Query 000320
Match_columns 1673
No_of_seqs 275 out of 306
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:13:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000320hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08214 KAT11: Histone acetyl 100.0 9.4E-56 2E-60 514.5 16.4 280 1189-1478 8-345 (346)
2 KOG1778 CREB binding protein/P 100.0 6.7E-33 1.5E-37 318.3 2.7 234 1389-1666 1-235 (319)
3 smart00551 ZnF_TAZ TAZ zinc fi 99.7 7.5E-17 1.6E-21 153.4 5.3 77 701-777 3-79 (79)
4 PF02135 zf-TAZ: TAZ zinc fing 99.4 3.9E-14 8.4E-19 133.2 1.9 73 704-776 2-75 (75)
5 cd02337 ZZ_CBP Zinc finger, ZZ 98.9 4.9E-10 1.1E-14 94.9 2.4 41 1593-1638 1-41 (41)
6 PF00569 ZZ: Zinc finger, ZZ t 98.9 4E-10 8.8E-15 97.4 1.1 44 1591-1635 3-46 (46)
7 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.7 1E-08 2.2E-13 89.7 3.1 46 1593-1638 1-48 (48)
8 cd02344 ZZ_HERC2 Zinc finger, 98.6 2E-08 4.2E-13 86.8 2.9 44 1593-1637 1-44 (45)
9 smart00551 ZnF_TAZ TAZ zinc fi 98.6 5.1E-08 1.1E-12 93.6 6.0 66 733-798 10-79 (79)
10 cd02340 ZZ_NBR1_like Zinc fing 98.6 2.6E-08 5.6E-13 85.3 2.8 43 1593-1638 1-43 (43)
11 smart00291 ZnF_ZZ Zinc-binding 98.6 3.8E-08 8.2E-13 84.5 3.2 42 1590-1633 2-43 (44)
12 cd02339 ZZ_Mind_bomb Zinc fing 98.5 4E-08 8.6E-13 85.0 2.9 43 1594-1637 2-44 (45)
13 cd02334 ZZ_dystrophin Zinc fin 98.4 1E-07 2.2E-12 83.9 2.9 44 1593-1636 1-47 (49)
14 cd02249 ZZ Zinc finger, ZZ typ 98.4 1.8E-07 3.9E-12 81.0 3.0 44 1593-1638 1-46 (46)
15 cd02345 ZZ_dah Zinc finger, ZZ 98.4 1.7E-07 3.7E-12 82.4 2.9 43 1594-1637 2-48 (49)
16 cd02342 ZZ_UBA_plant Zinc fing 98.3 2E-07 4.3E-12 79.5 2.1 35 1593-1627 1-35 (43)
17 cd02335 ZZ_ADA2 Zinc finger, Z 98.3 3.4E-07 7.4E-12 80.4 3.0 43 1593-1636 1-47 (49)
18 cd02338 ZZ_PCMF_like Zinc fing 98.3 2.9E-07 6.2E-12 81.0 2.4 33 1593-1625 1-33 (49)
19 cd02343 ZZ_EF Zinc finger, ZZ 98.2 8.6E-07 1.9E-11 77.7 3.1 43 1594-1637 2-47 (48)
20 PF06001 DUF902: Domain of Unk 98.2 3.7E-07 8.1E-12 77.0 0.0 35 1017-1051 6-41 (42)
21 PF02135 zf-TAZ: TAZ zinc fing 98.1 1.7E-06 3.6E-11 81.9 3.1 64 733-796 6-74 (75)
22 KOG4582 Uncharacterized conser 98.0 2E-06 4.3E-11 99.8 2.8 47 1592-1639 152-198 (278)
23 KOG1280 Uncharacterized conser 97.4 6E-05 1.3E-09 88.1 1.5 47 1591-1637 7-56 (381)
24 cd02334 ZZ_dystrophin Zinc fin 97.3 0.00014 2.9E-09 64.5 2.0 44 1470-1517 2-46 (49)
25 PF00569 ZZ: Zinc finger, ZZ t 97.2 0.0002 4.4E-09 62.4 2.1 38 1465-1506 1-38 (46)
26 cd02336 ZZ_RSC8 Zinc finger, Z 97.1 0.00025 5.4E-09 61.8 2.4 39 1593-1633 1-39 (45)
27 cd02338 ZZ_PCMF_like Zinc fing 97.1 0.00025 5.4E-09 62.7 2.0 44 1470-1517 2-46 (49)
28 cd02344 ZZ_HERC2 Zinc finger, 97.1 0.00025 5.4E-09 61.9 1.9 33 1470-1506 2-34 (45)
29 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.0 0.00035 7.6E-09 61.7 2.0 35 1469-1507 1-37 (48)
30 cd02342 ZZ_UBA_plant Zinc fing 97.0 0.00038 8.3E-09 59.9 2.0 34 1470-1507 2-35 (43)
31 cd02339 ZZ_Mind_bomb Zinc fing 96.9 0.00052 1.1E-08 59.9 2.2 32 1470-1505 2-33 (45)
32 cd02345 ZZ_dah Zinc finger, ZZ 96.9 0.00054 1.2E-08 60.6 2.1 44 1470-1517 2-46 (49)
33 cd02335 ZZ_ADA2 Zinc finger, Z 96.8 0.00063 1.4E-08 60.1 2.3 35 1469-1507 1-35 (49)
34 cd02249 ZZ Zinc finger, ZZ typ 96.8 0.00066 1.4E-08 59.1 2.1 34 1469-1507 1-34 (46)
35 cd02340 ZZ_NBR1_like Zinc fing 96.4 0.0015 3.3E-08 56.5 1.7 32 1470-1506 2-33 (43)
36 smart00291 ZnF_ZZ Zinc-binding 96.3 0.0019 4.1E-08 55.8 1.8 35 1467-1506 3-37 (44)
37 cd02337 ZZ_CBP Zinc finger, ZZ 96.3 0.0018 3.9E-08 55.5 1.4 32 1469-1506 1-32 (41)
38 cd02343 ZZ_EF Zinc finger, ZZ 96.3 0.0028 6.1E-08 56.2 2.5 43 1470-1517 2-45 (48)
39 KOG1280 Uncharacterized conser 96.3 0.0054 1.2E-07 72.3 5.5 89 1467-1564 7-104 (381)
40 KOG4582 Uncharacterized conser 95.6 0.0048 1E-07 72.3 1.5 34 1469-1506 153-186 (278)
41 KOG0457 Histone acetyltransfer 95.5 0.0051 1.1E-07 74.5 1.4 34 1592-1625 14-47 (438)
42 PF02172 KIX: KIX domain; Int 95.3 0.044 9.6E-07 53.7 6.7 55 67-121 12-67 (81)
43 KOG4286 Dystrophin-like protei 95.1 0.0081 1.8E-07 76.0 1.1 50 1590-1639 601-653 (966)
44 PF00628 PHD: PHD-finger; Int 94.8 0.0042 9.1E-08 54.4 -1.7 42 1092-1133 9-50 (51)
45 KOG4534 Uncharacterized conser 94.4 0.71 1.5E-05 53.8 13.9 128 1211-1355 24-156 (349)
46 COG5087 RTT109 Uncharacterized 94.4 0.71 1.5E-05 53.8 13.9 128 1211-1355 24-156 (349)
47 KOG0956 PHD finger protein AF1 94.0 0.018 4E-07 72.4 0.7 88 1017-1118 8-95 (900)
48 smart00249 PHD PHD zinc finger 93.8 0.044 9.5E-07 45.9 2.4 38 1093-1131 10-47 (47)
49 KOG1778 CREB binding protein/P 92.0 0.14 3E-06 61.3 4.0 51 745-795 231-283 (319)
50 COG5114 Histone acetyltransfer 91.9 0.057 1.2E-06 63.2 0.6 34 1592-1625 5-38 (432)
51 PF07649 C1_3: C1-like domain; 84.3 0.44 9.6E-06 38.2 0.9 28 1594-1622 2-29 (30)
52 KOG4274 Positive cofactor 2 (P 82.1 3.7 8E-05 52.1 7.8 57 68-136 10-66 (742)
53 KOG4286 Dystrophin-like protei 81.9 0.72 1.6E-05 59.5 1.9 46 1468-1517 603-649 (966)
54 KOG4301 Beta-dystrobrevin [Cyt 75.2 1.8 3.8E-05 52.0 2.2 57 1581-1638 229-289 (434)
55 KOG0457 Histone acetyltransfer 73.7 1.7 3.8E-05 53.6 1.8 46 1468-1517 14-60 (438)
56 KOG4323 Polycomb-like PHD Zn-f 70.6 1.4 3.1E-05 55.1 0.1 38 1096-1133 184-223 (464)
57 PF03107 C1_2: C1 domain; Int 69.4 2.9 6.3E-05 33.8 1.6 27 1594-1622 2-29 (30)
58 COG5141 PHD zinc finger-contai 66.7 1.9 4.2E-05 53.6 0.1 87 1015-1118 194-280 (669)
59 cd02336 ZZ_RSC8 Zinc finger, Z 63.3 4.5 9.8E-05 35.9 1.7 34 1469-1507 1-34 (45)
60 KOG0957 PHD finger protein [Ge 63.0 3 6.6E-05 52.0 0.8 89 1014-1120 119-217 (707)
61 KOG4369 RTK signaling protein 60.8 9.4 0.0002 51.9 4.5 22 150-171 1400-1421(2131)
62 KOG4786 Ubinuclein, nuclear pr 60.0 77 0.0017 41.9 11.9 64 327-397 972-1041(1136)
63 KOG4369 RTK signaling protein 59.9 11 0.00023 51.4 4.8 9 368-376 1766-1774(2131)
64 PF09606 Med15: ARC105 or Med1 59.0 6.8 0.00015 52.4 3.0 53 73-134 3-56 (799)
65 COG2888 Predicted Zn-ribbon RN 57.7 8.8 0.00019 36.1 2.6 28 1031-1066 9-36 (61)
66 COG5114 Histone acetyltransfer 43.4 9.8 0.00021 45.6 0.8 45 1469-1517 6-51 (432)
67 KOG1844 PHD Zn-finger proteins 42.9 12 0.00026 47.5 1.5 39 1094-1135 98-136 (508)
68 KOG0955 PHD finger protein BR1 39.5 17 0.00037 50.0 2.2 76 1014-1118 219-306 (1051)
69 KOG4301 Beta-dystrobrevin [Cyt 38.4 10 0.00022 45.9 -0.1 48 1446-1505 226-273 (434)
70 PF07227 DUF1423: Protein of u 36.4 22 0.00048 44.8 2.3 42 1093-1134 142-192 (446)
71 PF07496 zf-CW: CW-type Zinc F 36.3 13 0.00029 33.4 0.4 34 1095-1130 1-34 (50)
72 KOG1701 Focal adhesion adaptor 35.6 13 0.00028 46.3 0.2 123 1459-1624 270-429 (468)
73 PF13831 PHD_2: PHD-finger; PD 34.2 8 0.00017 32.8 -1.3 33 1096-1131 3-35 (36)
74 KOG4577 Transcription factor L 34.2 12 0.00027 44.2 -0.3 33 1568-1611 107-139 (383)
75 PF00412 LIM: LIM domain; Int 33.3 32 0.00069 30.6 2.2 39 1023-1066 18-56 (58)
76 KOG0336 ATP-dependent RNA heli 32.3 36 0.00079 42.5 3.1 33 1315-1350 164-197 (629)
77 TIGR03826 YvyF flagellar opero 32.2 4.1 8.8E-05 43.9 -4.2 26 1589-1625 78-103 (137)
78 KOG2462 C2H2-type Zn-finger pr 30.5 26 0.00056 41.7 1.5 37 1098-1134 188-224 (279)
79 KOG1973 Chromatin remodeling p 29.8 24 0.00053 41.9 1.2 35 1096-1134 231-268 (274)
80 PF07649 C1_3: C1-like domain; 29.0 31 0.00068 27.7 1.3 28 1470-1502 2-29 (30)
81 TIGR00515 accD acetyl-CoA carb 28.8 19 0.0004 43.2 -0.0 60 1231-1322 108-167 (285)
82 PF07500 TFIIS_M: Transcriptio 26.6 1.1E+02 0.0023 31.7 5.0 50 68-120 4-54 (115)
83 CHL00174 accD acetyl-CoA carbo 24.9 25 0.00055 42.4 0.2 58 1231-1320 121-178 (296)
84 KOG4552 Vitamin-D-receptor int 23.9 1E+02 0.0022 35.5 4.6 71 317-395 164-238 (272)
85 PLN03086 PRLI-interacting fact 23.6 1.1E+02 0.0023 40.3 5.2 15 713-727 424-438 (567)
86 PRK06266 transcription initiat 22.7 68 0.0015 36.1 2.9 53 1092-1170 112-164 (178)
87 TIGR03046 PS_II_psbV2 photosys 22.4 96 0.0021 34.5 3.9 39 1321-1359 110-148 (155)
88 TIGR00373 conserved hypothetic 22.4 57 0.0012 35.9 2.2 33 1092-1133 104-136 (158)
89 smart00642 Aamy Alpha-amylase 21.1 2.4E+02 0.0051 31.3 6.6 69 1299-1369 21-93 (166)
90 PHA03159 hypothetical protein; 20.6 36 0.00079 36.4 0.3 29 1548-1576 6-34 (160)
91 PF00150 Cellulase: Cellulase 20.4 2.1E+02 0.0045 32.7 6.3 55 1298-1363 22-79 (281)
No 1
>PF08214 KAT11: Histone acetylation protein; InterPro: IPR013178 Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal RTT109 protein, which is required for H3K56 acetylation. In Schizosaccharomyces pombe (Fission yeast) loss of RTT109 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin []. RTT109 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast []. This family also incorporates the p300/CBP histone acetyltransferase domain which has different catalytic properties and cofactor regulation to RTT109 []. This entry also contains CREB-binding proteins; these acetylate histones, giving a specific tag for transcriptional activation. They also acetylate non-histone proteins, like NCOA3 coactivator. They bind specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes [, ]. ; PDB: 3CZ7_A 2RIM_A 3Q66_C 2ZFN_A 3QM0_A 3Q68_C 3Q35_A 3Q33_A 3BIY_A.
