Query 000333
Match_columns 1650
No_of_seqs 305 out of 359
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:44:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000333.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000333hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1778 CREB binding protein/P 100.0 6E-57 1.3E-61 517.6 11.5 318 1271-1645 1-318 (319)
2 PF08214 KAT11: Histone acetyl 100.0 2.6E-55 5.7E-60 513.7 16.7 279 1071-1359 8-344 (346)
3 smart00551 ZnF_TAZ TAZ zinc fi 99.7 1.9E-17 4.1E-22 157.4 7.8 74 1536-1613 2-79 (79)
4 smart00551 ZnF_TAZ TAZ zinc fi 99.7 7.9E-17 1.7E-21 153.1 5.5 77 583-659 3-79 (79)
5 PF02135 zf-TAZ: TAZ zinc fing 99.4 5.1E-14 1.1E-18 132.7 1.6 73 586-658 2-75 (75)
6 PF02135 zf-TAZ: TAZ zinc fing 99.3 8.8E-13 1.9E-17 124.4 3.5 69 1540-1612 2-75 (75)
7 cd02337 ZZ_CBP Zinc finger, ZZ 98.9 6.8E-10 1.5E-14 93.7 2.6 41 1475-1520 1-41 (41)
8 PF00569 ZZ: Zinc finger, ZZ t 98.8 1.2E-09 2.6E-14 94.3 1.2 44 1473-1517 3-46 (46)
9 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.6 3.4E-08 7.3E-13 86.2 3.1 46 1475-1520 1-48 (48)
10 smart00291 ZnF_ZZ Zinc-binding 98.5 9.2E-08 2E-12 82.0 3.4 42 1472-1515 2-43 (44)
11 cd02344 ZZ_HERC2 Zinc finger, 98.4 1.2E-07 2.5E-12 81.7 3.1 43 1475-1518 1-43 (45)
12 cd02340 ZZ_NBR1_like Zinc fing 98.4 1.3E-07 2.9E-12 80.7 3.0 42 1475-1519 1-42 (43)
13 cd02345 ZZ_dah Zinc finger, ZZ 98.3 2.6E-07 5.5E-12 81.1 3.0 42 1476-1518 2-47 (49)
14 cd02339 ZZ_Mind_bomb Zinc fing 98.3 3.1E-07 6.6E-12 79.3 3.1 42 1476-1518 2-43 (45)
15 cd02249 ZZ Zinc finger, ZZ typ 98.3 4.7E-07 1E-11 78.3 3.0 43 1475-1519 1-45 (46)
16 cd02335 ZZ_ADA2 Zinc finger, Z 98.3 5.5E-07 1.2E-11 79.0 3.2 33 1475-1507 1-33 (49)
17 cd02334 ZZ_dystrophin Zinc fin 98.2 7.9E-07 1.7E-11 78.0 3.0 33 1475-1507 1-33 (49)
18 PF06001 DUF902: Domain of Unk 98.2 3.3E-07 7.1E-12 76.7 0.0 35 899-933 6-41 (42)
19 cd02338 ZZ_PCMF_like Zinc fing 98.1 1.9E-06 4.2E-11 75.6 2.6 33 1475-1507 1-33 (49)
20 cd02342 ZZ_UBA_plant Zinc fing 98.1 1.8E-06 3.8E-11 73.3 2.2 35 1475-1509 1-35 (43)
21 cd02343 ZZ_EF Zinc finger, ZZ 98.0 3.9E-06 8.5E-11 73.2 3.3 42 1476-1518 2-46 (48)
22 KOG4582 Uncharacterized conser 97.6 3.1E-05 6.6E-10 90.5 2.9 45 1474-1519 152-196 (278)
23 cd02336 ZZ_RSC8 Zinc finger, Z 96.9 0.00053 1.2E-08 59.5 2.6 37 1475-1513 1-37 (45)
24 KOG1280 Uncharacterized conser 96.8 0.00054 1.2E-08 80.3 1.7 47 1473-1519 7-56 (381)
25 cd02334 ZZ_dystrophin Zinc fin 96.5 0.0013 2.7E-08 58.3 1.7 34 1352-1389 2-35 (49)
26 PF00569 ZZ: Zinc finger, ZZ t 96.5 0.0015 3.4E-08 56.8 2.1 38 1347-1388 1-38 (46)
27 cd02344 ZZ_HERC2 Zinc finger, 96.3 0.0018 3.9E-08 56.3 1.7 32 1352-1387 2-33 (45)
28 cd02338 ZZ_PCMF_like Zinc fing 96.3 0.002 4.3E-08 56.9 1.7 34 1352-1389 2-35 (49)
29 cd02342 ZZ_UBA_plant Zinc fing 96.2 0.0026 5.6E-08 54.6 1.8 34 1352-1389 2-35 (43)
30 KOG0457 Histone acetyltransfer 95.9 0.0033 7.2E-08 76.1 1.6 35 1473-1507 13-47 (438)
31 cd02341 ZZ_ZZZ3 Zinc finger, Z 95.9 0.0047 1E-07 54.5 2.1 34 1351-1388 1-36 (48)
32 cd02339 ZZ_Mind_bomb Zinc fing 95.9 0.005 1.1E-07 53.6 2.2 32 1352-1387 2-33 (45)
33 cd02249 ZZ Zinc finger, ZZ typ 95.6 0.0066 1.4E-07 52.8 2.0 34 1351-1389 1-34 (46)
34 cd02335 ZZ_ADA2 Zinc finger, Z 95.6 0.0067 1.5E-07 53.6 1.9 34 1351-1388 1-34 (49)
35 cd02345 ZZ_dah Zinc finger, ZZ 95.6 0.0063 1.4E-07 53.8 1.8 33 1352-1388 2-34 (49)
36 KOG4286 Dystrophin-like protei 95.3 0.007 1.5E-07 76.6 1.3 49 1472-1520 601-652 (966)
37 KOG4534 Uncharacterized conser 95.0 0.3 6.5E-06 56.5 13.2 126 1095-1237 26-156 (349)
38 COG5087 RTT109 Uncharacterized 95.0 0.3 6.5E-06 56.5 13.2 126 1095-1237 26-156 (349)
39 cd02340 ZZ_NBR1_like Zinc fing 95.0 0.012 2.6E-07 50.8 1.7 32 1352-1388 2-33 (43)
40 PF00628 PHD: PHD-finger; Int 94.9 0.0038 8.2E-08 54.7 -1.8 42 974-1015 9-50 (51)
41 cd02343 ZZ_EF Zinc finger, ZZ 94.7 0.019 4.2E-07 50.7 2.0 33 1352-1389 2-34 (48)
42 smart00291 ZnF_ZZ Zinc-binding 94.6 0.019 4.1E-07 49.6 1.9 34 1350-1388 4-37 (44)
43 cd02337 ZZ_CBP Zinc finger, ZZ 94.3 0.018 3.9E-07 49.3 1.1 32 1351-1388 1-32 (41)
44 KOG3598 Thyroid hormone recept 94.3 0.0083 1.8E-07 79.6 -1.5 9 33-41 1845-1853(2220)
45 smart00249 PHD PHD zinc finger 93.7 0.044 9.6E-07 46.0 2.4 38 975-1013 10-47 (47)
46 COG5114 Histone acetyltransfer 93.5 0.029 6.3E-07 65.4 1.1 34 1474-1507 5-38 (432)
47 KOG4582 Uncharacterized conser 93.5 0.036 7.8E-07 65.3 1.8 34 1351-1388 153-186 (278)
48 KOG0956 PHD finger protein AF1 93.5 0.026 5.6E-07 71.2 0.7 88 899-1000 8-95 (900)
49 KOG1280 Uncharacterized conser 92.8 0.11 2.4E-06 61.7 4.4 88 1350-1446 8-104 (381)
50 PF07649 C1_3: C1-like domain; 87.2 0.29 6.3E-06 39.0 1.1 28 1476-1504 2-29 (30)
51 KOG3598 Thyroid hormone recept 87.0 0.23 5E-06 66.9 0.8 7 316-322 2065-2071(2220)
52 KOG1778 CREB binding protein/P 78.9 1.9 4E-05 52.1 3.9 65 604-670 231-299 (319)
53 KOG4369 RTK signaling protein 76.9 2.7 5.8E-05 56.5 4.6 63 31-93 1399-1465(2131)
54 KOG4369 RTK signaling protein 74.2 3.9 8.4E-05 55.1 5.0 9 250-258 1766-1774(2131)
55 KOG0957 PHD finger protein [Ge 72.5 3.4 7.5E-05 51.4 3.8 90 895-1002 118-217 (707)
56 KOG4786 Ubinuclein, nuclear pr 70.7 32 0.00068 45.0 11.4 64 209-279 972-1041(1136)
57 KOG4323 Polycomb-like PHD Zn-f 67.6 1.8 3.9E-05 54.3 0.1 37 979-1015 185-223 (464)
