ 376 (1482)
.|.+|.... -||+||.|+.+ ||+|||+|+ ++|-+.|||+.|.-
T Consensus 217 ~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 217 KCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 489997643 49999999999 999999997 49999999999953
No 14
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.58 E-value=2.1e-05 Score=92.00 Aligned_cols=48 Identities=23% Similarity=0.600 Sum_probs=46.5
Q ss_pred eeecCCCCCCCCcceEecCCCCCcccccc--ccCChhhhccCceEEcCCcC
Q 000462 1267 CYLCHEAEHTSTSNYIACEICGEWYHGDA--FGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1267 cclC~kpy~~~d~fyI~CD~C~~WfHG~C--Vglte~~a~~i~~y~Cp~Cr 1315 (1482)
+|.|.+++ +++.+||.||.|.+||||+| |||+++.+..++.|+|..|.
T Consensus 62 ~~~~~~~~-~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~ 111 (345)
T KOG1632|consen 62 YCKCYKPC-DPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECK 111 (345)
T ss_pred hhhccccc-CchhhhhccccccccccccccccCchhhcCCccccccccccc
Confidence 89999997 99989999999999999999 99999999999999999996
No 16
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.56 E-value=2.2e-05 Score=98.10 Aligned_cols=49 Identities=39% Similarity=1.046 Sum_probs=42.6
Q ss_pred CCCCccccccccCCceeecCCCCCcccccccCCC--CCCCCCccCcccccc
Q 000462 329 DWNSDECCLCKMDGSLLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALD 377 (1482)
Q Consensus 329 d~ndD~C~VC~~gG~LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~ 377 (1482)
+.+...|++|+++|++||||+|+.+||.+|++++ .+|.|+|.|+.|.+.
T Consensus 44 ~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 44 DAEQEACRICADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred hhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccC
Confidence 3445679999999999999999999999999986 478888999999543
No 17
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.45 E-value=4.7e-05 Score=85.81 Aligned_cols=44 Identities=34% Similarity=0.915 Sum_probs=37.4
Q ss_pred cccccccC---CceeecCCCCCcccccccCCCCCCCCCccCc-ccccc
Q 000462 334 ECCLCKMD---GSLLCCDGCPAAYHSKCVGVANVPEGDWFCP-ECALD 377 (1482)
Q Consensus 334 ~C~VC~~g---G~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp-~C~~~ 377 (1482)
.|.+|+++ .++++||.|+++||++|+|+..+|.|.|.|. .|...
T Consensus 316 lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD~~C~~~ 363 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDVCDRGPHTLCVGLQDLPRGEWICDMRCREA 363 (381)
T ss_pred hhhccCCcccchheeccccccCCCCccccccccccCccchhhhHHHHh
Confidence 46777764 4799999999999999999999999999998 46543
No 18
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.43 E-value=7e-05 Score=83.72 Aligned_cols=53 Identities=25% Similarity=0.614 Sum_probs=40.9
Q ss_pred CCCCCCCceeecCCCCCCCCcceEecCC--CC-CccccccccCChhhhccCceEEcCCcCCC
Q 000462 1259 TDTLDQPKCYLCHEAEHTSTSNYIACEI--CG-EWYHGDAFGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1259 ~~~~~~p~cclC~kpy~~~d~fyI~CD~--C~-~WfHG~CVglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
+.+.++++||.|+++-| +. ||+||. |+ +|||-+||||.+-=- -.|+|+.|+..
T Consensus 215 d~se~e~lYCfCqqvSy--Gq-MVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 215 DNSEGEELYCFCQQVSY--GQ-MVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred ccccCceeEEEeccccc--cc-ceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 34467899999999832 44 599995 65 799999999976431 46999999865
No 19
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.42 E-value=1.5e-05 Score=93.20 Aligned_cols=56 Identities=20% Similarity=0.525 Sum_probs=49.6
Q ss_pred CCCCCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCce----EEcCCcCC
Q 000462 1260 DTLDQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIG----FRCHVCRK 1316 (1482)
Q Consensus 1260 ~~~~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~----y~Cp~Cr~ 1316 (1482)
....+..|-.|+.+| ..+.|||+|+.|+.||||+||.|+++.+..+.. |+|+.|..
T Consensus 235 ~~~~~~~~~~cg~~~-~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 235 PDYSKLICDPCGLSD-ANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred cccccccccccCcch-HHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceee
Confidence 445667888999997 556999999999999999999999999999999 99999964
No 20
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=97.27 E-value=0.0002 Score=75.15 Aligned_cols=28 Identities=39% Similarity=1.095 Sum_probs=24.5
Q ss_pred cccccccCCC--CCCCCCccCccccccCCC
Q 000462 353 AYHSKCVGVA--NVPEGDWFCPECALDRHK 380 (1482)
Q Consensus 353 afHl~CL~Pp--~vPeGdW~Cp~C~~~~~~ 380 (1482)
+||++||.|| .+|+|+|+||.|..+...
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCC
Confidence 6999999997 599999999999876543
No 21
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.08 E-value=0.00046 Score=89.69 Aligned_cols=50 Identities=34% Similarity=1.018 Sum_probs=43.2
Q ss_pred CCccccccccCC-----ceeecCCCCCcccccccCCCCCCCCCccCccccccCCC
Q 000462 331 NSDECCLCKMDG-----SLLCCDGCPAAYHSKCVGVANVPEGDWFCPECALDRHK 380 (1482)
Q Consensus 331 ndD~C~VC~~gG-----~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~~~~ 380 (1482)
.|..|.||.++. .++.||+|..++|.+|.|.+.+|+|.|+|..|......
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSPQR 272 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCcCc
Confidence 356899998753 48999999999999999988999999999999876543
No 22
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.61 E-value=0.001 Score=81.96 Aligned_cols=44 Identities=43% Similarity=1.237 Sum_probs=38.6
Q ss_pred ccccccccC-----CceeecCC--CCCcccccccCCCCCCCCCccCccccc
Q 000462 333 DECCLCKMD-----GSLLCCDG--CPAAYHSKCVGVANVPEGDWFCPECAL 376 (1482)
Q Consensus 333 D~C~VC~~g-----G~LLcCD~--CprafHl~CL~Pp~vPeGdW~Cp~C~~ 376 (1482)
.-|+||-|. .-|+.||+ |.-+.|..|+++..||.|.|||..|..
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCES 56 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhh
Confidence 469999873 24999995 999999999999999999999999964
No 23
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=96.50 E-value=0.0015 Score=80.70 Aligned_cols=44 Identities=34% Similarity=0.920 Sum_probs=36.4
Q ss_pred cccccccCC---ceeecCCCCCcccccccCCC--CCCCCCccCcccccc
Q 000462 334 ECCLCKMDG---SLLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALD 377 (1482)
Q Consensus 334 ~C~VC~~gG---~LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~ 377 (1482)
.|..|+.+| .+++|+.|+.+||.||..|+ .+|.|.|+|+.|...
T Consensus 70 vCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 70 VCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred eeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHhh
Confidence 355566444 59999999999999999997 599999999999643
No 24
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.27 E-value=0.00087 Score=89.93 Aligned_cols=53 Identities=32% Similarity=0.852 Sum_probs=43.5
Q ss_pred CCCCCCccccccccCC---ceeecCCCCCcccccccCCC--CCCCCCccCccccccCC
Q 000462 327 ANDWNSDECCLCKMDG---SLLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALDRH 379 (1482)
Q Consensus 327 ~~d~ndD~C~VC~~gG---~LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~~~ 379 (1482)
........|.+|...+ +|++||.|..+||++|+.|. .+|.|+|+||.|+.+..