Probab=100.00 E-value=9.4e-56 Score=514.51 Aligned_cols=280 Identities=43% Similarity=0.700 Sum_probs=220.3
Q ss_pred CCCCCccEEEEEEeccchhhhhhHHHHHhhhhcCCCCcccceeEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEE
Q 000320 1189 EVPGAEALVIRVVSSVDKKLEVKQRFLEIFQEENYPTEFPYKSKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVY 1268 (1673)
Q Consensus 1189 ev~~a~~l~VRvVss~dK~~~Vk~~f~~~F~e~~yp~~fpYrsKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~Vy 1268 (1673)
.+|+++.++||+|++.+++++++..|...|.+..||.+|+||.|+|+|||++||+|||||+|+||||+..|+.||++|||
T Consensus 8 ~lp~~~~~~ir~v~S~~~~~~~~~~~~~~~~~~~~~~~~~y~~r~~~~fq~~~g~dv~~f~m~v~eY~~~~~~~~~~~v~ 87 (346)
T PF08214_consen 8 VLPKDEEFTIRHVSSPPKKCEVLFSFPPKFAEKGYPPEFTYKSRHFFVFQEIDGVDVLFFAMEVQEYGTICPAPNQRWVY 87 (346)
T ss_dssp CSCTT-EEEEEEEEEEEEEEE--TCHHHCTTTTTS-CCEEEEEEEEEEEEECTTEEEEEEEEEEEEEECCCSTCCCCEEE
T ss_pred hCCCCceEEEEEEEcCCEEccccccCCcccccccCCCCceeEEEEEEEEEEeCCccEEEEEEEEEEecCCCCCCCceEEE
Confidence 48999999999999999999999999999988789999999999999999999999999999999999999999999999
Q ss_pred EEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcCCcEEEEEeCCCCCCCCeeeccCCCCCCCCC-----hhH
Q 000320 1269 LSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIWACPPLKGEDYILYCHPEIQKTPK-----SDK 1343 (1673)
Q Consensus 1269 IsYLDSV~YfrP~~~~~~Ge~lRT~VYheILi~Yl~Y~k~~GF~~ahIWAcPP~~GDDYIF~~HP~~Qk~p~-----~~~ 1343 (1673)
|+|||||.||+|. .+||.|||++|++||+|++.+||.++|||||||.+|||||| |..|++|+ .++
T Consensus 88 IsylDSv~y~~~~-------~~r~~~~~~~ll~Yl~~~~~~g~~~~~~~a~~pr~~dqYlF---P~s~k~p~KhvL~~~~ 157 (346)
T PF08214_consen 88 ISYLDSVGYFKPS-------PSRTRVYHEILLSYLDYARPRGYTKAHIWACFPRAGDQYLF---PNSQKNPKKHVLDDDR 157 (346)
T ss_dssp EEEEEE-S--SSG-------GGHHHHHHHHHHHHHHCCHCHCHHCCEEEEEEE-CCS-SSS---TTCGGSTTS----HHH
T ss_pred EEECcccCCCCcc-------cccHHHHHHHHHHHHHHhhccCCcEEEEEEecCCCCCCeEc---CCcccCCccccccchH
Confidence 9999999999995 68999999999999999999999999999999999999999 88888888 999
Q ss_pred HHHHHHHHHHHHH-------hcCeEeeccchhhh--hhccccccc------------cccCccccCcccCCCccHHHHHH
Q 000320 1344 LREWYLAMLRKAA-------KENIVVDLTNLYDH--FFVSTGECR------------AKVTAARLPYFDGDYWPGAAEDL 1402 (1673)
Q Consensus 1344 L~~WY~~mL~kgk-------~eGIV~~~~n~yd~--~f~~~~e~~------------~~~~a~~LPyFeGd~Wp~~~E~i 1402 (1673)
|++||.+||++|+ +++||+...++|+. |+....... ....++.||||+||+||+.||++
T Consensus 158 L~~Wy~~~L~~~~~~~~~~~~~~~vvpg~d~~~~~~~~~~~~~~~~W~~g~~~~~~~~~~~~~~iP~FpdDpk~rfle~l 237 (346)
T PF08214_consen 158 LLKWYKKMLDKAKEESFKNAKAYLVVPGSDLYETRKYLPNTPDSNSWTYGHPFSQIKSDPAACLIPYFPDDPKPRFLEEL 237 (346)
T ss_dssp HHHHHHHHHHHHHHHHB-TTCCCCE-CCCEHHHHHHHHTCCCCTTTEEES-ST-SSSTSBGGGCSB--TT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhcccccccceEecCccHHHhhhhccccccccccccccccccccccCccccCCcCCCchHHHHHHHH
Confidence 9999999999999 99999999999987 333221100 11267889999999999999999
Q ss_pred HHH-------HHhccccc--ccc--------------------ccccchhhhHHHHHhcCC---CCCCCCcchhHHHHHH
Q 000320 1403 IYQ-------IRQDEDGK--KQN--------------------KGITKKTITKRALKASGQ---TDLSGNASKDLLLMHK 1450 (1673)
Q Consensus 1403 i~~-------l~~e~~~~--k~~--------------------k~~~kk~~~kr~~k~~g~---~~~~~~~~kd~~lm~k 1450 (1673)
+++ |+++.++. ++. +...++...|+.+++.+. .+.++.......+|++
T Consensus 238 ~~e~~~~~~s~~~fwe~~~~RqE~~~g~~vg~~~~~~~v~~~~~~~~s~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (346)
T PF08214_consen 238 IEEGRWKKVSLDQFWEELAFRQECSLGRLVGFIGLEDDVIDPPKKVKSKKQYKSIKSYITGEEFSTKEGAAEATQNLMDK 317 (346)
T ss_dssp HHTT-TTT-BHHHHHHHHHHTTTTTTSST-EEEEEETT-B------SSHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHH
T ss_pred HHhhhhccccHHHHHHHHHHHhhhhhccccccccccccccccccccccccchhhhhhhhcchhcccccCccchhHHHHHH
Confidence 999 87765442 110 111122222333333222 2223334455689999
Q ss_pred hhhccccCccceeEeeccccCccccccc
Q 000320 1451 LGETICPMKEDFIMVHLQHACNHCCILM 1478 (1673)
Q Consensus 1451 lg~~i~~~KEdF~vv~Lq~~C~~C~~~i 1478 (1673)
|+++|+++||+||+|++...|.+|++..
T Consensus 318 l~~~~~~~k~~~~~v~~~~~~~~~~~~~ 345 (346)
T PF08214_consen 318 LYETMEKHKEDFFVVRLKHQCTACSKPR 345 (346)
T ss_dssp HHHHHCHTGGGEEEEESSBGGG--SS-H
T ss_pred HHHHhcccccccEEEEEecccccccccC
Confidence 9999999999999999999999998653
No 2
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=99.97 E-value=6.7e-33 Score=318.34 Aligned_cols=234 Identities=35% Similarity=0.521 Sum_probs=198.8
Q ss_pred cccCCCccHHHHHHHHHHHhccccccccccccchhhhHHHHHhcCCCCCCCCcchhHHHHHHhhhccccCccceeEeecc
Q 000320 1389 YFDGDYWPGAAEDLIYQIRQDEDGKKQNKGITKKTITKRALKASGQTDLSGNASKDLLLMHKLGETICPMKEDFIMVHLQ 1468 (1673)
Q Consensus 1389 yFeGd~Wp~~~E~ii~~l~~e~~~~k~~k~~~kk~~~kr~~k~~g~~~~~~~~~kd~~lm~klg~~i~~~KEdF~vv~Lq 1468 (1673)
||+||+ +|+.|..+.++- ++-.++ .| .+...++.+|...|+++ +|.+++++|++++++
T Consensus 1 ~~~~~~----~ed~~~~~~~~~------~~~~~~---------~~-~~~~~~~~~~~~~~~s~--~l~~~~~~~~~~~~~ 58 (319)
T KOG1778|consen 1 YPIPDP----AEDLLSQMTQEV------SGDTRP---------TG-DVEIVTDVKDLIPAHSL--VLGPASPVFKKVLKQ 58 (319)
T ss_pred CCCCcH----HHHHHHhhhhhc------ccccCC---------cc-chhhhhhhhhhhHHHHh--cccccchHHHHHHhh
Confidence 566666 777777766551 111111 14 44556677888999999 899999999999999
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHhhhcccccCCCCCccccccccccccCCCCCCCCCccccccccc
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKREDRERHPVNSREVHILEEVPVTDVPADTKDKDEILESEF 1548 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~~~~~~e~HP~~~~~~h~L~pv~v~dvP~~t~D~D~~i~~ef 1548 (1673)
+ |++.++.+++|+|..| +++.+|++||.+. -+.|+.+.++.|.|.++.+..+|..+.|+|++++|++
T Consensus 59 ~----~~~~~~~~~~~~~~~c----~~~~~~~~~l~~~-----~ek~e~~~~~ihll~~~~~~~v~~~~~d~~~~~~~~~ 125 (319)
T KOG1778|consen 59 P----CRKSLVKGNKILGVPC----KAVNVFIRFLYSS-----LEKHEMVFFDIHLLALSHVYVVPQPKADCDPILECGL 125 (319)
T ss_pred h----cchhhhhcceeecccc----cccchhhhhhccc-----hhhhHHHHHHHHHHhhhhhhhccCccccCCccccchh
Confidence 8 8889999999999999 9999999999887 3689999999999998888999999999999999999
Q ss_pred cchhHHHHHhhhhCCCCccchhhccccchhhhhhhcCCCCCcccccccccccCccCCCccccCCCCCCccchhhhhcCCC
Q 000320 1549 FDTRQAFLSLCQGNHYQYDTLRRAKHSSMMVLYHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGG 1628 (1673)
Q Consensus 1549 fDtRqaFLslCQ~nHyQFDsLRRAKhSSMMvLyHLHNp~~~~f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~ 1628 (1673)
||+|++||.+|+.+||+|++||||||||||++||||+++.+.|+++|+.|+.++. .+|||++|+|||+|..||.++
T Consensus 126 ~~~r~~flvl~~~~~~~~~~lr~a~hss~~~~~~~H~~t~~~~~~~c~~c~~~~~--~~~~c~~~~d~d~~~~~~~k~-- 201 (319)
T KOG1778|consen 126 FDKRNVFLVLQLAEHCDFSDLRRAKHSSIMLLFDLHLQTEKWFAYTCPICKLEVL--TAWHCEVCPDYDRCRACEEKP-- 201 (319)
T ss_pred hhhHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHhcccCceeeecCccccccc--cccccccCCchhhhhcccCCC--
Confidence 9999999999999999999999999999999999999999999999999999994 579999999999999999985
Q ss_pred CCCCCCcccCCCcchhhhhhHHHHHHHHHHHHh-ccCCc
Q 000320 1629 IDHPHKLTNHPSTADRDAQNKEARQLRVLQVLY-TRCPS 1666 (1673)
Q Consensus 1629 ~~H~H~l~~~~s~~~~~~~~~e~r~~Rv~ql~~-t~~~~ 1666 (1673)
.|.|+++.+++ .....+.+.-|+.+|.+ ++-++
T Consensus 202 -~h~h~~~~~~~----~~~~~~~~~~~~~~i~~~~~~C~ 235 (319)
T KOG1778|consen 202 -LHPHLYEAMES----CTDGCATIGPRNKSINRRDANCS 235 (319)
T ss_pred -CCCcchhcccc----cccccccccchhhhhccCCCCCC
Confidence 39999999998 33344556667777774 34443
No 3
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.65 E-value=7.5e-17 Score=153.38 Aligned_cols=77 Identities=52% Similarity=1.032 Sum_probs=73.8
Q ss_pred HHhhhhchhhhhhhccccCCCCCCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchHH
Q 000320 701 QFRNQQRWLLFLRHARRCAAPEGKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVPV 777 (1673)
Q Consensus 701 ~~~~qqrwLllL~HA~kC~~~~g~C~~~~C~~~K~lL~Hm~~C~~~~C~~~~C~sSr~Ll~H~k~C~~~~CpvC~pv 777 (1673)
.+..+|+||+||+||.+|..+++.|..++|.+||.||+||..|+.++|.+++|..+|.||.||+.|++.+||||.++
T Consensus 3 ~~~~lq~~l~~L~Ha~~C~~~~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~H~k~C~~~~C~Vc~c~ 79 (79)
T smart00551 3 RYKQLQRWLELLVHARRCKAREAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQHSKHCKDSNCPVCKCV 79 (79)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 46688999999999999999999999999999999999999999999999999999999999999999999999764
No 4
>PF02135 zf-TAZ: TAZ zinc finger; InterPro: IPR000197 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. TAZ (Transcription Adaptor putative Zinc finger) domains are zinc-containing domains found in the homologous transcriptional co-activators CREB-binding protein (CBP) and the P300. CBP and P300 are histone acetyltransferases (2.3.1.48 from EC) that catalyse the reversible acetylation of all four histones in nucleosomes, acting to regulate transcription via chromatin remodelling. These large nuclear proteins interact with numerous transcription factors and viral oncoproteins, including p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1, and are involved in cell growth, differentiation and apoptosis []. Both CBP and P300 have two copies of the TAZ domain, one in the N-terminal region, the other in the C-terminal region. The TAZ1 domain of CBP and P300 forms a complex with CITED2 (CBP/P300-interacting transactivator with ED-rich tail), inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration []. Adaptation to hypoxia is mediated by transactivation of hypoxia-responsive genes by hypoxia-inducible factor-1 (HIF-1) in complex with the CBP and p300 transcriptional coactivators []. The TAZ domain adopts an all-alpha fold with zinc-binding sites in the loops connecting the helices. The TAZ1 domain in P300 and the TAZ2 (CH3) domain in CBP have each been shown to have four amphipathic helices, organised by three zinc-binding clusters with HCCC-type coordination [, , ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003712 transcription cofactor activity, 0004402 histone acetyltransferase activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1P4Q_B 1L3E_B 2KJE_A 1WO3_A 1WO4_A 1WO5_A 1LIQ_A 3P57_P 2K8F_A 3IO2_A ....