58 PF03107 C1_2: C1 domain; Int 63.3 4.5 9.8E-05 32.5 1.6 28 1476-1504 2-29 (30)
59 COG5141 PHD zinc finger-contai 59.7 3.1 6.7E-05 51.8 0.1 86 898-1000 195-280 (669)
60 KOG4301 Beta-dystrobrevin [Cyt 57.6 6.4 0.00014 47.4 2.2 45 1463-1507 229-273 (434)
61 KOG4286 Dystrophin-like protei 51.8 7.5 0.00016 50.8 1.6 37 1350-1390 603-639 (966)
62 COG2888 Predicted Zn-ribbon RN 47.3 15 0.00033 34.3 2.4 28 913-948 9-36 (61)
63 KOG0457 Histone acetyltransfer 45.5 11 0.00025 46.8 1.8 46 1350-1399 14-60 (438)
64 KOG1844 PHD Zn-finger proteins 39.9 12 0.00027 47.6 1.0 39 976-1017 98-136 (508)
65 PF07496 zf-CW: CW-type Zinc F 38.3 12 0.00026 33.5 0.3 34 977-1012 1-34 (50)
66 KOG0336 ATP-dependent RNA heli 36.9 28 0.00061 43.3 3.2 33 1197-1232 164-197 (629)
67 KOG0955 PHD finger protein BR1 36.1 22 0.00047 49.2 2.3 89 895-1000 218-306 (1051)
68 PF00412 LIM: LIM domain; Int 35.9 27 0.0006 31.0 2.3 39 905-948 18-56 (58)
69 PF13831 PHD_2: PHD-finger; PD 35.8 7.2 0.00016 32.8 -1.3 33 978-1013 3-35 (36)
70 PF07227 DUF1423: Protein of u 34.8 24 0.00052 44.4 2.3 41 975-1015 142-191 (446)
71 PF11498 Activator_LAG-3: Tran 34.1 13 0.00029 44.8 0.0 9 383-391 375-383 (468)
72 PF00150 Cellulase: Cellulase 31.3 1.9E+02 0.0041 33.2 8.7 54 1180-1244 22-78 (281)
73 KOG1701 Focal adhesion adaptor 29.7 39 0.00084 42.3 2.8 115 1341-1506 270-429 (468)
74 KOG4552 Vitamin-D-receptor int 28.7 76 0.0016 36.4 4.6 72 199-278 164-239 (272)
75 KOG4301 Beta-dystrobrevin [Cyt 27.8 20 0.00043 43.5 -0.0 46 1328-1385 226-271 (434)
76 KOG1973 Chromatin remodeling p 27.4 28 0.00061 41.5 1.1 35 978-1016 231-268 (274)
77 KOG2462 C2H2-type Zn-finger pr 26.5 34 0.00073 40.7 1.5 36 980-1015 188-223 (279)
78 cd02336 ZZ_RSC8 Zinc finger, Z 25.8 41 0.00088 29.9 1.5 33 1352-1389 2-34 (45)
79 TIGR03046 PS_II_psbV2 photosys 23.5 89 0.0019 34.6 3.9 39 1203-1241 110-148 (155)
80 COG2956 Predicted N-acetylgluc 23.4 34 0.00075 41.7 0.9 28 1470-1498 350-377 (389)
81 KOG4592 Uncharacterized conser 23.0 1.6E+02 0.0034 38.7 6.4 41 233-277 49-89 (728)
82 TIGR00515 accD acetyl-CoA carb 22.3 28 0.00062 41.8 -0.1 60 1113-1204 108-167 (285)
83 TIGR03826 YvyF flagellar opero 22.3 6.6 0.00014 42.3 -4.8 26 1471-1507 78-103 (137)
84 smart00642 Aamy Alpha-amylase 21.3 2.3E+02 0.005 31.4 6.6 65 1181-1247 21-89 (166)
No 1
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=100.00 E-value=6e-57 Score=517.57 Aligned_cols=318 Identities=38% Similarity=0.664 Sum_probs=278.9
Q ss_pred cccCCCccHHHHHHHHHHHhccccccccccccchhhhHHHHHhcCCCCCCCCcchhHHHHHHhhhccccCccceeEeecc
Q 000333 1271 YFDGDYWPGAAEDLIYQIRQDEDGKKQNKGITKKTITKRALKASGQTDLSGNASKDLLLMHKLGETICPMKEDFIMVHLQ 1350 (1650)
Q Consensus 1271 yF~Gd~Wp~~~E~~i~~l~~e~~~~k~~k~~~kk~~~kr~~k~~g~~~~~~~~~kd~~lm~kl~~~i~~~Ke~f~v~~Lq 1350 (1650)
||+||+ +||.|..+.++- ++-.++ .| .+...++.+|...|+++ +|.+++++|++++++
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 44556677889999999 899999999999999
Q ss_pred ccCcccccccccCceeeeeccccccccccchhhhhHHHhhcccccCCCCCccccccccccccCCCCCCCCCCCccccCcc
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKREDRERHPVNSREVHILEEVPVTDVPADTKDKDEILESEF 1430 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~~~~~~~~hp~~~~~~h~l~~~~v~~vp~~t~D~D~~i~sef 1430 (1650)
+ |.+.++.+++|+|..| +++++|++||.+. -+.|+.+.++.|.|.++.+..||..+.|+|++++|++
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 8899999999999999 9999999999887 3678999999999999889999999999999999999
Q ss_pred cccHHHHHHHhhhCCCCcchhhhcccchhhHHHhhcCCCCCcccccccccccCCCCCCceeccCCCCCccchhhhccCCC
Q 000333 1431 FDTRQAFLSLCQGNHYQYDTLRRAKHSSMMVLYHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGG 1510 (1650)
Q Consensus 1431 fdtR~~FL~lcq~nHyQFDsLRRAKhSSMMvLyhLHn~~~~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~ 1510 (1650)
||+|++||.||+.+||+|++||||||||||+|||||+++.+.|+++|+.|+.++. .+|||++|+|||+|..||.++.
T Consensus 126 ~~~r~~flvl~~~~~~~~~~lr~a~hss~~~~~~~H~~t~~~~~~~c~~c~~~~~--~~~~c~~~~d~d~~~~~~~k~~- 202 (319)
T KOG1778|consen 126 FDKRNVFLVLQLAEHCDFSDLRRAKHSSIMLLFDLHLQTEKWFAYTCPICKLEVL--TAWHCEVCPDYDRCRACEEKPL- 202 (319)
T ss_pred hhhHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHhcccCceeeecCccccccc--cccccccCCchhhhhcccCCCC-
Confidence 9999999999999999999999999999999999999999999999999999993 5899999999999999999954
Q ss_pred CCCCCCCcCCCCccchhHHhHHHHHHHHHHHHHHHHHHHHhccCCCCCCCChhhHHHHHHHHhhhccccccCCCChhHHH
Q 000333 1511 IDHPHKLTNHPSTADRDAQNKEARQLRVLQLRKMLDLLVHASQCRSPHCQYPNCRKVKGLFRHGIQCKTRASGGCVLCKK 1590 (1650)
Q Consensus 1511 ~~H~Hkl~~~ps~~~~~~~~~~~~q~r~~qL~~~m~~L~HA~~C~~a~C~~~~C~kmK~l~~H~~~C~~R~~ggC~~Ckr 1590 (1650)
|+|+++..++.. ++...+..|+..|.+ ++++|.++.|.+||+||+|++.|+.| |||++|++
T Consensus 203 --h~h~~~~~~~~~----~~~~~~~~~~~~i~~-----------~~~~C~~~~C~~~k~lirH~~~Ck~R--~gC~iCk~ 263 (319)
T KOG1778|consen 203 --HPHLYEAMESCT----DGCATIGPRNKSINR-----------RDANCSYPSCNGLKRLIRHFRGCKLR--GGCPICKR 263 (319)
T ss_pred --CCcchhcccccc----cccccccchhhhhcc-----------CCCCCCCchhHHHHHHHHHHHHHHhc--cCCchHHH
Confidence 999999988732 233445556666665 68999999999999999999999999 99999999
Q ss_pred HHHHHHHHHhhcCCCCCCCCCchhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 000333 1591 MWYLLQLHARACKESECHVPRCRDLKEHLRRLQQQSDTRRRQAVMEMMRQRAAEV 1645 (1650)
Q Consensus 1591 ~w~Ll~~HAk~C~~~~C~VP~C~~iK~~~~~~q~q~~~rrr~~v~~~~r~r~~~~ 1645 (1650)
||+|++|||++|++..|+||+|++||+++++++++.+++|+.+++++|+.+.+..