T Consensus 1103 ~~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1103 DRSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred ccccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 3334456799997644 59999999999999999985 69999999999987653
No 25
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.86 E-value=0.0031 Score=75.63 Aligned_cols=48 Identities=33% Similarity=0.895 Sum_probs=41.1
Q ss_pred CCCccccccccC-----CceeecCCCCCcccccccCCCCCCCCCccCcccccc
Q 000462 330 WNSDECCLCKMD-----GSLLCCDGCPAAYHSKCVGVANVPEGDWFCPECALD 377 (1482)
Q Consensus 330 ~ndD~C~VC~~g-----G~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~ 377 (1482)
.-++.|.+|... ..++.||+|+.+-|..|.|.+-+|+|.|+|..|...
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~ 243 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYG 243 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhccc
Confidence 346789999653 349999999999999999999999999999999643
No 26
>PF15612 WHIM1: WSTF, HB1, Itc1p, MBD9 motif 1; PDB: 2Y9Z_B 2Y9Y_B.
Probab=95.36 E-value=0.0082 Score=51.99 Aligned_cols=38 Identities=37% Similarity=0.679 Sum_probs=33.1
Q ss_pred eccCCccccchhhHHHHHHHhhhhhhhhHHHHHHHhcc
Q 000462 248 LFSSEYCKQPVSVKIEILRCLCDDMIEVEAIRMELNRR 285 (1482)
Q Consensus 248 ils~EYp~lpV~~KLeILqfLcD~~LeSeaIRdELd~R 285 (1482)
+...+|+-+++..|+.||++|||.++++..||++|+.+
T Consensus 9 l~~~~y~~L~~~~kl~iL~~L~~~~l~s~~vr~~i~~~ 46 (50)
T PF15612_consen 9 LETGEYYELSPEEKLEILRALCDQLLSSSSVRNEIEER 46 (50)
T ss_dssp CCCSTCCCS-HHHHHHHHHHHHHHHCC-CCHHHHHHHH
T ss_pred HHcCCcccCCHHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence 33678999999999999999999999999999999876
No 27
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.34 E-value=0.009 Score=72.44 Aligned_cols=52 Identities=21% Similarity=0.572 Sum_probs=39.2
Q ss_pred CceeecCCCCCCCCcceEecCCCCCcccccccc--CChhhhccC-ceEEcCCcCCCC
Q 000462 1265 PKCYLCHEAEHTSTSNYIACEICGEWYHGDAFG--LKVENISKL-IGFRCHVCRKRT 1318 (1482)
Q Consensus 1265 p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVg--lte~~a~~i-~~y~Cp~Cr~r~ 1318 (1482)
-.+|-|++|. .-+ -|++|+.|..|||=.|.. |+.+.+.+. -.|.|..|.++.
T Consensus 171 c~vC~~g~~~-~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 171 CSVCYCGGPG-AGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred eeeeecCCcC-ccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 3456666774 445 679999999999999986 666666654 469999998553
No 28
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.11 E-value=0.0099 Score=72.10 Aligned_cols=46 Identities=33% Similarity=0.795 Sum_probs=37.4
Q ss_pred ccccccccCC-----ceeecCCCCCcccccccCCC------CCCCCCccCccccccC
Q 000462 333 DECCLCKMDG-----SLLCCDGCPAAYHSKCVGVA------NVPEGDWFCPECALDR 378 (1482)
Q Consensus 333 D~C~VC~~gG-----~LLcCD~CprafHl~CL~Pp------~vPeGdW~Cp~C~~~~ 378 (1482)
-.|.+|+.|+ +||.|+.|..+||..|+-|. .-|...|||..|....
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 3499998654 69999999999999999874 2466789999997543
No 29
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.07 E-value=0.0057 Score=77.33 Aligned_cols=100 Identities=24% Similarity=0.334 Sum_probs=64.3
Q ss_pred CCCCcccccccCCC--CCCCCCccCccccccCCCCCcCCCCccccccccccCCCCcEEEEe---cCeEEEeecCCCCccc
Q 000462 349 GCPAAYHSKCVGVA--NVPEGDWFCPECALDRHKPWMKPRKSLRGAELLGVDPHGRLYFCS---CGYLLVSDSCDTELIL 423 (1482)
Q Consensus 349 ~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~~~~~~~k~r~~lrgaEilg~D~~gRkY~~~---CgrLLvcdsC~ses~l 423 (1482)
.|+++||..|+.|. ..|+++|.||.|.....+....... .+.+...+++. .+.+++|++|+ ..+
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~---------~~~~~~e~c~ic~~~g~~l~c~tC~--~s~ 69 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDD---------WDDAEQEACRICADGGELLWCDTCP--ASF 69 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccccccccCC---------cchhhhhhhhhhcCCCcEEEecccc--HHH
Confidence 59999999999985 4678999999998776554333221 11222333444 46799999997 345
Q ss_pred cccccCchhHHHHhhccC---------chhHHHHHHHHHHHhccCCCC
Q 000462 424 NYYCRDDLNFVIDVLKSS---------DTFYGGIINAICKQWDITVSS 462 (1482)
Q Consensus 424 ~YY~~~dL~~vL~~L~s~---------e~~y~~I~~~I~~~w~ip~~l 462 (1482)
|+|+. .+++...+.. ...-+++.+++.|+|..+.-.
T Consensus 70 h~~cl---~~pl~~~p~~~~~c~Rc~~p~~~~k~~~il~~~~~~~~~~ 114 (696)
T KOG0383|consen 70 HASCL---GPPLTPQPNGEFICPRCFCPKNAGKIEKILGWRWKPTPKP 114 (696)
T ss_pred HHHcc---CCCCCcCCccceeeeeeccCCCcccccccceeEecCCCCc
Confidence 55554 3333333322 234457889999999777633
No 30
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=94.86 E-value=0.012 Score=73.61 Aligned_cols=49 Identities=35% Similarity=0.921 Sum_probs=41.8
Q ss_pred CCccccccccC-----CceeecCCCCCcccccccCCCCCCCCCccCccccccCC
Q 000462 331 NSDECCLCKMD-----GSLLCCDGCPAAYHSKCVGVANVPEGDWFCPECALDRH 379 (1482)
Q Consensus 331 ndD~C~VC~~g-----G~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~~~ 379 (1482)
++-.|.||..+ .+|++||.|....|..|.|+..+|+|.|.|..|.-...
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg~~ 323 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALGIE 323 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCCCCeeehhccccCC
Confidence 34568888754 47999999999999999999999999999999976533
No 31
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=94.30 E-value=0.013 Score=48.52 Aligned_cols=34 Identities=50% Similarity=1.265 Sum_probs=20.6
Q ss_pred CceeecCCCCCcccccccCCCCCCCC-CccCcccc
Q 000462 342 GSLLCCDGCPAAYHSKCVGVANVPEG-DWFCPECA 375 (1482)
Q Consensus 342 G~LLcCD~CprafHl~CL~Pp~vPeG-dW~Cp~C~ 375 (1482)
..|+.|+.|.-..|..|.+...+|++ +|+|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 36899999999999999999888887 89999884
No 32
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=93.87 E-value=0.04 Score=66.64 Aligned_cols=50 Identities=36% Similarity=0.917 Sum_probs=36.5
Q ss_pred ceeecCCCCCCC---CcceEecCCCCCccccccccCChhhh-------c---cC-ceEEcCCcCCCC
Q 000462 1266 KCYLCHEAEHTS---TSNYIACEICGEWYHGDAFGLKVENI-------S---KL-IGFRCHVCRKRT 1318 (1482)
Q Consensus 1266 ~cclC~kpy~~~---d~fyI~CD~C~~WfHG~CVglte~~a-------~---~i-~~y~Cp~Cr~r~ 1318 (1482)
-||+|.+ | |. ...||+||.|+-|-|-+|- |....+ . .+ -+|+|-.|-+..