Probab=99.42 E-value=3.9e-14 Score=133.17 Aligned_cols=73 Identities=41% Similarity=0.957 Sum_probs=68.7
Q ss_pred hhhchhhhhhhccccCCCC-CCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchH
Q 000320 704 NQQRWLLFLRHARRCAAPE-GKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVP 776 (1673)
Q Consensus 704 ~qqrwLllL~HA~kC~~~~-g~C~~~~C~~~K~lL~Hm~~C~~~~C~~~~C~sSr~Ll~H~k~C~~~~CpvC~p 776 (1673)
.+++||+||+||..|..++ +.|..++|..||.||.|+..|.++.|.+++|..+|.||.||+.|++.+|+||.+
T Consensus 2 ~~~~~L~~L~Ha~~C~~~~~~~C~~~~C~~~K~ll~H~~~C~~~~C~~~~C~~~k~ll~H~~~C~~~~C~vc~C 75 (75)
T PF02135_consen 2 QLQRWLELLLHASSCRDPEHPNCSLPHCRKMKKLLKHMRTCRNRDCPVPGCQSCKRLLSHARSCKDSDCPVCFC 75 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHCTT-SSTTHHHHHHHHHHHCCSSSCCSSCCTHHHHHHHHHHHHHHTSTTSSSHHH
T ss_pred HHHHHHHHHHHHhHCcCCCCCCCCCcccHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcCCCCCCCCCCC
Confidence 4689999999999999988 899999999999999999999997799999999999999999999999999964
No 5
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=98.91 E-value=4.9e-10 Score=94.90 Aligned_cols=41 Identities=44% Similarity=1.125 Sum_probs=36.3
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCcccC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTNH 1638 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l~~~ 1638 (1673)
|+|+.|...+ |.||||.+|+|||||..||.+ ..|+|+|+++
T Consensus 1 y~C~~C~~~~--~~r~~C~~C~dfDLC~~C~~~---~~H~H~~~~~ 41 (41)
T cd02337 1 YTCNECKHHV--ETRWHCTVCEDYDLCITCYNT---KNHPHKMEKL 41 (41)
T ss_pred CcCCCCCCcC--CCceECCCCcchhhHHHHhCC---CCCCcccccC
Confidence 5899998833 689999999999999999987 5799999875
No 6
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=98.89 E-value=4e-10 Score=97.39 Aligned_cols=44 Identities=43% Similarity=0.955 Sum_probs=35.1
Q ss_pred ccccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCc
Q 000320 1591 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKL 1635 (1673)
Q Consensus 1591 f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l 1635 (1673)
++++|+.|+.+.+.|.||||.+|+|||||.+||.+ |...|.|+|
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~-g~~~~~H~~ 46 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK-GRHSHNHKM 46 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH---H-SSSSE
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC-cCCCCCcCc
Confidence 47899999998888999999999999999999998 778889987
No 7
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.68 E-value=1e-08 Score=89.69 Aligned_cols=46 Identities=26% Similarity=0.686 Sum_probs=39.2
Q ss_pred ccccccccCccCCCccccCCCC--CCccchhhhhcCCCCCCCCCcccC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCP--DYDVCNACYQKDGGIDHPHKLTNH 1638 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~--dyDLC~~Cy~~~g~~~H~H~l~~~ 1638 (1673)
|+|+.|....++|.||||.+|+ |||||..||.+...+...|+|+++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 5899999977789999999999 999999999983245557998764
No 8
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.62 E-value=2e-08 Score=86.85 Aligned_cols=44 Identities=25% Similarity=0.750 Sum_probs=37.3
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCccc
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1637 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l~~ 1637 (1673)
++|+.|...++.|.||+|.+|+|||||..||.+ +.+.-.|.+.+
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~-~~H~~~H~F~r 44 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKT-RKHNTRHTFGR 44 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCC-CCcCCCCceee
Confidence 489999998888999999999999999999998 33333787765
No 9
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=98.62 E-value=5.1e-08 Score=93.55 Aligned_cols=66 Identities=26% Similarity=0.578 Sum_probs=61.8
Q ss_pred HHHHHhcccccCC--CCCCCCCccchHHHHHHhhccCCCCCCC--chHHHHHHHHHHHhcCCCCCCCCCc
Q 000320 733 VQKLWRHMDNCTS--SQCPYPRCHHSKILIHHHKHCRDPSCPV--CVPVKNYLQQQKERARPKTDSCLPS 798 (1673)
Q Consensus 733 ~K~lL~Hm~~C~~--~~C~~~~C~sSr~Ll~H~k~C~~~~Cpv--C~pvR~~l~~~~~~s~~~~~vc~p~ 798 (1673)
.-++|.|+.+|+. ..|.+++|...+.||.|+..|+..+|++ |...|+++.|++.|.+..||||.|+
T Consensus 10 ~l~~L~Ha~~C~~~~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~H~k~C~~~~C~Vc~c~ 79 (79)
T smart00551 10 WLELLVHARRCKAREAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQHSKHCKDSNCPVCKCV 79 (79)
T ss_pred HHHHHHHHHhCCCCCCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 3489999999988 6999999999999999999999999977 9999999999999999999999764
No 10
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=98.59 E-value=2.6e-08 Score=85.34 Aligned_cols=43 Identities=37% Similarity=0.866 Sum_probs=36.6
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCcccC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTNH 1638 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l~~~ 1638 (1673)
++|+.|+..| .|.||+|.+|+|||||..||.. +.+ ..|+|.++
T Consensus 1 v~Cd~C~~~i-~G~ry~C~~C~d~dLC~~C~~~-~~H-~~H~f~~~ 43 (43)
T cd02340 1 VICDGCQGPI-VGVRYKCLVCPDYDLCESCEAK-GVH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCCcC-cCCeEECCCCCCccchHHhhCc-CCC-CCCCEEeC
Confidence 4799999954 6999999999999999999998 444 68998763
No 11
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=98.57 E-value=3.8e-08 Score=84.50 Aligned_cols=42 Identities=36% Similarity=0.918 Sum_probs=35.7
Q ss_pred cccccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCC
Q 000320 1590 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPH 1633 (1673)
Q Consensus 1590 ~f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H 1633 (1673)
.+.++|+.|+. .++|.||||.+|+|||||.+||.+ |...+.|
T Consensus 2 ~~~~~C~~C~~-~i~g~ry~C~~C~d~dlC~~Cf~~-~~~~~~h 43 (44)
T smart00291 2 HHSYSCDTCGK-PIVGVRYHCLVCPDYDLCQSCFAK-GSAGGEH 43 (44)
T ss_pred CCCcCCCCCCC-CCcCCEEECCCCCCccchHHHHhC-cCcCCCC
Confidence 46789999999 556999999999999999999997 5455555
No 12
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=98.55 E-value=4e-08 Score=85.00 Aligned_cols=43 Identities=33% Similarity=0.942 Sum_probs=37.7
Q ss_pred cccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCccc
Q 000320 1594 TCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1637 (1673)
Q Consensus 1594 tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l~~ 1637 (1673)
.|+.|+..++.|.||+|.+|+|||||..||.. +.+...|+|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~-~~H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG-DKHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC-CCCCCCCCEEe
Confidence 69999988888999999999999999999987 44556888865
No 13
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=98.45 E-value=1e-07 Score=83.85 Aligned_cols=44 Identities=32% Similarity=0.758 Sum_probs=36.2
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcC---CCCCCCCCcc
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKD---GGIDHPHKLT 1636 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~---g~~~H~H~l~ 1636 (1673)
++|+.|+..+++|.||+|.+|+|||||..||... +.+.-.|||.
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 4799999988889999999999999999999872 2334467664
No 14
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=98.39 E-value=1.8e-07 Score=81.00 Aligned_cols=44 Identities=36% Similarity=0.872 Sum_probs=36.1
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCCCC--CCCcccC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDH--PHKLTNH 1638 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H--~H~l~~~ 1638 (1673)
+.|+.|..+| .|.||||..|+|||||..||.+.. ..| .|+|+++
T Consensus 1 ~~C~~C~~~i-~g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPI-VGVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCC-cCCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeEC
Confidence 4799999966 589999999999999999999842 344 6887653
No 15
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=98.39 E-value=1.7e-07 Score=82.42 Aligned_cols=43 Identities=35% Similarity=0.876 Sum_probs=34.9
Q ss_pred ccccccc-CccCCCccccCCCCCCccchhhhhcC---CCCCCCCCccc
Q 000320 1594 TCNICHL-DIETGQGWRCEVCPDYDVCNACYQKD---GGIDHPHKLTN 1637 (1673)
Q Consensus 1594 tC~~C~~-~i~tG~r~hC~~C~dyDLC~~Cy~~~---g~~~H~H~l~~ 1637 (1673)
+|+.|.+ +|. |.||+|++|+|||||..||... +.+.-.|+|..
T Consensus 2 ~C~~C~~~~i~-g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 2 SCSACRKQDIS-GIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred cCCCCCCCCce-EeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 7999999 555 9999999999999999999973 12333788754
No 16
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.34 E-value=2e-07 Score=79.51 Aligned_cols=35 Identities=31% Similarity=0.767 Sum_probs=32.3
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDG 1627 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g 1627 (1673)
.+|+.|....+.|.||+|.+|+|||||..||.+.|
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 37999999999999999999999999999999844
No 17
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.32 E-value=3.4e-07 Score=80.40 Aligned_cols=43 Identities=33% Similarity=0.861 Sum_probs=36.0
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCC--CC--CCCcc
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGI--DH--PHKLT 1636 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~--~H--~H~l~ 1636 (1673)
++|+.|..+|..|.||+|..|+|||||..||.. |.. .| .|+|.
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~-g~~~~~H~~~H~~~ 47 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSA-GAEIGKHRNDHNYR 47 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhC-cCCCCCCCCCCCeE
Confidence 479999999999999999999999999999997 422 33 46654
No 18
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=98.31 E-value=2.9e-07 Score=80.99 Aligned_cols=33 Identities=36% Similarity=1.002 Sum_probs=29.5
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhc
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~ 1625 (1673)
..|+.|+...++|.||+|.+|+|||||.+||..
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~ 33 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLICYDYDLCADCYDS 33 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCCCCCccchhHHhC
Confidence 379999965556999999999999999999997
No 19
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.21 E-value=8.6e-07 Score=77.69 Aligned_cols=43 Identities=28% Similarity=0.750 Sum_probs=35.0
Q ss_pred cccccccCccCCCccccCCCCCCccchhhhhc---CCCCCCCCCccc
Q 000320 1594 TCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTN 1637 (1673)
Q Consensus 1594 tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~---~g~~~H~H~l~~ 1637 (1673)
.|+.|... .+|.||+|..|+|||||..||.. .+.+...|||..