T Consensus 264 m~~L~~lha~~c~~~~C~vP~c~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 318 (319)
T KOG1778|consen 264 LWQLLELHARHCDDSKCKVPLCRNLKQKLEKQQKQADERRWKLLVRRVAGTKADG 318 (319)
T ss_pred HHHHHHHHHHHcccccCCCCCCccHHHHHHHHHhhhhhHHHHHHHHHHHhhhccc
Confidence 9999999999999999999999999999999999999999888877777766543
No 2
>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=2.6e-55 Score=513.71 Aligned_cols=279 Identities=43% Similarity=0.702 Sum_probs=220.0
Q ss_pred CCCCCccEEEEEEecccchhhhhHHHHHhhhhcCCCCcccceeEEEEEEEEeCCeEEEEEEEEeeecCCCCCCCCCceEE
Q 000333 1071 EVPGAEALVIRVVSSVDKKLEVKQRFLEIFQEENYPTEFPYKSKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVY 1150 (1650)
Q Consensus 1071 e~~~a~~l~iRvVss~~k~~~Vk~~f~~~f~e~~yp~~f~YrsK~I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vy 1150 (1650)
.+|+++.++||+|++.+++++++..|...|.+..||.+|+||.|+|+|||++||+|||||+|+||||+..|+.||++|||
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 EEecccccccccccccccccchhHHHHHHHHHHHHHHHHhcCCcEEEEEeCCCCCCCCeeeccCCCCCCCCC-----hhH
Q 000333 1151 LSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIWACPPLKGEDYILYCHPEIQKTPK-----SDK 1225 (1650)
Q Consensus 1151 IsYLDSV~yf~P~~~~~~g~~~Rt~VYheILi~Yl~y~k~~GF~~ahiWAcPP~~GdDYIF~~HP~~Qk~p~-----~~~ 1225 (1650)
|+|||||.||+|. .+||.|||++|++||+|++.+||.++|||||||.+|||||| |..|++|+ .++
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 9999999999996 68999999999999999999999999999999999999999 88888888 999
Q ss_pred HHHHHHHHHHHHH-------hcCeEeeccchhhh--hhccccccc------------cccCccccCcccCCCccHHHHHH
Q 000333 1226 LREWYLAMLRKAA-------KENIVVDLTNLYDH--FFVSTGECR------------AKVTAARLPYFDGDYWPGAAEDL 1284 (1650)
Q Consensus 1226 L~~WY~~mL~ka~-------~egiV~~~~n~yd~--~f~~~~~~~------------~~~~~~~lPyF~Gd~Wp~~~E~~ 1284 (1650)
|++||.+||++|+ +++||+...++|+. |+....... ....++.||||+||+||+.||++
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 333321100 01267889999999999999999
Q ss_pred HHH-------HHhccccc--ccc--------------------ccccchhhhHHHHHhcCCC---CCCCCcchhHHHHHH
Q 000333 1285 IYQ-------IRQDEDGK--KQN--------------------KGITKKTITKRALKASGQT---DLSGNASKDLLLMHK 1332 (1650)
Q Consensus 1285 i~~-------l~~e~~~~--k~~--------------------k~~~kk~~~kr~~k~~g~~---~~~~~~~kd~~lm~k 1332 (1650)
+++ |+++.++. ++. +...++...|..+++.+.. +.++.......+|++
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 1111222223333332222 223334455689999
Q ss_pred hhhccccCccceeEeeccccCcccccc
Q 000333 1333 LGETICPMKEDFIMVHLQHACNHCCIL 1359 (1650)
Q Consensus 1333 l~~~i~~~Ke~f~v~~Lq~~C~~C~~~ 1359 (1650)
|+++|+++||+||+|+|+..|++|+.+
T Consensus 318 l~~~~~~~k~~~~~v~~~~~~~~~~~~ 344 (346)
T PF08214_consen 318 LYETMEKHKEDFFVVRLKHQCTACSKP 344 (346)
T ss_dssp HHHHHCHTGGGEEEEESSBGGG--SS-
T ss_pred HHHHhcccccccEEEEEeccccccccc
Confidence 999999999999999999999999865
No 3
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.70 E-value=1.9e-17 Score=157.35 Aligned_cols=74 Identities=47% Similarity=1.027 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHHhccCCC--CCCCChhhHHHHHHHHhhhccccc--cCCCChhHHHHHHHHHHHHhhcCCCCCCCCC
Q 000333 1536 LRVLQLRKMLDLLVHASQCRS--PHCQYPNCRKVKGLFRHGIQCKTR--ASGGCVLCKKMWYLLQLHARACKESECHVPR 1611 (1650)
Q Consensus 1536 ~r~~qL~~~m~~L~HA~~C~~--a~C~~~~C~kmK~l~~H~~~C~~R--~~ggC~~Ckr~w~Ll~~HAk~C~~~~C~VP~ 1611 (1650)
.+|.+|+++|++|+||+.|+. ++|.+++|.+||.||+|++.|+.| ..+||..||+||+ |++.|++.+|+||+
T Consensus 2 ~~~~~lq~~l~~L~Ha~~C~~~~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~----H~k~C~~~~C~Vc~ 77 (79)
T smart00551 2 TRYKQLQRWLELLVHARRCKAREAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQ----HSKHCKDSNCPVCK 77 (79)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHH----HHHhcCCCCCCCCC
Confidence 468899999999999999976 899999999999999999999999 7899999999999 99999999999999
Q ss_pred ch
Q 000333 1612 CR 1613 (1650)
Q Consensus 1612 C~ 1613 (1650)
|+
T Consensus 78 c~ 79 (79)
T smart00551 78 CV 79 (79)
T ss_pred CC
Confidence 95
No 4
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.65 E-value=7.9e-17 Score=153.11 Aligned_cols=77 Identities=52% Similarity=1.032 Sum_probs=74.3
Q ss_pred hhhhhhchhhhhhhccccCCCCCCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCcchhh
Q 000333 583 QFRNQQRWLLFLRHARRCAAPEGKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVPV 659 (1650)
Q Consensus 583 ~~~~qqrwLl~L~HA~~C~~~~g~C~~~~C~~~k~lL~H~~~C~~~~C~~~~C~ssr~ll~H~k~C~~~~CpvC~PV 659 (1650)
.+..+|+||+||+||.+|.++++.|..++|.+||.||+||.+|+.+.|.+++|.++|.||.||+.|++.+||||.||
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 36789999999999999999999999999999999999999999999999999999999999999999999999885
No 5
>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=99.41 E-value=5.1e-14 Score=132.68 Aligned_cols=73 Identities=41% Similarity=0.957 Sum_probs=68.8
Q ss_pred hhhchhhhhhhccccCCCC-CCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCcchh
Q 000333 586 NQQRWLLFLRHARRCAAPE-GKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVP 658 (1650)
Q Consensus 586 ~qqrwLl~L~HA~~C~~~~-g~C~~~~C~~~k~lL~H~~~C~~~~C~~~~C~ssr~ll~H~k~C~~~~CpvC~P 658 (1650)
.+++||+||+||..|..++ +.|..++|..||.||.|+..|..+.|.+++|..+|.||.||+.|++.+|+||.+
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 899999999999999999999997799999999999999999999999999975
No 6
>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=99.31 E-value=8.8e-13 Score=124.38 Aligned_cols=69 Identities=49% Similarity=1.058 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHhccCCC---CCCCChhhHHHHHHHHhhhcccccc--CCCChhHHHHHHHHHHHHhhcCCCCCCCCCc
Q 000333 1540 QLRKMLDLLVHASQCRS---PHCQYPNCRKVKGLFRHGIQCKTRA--SGGCVLCKKMWYLLQLHARACKESECHVPRC 1612 (1650)
Q Consensus 1540 qL~~~m~~L~HA~~C~~---a~C~~~~C~kmK~l~~H~~~C~~R~--~ggC~~Ckr~w~Ll~~HAk~C~~~~C~VP~C 1612 (1650)
+|++.|++|.||..|+. +.|.++.|.+||.||.|+..|..+. .++|..||+||. |++.|++.+|+||+|
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 QLQRWLELLLHASSCRDPEHPNCSLPHCRKMKKLLKHMRTCRNRDCPVPGCQSCKRLLS----HARSCKDSDCPVCFC 75 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHCTT-SSTTHHHHHHHHHHHCCSSSCCSSCCTHHHHHHHHH----HHHHHTSTTSSSHHH
T ss_pred HHHHHHHHHHHHhHCcCCCCCCCCCcccHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHH----HHhcCCCCCCCCCCC
Confidence 68999999999999998 9999999999999999999999887 689999999998 999999999999987
No 7
>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=98.90 E-value=6.8e-10 Score=93.65 Aligned_cols=41 Identities=44% Similarity=1.125 Sum_probs=35.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcCC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTNH 1520 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl~~~ 1520 (1650)
|+||.|...+ +.||||.+|+|||||..||.+ ..|+|+|+++
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 6899998843 389999999999999999988 5699999864
No 8
>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=98.81 E-value=1.2e-09 Score=94.34 Aligned_cols=44 Identities=43% Similarity=0.955 Sum_probs=34.5
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCC
Q 000333 1473 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKL 1517 (1650)
Q Consensus 1473 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl 1517 (1650)
..++|+.|..+...|.||||.+|+|||||.+||.+ |...|.|+|
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 47899999998888899999999999999999988 667788875
No 9
>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=98.57 E-value=3.4e-08 Score=86.16 Aligned_cols=46 Identities=26% Similarity=0.686 Sum_probs=38.3
Q ss_pred ccccccccCCCCCCceeccCCC--CCccchhhhccCCCCCCCCCCcCC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCP--DYDVCNACYQKDGGIDHPHKLTNH 1520 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~--DfDLC~~Cy~k~g~~~H~Hkl~~~ 1520 (1650)
|+|+.|..+..+|.||||.+|+ |||||.+||.+...|...|.|.++
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 6899999977778999999999 999999999984346666777653
No 10
>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=98.48 E-value=9.2e-08 Score=81.96 Aligned_cols=42 Identities=36% Similarity=0.918 Sum_probs=34.6
Q ss_pred cccccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCC
Q 000333 1472 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPH 1515 (1650)
Q Consensus 1472 ~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~H 1515 (1650)
.+.++|+.|.. ..+|.||||.+|+|||||.+||.+ |.+.+.|
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 456789999999999999999987 4344444
No 11
>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=98.44 E-value=1.2e-07 Score=81.71 Aligned_cols=43 Identities=26% Similarity=0.770 Sum_probs=35.4
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCc
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLT 1518 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl~ 1518 (1650)
++|+.|......|.||+|.+|+|||||..||.+.. |.-.|.+.