T Consensus 130 ~C~iC~k-f-D~~~n~~~Wi~Cd~CgH~cH~dCA-Lr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 130 MCCICSK-F-DDNKNTCSWIGCDVCGHWCHLDCA-LRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CccccCC-c-ccCCCCeeEEeccCCCceehhhhh-cccccccCCccCCCCCccCceEEEccCCCChh
Confidence 5899988 5 43 5789999999999999993 333332 1 11 379999997554
No 33
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=93.79 E-value=0.028 Score=68.59 Aligned_cols=55 Identities=22% Similarity=0.431 Sum_probs=47.3
Q ss_pred CCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC-Ccc
Q 000462 1264 QPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT-PVC 1321 (1482)
Q Consensus 1264 ~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~-p~C 1321 (1482)
...=|+|+... +.+.+||+|+.|..|=|+-|+|+..... .+.|.|..|+-+. .++
T Consensus 85 ~~~~c~c~~~~-~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~~~~ 140 (508)
T KOG1844|consen 85 EISRCDCGLED-DMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNKEVE 140 (508)
T ss_pred ccccccccccc-CCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccccccch
Confidence 34569999984 5489999999999999999999988776 7899999999776 665
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.65 E-value=0.026 Score=68.24 Aligned_cols=43 Identities=35% Similarity=0.917 Sum_probs=35.2
Q ss_pred cccccccCCc---eeecCCCCCcccccccCCC--CCCCC----CccCccccc
Q 000462 334 ECCLCKMDGS---LLCCDGCPAAYHSKCVGVA--NVPEG----DWFCPECAL 376 (1482)
Q Consensus 334 ~C~VC~~gG~---LLcCD~CprafHl~CL~Pp--~vPeG----dW~Cp~C~~ 376 (1482)
.|.+|+..-+ |+.||+|...||+.||+|| .+|.- -|.|.+|..
T Consensus 546 sCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred eeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence 4999987543 8899999999999999997 36653 499999943
No 35
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=93.50 E-value=0.047 Score=63.36 Aligned_cols=34 Identities=21% Similarity=0.344 Sum_probs=27.5
Q ss_pred cccccccccccccccccceecccccccccccccccc
Q 000462 1055 SEYYQCGHCSKDVLIRDAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1055 ~~~~~C~~C~kdV~~rdav~C~~Cqg~~Hk~c~~~s 1090 (1482)
.-.|+|-.|..+-- .|.-|-.|--.||-.|...-
T Consensus 53 Q~l~sClTC~P~~~--~agvC~~C~~~CH~~H~lve 86 (345)
T KOG2752|consen 53 QALFSCLTCTPAPE--MAGVCYACSLSCHDGHELVE 86 (345)
T ss_pred cceeEeecccCChh--hceeEEEeeeeecCCceeee
Confidence 46778888887754 88899999999999887655
No 36
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=92.10 E-value=0.043 Score=68.52 Aligned_cols=88 Identities=30% Similarity=0.501 Sum_probs=59.6
Q ss_pred CccccccccC-----CceeecCCCCCcccccccCCC---CCCCCCccCccccccCCCCCcCCCCccccccccccCCCCcE
Q 000462 332 SDECCLCKMD-----GSLLCCDGCPAAYHSKCVGVA---NVPEGDWFCPECALDRHKPWMKPRKSLRGAELLGVDPHGRL 403 (1482)
Q Consensus 332 dD~C~VC~~g-----G~LLcCD~CprafHl~CL~Pp---~vPeGdW~Cp~C~~~~~~~~~k~r~~lrgaEilg~D~~gRk 403 (1482)
...|.+|+.. |.|+-|..|..-||.+|+... .+-.+-|.||.|+......+ .-|.
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~-------------~gD~---- 80 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGT-------------TGDP---- 80 (694)
T ss_pred hhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccc-------------cCCc----
Confidence 4568888764 469999999999999999853 12234499999975321110 0111
Q ss_pred EEEecCeEEEeecCCCCccccccccCchhHHHHhhccCchhHH
Q 000462 404 YFCSCGYLLVSDSCDTELILNYYCRDDLNFVIDVLKSSDTFYG 446 (1482)
Q Consensus 404 Y~~~CgrLLvcdsC~ses~l~YY~~~dL~~vL~~L~s~e~~y~ 446 (1482)
.++++|+.|+. .||.+|+.|+++.+.+....+.
T Consensus 81 -----~kf~~Ck~cDv-----syh~yc~~P~~~~v~sg~~~ck 113 (694)
T KOG4443|consen 81 -----KKFLLCKRCDV-----SYHCYCQKPPNDKVPSGPWLCK 113 (694)
T ss_pred -----ccccccccccc-----cccccccCCccccccCcccccH
Confidence 24566777863 6888888888888888665333
No 37
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=90.08 E-value=0.15 Score=58.48 Aligned_cols=86 Identities=21% Similarity=0.288 Sum_probs=60.2
Q ss_pred CCceeecCCCCCcccccccCCC-----CCCCCCccCccccccCCCCCcCCCCccccccccccCCCCcEEEEecCeEEEee
Q 000462 341 DGSLLCCDGCPAAYHSKCVGVA-----NVPEGDWFCPECALDRHKPWMKPRKSLRGAELLGVDPHGRLYFCSCGYLLVSD 415 (1482)
Q Consensus 341 gG~LLcCD~CprafHl~CL~Pp-----~vPeGdW~Cp~C~~~~~~~~~k~r~~lrgaEilg~D~~gRkY~~~CgrLLvcd 415 (1482)
+.+|+-|..|.++=|..||-.. .|-.-.|.|.+|..-..-+.... | ..||.||
T Consensus 243 peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsen------------d----------dqllfcd 300 (336)
T KOG1244|consen 243 PEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEN------------D----------DQLLFCD 300 (336)
T ss_pred chhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCC------------C----------ceeEeec
Confidence 3479999999999999999753 36667899999986543222111 1 2478889
Q ss_pred cCCCCccccccccCchhHHHHhhccCchhHHHHHHHHH
Q 000462 416 SCDTELILNYYCRDDLNFVIDVLKSSDTFYGGIINAIC 453 (1482)
Q Consensus 416 sC~ses~l~YY~~~dL~~vL~~L~s~e~~y~~I~~~I~ 453 (1482)
.|+. =||.+||.|+|-.-+.....++-..+.+.