T Consensus 2 ~CdgC~~~-~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~~ 47 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMVN 47 (48)
T ss_pred CCCCCCCc-CCCceEECCCCCCchhHHHHHhCCccCCCCCCCCCccc
Confidence 69999995 46899999999999999999987 234455677754
No 20
>PF06001 DUF902: Domain of Unknown Function (DUF902); InterPro: IPR010303 This domain of unknown function is found in several transcriptional co-activators including the CREB-binding protein, 2.3.1.48 from EC, which is an acetyltransferase that acetylates histones, giving a specific tag for transcriptional activation. CREB-binding protein also acetylates non-histone proteins.; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
Probab=98.17 E-value=3.7e-07 Score=77.03 Aligned_cols=35 Identities=34% Similarity=0.640 Sum_probs=0.4
Q ss_pred cccccCcceeccCCccccCCC-CceecCCCeeeeec
Q 000320 1017 CQLCAVEKLTFEPPPIYCSPC-GTRIKRNAMYYTMG 1051 (1673)
Q Consensus 1017 C~~C~~~~L~F~p~~l~C~~c-~cRI~r~a~Yy~~~ 1051 (1673)
-++||+++|.|.|++|||+|. .|.|+||+.||+++
T Consensus 6 lGyCCgrk~~f~p~~L~C~Gk~lCtI~Rd~~Y~~Y~ 41 (42)
T PF06001_consen 6 LGYCCGRKLVFTPQVLYCYGKQLCTIPRDAVYYSYQ 41 (42)
T ss_dssp H-----------------------------------
T ss_pred cCcccCCceEecCceEEecCCceeeeecCCEEEEee
Confidence 479999999999999999997 59999999999985
No 21
>PF02135 zf-TAZ: TAZ zinc finger; InterPro: IPR000197 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. TAZ (Transcription Adaptor putative Zinc finger) domains are zinc-containing domains found in the homologous transcriptional co-activators CREB-binding protein (CBP) and the P300. CBP and P300 are histone acetyltransferases (2.3.1.48 from EC) that catalyse the reversible acetylation of all four histones in nucleosomes, acting to regulate transcription via chromatin remodelling. These large nuclear proteins interact with numerous transcription factors and viral oncoproteins, including p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1, and are involved in cell growth, differentiation and apoptosis []. Both CBP and P300 have two copies of the TAZ domain, one in the N-terminal region, the other in the C-terminal region. The TAZ1 domain of CBP and P300 forms a complex with CITED2 (CBP/P300-interacting transactivator with ED-rich tail), inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration []. Adaptation to hypoxia is mediated by transactivation of hypoxia-responsive genes by hypoxia-inducible factor-1 (HIF-1) in complex with the CBP and p300 transcriptional coactivators []. The TAZ domain adopts an all-alpha fold with zinc-binding sites in the loops connecting the helices. The TAZ1 domain in P300 and the TAZ2 (CH3) domain in CBP have each been shown to have four amphipathic helices, organised by three zinc-binding clusters with HCCC-type coordination [, , ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003712 transcription cofactor activity, 0004402 histone acetyltransferase activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1P4Q_B 1L3E_B 2KJE_A 1WO3_A 1WO4_A 1WO5_A 1LIQ_A 3P57_P 2K8F_A 3IO2_A ....
Probab=98.11 E-value=1.7e-06 Score=81.95 Aligned_cols=64 Identities=28% Similarity=0.711 Sum_probs=58.5
Q ss_pred HHHHHhcccccCC---CCCCCCCccchHHHHHHhhccCCCCCCC--chHHHHHHHHHHHhcCCCCCCCC
Q 000320 733 VQKLWRHMDNCTS---SQCPYPRCHHSKILIHHHKHCRDPSCPV--CVPVKNYLQQQKERARPKTDSCL 796 (1673)
Q Consensus 733 ~K~lL~Hm~~C~~---~~C~~~~C~sSr~Ll~H~k~C~~~~Cpv--C~pvR~~l~~~~~~s~~~~~vc~ 796 (1673)
.-++|.|+..|.. +.|.+++|...|.||.|...|.+..|++ |...|.++.|++.|.+..|++|.
T Consensus 6 ~L~~L~Ha~~C~~~~~~~C~~~~C~~~K~ll~H~~~C~~~~C~~~~C~~~k~ll~H~~~C~~~~C~vc~ 74 (75)
T PF02135_consen 6 WLELLLHASSCRDPEHPNCSLPHCRKMKKLLKHMRTCRNRDCPVPGCQSCKRLLSHARSCKDSDCPVCF 74 (75)
T ss_dssp HHHHHHHHHHHHHHHCTT-SSTTHHHHHHHHHHHCCSSSCCSSCCTHHHHHHHHHHHHHHTSTTSSSHH
T ss_pred HHHHHHHHhHCcCCCCCCCCCcccHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcCCCCCCCCCC
Confidence 3489999999999 8999999999999999999999999876 99999999999999988899873
No 22
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=98.05 E-value=2e-06 Score=99.79 Aligned_cols=47 Identities=28% Similarity=0.695 Sum_probs=39.0
Q ss_pred cccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCCCcccCC
Q 000320 1592 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTNHP 1639 (1673)
Q Consensus 1592 ~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H~l~~~~ 1639 (1673)
.+.|+.|....+.|.||||++|+|||||..||.+. .+.=.|.|.++.
T Consensus 152 ~v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~-~~h~~H~~lR~~ 198 (278)
T KOG4582|consen 152 SVPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN-EHHAAHAMLRLH 198 (278)
T ss_pred cccCCCccCCccccceeeecCCCccchhHHhhcCC-CCCcccceeecc
Confidence 47999999966679999999999999999999862 133389998843
No 23
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.38 E-value=6e-05 Score=88.08 Aligned_cols=47 Identities=28% Similarity=0.588 Sum_probs=40.9
Q ss_pred ccccccccccCccCCCccccCCCCCCccchhhhhc---CCCCCCCCCccc
Q 000320 1591 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTN 1637 (1673)
Q Consensus 1591 f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~---~g~~~H~H~l~~ 1637 (1673)
-++.|..|...-.++.||+|..|-|||||..||.. -+.+.|.|||.-
T Consensus 7 e~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqc 56 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQC 56 (381)
T ss_pred CCceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeE
Confidence 37899999999999999999999999999999987 345677898853
No 24
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=97.27 E-value=0.00014 Score=64.52 Aligned_cols=44 Identities=32% Similarity=0.844 Sum_probs=36.2
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
.|+.|++..|.|.||+|.+| .+|+||..||.... ...++..||+
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C----~d~DLC~~Cf~~g~~~~~H~~~Hp~ 46 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKC----FNYDLCQSCFFSGRTSKSHKNSHPM 46 (49)
T ss_pred CCCCCCCCCceeeeEECCCC----CCcCchHHHHhCCCcCCCCCCCCCe
Confidence 69999998888999999999 99999999998754 3344555665
No 25
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=97.17 E-value=0.0002 Score=62.35 Aligned_cols=38 Identities=29% Similarity=0.783 Sum_probs=30.3
Q ss_pred eeccccCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1465 VHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1465 v~Lq~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
+|..+.|+.|....+.|.||+|..| .+|+||+.||...
T Consensus 1 ~h~~~~C~~C~~~~i~g~Ry~C~~C----~d~dLC~~C~~~g 38 (46)
T PF00569_consen 1 IHHGYTCDGCGTDPIIGVRYHCLVC----PDYDLCEDCFSKG 38 (46)
T ss_dssp -CSSCE-SSS-SSSEESSEEEESSS----SS-EEEHHHHHH-
T ss_pred CCCCeECcCCCCCcCcCCeEECCCC----CCCchhhHHHhCc
Confidence 4667899999997778999999999 9999999999874
No 26
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=97.15 E-value=0.00025 Score=61.85 Aligned_cols=39 Identities=26% Similarity=0.560 Sum_probs=33.2
Q ss_pred ccccccccCccCCCccccCCCCCCccchhhhhcCCCCCCCC
Q 000320 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPH 1633 (1673)
Q Consensus 1593 ~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~H~H 1633 (1673)
|.|+.|..++. ..||||..+.|||||..||.+ |.-...|
T Consensus 1 y~C~~Cg~D~t-~vryh~~~~~~~dLC~~CF~~-G~f~~~~ 39 (45)
T cd02336 1 YHCFTCGNDCT-RVRYHNLKAKKYDLCPSCYQE-GRFPSNF 39 (45)
T ss_pred CcccCCCCccC-ceEEEecCCCccccChHHHhC-cCCCCCC
Confidence 57999999996 699999999999999999987 5444444
No 27
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=97.10 E-value=0.00025 Score=62.72 Aligned_cols=44 Identities=25% Similarity=0.708 Sum_probs=33.9
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
.|+.|++..+.|.||+|..| .+|+||+.||.... ...++..||+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C----~d~dlC~~Cf~~~~~~~~H~~~H~~ 46 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLIC----YDYDLCADCYDSGVTTERHLFDHPM 46 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCC----CCCccchhHHhCCCcCCCCCCCCCE
Confidence 69999966556999999999 99999999998753 2233444553
No 28
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.09 E-value=0.00025 Score=61.88 Aligned_cols=33 Identities=30% Similarity=1.114 Sum_probs=30.5
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
.|+.|....+.|.||+|.+| .+|+||+.||...
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C----~dyDLC~~Cf~~~ 34 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNC----DDFDFCENCFKTR 34 (45)
T ss_pred CCCCCCCCCCccCeEECCCC----CCccchHHhhCCC
Confidence 59999998889999999999 9999999999873
No 29
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.01 E-value=0.00035 Score=61.73 Aligned_cols=35 Identities=31% Similarity=0.909 Sum_probs=30.9
Q ss_pred ccCcccccccccCceeeecccccccc--cchhhhhhHHHhh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNK--NFQLCDKCFEAEK 1507 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k--~f~LCe~Cy~~e~ 1507 (1673)
+.|+.|....+.|.||+|..| . +|+||+.||....
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C----~~~d~DlC~~C~~~~~ 37 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSEC----DDGDFDLCQDCVVKGE 37 (48)
T ss_pred CCCCCCCCCccccceEECCCC----CCCCCccCHHHHhCcC
Confidence 479999996667999999999 8 9999999998753
No 30
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=96.98 E-value=0.00038 Score=59.95 Aligned_cols=34 Identities=26% Similarity=0.721 Sum_probs=31.4
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHhh
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~ 1507 (1673)
.|+.|+...+.|.||+|..| .+|+||+.||....
T Consensus 2 ~CDgCg~~PI~G~RykC~~C----~dyDLC~~C~~~~~ 35 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVK----EDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCcccccceEeCCC----CCCccHHHHhhhhc
Confidence 69999999999999999999 99999999998654
No 31
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=96.91 E-value=0.00052 Score=59.89 Aligned_cols=32 Identities=31% Similarity=0.937 Sum_probs=30.1
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHH
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~ 1505 (1673)
.|+.|++..+.|.||+|.+| .+|+||+.|+..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C----~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAEC----PNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCC----CCccchHHHhCC
Confidence 69999998999999999999 999999999985
No 32
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=96.87 E-value=0.00054 Score=60.63 Aligned_cols=44 Identities=25% Similarity=0.734 Sum_probs=34.0
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
.|+.|.+..+.|.||+|..| .+|+||..||.... ...++..||+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C----~dydLC~~Cf~~~~~~~~H~~~H~~ 46 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVC----RDYSLCLGCYTKGRETKRHNSLHIM 46 (49)
T ss_pred cCCCCCCCCceEeeEECCCC----CCcCchHHHHhCCCcCCCCCCCCCc
Confidence 69999994445999999999 99999999998653 2334445554
No 33
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=96.84 E-value=0.00063 Score=60.07 Aligned_cols=35 Identities=31% Similarity=0.777 Sum_probs=32.1
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHhh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~ 1507 (1673)
+.|+.|.+.++.|.||+|.+| .+|+||..||....
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C----~d~dLC~~Cf~~g~ 35 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAEC----PDFDLCLECFSAGA 35 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCC----CCcchhHHhhhCcC
Confidence 469999999999999999999 99999999998653
No 34
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=96.80 E-value=0.00066 Score=59.06 Aligned_cols=34 Identities=32% Similarity=0.873 Sum_probs=29.8
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHhh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~ 1507 (1673)
+.|+.|...| .|.||+|.+| .+|+||..||....
T Consensus 1 ~~C~~C~~~i-~g~r~~C~~C----~d~dLC~~Cf~~~~ 34 (46)
T cd02249 1 YSCDGCLKPI-VGVRYHCLVC----EDFDLCSSCYAKGK 34 (46)
T ss_pred CCCcCCCCCC-cCCEEECCCC----CCCcCHHHHHCcCc
Confidence 4699999955 6799999999 99999999998764
No 35
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=96.42 E-value=0.0015 Score=56.46 Aligned_cols=32 Identities=28% Similarity=0.762 Sum_probs=28.8
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
.|+.|++ .+.|.||+|.+| .+|+||+.||...
T Consensus 2 ~Cd~C~~-~i~G~ry~C~~C----~d~dLC~~C~~~~ 33 (43)
T cd02340 2 ICDGCQG-PIVGVRYKCLVC----PDYDLCESCEAKG 33 (43)
T ss_pred CCCCCCC-cCcCCeEECCCC----CCccchHHhhCcC
Confidence 5999999 558899999999 9999999999865
No 36
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=96.33 E-value=0.0019 Score=55.85 Aligned_cols=35 Identities=29% Similarity=0.799 Sum_probs=30.9
Q ss_pred ccccCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1467 LQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1467 Lq~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
....|+.|.. .+.|.||+|..| .+|+||..||...
T Consensus 3 ~~~~C~~C~~-~i~g~ry~C~~C----~d~dlC~~Cf~~~ 37 (44)
T smart00291 3 HSYSCDTCGK-PIVGVRYHCLVC----PDYDLCQSCFAKG 37 (44)
T ss_pred CCcCCCCCCC-CCcCCEEECCCC----CCccchHHHHhCc
Confidence 4567999999 667899999999 9999999999864
No 37
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=96.28 E-value=0.0018 Score=55.54 Aligned_cols=32 Identities=28% Similarity=0.862 Sum_probs=27.8
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
+.|+.|.. + .|.||+|..| .+|+||+.||...