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~-H~~~H~F~ 43 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRK-HNTRHTFG 43 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCCCC-cCCCCcee
Confidence 48999999888889999999999999999998832 33356554
No 12
>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=98.43 E-value=1.3e-07 Score=80.75 Aligned_cols=42 Identities=36% Similarity=0.853 Sum_probs=34.8
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1519 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl~~ 1519 (1650)
++|+.|+..| .|.||+|.+|+|||||.+||.+. +| ..|+|.+
T Consensus 1 v~Cd~C~~~i-~G~ry~C~~C~d~dLC~~C~~~~-~H-~~H~f~~ 42 (43)
T cd02340 1 VICDGCQGPI-VGVRYKCLVCPDYDLCESCEAKG-VH-PEHAMLK 42 (43)
T ss_pred CCCCCCCCcC-cCCeEECCCCCCccchHHhhCcC-CC-CCCCEEe
Confidence 4799999955 66899999999999999999984 45 5677654
No 13
>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=98.35 E-value=2.6e-07 Score=81.11 Aligned_cols=42 Identities=36% Similarity=0.890 Sum_probs=33.7
Q ss_pred ccccccc-CCCCCCceeccCCCCCccchhhhccC---CCCCCCCCCc
Q 000333 1476 TCNICHL-DIETGQGWRCEVCPDYDVCNACYQKD---GGIDHPHKLT 1518 (1650)
Q Consensus 1476 tCn~C~~-~I~t~~rwhC~vC~DfDLC~~Cy~k~---g~~~H~Hkl~ 1518 (1650)
+|+.|.+ +|. |.||+|.+|+|||||..||.+. ++|.-.|+|.
T Consensus 2 ~C~~C~~~~i~-g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~ 47 (49)
T cd02345 2 SCSACRKQDIS-GIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMY 47 (49)
T ss_pred cCCCCCCCCce-EeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcc
Confidence 7999999 777 7999999999999999999873 2233366654
No 14
>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=98.34 E-value=3.1e-07 Score=79.26 Aligned_cols=42 Identities=33% Similarity=0.962 Sum_probs=35.8
Q ss_pred cccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCc
Q 000333 1476 TCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLT 1518 (1650)
Q Consensus 1476 tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl~ 1518 (1650)
.|+.|+.....|.||+|.+|+|||||..||.. +.|...|++.
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~-~~H~~~H~f~ 43 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG-DKHDLEHRFY 43 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC-CCCCCCCCEE
Confidence 69999988888899999999999999999987 4455566664
No 15
>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=98.28 E-value=4.7e-07 Score=78.29 Aligned_cols=43 Identities=37% Similarity=0.895 Sum_probs=34.6
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCC--CCCCcC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDH--PHKLTN 1519 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H--~Hkl~~ 1519 (1650)
++|+.|..+|. |.||+|..|+|||||..||.+.. ..| .|.+.+
T Consensus 1 ~~C~~C~~~i~-g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~ 45 (46)
T cd02249 1 YSCDGCLKPIV-GVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTE 45 (46)
T ss_pred CCCcCCCCCCc-CCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeE
Confidence 57999999776 58999999999999999998842 344 566543
No 16
>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=98.27 E-value=5.5e-07 Score=78.98 Aligned_cols=33 Identities=33% Similarity=0.952 Sum_probs=31.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
++|+.|.+++..|.||+|.+|+|||||.+||..
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhC
Confidence 589999999999999999999999999999987
No 17
>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=98.21 E-value=7.9e-07 Score=78.05 Aligned_cols=33 Identities=39% Similarity=0.933 Sum_probs=30.6
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
++|+.|+.....|.||+|.+|+|||||..||.+
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~ 33 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFS 33 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhC
Confidence 479999998778899999999999999999987
No 18
>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=98.18 E-value=3.3e-07 Score=76.71 Aligned_cols=35 Identities=34% Similarity=0.640 Sum_probs=0.5
Q ss_pred cccccccceeccCCccccCCC-CceecCCCeeeeec
Q 000333 899 CQLCAVEKLTFEPPPIYCSPC-GTRIKRNAMYYTMG 933 (1650)
Q Consensus 899 C~~C~~~~l~f~p~~l~C~~c-~cRI~r~~~Yy~~~ 933 (1650)
-++||+++|.|.|++|||+|. .|.|+||+.||+|+
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 59999999999986
No 19
>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=98.08 E-value=1.9e-06 Score=75.62 Aligned_cols=33 Identities=36% Similarity=1.002 Sum_probs=28.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
.+|+.|......|.||+|.+|+|||||.+||.+
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 379999954444899999999999999999987
No 20
>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=98.07 E-value=1.8e-06 Score=73.29 Aligned_cols=35 Identities=31% Similarity=0.767 Sum_probs=31.8
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDG 1509 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g 1509 (1650)
.+|..|...-..|.||+|.+|+|||||..||.+-|
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 37999999888899999999999999999998844
No 21
>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=98.01 E-value=3.9e-06 Score=73.22 Aligned_cols=42 Identities=26% Similarity=0.732 Sum_probs=33.0
Q ss_pred cccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCc
Q 000333 1476 TCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLT 1518 (1650)
Q Consensus 1476 tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k---~g~~~H~Hkl~ 1518 (1650)
.|+.|...+ ++.||+|..|+|||||.+||.+ -++|...|+|.
T Consensus 2 ~CdgC~~~~-~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 2 SCDGCDEIA-PWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCcC-CCceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 699999854 6789999999999999999987 23344455553
No 22
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.60 E-value=3.1e-05 Score=90.48 Aligned_cols=45 Identities=29% Similarity=0.748 Sum_probs=36.5
Q ss_pred cccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcC
Q 000333 1474 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1519 (1650)
Q Consensus 1474 ~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H~Hkl~~ 1519 (1650)
..-|++|......|.||+|++|+|||||..||.+.+ +.=+|.|..
T Consensus 152 ~v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~-~h~~H~~lR 196 (278)
T KOG4582|consen 152 SVPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNE-HHAAHAMLR 196 (278)
T ss_pred cccCCCccCCccccceeeecCCCccchhHHhhcCCC-CCcccceee
Confidence 379999999777789999999999999999998842 333456654
No 23
>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=96.94 E-value=0.00053 Score=59.54 Aligned_cols=37 Identities=27% Similarity=0.606 Sum_probs=32.0
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCC
Q 000333 1475 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDH 1513 (1650)
Q Consensus 1475 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k~g~~~H 1513 (1650)
|.|+.|..|+.+ .||||..+.|||||..||.+ |....