T Consensus 301 dcdr-----gyhmyclsppm~eppegswsc~KOG~~~~ 333 (336)
T KOG1244|consen 301 DCDR-----GYHMYCLSPPMVEPPEGSWSCHLCLEELK 333 (336)
T ss_pred ccCC-----ceeeEecCCCcCCCCCCchhHHHHHHHHh
Confidence 9973 57788888888887766655554444443
No 38
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.95 E-value=0.16 Score=64.42 Aligned_cols=50 Identities=18% Similarity=0.529 Sum_probs=43.0
Q ss_pred CCCceeecCCCCCCCCcceEecCCCCCc-cccccccCChhhhccCceEEcCCcC
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEICGEW-YHGDAFGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~C~~W-fHG~CVglte~~a~~i~~y~Cp~Cr 1315 (1482)
....|-||..+ ++..++|-||.|++= ||-.|+..+..++- |..|+|+.|.
T Consensus 214 E~~~C~IC~~~--DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~ 264 (1134)
T KOG0825|consen 214 EEVKCDICTVH--DPEDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCS 264 (1134)
T ss_pred ccccceeeccC--ChHHhheeecccccceeeccccCccccccc-ccceecCcch
Confidence 33469999987 888999999999998 99999998776654 6789999996
No 39
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.71 E-value=0.15 Score=58.62 Aligned_cols=46 Identities=26% Similarity=0.444 Sum_probs=36.4
Q ss_pred ccccccccCC---------ceeecCCCCCcccccccCCC-----CCCCCCccCccccccC
Q 000462 333 DECCLCKMDG---------SLLCCDGCPAAYHSKCVGVA-----NVPEGDWFCPECALDR 378 (1482)
Q Consensus 333 D~C~VC~~gG---------~LLcCD~CprafHl~CL~Pp-----~vPeGdW~Cp~C~~~~ 378 (1482)
..|.+|-++- .+++|..|..++|.+|+..+ .+-.-.|.|-.|+-..
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~ 318 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCR 318 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhh
Confidence 4688886642 49999999999999999965 2555689999997543
No 40
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=86.76 E-value=0.33 Score=60.82 Aligned_cols=46 Identities=35% Similarity=0.907 Sum_probs=38.8
Q ss_pred CccccccccCCceeecCCCCCcccccccCCCC---CCCCCccCcccccc
Q 000462 332 SDECCLCKMDGSLLCCDGCPAAYHSKCVGVAN---VPEGDWFCPECALD 377 (1482)
Q Consensus 332 dD~C~VC~~gG~LLcCD~CprafHl~CL~Pp~---vPeGdW~Cp~C~~~ 377 (1482)
-+.|.+|..+|+++||+.|+.+||..|.+++. .+-+.|.|..|...
T Consensus 47 ~ts~~~~~~~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 47 ATSCGICKSGGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhhcchhhhcCCccccccCccccchhccCcccCcccccccccccCCCcc
Confidence 45799999999999999999999999999753 44567888888654
No 41
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=81.28 E-value=0.34 Score=40.33 Aligned_cols=34 Identities=18% Similarity=0.465 Sum_probs=19.4
Q ss_pred ceEecCCCCCccccccccCChhhhccCceEEcCCcC
Q 000462 1280 NYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1280 fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr 1315 (1482)
.+|.|+.|+-..|-.|.||.+.... ..|.|..|+
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred ceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 4699999999999999999988655 349998885
No 42
>PLN00163 histone H4; Provisional
Probab=81.14 E-value=0.85 Score=41.97 Aligned_cols=26 Identities=27% Similarity=0.695 Sum_probs=24.4
Q ss_pred CcHHHHHHHHHhcCccccCccccCCC
Q 000462 863 LPRSLVSKAARQAGCMKIPGILYPEN 888 (1482)
Q Consensus 863 Lp~s~v~KAARQgG~~ki~gi~Y~d~ 888 (1482)
+.+.+|++-||-||.++|+|.+|.|.
T Consensus 30 ItKpaIrRLARRgGVKRIs~~iY~e~ 55 (59)
T PLN00163 30 ITKPAIRRLARRGGVKRISGLIYEET 55 (59)
T ss_pred cchHHHHHHHHhcCceeecchhhHhH
Confidence 78999999999999999999999874
No 43
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=80.39 E-value=1.1 Score=55.17 Aligned_cols=43 Identities=42% Similarity=1.132 Sum_probs=35.3
Q ss_pred ccccccc-----CCceeecCCCCCcccccccCCC---CCCCC-------CccCccccc
Q 000462 334 ECCLCKM-----DGSLLCCDGCPAAYHSKCVGVA---NVPEG-------DWFCPECAL 376 (1482)
Q Consensus 334 ~C~VC~~-----gG~LLcCD~CprafHl~CL~Pp---~vPeG-------dW~Cp~C~~ 376 (1482)
.|+||-. .|++|-||.|....|-.|.|.. ++|.| .|||.-|..
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY 178 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence 7999953 5789999999999999999863 35654 599988865
No 44
>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=78.97 E-value=1.3 Score=38.61 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=29.6
Q ss_pred cccccccccccc--ccccceecccccccccccccccc
Q 000462 1056 EYYQCGHCSKDV--LIRDAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1056 ~~~~C~~C~kdV--~~rdav~C~~Cqg~~Hk~c~~~s 1090 (1482)
....|..|++-+ +.+.+..|+.|+-.+|++|...-
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 456899999999 89999999999999999998754
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=75.61 E-value=0.51 Score=39.75 Aligned_cols=43 Identities=23% Similarity=0.563 Sum_probs=32.2
Q ss_pred ceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcC
Q 000462 1266 KCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1266 ~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr 1315 (1482)
.|.||...+ .++..++... |+..||-+|+.-=-.. .+.||-||
T Consensus 2 ~C~IC~~~~-~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEF-EDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR 44 (44)
T ss_dssp CETTTTCBH-HTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred CCcCCChhh-cCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence 489999998 6666777777 9999999997643333 24899886
No 46
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=69.41 E-value=3.7 Score=55.12 Aligned_cols=69 Identities=14% Similarity=0.363 Sum_probs=47.2
Q ss_pred ccccccceeccccccCCCCCCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCC
Q 000462 1244 MQFTRKNFLAASELLTDTLDQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1244 ~~Fr~~~v~~~g~~~~~~~~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
..|....+..+.. .+.....+||+|.+--..+..+-+.||.|+-=+|-+|+||..-- =-+|-|-+|-..
T Consensus 201 ~~f~~~e~~~~~~--~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ip---eg~WlCr~Cl~s 269 (1051)
T KOG0955|consen 201 SYFKNYELGDPKD--ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIP---EGQWLCRRCLQS 269 (1051)
T ss_pred HHhhhhhccCCCc--cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCC---CCcEeehhhccC
Confidence 3455555555543 44456679999988732223666999999999999999943211 146999999643
No 47
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=63.88 E-value=3.6 Score=40.64 Aligned_cols=42 Identities=21% Similarity=0.443 Sum_probs=32.4
Q ss_pred CcHHHHHHHHHhcCccccCccccCCCchhhhh-hhhhhhhhhh
Q 000462 863 LPRSLVSKAARQAGCMKIPGILYPENSDFARR-SRTVAWRAAV 904 (1482)
Q Consensus 863 Lp~s~v~KAARQgG~~ki~gi~Y~d~se~~rR-sr~~aWraaV 904 (1482)
+-+.+|++-||.||.++|.|++|-|-....|= -+.++|-|+.