T Consensus 1 y~C~~C~~-~-~~~r~~C~~C----~dfDLC~~C~~~~ 32 (41)
T cd02337 1 YTCNECKH-H-VETRWHCTVC----EDYDLCITCYNTK 32 (41)
T ss_pred CcCCCCCC-c-CCCceECCCC----cchhhHHHHhCCC
Confidence 46999987 4 4699999999 9999999999764
No 38
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=96.26 E-value=0.0028 Score=56.15 Aligned_cols=43 Identities=26% Similarity=0.662 Sum_probs=34.3
Q ss_pred cCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
.|+.|.+. +.|.||+|.+| .+|+||..||.... ...++..||+
T Consensus 2 ~CdgC~~~-~~~~RykCl~C----~d~DlC~~Cf~~g~~~~~H~~~Hpm 45 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQC----TDMDLCKTCFLGGVKPEGHEDDHEM 45 (48)
T ss_pred CCCCCCCc-CCCceEECCCC----CCchhHHHHHhCCccCCCCCCCCCc
Confidence 59999985 57899999999 99999999998865 3334445665
No 39
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=96.25 E-value=0.0054 Score=72.33 Aligned_cols=89 Identities=21% Similarity=0.406 Sum_probs=60.9
Q ss_pred ccccCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCCCccccccccccccCCC----CCCCCCcc
Q 000320 1467 LQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPVNSREVHILEEVPVTDV----PADTKDKD 1541 (1673)
Q Consensus 1467 Lq~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~~~~~~h~L~pv~v~dv----P~~t~D~D 1541 (1673)
-...|+.|.+--+.+.||+|..| .+|+||..||+... .--+.+-||+. -+|.+++++-. |-...+++
T Consensus 7 e~v~CdgC~k~~~t~rrYkCL~C----~DyDlC~sCyen~~tt~~H~~dHPmq----cil~~~dfeL~f~Ge~i~~y~~q 78 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFTFRRYKCLRC----SDYDLCFSCYENGATTPIHDEDHPMQ----CILSRVDFELYFGGEPISHYDPQ 78 (381)
T ss_pred CCceeccccccceeeeeeEeeee----cchhHHHHHhhcCCCCcccCCCCcee----EEeeccceeeEecCccccccccc
Confidence 34689999999999999999999 99999999999865 23345557763 34555555422 22233333
Q ss_pred ccccccccchh----HHHHHhhhhCCC
Q 000320 1542 EILESEFFDTR----QAFLSLCQGNHY 1564 (1673)
Q Consensus 1542 ~~i~~effDtR----qaFLslCQ~nHy 1564 (1673)
-..|.....+ ..|+.++...|.
T Consensus 79 -SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 -SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred -cccCCcccccccchhHHHHHhhhcCc
Confidence 6777776544 566666666654
No 40
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.62 E-value=0.0048 Score=72.28 Aligned_cols=34 Identities=26% Similarity=0.826 Sum_probs=31.7
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e 1506 (1673)
..|+.|....|.|.||+|.+| .+|+||++|+...
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C----~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVC----PDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCC----CccchhHHhhcCC
Confidence 789999998888999999999 9999999999875
No 41
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.54 E-value=0.0051 Score=74.51 Aligned_cols=34 Identities=35% Similarity=0.928 Sum_probs=31.3
Q ss_pred cccccccccCccCCCccccCCCCCCccchhhhhc
Q 000320 1592 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1673)
Q Consensus 1592 ~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~ 1625 (1673)
-|.|+.|..+|..-.|.+|.+|||||||..|+..
T Consensus 14 ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~ 47 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSV 47 (438)
T ss_pred CCCCccHhHHhccceEEEeecCCCcchhHHHHhc
Confidence 5799999999987777999999999999999987
No 42
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=95.34 E-value=0.044 Score=53.66 Aligned_cols=55 Identities=11% Similarity=0.429 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHhhcc-CCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc
Q 000320 67 LRARGFMRDRIFGMLLHRQ-TQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM 121 (1673)
Q Consensus 67 ~~~R~~m~~rI~~~L~~R~-~~p~~~~~k~rl~dlakRLEe~lfk~a~tKeeY~n~ 121 (1673)
..||..|++||+..|+-.. |.+..+.--..|-+-||++|.-+|.+|.|++|||.+
T Consensus 12 ~~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~l~~yarkvE~~~fe~A~sreeYY~l 67 (81)
T PF02172_consen 12 PDLRNHLVHKLVQAIFPTPDPNAMNDPRMKNLIEYARKVEKDMFETAQSREEYYHL 67 (81)
T ss_dssp HHHHHHHHHHHHHHHS-SSSCCCCCSHHHHHHHHHHHHHHHHHHHC-SSHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence 3689999999999998662 334444444567788999999999999999999998
No 43
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.06 E-value=0.0081 Score=76.05 Aligned_cols=50 Identities=22% Similarity=0.417 Sum_probs=41.5
Q ss_pred cccccccccccCccCCCccccCCCCCCccchhhhhc---CCCCCCCCCcccCC
Q 000320 1590 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTNHP 1639 (1673)
Q Consensus 1590 ~f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~---~g~~~H~H~l~~~~ 1639 (1673)
+....||+|+.-.+.|.||+|.+|=+||||..||-. -+++.-.|||...-
T Consensus 601 kH~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~ 653 (966)
T KOG4286|consen 601 KHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYC 653 (966)
T ss_pred HhhhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeee
Confidence 456799999999999999999999999999999965 23344578987643
No 44
>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=94.81 E-value=0.0042 Score=54.40 Aligned_cols=42 Identities=29% Similarity=0.696 Sum_probs=31.5
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCch
Q 000320 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYI 1133 (1673)
Q Consensus 1092 ~~~E~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~ 1133 (1673)
...+.+|.|+.|++|+|..|.-............|+|+.|..
T Consensus 9 ~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 9 DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 457789999999999999999776442221134799999853
No 45
>KOG4534 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.36 E-value=0.71 Score=53.80 Aligned_cols=128 Identities=20% Similarity=0.347 Sum_probs=88.0
Q ss_pred hHHHHHhhhhcCCCCcccce-eEEE-EEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccc
Q 000320 1211 KQRFLEIFQEENYPTEFPYK-SKVV-LLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGE 1288 (1673)
Q Consensus 1211 k~~f~~~F~e~~yp~~fpYr-sKaI-~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge 1288 (1673)
+..+...|...+-...|++- .|-+ +||. .+++||+|-+|-|..+ ..++|||+=-||--|-. .|.
T Consensus 24 ~~~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gv 89 (349)
T KOG4534|consen 24 RRHMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGV 89 (349)
T ss_pred HHhhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------ccc
Confidence 33444445444444444443 3333 3443 6799999999999654 35899999999999974 245
Q ss_pred hhhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000320 1289 ALRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1673)
Q Consensus 1289 ~lRT~VYheILi~Yl~Y~k~~GF~~a-hIWAcPP~~GDDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~kg 1355 (1673)
.-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
T Consensus 90 s~~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T KOG4534|consen 90 SRGTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred cccchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 67899999988887665555555444 5677664 56999765443 34899999999999777643
No 46
>COG5087 RTT109 Uncharacterized conserved protein [Function unknown]
Probab=94.36 E-value=0.71 Score=53.80 Aligned_cols=128 Identities=20% Similarity=0.347 Sum_probs=88.0
Q ss_pred hHHHHHhhhhcCCCCcccce-eEEE-EEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccc
Q 000320 1211 KQRFLEIFQEENYPTEFPYK-SKVV-LLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGE 1288 (1673)
Q Consensus 1211 k~~f~~~F~e~~yp~~fpYr-sKaI-~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge 1288 (1673)
+..+...|...+-...|++- .|-+ +||. .+++||+|-+|-|..+ ..++|||+=-||--|-. .|.
T Consensus 24 ~~~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gv 89 (349)
T COG5087 24 RRHMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGV 89 (349)
T ss_pred HHhhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------ccc
Confidence 33444445444444444443 3333 3443 6799999999999654 35899999999999974 245
Q ss_pred hhhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000320 1289 ALRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1673)
Q Consensus 1289 ~lRT~VYheILi~Yl~Y~k~~GF~~a-hIWAcPP~~GDDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~kg 1355 (1673)
.-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
T Consensus 90 s~~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T COG5087 90 SRGTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred cccchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 67899999988887665555555444 5677664 56999765443 34899999999999777643
No 47
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=93.98 E-value=0.018 Score=72.43 Aligned_cols=88 Identities=25% Similarity=0.505 Sum_probs=57.9
Q ss_pred cccccCcceeccCCccccCCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCCccc
Q 000320 1017 CQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEEW 1096 (1673)
Q Consensus 1017 C~~C~~~~L~F~p~~l~C~~c~cRI~r~a~Yy~~~~g~~~~~~C~kCf~~~~~~~i~~~~~~i~K~~~~KkkNd~~~~E~ 1096 (1673)
|-+|-.|+=.-|-|-+||.|-.|.+.-..-.|..-.-.+--|||-||-..-+.-.|.-+-.+.+--.|+|. |
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGALKkT--D------ 79 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGALKKT--D------ 79 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccceecc--c------
Confidence 44777788889999999999889999988888754322336999999876443222111111111111111 1
Q ss_pred ceeccccccccccccccccccc
Q 000320 1097 WVQCDKCEAWQHQICALFNGRR 1118 (1673)
Q Consensus 1097 ~V~C~~C~r~~HqiCaLfn~~~ 1118 (1673)
=+.|-|.|||||.++.
T Consensus 80 ------n~GWAHVVCALYIPEV 95 (900)
T KOG0956|consen 80 ------NGGWAHVVCALYIPEV 95 (900)
T ss_pred ------CCCceEEEEEeeccce
Confidence 1689999999998765
No 48
>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 KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=92.00 E-value=0.14 Score=61.33 Aligned_cols=51 Identities=27% Similarity=0.645 Sum_probs=42.9
Q ss_pred CCCCCCCCccchHHHHHHhhccCCC-CCCCchHHHHHHHH-HHHhcCCCCCCC
Q 000320 745 SSQCPYPRCHHSKILIHHHKHCRDP-SCPVCVPVKNYLQQ-QKERARPKTDSC 795 (1673)
Q Consensus 745 ~~~C~~~~C~sSr~Ll~H~k~C~~~-~CpvC~pvR~~l~~-~~~~s~~~~~vc 795 (1673)
...|.|+.|..++.|+.|+..|+.. .|++|-..+.++.= +..|.+..|+|.
T Consensus 231 ~~~C~~~~C~~~k~lirH~~~Ck~R~gC~iCk~m~~L~~lha~~c~~~~C~vP 283 (319)
T KOG1778|consen 231 DANCSYPSCNGLKRLIRHFRGCKLRGGCPICKRLWQLLELHARHCDDSKCKVP 283 (319)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHcccccCCCC
Confidence 3589999999999999999999995 99999999999854 468887778775
No 50
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=91.86 E-value=0.057 Score=63.23 Aligned_cols=34 Identities=29% Similarity=0.856 Sum_probs=31.7
Q ss_pred cccccccccCccCCCccccCCCCCCccchhhhhc
Q 000320 1592 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1673)
Q Consensus 1592 ~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~ 1625 (1673)
-+-|+.|.+++....+-+|..||+||||..|+..
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~ 38 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVN 38 (432)
T ss_pred eeeehHHHHhhhcceeeeeecccccceehhhhhc
Confidence 4689999999998899999999999999999986
No 51
>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=84.28 E-value=0.44 Score=38.19 Aligned_cols=28 Identities=36% Similarity=0.973 Sum_probs=13.0
Q ss_pred cccccccCccCCCccccCCCCCCccchhh
Q 000320 1594 TCNICHLDIETGQGWRCEVCPDYDVCNAC 1622 (1673)
Q Consensus 1594 tC~~C~~~i~tG~r~hC~~C~dyDLC~~C 1622 (1673)
.|+.|+..+..+..|+|..| ||+|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccC-CCccChhc
Confidence 69999999986689999999 99999887
No 52
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=82.08 E-value=3.7 Score=52.06 Aligned_cols=57 Identities=25% Similarity=0.358 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCcchHHHHHHHHHhcCC
Q 000320 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNMDTLEARLSYLIKGRP 136 (1673)
Q Consensus 68 ~~R~~m~~rI~~~L~~R~~~p~~~~~k~rl~dlakRLEe~lfk~a~tKeeY~n~~tle~rLq~~ik~~~ 136 (1673)
+.|...+.||-. ++.|..+..+ .=||-.|+-+|+|+.||+|||.+ -.+|-..+|-+.
T Consensus 10 kFRq~vIsried-~l~~n~q~~~--------k~a~~mE~hVF~K~~tkDEYl~l---vAkli~h~~d~s 66 (742)
T KOG4274|consen 10 KFRQHVISRIED-ELRKNGQAHS--------KSAKDMESHVFLKAKTKDEYLSL---VAKLIIHFRDIS 66 (742)
T ss_pred HHHHHHHHHhhh-hhhhhhhccC--------cchHHHHHHHHHhhhhHHHHHHH---HHHHHHHHHhhh
Confidence 568899999755 6677766654 45899999999999999999975 344444454444
No 53
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=81.93 E-value=0.72 Score=59.49 Aligned_cols=46 Identities=24% Similarity=0.494 Sum_probs=38.4
Q ss_pred cccCcccccccccCceeeecccccccccchhhhhhHHHhhhcc-cccCCCC
Q 000320 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKRE-DRERHPV 1517 (1673)
Q Consensus 1468 q~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~~~~-~~e~HP~ 1517 (1673)
+.+|+.|++..|.|.||.|..| .|++||..||......+ ++..||+
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~----fn~dlCq~CF~sgraak~hk~~~pM 649 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKH----FNYDICQSCFFSGRAAKGHKMHYPM 649 (966)
T ss_pred hhhcchhhhCccceeeeeehhh----cChhHHhhHhhhcccccCCCCCCCc
Confidence 6799999999999999999999 99999999998865322 3445666
No 54
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=75.21 E-value=1.8 Score=51.98 Aligned_cols=57 Identities=23% Similarity=0.617 Sum_probs=44.0
Q ss_pred hhhcCCCCCcccccccccccCccCCCccccCCCCCCccchhhhhcCCCCC--C--CCCcccC
Q 000320 1581 YHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGID--H--PHKLTNH 1638 (1673)
Q Consensus 1581 yHLHNp~~~~f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~~g~~~--H--~H~l~~~ 1638 (1673)
+-|-+....-.-+.|+.|...-..|-||+|--|-.|.||..|+=+ |+.+ | .|.|...