T Consensus 1 y~C~~Cg~D~t~-vryh~~~~~~~dLC~~CF~~-G~f~~ 37 (45)
T cd02336 1 YHCFTCGNDCTR-VRYHNLKAKKYDLCPSCYQE-GRFPS 37 (45)
T ss_pred CcccCCCCccCc-eEEEecCCCccccChHHHhC-cCCCC
Confidence 579999999975 89999999999999999988 53333
No 24
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=96.77 E-value=0.00054 Score=80.26 Aligned_cols=47 Identities=28% Similarity=0.588 Sum_probs=40.5
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCcC
Q 000333 1473 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTN 1519 (1650)
Q Consensus 1473 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k---~g~~~H~Hkl~~ 1519 (1650)
-.+.|..|...--++.||+|..|-|||||.+||.. .+.|.|.|+|.-
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 46789999999999999999999999999999987 345777888753
No 25
>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=96.50 E-value=0.0013 Score=58.27 Aligned_cols=34 Identities=35% Similarity=0.877 Sum_probs=30.8
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
.|+.|.+..+.|.||+|..| .+|+||..||....
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C----~d~DLC~~Cf~~g~ 35 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKC----FNYDLCQSCFFSGR 35 (49)
T ss_pred CCCCCCCCCceeeeEECCCC----CCcCchHHHHhCCC
Confidence 69999998888999999999 99999999998654
No 26
>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=96.48 E-value=0.0015 Score=56.78 Aligned_cols=38 Identities=29% Similarity=0.783 Sum_probs=29.8
Q ss_pred eeccccCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1347 VHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1347 ~~Lq~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
||-...|+.|....+.|.||.|..| .+|+||+.||...
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 3566789999997778899999999 9999999999874
No 27
>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=96.34 E-value=0.0018 Score=56.33 Aligned_cols=32 Identities=31% Similarity=1.144 Sum_probs=29.8
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHH
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1387 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~ 1387 (1650)
.|+.|....+.|.||+|..| .+|+||+.||..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C----~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNC----DDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCC----CCccchHHhhCC
Confidence 59999998888999999999 999999999976
No 28
>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=96.28 E-value=0.002 Score=56.93 Aligned_cols=34 Identities=26% Similarity=0.816 Sum_probs=29.5
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
.|+.|.+..+.|.||+|..| .+|.||+.||....
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C----~d~dlC~~Cf~~~~ 35 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLIC----YDYDLCADCYDSGV 35 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCC----CCCccchhHHhCCC
Confidence 69999965555999999999 99999999998653
No 29
>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=96.19 E-value=0.0026 Score=54.60 Aligned_cols=34 Identities=26% Similarity=0.721 Sum_probs=31.1
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
.|+.|...-+.|.||+|..| .+|+||+.||....
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 59999998889999999999 99999999997654
No 30
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.89 E-value=0.0033 Score=76.06 Aligned_cols=35 Identities=34% Similarity=0.852 Sum_probs=32.9
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1473 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1473 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
--|.|+.|..+|..-.+.+|.+|||||||..|+..
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~ 47 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSV 47 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhc
Confidence 46799999999999989999999999999999987
No 31
>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=95.88 E-value=0.0047 Score=54.48 Aligned_cols=34 Identities=32% Similarity=0.924 Sum_probs=29.7
Q ss_pred ccCcccccccccCceeeeeccccccc--cccchhhhhHHH
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNK--NFQLCDKCFEAE 1388 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k--~f~lC~~Cy~~e 1388 (1650)
+.|+.|....+.|.||.|..| . +|.||+.||...
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C----~~~d~DlC~~C~~~~ 36 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSEC----DDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCCccccceEECCCC----CCCCCccCHHHHhCc
Confidence 369999995666999999999 8 999999999864
No 32
>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=95.88 E-value=0.005 Score=53.61 Aligned_cols=32 Identities=31% Similarity=0.937 Sum_probs=30.0
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHH
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1387 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~ 1387 (1650)
.|+.|.+..+.|.||+|..| .+|+||+.|+..
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 59999999999999999999 999999999984
No 33
>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=95.62 E-value=0.0066 Score=52.79 Aligned_cols=34 Identities=32% Similarity=0.873 Sum_probs=29.4
Q ss_pred ccCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
+.|+.|...| .|.||.|.+| .+|.||.+||....
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 3699999955 5799999999 99999999998654
No 34
>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=95.59 E-value=0.0067 Score=53.55 Aligned_cols=34 Identities=32% Similarity=0.804 Sum_probs=31.4
Q ss_pred ccCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
+.|+.|.+.++.|.||+|.+| .+|.||..||...
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C----~d~dLC~~Cf~~g 34 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAEC----PDFDLCLECFSAG 34 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCC----CCcchhHHhhhCc
Confidence 369999999999999999999 9999999999865
No 35
>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=95.58 E-value=0.0063 Score=53.82 Aligned_cols=33 Identities=30% Similarity=0.881 Sum_probs=28.6
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
.|+.|.+.-+.|.||+|..| .+|.||..||...
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C----~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVC----RDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCceEeeEECCCC----CCcCchHHHHhCC
Confidence 59999993344899999999 9999999999865
No 36
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.26 E-value=0.007 Score=76.57 Aligned_cols=49 Identities=22% Similarity=0.447 Sum_probs=40.2
Q ss_pred cccccccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCcCC
Q 000333 1472 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTNH 1520 (1650)
Q Consensus 1472 ~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k---~g~~~H~Hkl~~~ 1520 (1650)
+-...||.|+..-.-|.||+|.+|-+||||.+||-. -++|.-+|+|...
T Consensus 601 kH~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey 652 (966)
T KOG4286|consen 601 KHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEY 652 (966)
T ss_pred HhhhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceee
Confidence 345689999999999999999999999999999965 3445556777654
No 37
>KOG4534 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.05 E-value=0.3 Score=56.53 Aligned_cols=126 Identities=20% Similarity=0.339 Sum_probs=87.4
Q ss_pred HHHHhhhhcCCCCcccce-eEEE-EEEEEeCCeEEEEEEEEeeecCCCCCCCCCceEEEEecccccccccccccccccch
Q 000333 1095 RFLEIFQEENYPTEFPYK-SKVV-LLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEAL 1172 (1650)
Q Consensus 1095 ~f~~~f~e~~yp~~f~Yr-sK~I-~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~g~~~ 1172 (1650)
.+...|...+-...|++- .+-+ +||. .+++||+|-+|-|..+ ..++|||+=-||--|-.- |...
T Consensus 26 ~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn~------gvs~ 91 (349)
T KOG4534|consen 26 HMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGNR------GVSR 91 (349)
T ss_pred hhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCcc------cccc
Confidence 344444433334444433 3333 3443 6899999999999544 358999999999999643 4567
Q ss_pred hHHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000333 1173 RTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1237 (1650)
Q Consensus 1173 Rt~VYheILi~Yl~y~k~~GF~~a-hiWAcPP~~GdDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~ka 1237 (1650)
||.++-|+|++-..--|+.|=.-+ -+++-|- ..|||..--.. ..++++..|.+|+..+|+--
T Consensus 92 ~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T KOG4534|consen 92 GTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred cchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 899999998887775566655544 6777664 56999765443 34899999999999777644
No 38
>COG5087 RTT109 Uncharacterized conserved protein [Function unknown]
Probab=95.05 E-value=0.3 Score=56.53 Aligned_cols=126 Identities=20% Similarity=0.339 Sum_probs=87.4
Q ss_pred HHHHhhhhcCCCCcccce-eEEE-EEEEEeCCeEEEEEEEEeeecCCCCCCCCCceEEEEecccccccccccccccccch
Q 000333 1095 RFLEIFQEENYPTEFPYK-SKVV-LLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEAL 1172 (1650)
Q Consensus 1095 ~f~~~f~e~~yp~~f~Yr-sK~I-~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~g~~~ 1172 (1650)
.+...|...+-...|++- .+-+ +||. .+++||+|-+|-|..+ ..++|||+=-||--|-.- |...