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 35789999999999999999999886554443 3456777654
No 48
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=60.97 E-value=6.4 Score=48.94 Aligned_cols=48 Identities=27% Similarity=0.529 Sum_probs=40.2
Q ss_pred CCCCccccccccCCceeecCCCCCcccccccCCCCCCCCCccCcccccc
Q 000462 329 DWNSDECCLCKMDGSLLCCDGCPAAYHSKCVGVANVPEGDWFCPECALD 377 (1482)
Q Consensus 329 d~ndD~C~VC~~gG~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~ 377 (1482)
..+.+.|.+|.+||.+++|+.|+.++|-.|... ..|++-|.|..|..-
T Consensus 86 ~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~-~~~~c~~~~~d~~~~ 133 (463)
T KOG1081|consen 86 KIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPA-QLEKCSKRCTDCRAF 133 (463)
T ss_pred CCCcchhccccCCCccceeccccccccccCcCc-cCcccccCCcceeee
Confidence 345678999999999999999999999999864 577788988888654
No 49
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=60.45 E-value=4.5 Score=52.04 Aligned_cols=56 Identities=18% Similarity=0.535 Sum_probs=43.5
Q ss_pred CCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC-Ccc
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT-PVC 1321 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~-p~C 1321 (1482)
..-+|=.|+-|-.....=||+||.|+-=-|-.|.||++--- ..|.|-.|..-. |.|
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~~ppC 326 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGIEPPC 326 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccCCCCe
Confidence 44579999999323344569999999999999999987544 789999998654 544
No 50
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=59.09 E-value=5.5 Score=44.33 Aligned_cols=42 Identities=36% Similarity=0.850 Sum_probs=34.2
Q ss_pred ccccccccc-ccc----cccceeccccccccccccccccCccccceeeeeecccccC
Q 000462 1057 YYQCGHCSK-DVL----IRDAVCCQDCKGYFHKRHIRKSAGAVTTECKYTCYQCQDG 1108 (1482)
Q Consensus 1057 ~~~C~~C~k-dV~----~rdav~C~~Cqg~~Hk~c~~~s~g~~~~~~~~~C~~C~~~ 1108 (1482)
+..|..|+. ||+ +..++.|..|...||+.|..+. .|.+|..-
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~----------~CpkC~R~ 198 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK----------SCPKCARR 198 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC----------CCCCcHhH
Confidence 467899996 555 4589999999999999999964 49888653
No 51
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=58.13 E-value=10 Score=38.56 Aligned_cols=53 Identities=23% Similarity=0.491 Sum_probs=39.6
Q ss_pred CCCceeecCCCCCCCCcceEe-----cCCC---CCcccccc----ccCChhhhccCceEEcCCcCCC
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIA-----CEIC---GEWYHGDA----FGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~-----CD~C---~~WfHG~C----Vglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
....|+.|++- ..+..+++ +..| ..=|=|.| ++...+++.....|.||.||..
T Consensus 6 ~g~~CHqCrqK--t~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 6 NGKTCHQCRQK--TLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred CCCCchhhcCC--CCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 45679999997 55666443 2666 77788888 5667777777889999999974
No 52
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=57.03 E-value=13 Score=46.87 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=39.6
Q ss_pred CCCccccccccCCceeecCCCCCcccccccCCC-CCCC--CCccCccccccC
Q 000462 330 WNSDECCLCKMDGSLLCCDGCPAAYHSKCVGVA-NVPE--GDWFCPECALDR 378 (1482)
Q Consensus 330 ~ndD~C~VC~~gG~LLcCD~CprafHl~CL~Pp-~vPe--GdW~Cp~C~~~~ 378 (1482)
..+-+|+.|+..|..+-|+-|-+.||..|..|. ..+. ..|.||.|..-+
T Consensus 58 N~d~~cfechlpg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 58 NIDPFCFECHLPGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFK 109 (588)
T ss_pred CCCcccccccCCcceeeeehhhccccccccCcchhhccccccccCCcccccC
Confidence 334579999999999999999999999999985 3333 359999997544
No 53
>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=56.02 E-value=4.2 Score=34.02 Aligned_cols=33 Identities=27% Similarity=0.488 Sum_probs=28.2
Q ss_pred ccccccccccccc-cceecccccccccccccccc
Q 000462 1058 YQCGHCSKDVLIR-DAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1058 ~~C~~C~kdV~~r-dav~C~~Cqg~~Hk~c~~~s 1090 (1482)
..|..|++-+... .+.+|..|+-.+|++|...-
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 4599999988755 49999999999999998753
No 54
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=55.63 E-value=3 Score=57.69 Aligned_cols=58 Identities=16% Similarity=0.358 Sum_probs=46.2
Q ss_pred CCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC---Ccccc
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT---PVCSC 1323 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~---p~Cp~ 1323 (1482)
....|-+|+.- +-+.-|+-||.|..|||--|+....+.+. +.+|.||.|+... ..|..
T Consensus 1107 ~~~~c~~cr~k--~~~~~m~lc~~c~~~~h~~C~rp~~~~~~-~~dW~C~~c~~e~~~rr~~~~ 1167 (1404)
T KOG1245|consen 1107 VNALCKVCRRK--KQDEKMLLCDECLSGFHLFCLRPALSSVP-PGDWMCPSCRKEHRARRQKRF 1167 (1404)
T ss_pred chhhhhhhhhc--ccchhhhhhHhhhhhHHHHhhhhhhccCC-cCCccCCccchhhhhhhhhhh
Confidence 55689999998 44567799999999999999999988765 5669999998442 44444
No 55
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=55.51 E-value=5.5 Score=43.67 Aligned_cols=41 Identities=37% Similarity=0.997 Sum_probs=30.3
Q ss_pred cccccc------CCceeecCCCCCcccccccCCCC--------CCCCC--ccCcccc
Q 000462 335 CCLCKM------DGSLLCCDGCPAAYHSKCVGVAN--------VPEGD--WFCPECA 375 (1482)
Q Consensus 335 C~VC~~------gG~LLcCD~CprafHl~CL~Pp~--------vPeGd--W~Cp~C~ 375 (1482)
|.+|+. -|.|+.|-+|-.+||..|||+-+ |-+++ ..|.+|.
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Ci 58 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCI 58 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhc
Confidence 778853 36799999999999999999842 33332 5677774
No 56
>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=53.37 E-value=5.8 Score=33.59 Aligned_cols=33 Identities=27% Similarity=0.490 Sum_probs=28.9
Q ss_pred cccccccccccc--ccceecccccccccccccccc
Q 000462 1058 YQCGHCSKDVLI--RDAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1058 ~~C~~C~kdV~~--rdav~C~~Cqg~~Hk~c~~~s 1090 (1482)
..|.+|++-+.. ..+.+|..|+-.+|++|...-
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 459999998876 699999999999999998764
No 57
>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=52.15 E-value=5.8 Score=37.50 Aligned_cols=43 Identities=30% Similarity=0.662 Sum_probs=28.6
Q ss_pred ceeecCCCCCCC--------CcceEecCCCCCcccccccc--CChhhhccCceEEcCCcC
Q 000462 1266 KCYLCHEAEHTS--------TSNYIACEICGEWYHGDAFG--LKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1266 ~cclC~kpy~~~--------d~fyI~CD~C~~WfHG~CVg--lte~~a~~i~~y~Cp~Cr 1315 (1482)
.|.||+.++.++ +...|.=..|+--||..|+. |+... .||-||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~-------~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN-------TCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS-------B-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC-------cCCCCC
Confidence 499999997333 23444445699999999995 32222 899887
No 58
>smart00417 H4 Histone H4.