T Consensus 229 hrla~v~nv~hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwr-G~~g~~hsnqh~mke~ 289 (434)
T KOG4301|consen 229 HRLATVENVFHPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWR-GHAGGSHSNQHQMKEY 289 (434)
T ss_pred HHHHhhcccCCCccCcceecccccchhhhHhhcCCccccchhhcc-ccCCCCcchHHHHHHh
Confidence 334555555566799999999999999999999999999999987 4333 3 5666554
No 55
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=73.74 E-value=1.7 Score=53.58 Aligned_cols=46 Identities=26% Similarity=0.714 Sum_probs=36.7
Q ss_pred cccCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1468 q~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
.+.|+.|...|-.-.|.+|.+| .+|+||-.|+.... --.|+..||=
T Consensus 14 ky~C~~C~~dit~~i~ikCaeC----p~fdLCl~CFs~GaE~~~H~~~H~Y 60 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAEC----PDFDLCLQCFSVGAETGKHQNDHPY 60 (438)
T ss_pred CCCCccHhHHhccceEEEeecC----CCcchhHHHHhcccccCCCCCCCCc
Confidence 4789999998877677999999 99999999998855 3345555664
No 56
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=70.56 E-value=1.4 Score=55.06 Aligned_cols=38 Identities=32% Similarity=0.605 Sum_probs=27.0
Q ss_pred cceeccccccccccccccccccc--CCCCCCcccCCCCch
Q 000320 1096 WWVQCDKCEAWQHQICALFNGRR--NDGGQAEYTCPNCYI 1133 (1673)
Q Consensus 1096 ~~V~C~~C~r~~HqiCaLfn~~~--~~~~~a~FiC~~C~~ 1133 (1673)
-+|+|++|+.|||+-|.--.-.. ..+..-+|.|..|..
T Consensus 184 rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 184 RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 36999999999999998422111 012246899999975
No 57
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=69.39 E-value=2.9 Score=33.76 Aligned_cols=27 Identities=26% Similarity=0.819 Sum_probs=23.7
Q ss_pred cccccccCccCCC-ccccCCCCCCccchhh
Q 000320 1594 TCNICHLDIETGQ-GWRCEVCPDYDVCNAC 1622 (1673)
Q Consensus 1594 tC~~C~~~i~tG~-r~hC~~C~dyDLC~~C 1622 (1673)
.|..|.+.+. |. .|+|..|. |+|...|
T Consensus 2 ~C~~C~~~~~-~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKID-GFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCcC-CCEeEEeCCCC-CeEcCcc
Confidence 6999999887 67 99999997 9998877
No 58
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=66.73 E-value=1.9 Score=53.59 Aligned_cols=87 Identities=21% Similarity=0.382 Sum_probs=46.4
Q ss_pred cccccccCcceeccCCccccCCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCCc
Q 000320 1015 NSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETE 1094 (1673)
Q Consensus 1015 ~~C~~C~~~~L~F~p~~l~C~~c~cRI~r~a~Yy~~~~g~~~~~~C~kCf~~~~~~~i~~~~~~i~K~~~~KkkNd~~~~ 1094 (1673)
..|..|.+-.-.=.-.-.||.|| .|--....|...--..-.++|-+|-=.. ..|.-.....+.+.--|.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC--~i~VHq~CYGI~f~peG~WlCrkCi~~~--~~i~~C~fCps~dGaFkq------- 262 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGC--EICVHQSCYGIQFLPEGFWLCRKCIYGE--YQIRCCSFCPSSDGAFKQ------- 262 (669)
T ss_pred hhhHhccccccCCcceEEEecCc--chhhhhhcccceecCcchhhhhhhcccc--cceeEEEeccCCCCceee-------
Confidence 46666665443333455688876 5777777787543122268899996431 111100000000000000
Q ss_pred ccceeccccccccccccccccccc
Q 000320 1095 EWWVQCDKCEAWQHQICALFNGRR 1118 (1673)
Q Consensus 1095 E~~V~C~~C~r~~HqiCaLfn~~~ 1118 (1673)
..=|||-|-|||+|++..
T Consensus 263 ------T~dgrW~H~iCA~~~pel 280 (669)
T COG5141 263 ------TSDGRWGHVICAMFNPEL 280 (669)
T ss_pred ------ccCCchHhHhHHHhcchh
Confidence 122899999999999754
No 59
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=63.33 E-value=4.5 Score=35.92 Aligned_cols=34 Identities=21% Similarity=0.470 Sum_probs=28.8
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHhh
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~ 1507 (1673)
+.|..|+.... ..||+|..+ ++++||..||....
T Consensus 1 y~C~~Cg~D~t-~vryh~~~~----~~~dLC~~CF~~G~ 34 (45)
T cd02336 1 YHCFTCGNDCT-RVRYHNLKA----KKYDLCPSCYQEGR 34 (45)
T ss_pred CcccCCCCccC-ceEEEecCC----CccccChHHHhCcC
Confidence 36899998885 589999998 89999999997653
No 60
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=63.01 E-value=3 Score=51.99 Aligned_cols=89 Identities=19% Similarity=0.332 Sum_probs=54.3
Q ss_pred CcccccccCcceeccCCccccCCCCceecCCCeeeeecC----------CccceeeccccccccCCCceeecCchhhHHH
Q 000320 1014 ENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGA----------GDTRHYFCIKCYNEARGDTIVVDGTTIAKAR 1083 (1673)
Q Consensus 1014 e~~C~~C~~~~L~F~p~~l~C~~c~cRI~r~a~Yy~~~~----------g~~~~~~C~kCf~~~~~~~i~~~~~~i~K~~ 1083 (1673)
-+.|.+|-+++..=.---+.|..||..+..| .|..-+ ..+.-|||..|--......-+|
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~CGi~VHEg--CYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CEl--------- 187 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDKCGINVHEG--CYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCEL--------- 187 (707)
T ss_pred ceEEEEeecCccccccceeeccccCceeccc--ccccccccccCCCCccCCCCchhhhhHhcCCCCCcccc---------
Confidence 3478899888877777788999887666655 555321 1246799999976543211111
Q ss_pred HHHhhcCCCCcccceecccccccccccccccccccCC
Q 000320 1084 LEKKKNDEETEEWWVQCDKCEAWQHQICALFNGRRND 1120 (1673)
Q Consensus 1084 ~~KkkNd~~~~E~~V~C~~C~r~~HqiCaLfn~~~~~ 1120 (1673)
.-|.- .+++=..=+||+|-|||||....+-
T Consensus 188 ---CPn~~----GifKetDigrWvH~iCALYvpGVaf 217 (707)
T KOG0957|consen 188 ---CPNRF----GIFKETDIGRWVHAICALYVPGVAF 217 (707)
T ss_pred ---CCCcC----CcccccchhhHHHHHHHhhcCcccc
Confidence 11100 0011113479999999999877653
No 61
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=60.79 E-value=9.4 Score=51.89 Aligned_cols=22 Identities=36% Similarity=0.458 Sum_probs=9.5
Q ss_pred CCCCccccccCCCCCCCCCcce
Q 000320 150 SSSSIGTMIPTPGMSHCGNSSL 171 (1673)
Q Consensus 150 sSs~~gtmiptPg~s~~~ns~~ 171 (1673)
+-+.||.||=-|+.+.-.|+++
T Consensus 1400 a~~~I~~~i~Dpdv~~~~~ssi 1421 (2131)
T KOG4369|consen 1400 ATSPIGLPIIDPDVSSPSSSSI 1421 (2131)
T ss_pred hhccccceeecCCcCccccccc
Confidence 3444455554444333333333
No 62
>KOG4786 consensus Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription; Signal transduction mechanisms]
Probab=59.95 E-value=77 Score=41.87 Aligned_cols=64 Identities=17% Similarity=0.158 Sum_probs=30.7
Q ss_pred cCCCCCcccCCccccccceeccCCCC------CCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCCCCCcc
Q 000320 327 YGFSNGALNGGLGMIGNNLLINEPGT------SEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADSYGTGN 397 (1673)
Q Consensus 327 ~g~s~~s~nggmg~~g~n~min~pg~------s~gy~n~~~y~~spk~~Qq~~~~qrs~~q~~~Yg~sn~d~~gs~~ 397 (1673)
-|-+++...||-| |.|.+.|.||. +.+-....+++.|-.-+| + .+.+|.-.|-.++-..+|++.
T Consensus 972 ~~~P~~~sS~~s~--GV~~~~~~~~~~P~~V~~~~~~~~~S~~~S~sV~~-~----~S~L~~~~Y~S~S~~~~~s~~ 1041 (1136)
T KOG4786|consen 972 HQNPQIATSSSSG--GVNQFYNNGGAAPPVVEQQAANRRSSFTMSHSVQQ-H----QSPLQQQFYQSPSHHNNSSSM 1041 (1136)
T ss_pred CCCCCccccCCch--hHHHHhcCCCCCCchhhhhhhccccccccchhhhh-c----cChhhhccccCCCcccccccc
Confidence 4556666655544 66677777771 122233344455432111 1 233344456555555555443
No 63
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=59.93 E-value=11 Score=51.40 Aligned_cols=9 Identities=33% Similarity=0.025 Sum_probs=3.9
Q ss_pred ccccccCCC
Q 000320 368 PLQHHFDHQ 376 (1673)
Q Consensus 368 ~~Qq~~~~q 376 (1673)
..|+.|-.|
T Consensus 1766 ~~q~~~~sq 1774 (2131)
T KOG4369|consen 1766 WGQNEFISQ 1774 (2131)
T ss_pred hhccchhhh
Confidence 333344454
No 64
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=58.96 E-value=6.8 Score=52.42 Aligned_cols=53 Identities=19% Similarity=0.365 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc-chHHHHHHHHHhc
Q 000320 73 MRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM-DTLEARLSYLIKG 134 (1673)
Q Consensus 73 m~~rI~~~L~~R~~~p~~~~~k~rl~dlakRLEe~lfk~a~tKeeY~n~-~tle~rLq~~ik~ 134 (1673)
.+.||=+ .++|...+++ .=||-+|+-+|.||.||||||++ .-|--|+...-+.
T Consensus 3 vi~~ie~-a~~~~~~~~~--------k~a~emE~hvF~Ka~tkdEYl~~varli~h~r~~~~~ 56 (799)
T PF09606_consen 3 VISKIEE-AMRKNGQNTP--------KSAREMENHVFQKAKTKDEYLSLVARLILHIRDMSKK 56 (799)
T ss_dssp HHHHHHH-HHHHH----S--------S-HHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHH-HHHHhCCCCC--------CCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhhhc
Confidence 4556544 4455555543 34788999999999999999997 5555555554433
No 65
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=57.73 E-value=8.8 Score=36.09 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=21.0
Q ss_pred ccccCCCCceecCCCeeeeecCCccceeeccccccc
Q 000320 1031 PIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 1066 (1673)
Q Consensus 1031 ~l~C~~c~cRI~r~a~Yy~~~~g~~~~~~C~kCf~~ 1066 (1673)
+-.|..|+..|.+++.|= ...|..|=++
T Consensus 9 ~~~CtSCg~~i~p~e~~v--------~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGETAV--------KFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCcee--------EeeCCCCCce
Confidence 678999999998887662 3568888654
No 66
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=43.39 E-value=9.8 Score=45.57 Aligned_cols=45 Identities=22% Similarity=0.456 Sum_probs=35.9
Q ss_pred ccCcccccccccCceeeecccccccccchhhhhhHHHhh-hcccccCCCC
Q 000320 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK-KREDRERHPV 1517 (1673)
Q Consensus 1469 ~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~e~-~~~~~e~HP~ 1517 (1673)
+-|+.|...|..-.+-.|.+| ..|+||-.|+.... --.|+..|+-
T Consensus 6 ~hCdvC~~d~T~~~~i~C~eC----~~~DLC~pCF~~g~~tg~H~pyH~Y 51 (432)
T COG5114 6 IHCDVCFLDMTDLTFIKCNEC----PAVDLCLPCFVNGIETGVHSPYHGY 51 (432)
T ss_pred eeehHHHHhhhcceeeeeecc----cccceehhhhhccccccccCCCCCe
Confidence 459999999988899999999 99999999998754 2334555654
No 67
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=42.87 E-value=12 Score=47.46 Aligned_cols=39 Identities=33% Similarity=0.714 Sum_probs=32.3
Q ss_pred cccceecccccccccccccccccccCCCCCCcccCCCCchhh
Q 000320 1094 EEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITE 1135 (1673)
Q Consensus 1094 ~E~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~~ 1135 (1673)
..-.++|+.|++|.|.+|..+.+... ...|.|..|....