T Consensus 26 ~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn~------gvs~ 91 (349)
T COG5087 26 HMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGNR------GVSR 91 (349)
T ss_pred hhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCcc------cccc
Confidence 344444433334444433 3333 3443 6899999999999544 358999999999999643 4567
Q ss_pred hHHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000333 1173 RTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1237 (1650)
Q Consensus 1173 Rt~VYheILi~Yl~y~k~~GF~~a-hiWAcPP~~GdDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~ka 1237 (1650)
||.++-|+|++-..--|+.|=.-+ -+++-|- ..|||..--.. ..++++..|.+|+..+|+--
T Consensus 92 ~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T COG5087 92 GTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred cchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 899999998887775566655544 6777664 56999765443 34899999999999777644
No 39
>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=95.04 E-value=0.012 Score=50.81 Aligned_cols=32 Identities=28% Similarity=0.762 Sum_probs=28.5
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
.|+.|.+ .+.|.||.|.+| .+|+||+.||...
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 557799999999 9999999999854
No 40
>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=94.87 E-value=0.0038 Score=54.72 Aligned_cols=42 Identities=29% Similarity=0.696 Sum_probs=31.6
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCch
Q 000333 974 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYI 1015 (1650)
Q Consensus 974 ~~~E~~v~C~~C~r~~HqiCaLfn~~~~~~~~~~f~C~~C~~ 1015 (1650)
...+.+|.|+.|++|+|..|.-..........+.|+|+.|..
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 41
>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=94.66 E-value=0.019 Score=50.71 Aligned_cols=33 Identities=30% Similarity=0.769 Sum_probs=29.4
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
.|+.|.+. +.|.||+|.+| .+|+||..||....
T Consensus 2 ~CdgC~~~-~~~~RykCl~C----~d~DlC~~Cf~~g~ 34 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQC----TDMDLCKTCFLGGV 34 (48)
T ss_pred CCCCCCCc-CCCceEECCCC----CCchhHHHHHhCCc
Confidence 59999985 57899999999 99999999998765
No 42
>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=94.65 E-value=0.019 Score=49.61 Aligned_cols=34 Identities=29% Similarity=0.841 Sum_probs=29.9
Q ss_pred cccCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1350 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1350 q~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
...|..|.. .+.|.||.|..| .+|+||..||...
T Consensus 4 ~~~C~~C~~-~i~g~ry~C~~C----~d~dlC~~Cf~~~ 37 (44)
T smart00291 4 SYSCDTCGK-PIVGVRYHCLVC----PDYDLCQSCFAKG 37 (44)
T ss_pred CcCCCCCCC-CCcCCEEECCCC----CCccchHHHHhCc
Confidence 457999999 667899999999 9999999999753
No 43
>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=94.33 E-value=0.018 Score=49.30 Aligned_cols=32 Identities=28% Similarity=0.862 Sum_probs=27.1
Q ss_pred ccCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
+.|..|.. + .|.||.|..| .+|+||+.||...
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 35889977 4 3699999999 9999999999763
No 44
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=94.29 E-value=0.0083 Score=79.63 Aligned_cols=9 Identities=11% Similarity=0.117 Sum_probs=4.6
Q ss_pred CCCcccccc
Q 000333 33 SSSIGTMIP 41 (1650)
Q Consensus 33 ss~~gtmip 41 (1650)
+|++|..||
T Consensus 1845 ~~p~~~~~s 1853 (2220)
T KOG3598|consen 1845 ASPKDDVTS 1853 (2220)
T ss_pred CCCCCCCCC
Confidence 455555443
No 45
>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 COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=93.51 E-value=0.029 Score=65.40 Aligned_cols=34 Identities=29% Similarity=0.856 Sum_probs=32.1
Q ss_pred cccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1474 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1474 ~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
-+-|+.|..++....+-+|..|++||||..|+..
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 4689999999999999999999999999999987
No 47
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=93.46 E-value=0.036 Score=65.34 Aligned_cols=34 Identities=26% Similarity=0.826 Sum_probs=31.3
Q ss_pred ccCcccccccccCceeeeeccccccccccchhhhhHHH
Q 000333 1351 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1388 (1650)
Q Consensus 1351 ~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e 1388 (1650)
..|+.|....+.|.||+|++| .+|+||++|+...
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 689999997788899999999 9999999999764
No 48
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=93.46 E-value=0.026 Score=71.17 Aligned_cols=88 Identities=26% Similarity=0.494 Sum_probs=58.4
Q ss_pred cccccccceeccCCccccCCCCceecCCCeeeeecCCccceEEccccccccCCCeeeecCchhHHHHHHHhhcCCCCccc
Q 000333 899 CQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEEW 978 (1650)
Q Consensus 899 C~~C~~~~l~f~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~~Cf~~~~~~~i~~~~~~~~K~~~~kkkNd~~~~E~ 978 (1650)
|-.|-.|+=.-|-|-+||.|-.|.+.-..-.|..-.-.+--|||-||-...+.-.|.-+--+ .|+.-.||. |
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP-~kdGALKkT-D------ 79 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCP-HKDGALKKT-D------ 79 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeeccc-Ccccceecc-c------
Confidence 55788888899999999999888999999888764423347999999876543222111111 111111111 1
Q ss_pred ceeccccccccccccccccccc
Q 000333 979 WVQCDKCEAWQHQICALFNGRR 1000 (1650)
Q Consensus 979 ~v~C~~C~r~~HqiCaLfn~~~ 1000 (1650)
=+.|-|.|||||.++.
T Consensus 80 ------n~GWAHVVCALYIPEV 95 (900)
T KOG0956|consen 80 ------NGGWAHVVCALYIPEV 95 (900)
T ss_pred ------CCCceEEEEEeeccce
Confidence 2689999999998765
No 49
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=92.76 E-value=0.11 Score=61.73 Aligned_cols=88 Identities=23% Similarity=0.443 Sum_probs=58.5
Q ss_pred cccCcccccccccCceeeeeccccccccccchhhhhHHHhhcc-cccCCCCCccccccccccccCCC----CCCCCCCCc
Q 000333 1350 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKRE-DRERHPVNSREVHILEEVPVTDV----PADTKDKDE 1424 (1650)
Q Consensus 1350 q~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~~~~-~~~~hp~~~~~~h~l~~~~v~~v----p~~t~D~D~ 1424 (1650)
...|+.|.+.-+.++||+|..| .+|+||..||+...... ..+-||+ .-+|.++.++-. |-...+++
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C----~DyDlC~sCyen~~tt~~H~~dHPm----qcil~~~dfeL~f~Ge~i~~y~~q- 78 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRC----SDYDLCFSCYENGATTPIHDEDHPM----QCILSRVDFELYFGGEPISHYDPQ- 78 (381)
T ss_pred CceeccccccceeeeeeEeeee----cchhHHHHHhhcCCCCcccCCCCce----eEEeeccceeeEecCccccccccc-
Confidence 3589999999999999999999 99999999998765221 2223554 235566654422 22233433
Q ss_pred cccCcccc----cHHHHHHHhhhCCC
Q 000333 1425 ILESEFFD----TRQAFLSLCQGNHY 1446 (1650)
Q Consensus 1425 ~i~seffd----tR~~FL~lcq~nHy 1446 (1650)
-.+|.... |=..|+.++...|.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCc
Confidence 67777654 34567777766663
No 50
>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=87.15 E-value=0.29 Score=39.02 Aligned_cols=28 Identities=36% Similarity=0.973 Sum_probs=13.1
Q ss_pred cccccccCCCCCCceeccCCCCCccchhh
Q 000333 1476 TCNICHLDIETGQGWRCEVCPDYDVCNAC 1504 (1650)
Q Consensus 1476 tCn~C~~~I~t~~rwhC~vC~DfDLC~~C 1504 (1650)
+|+.|...+..+..|+|..| ||+|...|
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 69999999998789999999 99999887
No 51
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=87.02 E-value=0.23 Score=66.92 Aligned_cols=7 Identities=14% Similarity=0.188 Sum_probs=2.7
Q ss_pred cccccCC
Q 000333 316 NQSNFHG 322 (1650)
Q Consensus 316 ~q~n~q~ 322 (1650)
+++.|++
T Consensus 2065 ~~~~m~p 2071 (2220)
T KOG3598|consen 2065 NRPLMNP 2071 (2220)
T ss_pred chhhccc
Confidence 3333333
No 52
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=78.93 E-value=1.9 Score=52.15 Aligned_cols=65 Identities=32% Similarity=0.768 Sum_probs=55.2
Q ss_pred CCCCCCCCchhHHHHHhcccccCCC-CCCCCCccchHHHHHHh-hccCCCCCCc--chhhhhHHHHHHHHh
Q 000333 604 EGKCQDVNCITVQKLWRHMDNCTSS-QCPYPRCHHSKILIHHH-KHCRDPSCPV--CVPVKNYLQQQKERA 670 (1650)
Q Consensus 604 ~g~C~~~~C~~~k~lL~H~~~C~~~-~C~~~~C~ssr~ll~H~-k~C~~~~Cpv--C~PVr~~v~k~~qq~ 670 (1650)
...|..+.|..++.|++|...|+.. .| +.|....+|+.=| +.|.+..|+| |-.+|.-+++..++.