Probab=48.42 E-value=6.4 Score=37.95 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=27.4
Q ss_pred CcHHHHHHHHHhcCccccCccccCCCchhh
Q 000462 863 LPRSLVSKAARQAGCMKIPGILYPENSDFA 892 (1482)
Q Consensus 863 Lp~s~v~KAARQgG~~ki~gi~Y~d~se~~ 892 (1482)
||+..|++-||.||.++|+|-.|.+-.++-
T Consensus 14 I~k~~IrRLaRr~GvkRIS~~~y~elr~vl 43 (74)
T smart00417 14 ITKPAIRRLARRGGVKRISGLIYDETRNVL 43 (74)
T ss_pred CCHHHHHHHHHHcCcchhhHHHHHHHHHHH
Confidence 999999999999999999999998876664
No 59
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=47.88 E-value=12 Score=50.04 Aligned_cols=45 Identities=40% Similarity=1.054 Sum_probs=37.7
Q ss_pred ccccccccCCc--eeecCCCCCcccccccCCC--CCCCCCccCcccccc
Q 000462 333 DECCLCKMDGS--LLCCDGCPAAYHSKCVGVA--NVPEGDWFCPECALD 377 (1482)
Q Consensus 333 D~C~VC~~gG~--LLcCD~CprafHl~CL~Pp--~vPeGdW~Cp~C~~~ 377 (1482)
..|..|..+.. ++.|+.|...||.+|..++ .+|+|+|.|+.|...
T Consensus 156 ~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 156 PQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred hhhhccccCCCccceecccccCcccccccCCCCCcCCcCcccCCccccc
Confidence 45888987653 3499999999999999975 599999999999765
No 60
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.73 E-value=10 Score=34.76 Aligned_cols=29 Identities=28% Similarity=0.754 Sum_probs=25.3
Q ss_pred cccccccc----CCceeecCCCCCcccccccCC
Q 000462 333 DECCLCKM----DGSLLCCDGCPAAYHSKCVGV 361 (1482)
Q Consensus 333 D~C~VC~~----gG~LLcCD~CprafHl~CL~P 361 (1482)
..|.+|++ +++++.|..|...||-.|...
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 46999986 678999999999999999964
No 61
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=38.86 E-value=14 Score=32.74 Aligned_cols=35 Identities=11% Similarity=0.262 Sum_probs=16.4
Q ss_pred ceEecCCCCCccccccccCChhhhccCceEEcCCcC
Q 000462 1280 NYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1280 fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr 1315 (1482)
.||+||.|.+|=.-. .++.......-+.|.|..=.
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~n~ 36 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSMNP 36 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGGSS
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCCCC
Confidence 589999999998765 23322111122388887643
No 62
>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=38.69 E-value=17 Score=30.10 Aligned_cols=23 Identities=35% Similarity=0.934 Sum_probs=18.0
Q ss_pred ccccccccccc--cccceecccccc
Q 000462 1058 YQCGHCSKDVL--IRDAVCCQDCKG 1080 (1482)
Q Consensus 1058 ~~C~~C~kdV~--~rdav~C~~Cqg 1080 (1482)
|.|+.|..+|. .+|.|+|.+|-.
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCC
Confidence 67999999987 578899999953
No 63
>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=37.99 E-value=13 Score=36.82 Aligned_cols=28 Identities=25% Similarity=0.536 Sum_probs=26.0
Q ss_pred CcHHHHHHHHHhcCccccCccccCCCch
Q 000462 863 LPRSLVSKAARQAGCMKIPGILYPENSD 890 (1482)
Q Consensus 863 Lp~s~v~KAARQgG~~ki~gi~Y~d~se 890 (1482)
||+..|++-||.||.++|++-.|.+-.+
T Consensus 14 i~k~~I~RLarr~GvkRIS~d~y~e~~~ 41 (85)
T cd00076 14 ITKPAIRRLARRGGVKRISGGVYDEVRN 41 (85)
T ss_pred CCHHHHHHHHHHcCcchhhHHHHHHHHH
Confidence 9999999999999999999999987665
No 64
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.87 E-value=25 Score=42.63 Aligned_cols=45 Identities=29% Similarity=0.642 Sum_probs=31.2
Q ss_pred cccccccc---CCceeecCCCCCcccccccCCCCCCCCCccCccccccC
Q 000462 333 DECCLCKM---DGSLLCCDGCPAAYHSKCVGVANVPEGDWFCPECALDR 378 (1482)
Q Consensus 333 D~C~VC~~---gG~LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~~ 378 (1482)
+.|.+|-+ .|+.|-==-|.-.||..|++|.-..- .=+||.|+.+-
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 68999976 35533334567789999999864322 34699998753
No 65
>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=35.34 E-value=10 Score=32.51 Aligned_cols=31 Identities=23% Similarity=0.449 Sum_probs=23.5
Q ss_pred HHHHhhccceeeecCCccccccccccccccccccc
Q 000462 658 MKAILKKWDKFYWPNTQKLNADTQKEKCGWCFSCK 692 (1482)
Q Consensus 658 ~Kafs~~~~~F~Wps~ekk~~ev~rerCGWC~sCk 692 (1482)
-|++++-+.+|+||...+-+.++-| -|..||
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 3788899999999999887766544 366664
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.57 E-value=22 Score=31.22 Aligned_cols=24 Identities=38% Similarity=0.982 Sum_probs=20.6
Q ss_pred cccccccccccccc--cceecccccc
Q 000462 1057 YYQCGHCSKDVLIR--DAVCCQDCKG 1080 (1482)
Q Consensus 1057 ~~~C~~C~kdV~~r--dav~C~~Cqg 1080 (1482)
.|-|+.|..+|.+. |.|+|.+|-.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCc
Confidence 47899999999876 8999999964
No 67
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=33.42 E-value=8.8 Score=48.40 Aligned_cols=42 Identities=33% Similarity=0.609 Sum_probs=32.1
Q ss_pred eeccccccccccccccccccc--ccccceecccccccccccccccc
Q 000462 1047 YLFSKAARSEYYQCGHCSKDV--LIRDAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1047 yL~~k~~~~~~~~C~~C~kdV--~~rdav~C~~Cqg~~Hk~c~~~s 1090 (1482)
++.|-+.+. --|-+|+|.. ++|.-..|-.|+-+|||+|..+-
T Consensus 270 f~vHSY~rp--TVCq~CkkLLkGL~rQGlqCkDCk~NcHkrCa~~v 313 (888)
T KOG4236|consen 270 FIVHSYTRP--TVCQYCKKLLKGLFRQGLQCKDCKFNCHKRCAMKV 313 (888)
T ss_pred EEEeeccCc--hHHHHHHHHHHHHHhcCcccccCCcchhhhhhhhc
Confidence 344444332 3478999977 49999999999999999998654
No 68
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=33.30 E-value=16 Score=29.09 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=11.9
Q ss_pred ceeecCCCCCCCCcceEecCCCCCccccccc
Q 000462 1266 KCYLCHEAEHTSTSNYIACEICGEWYHGDAF 1296 (1482)
Q Consensus 1266 ~cclC~kpy~~~d~fyI~CD~C~~WfHG~CV 1296 (1482)
.|-+|+++- +. .++-.|..|+=.+|-+|+
T Consensus 2 ~C~~C~~~~-~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPI-DG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS-----S---EEE-TTT-----HHHH
T ss_pred cCCcCCCcC-CC-CceEECccCCCccChhcC
Confidence 488999995 43 355568999999999884
No 69
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=33.04 E-value=38 Score=42.39 Aligned_cols=46 Identities=7% Similarity=-0.232 Sum_probs=41.6