T Consensus 98 ~g~~i~c~~c~~Wqh~~C~g~~~~~~---p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 98 EGLMIQCDWCGRWQHKICCGSFKSTK---PDKYVCEICTPRN 136 (508)
T ss_pred CceeeCCcccCcccCceeeeecCCCC---chhceeeeecccc
Confidence 56789999999999999999876542 4579999998753
No 68
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=39.52 E-value=17 Score=50.03 Aligned_cols=76 Identities=18% Similarity=0.560 Sum_probs=50.2
Q ss_pred CcccccccCcceeccCCccccCCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCC
Q 000320 1014 ENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEET 1093 (1673)
Q Consensus 1014 e~~C~~C~~~~L~F~p~~l~C~~c~cRI~r~a~Yy~~~~g~~~~~~C~kCf~~~~~~~i~~~~~~i~K~~~~KkkNd~~~ 1093 (1673)
...|.+|...+-.=.-.-+||.+| .|--+...|..+---.-.+.|-.|--.-.+.
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~C--nl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~----------------------- 273 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGC--NLAVHQECYGIPFIPEGQWLCRRCLQSPQRP----------------------- 273 (1051)
T ss_pred CccceeecccccCCCceEEEcCCC--cchhhhhccCCCCCCCCcEeehhhccCcCcc-----------------------
Confidence 357888877666555667899976 5666777776332112258899997653321
Q ss_pred cccceecccc------------ccccccccccccccc
Q 000320 1094 EEWWVQCDKC------------EAWQHQICALFNGRR 1118 (1673)
Q Consensus 1094 ~E~~V~C~~C------------~r~~HqiCaLfn~~~ 1118 (1673)
|.|.-| |+|.|.+||++.+..
T Consensus 274 ----v~c~~cp~~~gAFkqt~dgrw~Hv~caiwipev 306 (1051)
T KOG0955|consen 274 ----VRCLLCPSKGGAFKQTDDGRWAHVVCAIWIPEV 306 (1051)
T ss_pred ----cceEeccCCCCcceeccCCceeeeehhhccccc
Confidence 333333 899999999997755
No 69
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=38.41 E-value=10 Score=45.89 Aligned_cols=48 Identities=42% Similarity=0.873 Sum_probs=37.1
Q ss_pred HHHHHhhhccccCccceeEeeccccCcccccccccCceeeecccccccccchhhhhhHHH
Q 000320 1446 LLMHKLGETICPMKEDFIMVHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1673)
Q Consensus 1446 ~lm~klg~~i~~~KEdF~vv~Lq~~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~Cy~~ 1505 (1673)
.||++|+ ++ |. |.| --.|++|...-+-|.||.|..| -++++|..|+=.
T Consensus 226 pLmhrla-~v----~n--v~h-pv~cs~c~srs~~gfry~cq~C----~nyqlcq~cfwr 273 (434)
T KOG4301|consen 226 PLMHRLA-TV----EN--VFH-PVECSYCRSRSMMGFRYRCQQC----HNYQLCQQCFWR 273 (434)
T ss_pred HHHHHHH-hh----cc--cCC-CccCcceecccccchhhhHhhc----CCccccchhhcc
Confidence 5788874 22 11 222 3579999999999999999999 999999999643
No 70
>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=36.45 E-value=22 Score=44.78 Aligned_cols=42 Identities=31% Similarity=0.680 Sum_probs=31.8
Q ss_pred CcccceecccccccccccccccccccC-----CC----CCCcccCCCCchh
Q 000320 1093 TEEWWVQCDKCEAWQHQICALFNGRRN-----DG----GQAEYTCPNCYIT 1134 (1673)
Q Consensus 1093 ~~E~~V~C~~C~r~~HqiCaLfn~~~~-----~~----~~a~FiC~~C~~~ 1134 (1673)
..=-||.|+.|+-|-|--|||-...+- .+ -+..|.|..|...
T Consensus 142 n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 142 NTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred CCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 445799999999999999999755431 11 1457999999853
No 71
>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=36.31 E-value=13 Score=33.36 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=15.0
Q ss_pred ccceecccccccccccccccccccCCCCCCcccCCC
Q 000320 1095 EWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPN 1130 (1673)
Q Consensus 1095 E~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~ 1130 (1673)
+-||+|+.|++|=.-- .-+...+... ...|.|..
T Consensus 1 ~~WVQCd~C~KWR~lp-~~~~~~~~~~-~d~W~C~~ 34 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLP-EEVDPIREEL-PDPWYCSM 34 (50)
T ss_dssp -EEEE-TTT--EEEE--CCHHCTSCCS-STT--GGG
T ss_pred CeEEECCCCCceeeCC-hhhCcccccC-CCeEEcCC
Confidence 3599999999997554 3233322112 23788844
No 72
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=35.57 E-value=13 Score=46.30 Aligned_cols=123 Identities=21% Similarity=0.488 Sum_probs=0.0
Q ss_pred ccceeEeeccccCcccccccccCc-------------eeeeccccc--ccccch------hhhhhHHHhhhcccccCCCC
Q 000320 1459 KEDFIMVHLQHACNHCCILMVSGS-------------RHVCEQCTK--LNKNFQ------LCDKCFEAEKKREDRERHPV 1517 (1673)
Q Consensus 1459 KEdF~vv~Lq~~C~~C~~~iV~g~-------------Rw~C~~C~~--~~k~f~------LCe~Cy~~e~~~~~~e~HP~ 1517 (1673)
+|++|. .|..|++.|+... -|+|.+|.+ .++.|+ +||.||......=..=.|++
T Consensus 270 ~~~~~~-----iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I 344 (468)
T KOG1701|consen 270 VEDYFG-----ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPI 344 (468)
T ss_pred hhhhhh-----hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHH
Q ss_pred Ccccccccccc-------------ccCCCCCCCCCccccccccccchhHHHHHhhhhCCCCccchhhccccchhhhhhhc
Q 000320 1518 NSREVHILEEV-------------PVTDVPADTKDKDEILESEFFDTRQAFLSLCQGNHYQYDTLRRAKHSSMMVLYHLH 1584 (1673)
Q Consensus 1518 ~~~~~h~L~pv-------------~v~dvP~~t~D~D~~i~~effDtRqaFLslCQ~nHyQFDsLRRAKhSSMMvLyHLH 1584 (1673)
..+.+.++..+ -+++||- |-|.+-.+.| +--+|
T Consensus 345 ~d~iLrA~GkayHp~CF~Cv~C~r~ldgipF-tvd~~n~v~C---------------------------------v~dfh 390 (468)
T KOG1701|consen 345 MDRILRALGKAYHPGCFTCVVCARCLDGIPF-TVDSQNNVYC---------------------------------VPDFH 390 (468)
T ss_pred HHHHHHhcccccCCCceEEEEeccccCCccc-cccCCCceee---------------------------------ehhhh
Q ss_pred CCCCCcccccccccccCccCCCccccC---CCCCCccchhhhh
Q 000320 1585 NPTAPAFVTTCNICHLDIETGQGWRCE---VCPDYDVCNACYQ 1624 (1673)
Q Consensus 1585 Np~~~~f~~tC~~C~~~i~tG~r~hC~---~C~dyDLC~~Cy~ 1624 (1673)
. +|.-.|++|...|....+-.=+ +|-|-|.=.+||+
T Consensus 391 ~----kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~ 429 (468)
T KOG1701|consen 391 K----KFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYK 429 (468)
T ss_pred h----hcCcchhhccCCccCCCCCcceEEEEEcccccccccee
No 73
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=34.24 E-value=8 Score=32.78 Aligned_cols=33 Identities=27% Similarity=0.591 Sum_probs=16.9
Q ss_pred cceecccccccccccccccccccCCCCCCcccCCCC
Q 000320 1096 WWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNC 1131 (1673)
Q Consensus 1096 ~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C 1131 (1673)
+++.|+.|+-.+|+.|.=..... + ...+.|..|
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~~~-~--~~~W~C~~C 35 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSEVP-D--GDDWLCDRC 35 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS---S--S-----HHH
T ss_pred ceEEeCCCCCcCChhhCCcccCC-C--CCcEECCcC
Confidence 68999999999999997543322 1 235888766
No 74
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=34.16 E-value=12 Score=44.23 Aligned_cols=33 Identities=33% Similarity=0.666 Sum_probs=26.9
Q ss_pred chhhccccchhhhhhhcCCCCCcccccccccccCccCCCccccC
Q 000320 1568 TLRRAKHSSMMVLYHLHNPTAPAFVTTCNICHLDIETGQGWRCE 1611 (1673)
Q Consensus 1568 sLRRAKhSSMMvLyHLHNp~~~~f~~tC~~C~~~i~tG~r~hC~ 1611 (1673)
..|||. =.+||||- ..|.+|++.++||..|-=.
T Consensus 107 VVRkAq----d~VYHl~C-------F~C~iC~R~L~TGdEFYLm 139 (383)
T KOG4577|consen 107 VVRKAQ----DFVYHLHC-------FACFICKRQLATGDEFYLM 139 (383)
T ss_pred HHHHhh----cceeehhh-------hhhHhhhcccccCCeeEEe
Confidence 568875 46899996 3899999999999887654
No 75
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=33.35 E-value=32 Score=30.63 Aligned_cols=39 Identities=23% Similarity=0.675 Sum_probs=31.0
Q ss_pred cceeccCCccccCCCCceecCCCeeeeecCCccceeeccccccc
Q 000320 1023 EKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 1066 (1673)
Q Consensus 1023 ~~L~F~p~~l~C~~c~cRI~r~a~Yy~~~~g~~~~~~C~kCf~~ 1066 (1673)
....|.+.=+.|..|+..|..+. ||.... ..||..||.+
T Consensus 18 ~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~----~~~C~~c~~~ 56 (58)
T PF00412_consen 18 MGKFWHPECFKCSKCGKPLNDGD-FYEKDG----KPYCKDCYQK 56 (58)
T ss_dssp TTEEEETTTSBETTTTCBTTTSS-EEEETT----EEEEHHHHHH
T ss_pred CCcEEEccccccCCCCCccCCCe-eEeECC----EEECHHHHhh
Confidence 35679999999999999998888 555432 6899999975
No 76
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=32.31 E-value=36 Score=42.52 Aligned_cols=33 Identities=27% Similarity=0.679 Sum_probs=27.5
Q ss_pred EEEe-CCCCCCCCeeeccCCCCCCCCChhHHHHHHHH
Q 000320 1315 YIWA-CPPLKGEDYILYCHPEIQKTPKSDKLREWYLA 1350 (1673)
Q Consensus 1315 hIWA-cPP~~GDDYIF~~HP~~Qk~p~~~~L~~WY~~ 1350 (1673)
.=|| |||.+-+ ||.-|..++.+++.+|++||..
T Consensus 164 ~kW~~lpPi~kn---fYke~~e~s~ls~~q~~~~r~e 197 (629)
T KOG0336|consen 164 FKWAKLPPIKKN---FYKESNETSNLSKEQLQEWRKE 197 (629)
T ss_pred cccccCCchhhh---hhhcCchhccCCHHHHHHHHHc
Confidence 4587 5888776 7788999999999999999953
No 77
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=32.15 E-value=4.1 Score=43.93 Aligned_cols=26 Identities=27% Similarity=0.772 Sum_probs=21.6
Q ss_pred CcccccccccccCccCCCccccCCCCCCccchhhhhc
Q 000320 1589 PAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1673)
Q Consensus 1589 ~~f~~tC~~C~~~i~tG~r~hC~~C~dyDLC~~Cy~~ 1625 (1673)
+..++.|-.|...|-+| -+|+.|..+
T Consensus 78 ~nl~~~CE~CG~~I~~G-----------r~C~~C~~~ 103 (137)
T TIGR03826 78 PNLGYPCERCGTSIREG-----------RLCDSCAGE 103 (137)
T ss_pred CCCcCcccccCCcCCCC-----------CccHHHHHH
Confidence 45689999999999987 378888876
No 78
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=30.50 E-value=26 Score=41.73 Aligned_cols=37 Identities=22% Similarity=0.493 Sum_probs=25.0
Q ss_pred eecccccccccccccccccccCCCCCCcccCCCCchh
Q 000320 1098 VQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1673)
Q Consensus 1098 V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~ 1134 (1673)
-+|..||+.|++-=-|---.|...||++|.|+.|.+.
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kA 224 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKA 224 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccch
Confidence 5688888887766555433344556788888888754
No 79
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=29.84 E-value=24 Score=41.91 Aligned_cols=35 Identities=26% Similarity=0.802 Sum_probs=26.1
Q ss_pred cceeccc--cc-ccccccccccccccCCCCCCcccCCCCchh
Q 000320 1096 WWVQCDK--CE-AWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1673)
Q Consensus 1096 ~~V~C~~--C~-r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~ 1134 (1673)
++|.||- |. .|||-.|+=.... + .-...|+.|...