T Consensus 231 ~~~C~~~~C~~~k~lirH~~~Ck~R~gC--~iCk~m~~L~~lha~~c~~~~C~vP~c~~~k~~~~~~~~~~ 299 (319)
T KOG1778|consen 231 DANCSYPSCNGLKRLIRHFRGCKLRGGC--PICKRLWQLLELHARHCDDSKCKVPLCRNLKQKLEKQQKQA 299 (319)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHhccCC--chHHHHHHHHHHHHHHcccccCCCCCCccHHHHHHHHHhhh
Confidence 4678899999999999999999994 77 4788888888655 9999999999 999999888766543
No 53
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=76.92 E-value=2.7 Score=56.50 Aligned_cols=63 Identities=21% Similarity=0.132 Sum_probs=36.9
Q ss_pred cCCCCccccccCCCCCCCCCCcceEeecccc--ccccccCCCcccccccccCcc--cccCCcccCCC
Q 000333 31 NSSSSIGTMIPTPGMSHCGNSSLMVTSSVDS--SMIAASGCNTIAPTTVNSGSL--LSTGGIQSNSY 93 (1650)
Q Consensus 31 ~~ss~~gtmiptpg~~~~~n~~~~~~~~~~~--~~~~~~~~~~~~~~~~n~~~~--l~~~~~~~~~~ 93 (1650)
++-|+||.||=-|+.+.-.||++..++.-.+ ++.+.+|-....++++|.-.. .|.+-..++++
T Consensus 1399 ~a~~~I~~~i~Dpdv~~~~~ssi~~as~gg~s~~~sf~~~~~~agS~S~~rq~~Sp~P~~tS~sna~ 1465 (2131)
T KOG4369|consen 1399 VATSPIGLPIIDPDVSSPSSSSIPLASFGGISGTRSFLQGPAPAGSPSFNRQHFSPHPQWTSASNAC 1465 (2131)
T ss_pred hhhccccceeecCCcCccccccchhhhcCCCccccccccCCCcCCCcccccccCCCCcccccccccc
Confidence 4678889999888877777877766654222 233444555555566655433 34344444333
No 54
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=74.20 E-value=3.9 Score=55.13 Aligned_cols=9 Identities=33% Similarity=0.025 Sum_probs=4.0
Q ss_pred ccccccCCC
Q 000333 250 PLQHHFDHQ 258 (1650)
Q Consensus 250 ~~Qq~~~~q 258 (1650)
..|+.|-.|
T Consensus 1766 ~~q~~~~sq 1774 (2131)
T KOG4369|consen 1766 WGQNEFISQ 1774 (2131)
T ss_pred hhccchhhh
Confidence 333344454
No 55
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=72.51 E-value=3.4 Score=51.43 Aligned_cols=90 Identities=19% Similarity=0.360 Sum_probs=55.4
Q ss_pred CCcccccccccceeccCCccccCCCCceecCCCeeeeecC----------CccceEEccccccccCCCeeeecCchhHHH
Q 000333 895 SENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGA----------GDTRHYFCIKCYNEARGDTIVVDGTTIAKA 964 (1650)
Q Consensus 895 ~~~~C~~C~~~~l~f~p~~l~C~~c~cRI~r~~~Yy~~~~----------~~~~~~~C~~Cf~~~~~~~i~~~~~~~~K~ 964 (1650)
.-+.|..|-+++..=.---+.|..||..+-.| .|..-+ ..+.-|||..|--......-+|.- .|.
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~CGi~VHEg--CYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElCP---n~~ 192 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDKCGINVHEG--CYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELCP---NRF 192 (707)
T ss_pred cceEEEEeecCccccccceeeccccCceeccc--ccccccccccCCCCccCCCCchhhhhHhcCCCCCccccCC---CcC
Confidence 34478899998877777788999887665555 565431 124678999997654311111100 011
Q ss_pred HHHHhhcCCCCcccceecccccccccccccccccccCC
Q 000333 965 RLEKKKNDEETEEWWVQCDKCEAWQHQICALFNGRRND 1002 (1650)
Q Consensus 965 ~~~kkkNd~~~~E~~v~C~~C~r~~HqiCaLfn~~~~~ 1002 (1650)
..-|. ..=|||+|-|||||....+-
T Consensus 193 GifKe-------------tDigrWvH~iCALYvpGVaf 217 (707)
T KOG0957|consen 193 GIFKE-------------TDIGRWVHAICALYVPGVAF 217 (707)
T ss_pred Ccccc-------------cchhhHHHHHHHhhcCcccc
Confidence 10011 13479999999999887753
No 56
>KOG4786 consensus Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription; Signal transduction mechanisms]
Probab=70.65 E-value=32 Score=45.05 Aligned_cols=64 Identities=17% Similarity=0.158 Sum_probs=31.0
Q ss_pred cCCCCCcccCCccccccceeccCCCC------CCCcccccccCCCCCccccccCCCCCcccCCCCCCCCCCCCCCcc
Q 000333 209 YGFSNGALNGGLGMIGNNLLINEPGT------SEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADSYGTGN 279 (1650)
Q Consensus 209 ~g~s~~s~nggmg~~g~~~min~pg~------s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~~g~~~ 279 (1650)
-|-+++...||-| |.|.+.|.||. +.+-....+++.|..-+| + .+.+|.-.|-.++-..+|++.
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 122233334444432111 1 233344456555555555443
No 57
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=67.59 E-value=1.8 Score=54.26 Aligned_cols=37 Identities=32% Similarity=0.636 Sum_probs=26.8
Q ss_pred ceeccccccccccccccccccc--CCCCCCcccCCCCch
Q 000333 979 WVQCDKCEAWQHQICALFNGRR--NDGGQAEYTCPNCYI 1015 (1650)
Q Consensus 979 ~v~C~~C~r~~HqiCaLfn~~~--~~~~~~~f~C~~C~~ 1015 (1650)
+|+|++|+.||||-|.--.-.. ..+...+|.|..|..
T Consensus 185 mlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 185 MLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 6999999999999998422111 112356899999975
No 58
>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=63.30 E-value=4.5 Score=32.47 Aligned_cols=28 Identities=21% Similarity=0.648 Sum_probs=23.7
Q ss_pred cccccccCCCCCCceeccCCCCCccchhh
Q 000333 1476 TCNICHLDIETGQGWRCEVCPDYDVCNAC 1504 (1650)
Q Consensus 1476 tCn~C~~~I~t~~rwhC~vC~DfDLC~~C 1504 (1650)
.|..|.+.++...+|+|..|. |+|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC-CeEcCcc
Confidence 599998888773399999998 9998877
No 59
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=59.70 E-value=3.1 Score=51.79 Aligned_cols=86 Identities=21% Similarity=0.382 Sum_probs=46.1
Q ss_pred ccccccccceeccCCccccCCCCceecCCCeeeeecCCccceEEccccccccCCCeeeecCchhHHHHHHHhhcCCCCcc
Q 000333 898 SCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEE 977 (1650)
Q Consensus 898 ~C~~C~~~~l~f~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~~Cf~~~~~~~i~~~~~~~~K~~~~kkkNd~~~~E 977 (1650)
.|..|-+-.-.=.-.-.||.|| .|--....|...--..-.++|-+|.=..- .|.-...-.+.+.--|.
T Consensus 195 ~C~~c~~t~~eN~naiVfCdgC--~i~VHq~CYGI~f~peG~WlCrkCi~~~~--~i~~C~fCps~dGaFkq-------- 262 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDGC--EICVHQSCYGIQFLPEGFWLCRKCIYGEY--QIRCCSFCPSSDGAFKQ-------- 262 (669)
T ss_pred hhHhccccccCCcceEEEecCc--chhhhhhcccceecCcchhhhhhhccccc--ceeEEEeccCCCCceee--------
Confidence 5666655433333455688876 57777778876532223688999865321 11100000000000000
Q ss_pred cceeccccccccccccccccccc
Q 000333 978 WWVQCDKCEAWQHQICALFNGRR 1000 (1650)
Q Consensus 978 ~~v~C~~C~r~~HqiCaLfn~~~ 1000 (1650)
..=|||-|-|||+|++..