Q ss_pred CceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcC
Q 000462 1265 PKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCR 1315 (1482)
Q Consensus 1265 p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr 1315 (1482)
-.||.|++.| ++++.+-.|..|+.|+|-+|++.+. .++.++|-.|+
T Consensus 171 ~~~~~~~k~e-~d~~~~kt~~~~~~~~~p~~~~t~~----~~~~~~~~~~s 216 (464)
T KOG1886|consen 171 GDFGDGQKLE-IDMLVPKTGPRRGTLPDPKKVQTLN----AAASKRSQQKS 216 (464)
T ss_pred cchhcccccC-CccchhhhcccCCCCCCcccccccc----ccccceecccc
Confidence 4699999997 9999999999999999999999998 66888898883
No 70
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=31.80 E-value=11 Score=48.17 Aligned_cols=28 Identities=25% Similarity=0.596 Sum_probs=19.5
Q ss_pred EecCCCCCccccccccCChhhhccCceEEcCCcCCC
Q 000462 1282 IACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1282 I~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
+.|+.|.-|||-+|....--. ||+|-|+
T Consensus 532 ~rC~~C~avfH~~C~~r~s~~--------CPrC~R~ 559 (580)
T KOG1829|consen 532 RRCSTCLAVFHKKCLRRKSPC--------CPRCERR 559 (580)
T ss_pred eeHHHHHHHHHHHHHhccCCC--------CCchHHH
Confidence 668899999998887643222 7777543
No 71
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=31.54 E-value=25 Score=32.37 Aligned_cols=35 Identities=29% Similarity=0.586 Sum_probs=31.0
Q ss_pred ccccccccccccc-cccceecccccccccccccccc
Q 000462 1056 EYYQCGHCSKDVL-IRDAVCCQDCKGYFHKRHIRKS 1090 (1482)
Q Consensus 1056 ~~~~C~~C~kdV~-~rdav~C~~Cqg~~Hk~c~~~s 1090 (1482)
+...|..|.+.+. -.|+|-|..|...-|++|-..-
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 5678999999997 8899999999999999998654
No 72
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=31.52 E-value=27 Score=34.69 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=24.9
Q ss_pred CCCceeecCCCCCCCCcceEecCC--CCCccccccc
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEI--CGEWYHGDAF 1296 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~--C~~WfHG~CV 1296 (1482)
....|.+|++.. -..|.|.. |..+||--|-
T Consensus 54 ~~~~C~iC~~~~----G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 54 FKLKCSICGKSG----GACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred cCCcCcCCCCCC----ceeEEcCCCCCCcCCCHHHH
Confidence 467899999873 34699999 9999999885
No 73
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=29.85 E-value=30 Score=35.65 Aligned_cols=21 Identities=19% Similarity=0.536 Sum_probs=18.3
Q ss_pred CCCceeecCCCCCCCCcceEec
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIAC 1284 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~C 1284 (1482)
..+..|+|..+| |++..||.|
T Consensus 101 ~~~d~~~Ce~~y-n~~~~~~~c 121 (121)
T cd04714 101 DGVDFYYCAGTY-NPDTGMLKC 121 (121)
T ss_pred cCCCEEEEeccC-CCCcCcccC
Confidence 345679999998 999999998
No 74
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=29.63 E-value=26 Score=33.45 Aligned_cols=30 Identities=30% Similarity=0.909 Sum_probs=25.6
Q ss_pred CccccccccC-CceeecC--CCCCcccccccCC
Q 000462 332 SDECCLCKMD-GSLLCCD--GCPAAYHSKCVGV 361 (1482)
Q Consensus 332 dD~C~VC~~g-G~LLcCD--~CprafHl~CL~P 361 (1482)
...|.+|+.. |-.+-|. +|.+.||+.|..-
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 3469999998 9888897 5999999999864
No 75
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=29.58 E-value=27 Score=34.71 Aligned_cols=30 Identities=27% Similarity=0.811 Sum_probs=25.1
Q ss_pred Ccccccccc-CCceeecCC--CCCcccccccCC
Q 000462 332 SDECCLCKM-DGSLLCCDG--CPAAYHSKCVGV 361 (1482)
Q Consensus 332 dD~C~VC~~-gG~LLcCD~--CprafHl~CL~P 361 (1482)
...|.+|+. +|-.+-|.. |...||..|...
T Consensus 55 ~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKSGGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHH
Confidence 356999987 577888987 999999999854
No 76
>PTZ00015 histone H4; Provisional
Probab=28.78 E-value=26 Score=35.87 Aligned_cols=40 Identities=18% Similarity=0.344 Sum_probs=30.6
Q ss_pred cchhhhhcccc--CcHHHHHHHHHhcCccccCccccCCCchh
Q 000462 852 RLSCQLFSWKR--LPRSLVSKAARQAGCMKIPGILYPENSDF 891 (1482)
Q Consensus 852 ~lsr~if~~~~--Lp~s~v~KAARQgG~~ki~gi~Y~d~se~ 891 (1482)
+=.|.++.-.+ ||+..|++-||.||.++|++-.|.|-.++
T Consensus 18 kr~rk~~r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~v 59 (102)
T PTZ00015 18 KRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGV 59 (102)
T ss_pred hhHHHHHhhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHH
Confidence 33455553332 89999999999999999999999865553
No 77
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=28.49 E-value=24 Score=35.10 Aligned_cols=30 Identities=20% Similarity=0.511 Sum_probs=20.6
Q ss_pred CCCCCcccccccCCC-CCCCCCccCcccccc
Q 000462 348 DGCPAAYHSKCVGVA-NVPEGDWFCPECALD 377 (1482)
Q Consensus 348 D~CprafHl~CL~Pp-~vPeGdW~Cp~C~~~ 377 (1482)
..|.-.||+.|+.-- +-....=.||.|+..
T Consensus 50 g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQSSKGQCPMCRQP 80 (85)
T ss_pred ccCccHHHHHHHHHHHccccCCCCCCCcCCe
Confidence 358999999999742 122234489999864
No 78
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.28 E-value=47 Score=44.96 Aligned_cols=42 Identities=26% Similarity=0.612 Sum_probs=30.6
Q ss_pred CCCceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC--Ccccc
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT--PVCSC 1323 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~--p~Cp~ 1323 (1482)
....|.-|+... ++..|..|+.. .-..|+||+|+... ..||-
T Consensus 625 g~RfCpsCG~~t-----~~frCP~CG~~--------------Te~i~fCP~CG~~~~~y~CPK 668 (1121)
T PRK04023 625 GRRKCPSCGKET-----FYRRCPFCGTH--------------TEPVYRCPRCGIEVEEDECEK 668 (1121)
T ss_pred cCccCCCCCCcC-----CcccCCCCCCC--------------CCcceeCccccCcCCCCcCCC
Confidence 456799998873 66899999987 22458899998664 44554
No 79
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=25.76 E-value=38 Score=32.40 Aligned_cols=33 Identities=21% Similarity=0.501 Sum_probs=25.8
Q ss_pred CCCceeecCCCCCCCCcceEecCC--CCCccccccccCC
Q 000462 1263 DQPKCYLCHEAEHTSTSNYIACEI--CGEWYHGDAFGLK 1299 (1482)
Q Consensus 1263 ~~p~cclC~kpy~~~d~fyI~CD~--C~~WfHG~CVglt 1299 (1482)
...+|.+|++++ + --|.|.. |..+||--|-.-.