T Consensus 231 ~Mi~CDn~~C~~eWFH~~CVGL~~~--P--kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 231 KMIGCDNPGCPIEWFHFTCVGLKTK--P--KGKWYCPRCKAE 268 (274)
T ss_pred cccccCCCCCCcceEEEeccccccC--C--CCcccchhhhhh
Confidence 4688888 99 9999999954422 1 234899999865
No 80
>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=29.03 E-value=31 Score=27.75 Aligned_cols=28 Identities=29% Similarity=0.790 Sum_probs=11.8
Q ss_pred cCcccccccccCceeeecccccccccchhhhhh
Q 000320 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKC 1502 (1673)
Q Consensus 1470 ~C~~C~~~iV~g~Rw~C~~C~~~~k~f~LCe~C 1502 (1673)
.|..|++.+-.+..|.|.+| +|.|..+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-----df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-----DFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT----------HHH
T ss_pred cCCcCCCcCCCCceEECccC-----CCccChhc
Confidence 58889998866578999999 78877666
No 81
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=28.78 E-value=19 Score=43.24 Aligned_cols=60 Identities=13% Similarity=0.019 Sum_probs=43.9
Q ss_pred eEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcC
Q 000320 1231 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1310 (1673)
Q Consensus 1231 sKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYheILi~Yl~Y~k~~G 1310 (1673)
.=+|.-|=+|||..|.++++--.-.|- .+ +.+..|=+...+++|-+.|
T Consensus 108 d~vVtG~g~I~G~~V~v~a~D~~f~gG-------------------------------Sm-g~~~geKi~r~~e~A~~~~ 155 (285)
T TIGR00515 108 DAVVTGKGTLYGMPIVVAVFDFAFMGG-------------------------------SM-GSVVGEKFVRAIEKALEDN 155 (285)
T ss_pred CcEEEEEEEECCEEEEEEEEeccccCC-------------------------------Cc-cHHHHHHHHHHHHHHHHcC
Confidence 468999999999999988883333321 11 1355666778899999999
Q ss_pred CcEEEEEeCCCC
Q 000320 1311 FTSCYIWACPPL 1322 (1673)
Q Consensus 1311 F~~ahIWAcPP~ 1322 (1673)
.=-+.|.+.+=.
T Consensus 156 lPlV~l~dSgGa 167 (285)
T TIGR00515 156 CPLIIFSASGGA 167 (285)
T ss_pred CCEEEEEcCCCc
Confidence 999998888753
No 82
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=26.61 E-value=1.1e+02 Score=31.73 Aligned_cols=50 Identities=26% Similarity=0.420 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhc-CChhhhcC
Q 000320 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAA-STKEDYMN 120 (1673)
Q Consensus 68 ~~R~~m~~rI~~~L~~R~~~p~~~~~k~rl~dlakRLEe~lfk~a-~tKeeY~n 120 (1673)
.+|..+++.++.-|......+. --..+..||..+|+.||... .++.+|..
T Consensus 4 ~~R~k~~~~L~~~l~~~~~~~~---~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~ 54 (115)
T PF07500_consen 4 KVRDKARKLLYKALQKRSDEQD---DPEDAKELAKEIEEALFDKFGSTSKKYKQ 54 (115)
T ss_dssp HHHHHHHHHHHHHHHHCCCCCC---CTCCHHHHHHHHHHHHHHHHTSTSHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCcccc---chhHHHHHHHHHHHHHHHHHccCcHHHHH
Confidence 5788889888888877754411 13467899999999999998 35566654
No 83
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=24.90 E-value=25 Score=42.39 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=40.7
Q ss_pred eEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcC
Q 000320 1231 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1310 (1673)
Q Consensus 1231 sKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYheILi~Yl~Y~k~~G 1310 (1673)
.=+|.-+=+|||.+|++++| +|.- -|..+ +.|..|-|.-=+++|.+.|
T Consensus 121 dgVVtG~G~I~Gr~v~v~a~---Dftf----------------------------~gGSm-G~v~geKi~ra~e~A~~~r 168 (296)
T CHL00174 121 DAVQTGIGQLNGIPVALGVM---DFQF----------------------------MGGSM-GSVVGEKITRLIEYATNES 168 (296)
T ss_pred ccEEEEEEEECCEEEEEEEE---CCcc----------------------------cccCc-CHHHHHHHHHHHHHHHHcC
Confidence 35788899999999998777 4421 11122 2356666677789999999
Q ss_pred CcEEEEEeCC
Q 000320 1311 FTSCYIWACP 1320 (1673)
Q Consensus 1311 F~~ahIWAcP 1320 (1673)
-=-+.|.+..
T Consensus 169 lPlV~l~~SG 178 (296)
T CHL00174 169 LPLIIVCASG 178 (296)
T ss_pred CCEEEEECCC
Confidence 8888777765
No 84
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=23.93 E-value=1e+02 Score=35.52 Aligned_cols=71 Identities=24% Similarity=0.235 Sum_probs=36.9
Q ss_pred CCCCCccccc----cCCCCCcccCCccccccceeccCCCCCCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCC
Q 000320 317 GMRSGLQHKS----YGFSNGALNGGLGMIGNNLLINEPGTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADS 392 (1673)
Q Consensus 317 gm~sg~qq~s----~g~s~~s~nggmg~~g~n~min~pg~s~gy~n~~~y~~spk~~Qq~~~~qrs~~q~~~Yg~sn~d~ 392 (1673)
-||+|++-++ .|-|..+.||||-.--...||+.-++.++-.. -+--|.++|++|.-|- ..|.|.-..+
T Consensus 164 EmR~GLlGk~~~~in~ps~s~~Ngg~P~~~~~tl~gsA~tg~~sga---gg~~P~~~q~Q~~Wq~-----~~~~m~m~~p 235 (272)
T KOG4552|consen 164 EMRAGLLGKQRPLINSPSASSSNGGAPIRTVGTLIGSAPTGDFSGA---GGDEPPPIQQQVLWQN-----SPYNMVMQSP 235 (272)
T ss_pred HHhccCccccccccCCCCcCCCCCCCCchhhccccccCCCCCcccc---CCCCCchhhhhccccC-----CcchhhccCC
Confidence 3566655533 44555666777654222226666655543222 2345778888877432 3444544444
Q ss_pred CCC
Q 000320 393 YGT 395 (1673)
Q Consensus 393 ~gs 395 (1673)
+.+
T Consensus 236 ~~s 238 (272)
T KOG4552|consen 236 SSS 238 (272)
T ss_pred CCC
Confidence 443
No 85
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.63 E-value=1.1e+02 Score=40.30 Aligned_cols=15 Identities=20% Similarity=0.443 Sum_probs=10.0
Q ss_pred hhccccCCCCCCCCC
Q 000320 713 RHARRCAAPEGKCQD 727 (1673)
Q Consensus 713 ~HA~kC~~~~g~C~~ 727 (1673)
+|-..|..-.-.|+.
T Consensus 424 lHe~~C~r~~V~Cp~ 438 (567)
T PLN03086 424 LHEAYCSRHNVVCPH 438 (567)
T ss_pred HHHhhCCCcceeCCc
Confidence 677777776666653
No 86
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.65 E-value=68 Score=36.06 Aligned_cols=53 Identities=17% Similarity=0.382 Sum_probs=33.6
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCchhhhccccccCCCcccccccCCCCCCcchHHHHHHHHH
Q 000320 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITEVERGERKPLPQSAVLGAKDLPRTILSDHIEHRLFR 1170 (1673)
Q Consensus 1092 ~~~E~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~~~~~~~r~p~p~~~~~~AkdLP~T~LS~fiE~rLn~ 1170 (1673)
+....++.|..|++.|=.-=|+ +..|+||.|... +. .+..+.+...|++++..
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~---------~~~F~Cp~Cg~~---------L~--------~~dn~~~~~~l~~~I~~ 164 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAM---------EYGFRCPQCGEM---------LE--------EYDNSELIKELKEQIKE 164 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHh---------hcCCcCCCCCCC---------Ce--------ecccHHHHHHHHHHHHH
Confidence 3345789999999888333222 236999999753 11 12345566777777753
No 87
>TIGR03046 PS_II_psbV2 photosystem II cytochrome PsbV2. Members of this protein family are PsbV2, a protein closely related cytochrome c-550 (PsbV), a protein important to the water-splitting and oxygen-evolving activity of photosystem II. Mutant studies in Thermosynechococcus elongatus showed PsbV2 can partially replace PsbV, from which it appears to have arisen first by duplication, then by intergenic recombination with a different gene.
Probab=22.44 E-value=96 Score=34.48 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=32.9
Q ss_pred CCCCCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcC
Q 000320 1321 PLKGEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKEN 1359 (1673)
Q Consensus 1321 P~~GDDYIF~~HP~~Qk~p~~~~L~~WY~~mL~kgk~eG 1359 (1673)
+.+|+||+|.|||.....++.+.|..=..=+|+.|++.+
T Consensus 110 s~kG~~~~~~~~mp~~~~LsdeEL~aIAaYLl~qa~~~~ 148 (155)
T TIGR03046 110 SYDGSEESYGCRPVPEDWMDDEEVENLAAFILRAAQKAP 148 (155)
T ss_pred ccCcccccccccCCcccCCCHHHHHHHHHHHHHhhhhcC
Confidence 568999999999999999999999877777777776654
No 88
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.41 E-value=57 Score=35.93 Aligned_cols=33 Identities=24% Similarity=0.445 Sum_probs=23.8
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCch
Q 000320 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYI 1133 (1673)
Q Consensus 1092 ~~~E~~V~C~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~ 1133 (1673)
+....+.-|..|+..|=.-=|+ +..|+||.|..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~---------~~~F~Cp~Cg~ 136 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAM---------ELNFTCPRCGA 136 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHH---------HcCCcCCCCCC
Confidence 4556789999999887433333 23699999975
No 89
>smart00642 Aamy Alpha-amylase domain.
Probab=21.13 E-value=2.4e+02 Score=31.26 Aligned_cols=69 Identities=22% Similarity=0.220 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcCCcEEEEEeCCCCCCCC---eeeccCCCCCCCCChh-HHHHHHHHHHHHHHhcCeEeeccchhh
Q 000320 1299 LIGYLEYCKLRGFTSCYIWACPPLKGED---YILYCHPEIQKTPKSD-KLREWYLAMLRKAAKENIVVDLTNLYD 1369 (1673)
Q Consensus 1299 Li~Yl~Y~k~~GF~~ahIWAcPP~~GDD---YIF~~HP~~Qk~p~~~-~L~~WY~~mL~kgk~eGIV~~~~n~yd 1369 (1673)
|+.-|+|.+..||+. ||..|+.+... .-..-.|.+-..+++. .=.+=+++|+++|.+.||-+=+.-...
T Consensus 21 i~~~l~yl~~lG~~~--I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vilD~V~N 93 (166)
T smart00642 21 IIEKLDYLKDLGVTA--IWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVILDVVIN 93 (166)
T ss_pred HHHHHHHHHHCCCCE--EEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEEEECCC
Confidence 567789999999986 56688865332 1011122222111110 013457789999999987664443333
No 90
>PHA03159 hypothetical protein; Provisional
Probab=20.63 E-value=36 Score=36.42 Aligned_cols=29 Identities=38% Similarity=0.485 Sum_probs=25.4
Q ss_pred ccchhHHHHHhhhhCCCCccchhhccccc
Q 000320 1548 FFDTRQAFLSLCQGNHYQYDTLRRAKHSS 1576 (1673)
Q Consensus 1548 ffDtRqaFLslCQ~nHyQFDsLRRAKhSS 1576 (1673)
|-.+-...|+-||++|-|-|+.-||-||-
T Consensus 6 fq~~ie~il~~cq~~~~~~dsivraihsv 34 (160)
T PHA03159 6 FQKIIENILKECQDCHHQQDSIVRAIHSV 34 (160)
T ss_pred HHHHHHHHHHHHHhcchhhhHHHHHHHHH
Confidence 44566789999999999999999999985
No 91
>PF00150 Cellulase: Cellulase (glycosyl hydrolase family 5); InterPro: IPR001547 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 5 GH5 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); beta-mannanase (3.2.1.78 from EC); exo-1,3-glucanase (3.2.1.58 from EC); endo-1,6-glucanase (3.2.1.75 from EC); xylanase (3.2.1.8 from EC); endoglycoceramidase (3.2.1.123 from EC). The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A [] or as the glycosyl hydrolases family 5 []. One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved [] in the catalytic mechanism.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3NDY_A 3NDZ_B 1LF1_A 1TVP_B 1TVN_A 3AYR_A 3AYS_A 1QI0_A 1W3K_A 1OCQ_A ....
Probab=20.43 E-value=2.1e+02 Score=32.68 Aligned_cols=55 Identities=16% Similarity=0.075 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhcCCcEEEEEeCC-CCC--CCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcCeEee
Q 000320 1298 ILIGYLEYCKLRGFTSCYIWACP-PLK--GEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKENIVVD 1363 (1673)
Q Consensus 1298 ILi~Yl~Y~k~~GF~~ahIWAcP-P~~--GDDYIF~~HP~~Qk~p~~~~L~~WY~~mL~kgk~eGIV~~ 1363 (1673)
+...+|+.++..||..+.|+... ... ..+| .-.+...+.+.++|+.|.+.||.+=
T Consensus 22 ~~~~~~~~~~~~G~n~VRi~v~~~~~~~~~~~~-----------~~~~~~~~~ld~~v~~a~~~gi~vi 79 (281)
T PF00150_consen 22 ITEADFDQLKALGFNTVRIPVGWEAYQEPNPGY-----------NYDETYLARLDRIVDAAQAYGIYVI 79 (281)
T ss_dssp SHHHHHHHHHHTTESEEEEEEESTSTSTTSTTT-----------SBTHHHHHHHHHHHHHHHHTT-EEE
T ss_pred CHHHHHHHHHHCCCCEEEeCCCHHHhcCCCCCc-----------cccHHHHHHHHHHHHHHHhCCCeEE
Confidence 45689999999999999999984 111 1122 2234566778999999999998773
Done!