T Consensus 35 ~~~~C~~C~~~~---G-a~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 35 RKLKCSICKKKG---G-ACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred hCCCCcCCCCCC---C-eEEEEeCCCCCcEEChHHHccC
Confidence 345899999994 2 4499988 9999999886543
No 80
>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=25.51 E-value=20 Score=28.66 Aligned_cols=42 Identities=19% Similarity=0.442 Sum_probs=28.2
Q ss_pred eeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCC
Q 000462 1267 CYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRK 1316 (1482)
Q Consensus 1267 cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~ 1316 (1482)
|.+|...+ ... +.-..|+.-||..|+.--.++ ...+||.|+.
T Consensus 2 C~iC~~~~-~~~---~~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF-REP---VVLLPCGHVFCRSCIDKWLKS----GKNTCPLCRT 43 (45)
T ss_pred CCcCchhh-hCc---eEecCCCChhcHHHHHHHHHh----CcCCCCCCCC
Confidence 77887775 322 333458888999998643332 5667999875
No 81
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=24.18 E-value=23 Score=35.24 Aligned_cols=50 Identities=18% Similarity=0.389 Sum_probs=29.7
Q ss_pred CceeecCCCCCCC---Ccce--Eec----CCCCCccccccccCChhhhccCceEEcCCcCCC
Q 000462 1265 PKCYLCHEAEHTS---TSNY--IAC----EICGEWYHGDAFGLKVENISKLIGFRCHVCRKR 1317 (1482)
Q Consensus 1265 p~cclC~kpy~~~---d~fy--I~C----D~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r 1317 (1482)
.+|.||+.+| +. +-.+ -.| -.|+.=||..|+.-=.+... - +=.||.||+.
T Consensus 22 d~CgICr~~f-dg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~-~-~~~CPmCR~~ 80 (85)
T PF12861_consen 22 DVCGICRMPF-DGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS-S-KGQCPMCRQP 80 (85)
T ss_pred CceeeEeccc-ccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc-C-CCCCCCcCCe
Confidence 4688888887 52 1111 122 26999999999753322211 1 2389999863
No 82
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=23.07 E-value=22 Score=45.47 Aligned_cols=46 Identities=24% Similarity=0.685 Sum_probs=34.0
Q ss_pred ccccccccccccc-----cccceeccccccccccccccccCccccceeeeeecccccCc
Q 000462 1056 EYYQCGHCSKDVL-----IRDAVCCQDCKGYFHKRHIRKSAGAVTTECKYTCYQCQDGR 1109 (1482)
Q Consensus 1056 ~~~~C~~C~kdV~-----~rdav~C~~Cqg~~Hk~c~~~s~g~~~~~~~~~C~~C~~~~ 1109 (1482)
-...|..|+++=+ .+.+.+|..|...|||+|.++. +-.|.+|..-+
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~--------s~~CPrC~R~q 560 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK--------SPCCPRCERRQ 560 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc--------CCCCCchHHHH
Confidence 4456777776543 5777899999999999999887 44488886543
No 83
>PLN00035 histone H4; Provisional
Probab=22.52 E-value=38 Score=34.80 Aligned_cols=29 Identities=24% Similarity=0.623 Sum_probs=25.9
Q ss_pred CcHHHHHHHHHhcCccccCccccCCCchh
Q 000462 863 LPRSLVSKAARQAGCMKIPGILYPENSDF 891 (1482)
Q Consensus 863 Lp~s~v~KAARQgG~~ki~gi~Y~d~se~ 891 (1482)
||...|++-||.||.++|++-.|.+-.+.
T Consensus 30 ipk~~IrRLARr~GvkRIS~~ay~elr~v 58 (103)
T PLN00035 30 ITKPAIRRLARRGGVKRISGLIYEETRGV 58 (103)
T ss_pred CCHHHHHHHHHHcCcccchHHHHHHHHHH
Confidence 99999999999999999999888765544
No 84
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=22.15 E-value=54 Score=36.71 Aligned_cols=43 Identities=21% Similarity=0.532 Sum_probs=31.4
Q ss_pred CCceeecCC-----CCCCCCcceEecCCCCCccccccccCChhhhccCceEEcCCcCCCC
Q 000462 1264 QPKCYLCHE-----AEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGFRCHVCRKRT 1318 (1482)
Q Consensus 1264 ~p~cclC~k-----py~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y~Cp~Cr~r~ 1318 (1482)
.-+|-+|.. || +.+ --+.|+.|.-=||-.|+.- =.||+|.++.
T Consensus 152 GfiCe~C~~~~~IfPF-~~~-~~~~C~~C~~v~H~~C~~~----------~~CpkC~R~~ 199 (202)
T PF13901_consen 152 GFICEICNSDDIIFPF-QID-TTVRCPKCKSVFHKSCFRK----------KSCPKCARRQ 199 (202)
T ss_pred CCCCccCCCCCCCCCC-CCC-CeeeCCcCccccchhhcCC----------CCCCCcHhHh
Confidence 346888876 34 222 4589999999999999982 1299997653
No 85
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=22.14 E-value=42 Score=31.73 Aligned_cols=29 Identities=31% Similarity=0.889 Sum_probs=0.0
Q ss_pred CCcccccccc----CCce--eecC--CCCCccccccc
Q 000462 331 NSDECCLCKM----DGSL--LCCD--GCPAAYHSKCV 359 (1482)
Q Consensus 331 ndD~C~VC~~----gG~L--LcCD--~CprafHl~CL 359 (1482)
.+..|.||.. .+++ +.|+ .|...||..||
T Consensus 1 ~~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL 37 (70)
T PF11793_consen 1 QELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCL 37 (70)
T ss_dssp ---S-SSS--SS-TT-----B--S-TT----B-SGGG
T ss_pred CCCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHH
No 86
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.22 E-value=33 Score=40.29 Aligned_cols=46 Identities=17% Similarity=0.371 Sum_probs=28.8
Q ss_pred CccccccccCCc----------eeecCCCCCcccccccCCCCCCCCCccCcccccc
Q 000462 332 SDECCLCKMDGS----------LLCCDGCPAAYHSKCVGVANVPEGDWFCPECALD 377 (1482)
Q Consensus 332 dD~C~VC~~gG~----------LLcCD~CprafHl~CL~Pp~vPeGdW~Cp~C~~~ 377 (1482)
|..|.||++.=+ -+.==.|.-+||-+|..-.-+-.-.=.||.|..+
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKek 279 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEK 279 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHH
Confidence 567999986311 0111158899999999754322224569999754
No 87
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.03 E-value=2.5e+02 Score=34.56 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=33.7
Q ss_pred CceeecCCCCCCCCcceEecCCCCCccccccccCChhhhccCceE--EcCCcCCCC
Q 000462 1265 PKCYLCHEAEHTSTSNYIACEICGEWYHGDAFGLKVENISKLIGF--RCHVCRKRT 1318 (1482)
Q Consensus 1265 p~cclC~kpy~~~d~fyI~CD~C~~WfHG~CVglte~~a~~i~~y--~Cp~Cr~r~ 1318 (1482)
-.|+||-+-|-.-|.+-| =-|.-=||..||.- =|.++ .||-|++..
T Consensus 230 ~~CaIClEdY~~GdklRi--LPC~H~FH~~CIDp------WL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRI--LPCSHKFHVNCIDP------WLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeE--ecCCCchhhccchh------hHhhcCccCCCCCCcC
Confidence 489999999955566666 78999999999852 12222 499988653
Done!