T Consensus 263 -----T~dgrW~H~iCA~~~pel 280 (669)
T COG5141 263 -----TSDGRWGHVICAMFNPEL 280 (669)
T ss_pred -----ccCCchHhHhHHHhcchh
Confidence 123899999999999755
No 60
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=57.62 E-value=6.4 Score=47.38 Aligned_cols=45 Identities=22% Similarity=0.637 Sum_probs=37.2
Q ss_pred HhhcCCCCCcccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1463 YHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1463 yhLHn~~~~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
+-|-+.+...--+.|+.|..+-..|.||+|.-|-.|.||+.|+-+
T Consensus 229 hrla~v~nv~hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwr 273 (434)
T KOG4301|consen 229 HRLATVENVFHPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWR 273 (434)
T ss_pred HHHHhhcccCCCccCcceecccccchhhhHhhcCCccccchhhcc
Confidence 334455444445789999999999999999999999999999977
No 61
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=51.82 E-value=7.5 Score=50.82 Aligned_cols=37 Identities=27% Similarity=0.530 Sum_probs=33.9
Q ss_pred cccCcccccccccCceeeeeccccccccccchhhhhHHHhh
Q 000333 1350 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1390 (1650)
Q Consensus 1350 q~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~~ 1390 (1650)
+.+|..|++.-+.|.||.|..| .|+.||..||...-.
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~----fn~dlCq~CF~sgra 639 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKH----FNYDICQSCFFSGRA 639 (966)
T ss_pred hhhcchhhhCccceeeeeehhh----cChhHHhhHhhhccc
Confidence 5699999999999999999999 999999999987654
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.27 E-value=15 Score=34.27 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=20.5
Q ss_pred ccccCCCCceecCCCeeeeecCCccceEEccccccc
Q 000333 913 PIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 948 (1650)
Q Consensus 913 ~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~~Cf~~ 948 (1650)
+-.|..|+..|.+++.|= ...|..|=++
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 678999999998887762 3568777543
No 63
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=45.51 E-value=11 Score=46.79 Aligned_cols=46 Identities=26% Similarity=0.728 Sum_probs=35.8
Q ss_pred cccCcccccccccCceeeeeccccccccccchhhhhHHHhhc-ccccCCCC
Q 000333 1350 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKR-EDRERHPV 1399 (1650)
Q Consensus 1350 q~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~~~-~~~~~hp~ 1399 (1650)
.+.|.-|...|-.-.|.+|.+| .+|.||-.|+...... +.+..||=
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 3679999998877778999999 9999999999886532 23334553
No 64
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=39.94 E-value=12 Score=47.56 Aligned_cols=39 Identities=33% Similarity=0.714 Sum_probs=32.2
Q ss_pred cccceecccccccccccccccccccCCCCCCcccCCCCchhh
Q 000333 976 EEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITE 1017 (1650)
Q Consensus 976 ~E~~v~C~~C~r~~HqiCaLfn~~~~~~~~~~f~C~~C~~~~ 1017 (1650)
..-.++|+.|++|.|.+|..+.+... ...|.|..|....
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 56789999999999999998876542 3579999998753
No 65
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=38.25 E-value=12 Score=33.54 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=15.1
Q ss_pred ccceecccccccccccccccccccCCCCCCcccCCC
Q 000333 977 EWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPN 1012 (1650)
Q Consensus 977 E~~v~C~~C~r~~HqiCaLfn~~~~~~~~~~f~C~~ 1012 (1650)
+-||||+.|++|=.-. .-+...+... ...|.|..
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 3599999999997655 3333322112 23788844
No 66
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=36.93 E-value=28 Score=43.32 Aligned_cols=33 Identities=27% Similarity=0.679 Sum_probs=27.7
Q ss_pred EEEe-CCCCCCCCeeeccCCCCCCCCChhHHHHHHHH
Q 000333 1197 YIWA-CPPLKGEDYILYCHPEIQKTPKSDKLREWYLA 1232 (1650)
Q Consensus 1197 hiWA-cPP~~GdDYIF~~HP~~Qk~p~~~~L~~WY~~ 1232 (1650)
.=|| |||.+-+ ||.-|..++.++..+|++||..
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 5888766 7788999999999999999973
No 67
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=36.06 E-value=22 Score=49.22 Aligned_cols=89 Identities=12% Similarity=0.337 Sum_probs=52.0
Q ss_pred CCcccccccccceeccCCccccCCCCceecCCCeeeeecCCccceEEccccccccCCCeeeecCchhHHHHHHHhhcCCC
Q 000333 895 SENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEE 974 (1650)
Q Consensus 895 ~~~~C~~C~~~~l~f~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~~Cf~~~~~~~i~~~~~~~~K~~~~kkkNd~~ 974 (1650)
....|.+|...+-.=.-.-+||.+| .|.-+...|..+-.-.-.+.|-.|--.-.+. |. +.-.-+.+-
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~C--nl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~-v~----------c~~cp~~~g 284 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGC--NLAVHQECYGIPFIPEGQWLCRRCLQSPQRP-VR----------CLLCPSKGG 284 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCC--cchhhhhccCCCCCCCCcEeehhhccCcCcc-cc----------eEeccCCCC
Confidence 4457888987766666677899976 4667777777432222368899997654321 10 000000000
Q ss_pred Ccccceeccccccccccccccccccc
Q 000333 975 TEEWWVQCDKCEAWQHQICALFNGRR 1000 (1650)
Q Consensus 975 ~~E~~v~C~~C~r~~HqiCaLfn~~~ 1000 (1650)
+.+. ..=|+|.|.+||++.+..
T Consensus 285 AFkq----t~dgrw~Hv~caiwipev 306 (1051)
T KOG0955|consen 285 AFKQ----TDDGRWAHVVCAIWIPEV 306 (1051)
T ss_pred ccee----ccCCceeeeehhhccccc
Confidence 0000 012899999999998765
No 68
>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=35.89 E-value=27 Score=31.02 Aligned_cols=39 Identities=23% Similarity=0.675 Sum_probs=31.1
Q ss_pred cceeccCCccccCCCCceecCCCeeeeecCCccceEEccccccc
Q 000333 905 EKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 948 (1650)
Q Consensus 905 ~~l~f~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~~Cf~~ 948 (1650)
....|.+.=+.|..|+..|..+. ||...+ ..||..||.+
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 69
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=35.81 E-value=7.2 Score=32.81 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=16.9
Q ss_pred cceecccccccccccccccccccCCCCCCcccCCCC
Q 000333 978 WWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNC 1013 (1650)
Q Consensus 978 ~~v~C~~C~r~~HqiCaLfn~~~~~~~~~~f~C~~C 1013 (1650)
+++.|+.|+-.+|+.|.=..... ....+.|..|
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~~~~---~~~~W~C~~C 35 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVSEVP---DGDDWLCDRC 35 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-SS-----SS-----HHH
T ss_pred ceEEeCCCCCcCChhhCCcccCC---CCCcEECCcC
Confidence 68999999999999997543322 1235888766
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=34.76 E-value=24 Score=44.41 Aligned_cols=41 Identities=29% Similarity=0.677 Sum_probs=31.5
Q ss_pred CcccceecccccccccccccccccccC-----CC----CCCcccCCCCch
Q 000333 975 TEEWWVQCDKCEAWQHQICALFNGRRN-----DG----GQAEYTCPNCYI 1015 (1650)
Q Consensus 975 ~~E~~v~C~~C~r~~HqiCaLfn~~~~-----~~----~~~~f~C~~C~~ 1015 (1650)
..=-||.|+.|+-|-|--|||-...+- .| -+..|.|..|..
T Consensus 142 n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~ 191 (446)
T PF07227_consen 142 NTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGK 191 (446)
T ss_pred CCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCC
Confidence 445799999999999999999765431 11 145899999975
No 71
>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12 []. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1 []. ; PDB: 2FO1_D.
Probab=34.14 E-value=13 Score=44.85 Aligned_cols=9 Identities=67% Similarity=0.815 Sum_probs=0.0
Q ss_pred chhhhhhcc
Q 000333 383 QSQQQHLLN 391 (1650)
Q Consensus 383 Q~qqq~~l~ 391 (1650)
|.+||+.++
T Consensus 375 Q~qQq~qmn 383 (468)
T PF11498_consen 375 QQQQQHQMN 383 (468)
T ss_dssp ---------
T ss_pred hhhhhhhcc
Confidence 334444554
No 72
>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=31.29 E-value=1.9e+02 Score=33.18 Aligned_cols=54 Identities=17% Similarity=0.100 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhcCCcEEEEEeCC-CCC--CCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcCeEe
Q 000333 1180 ILIGYLEYCKLRGFTSCYIWACP-PLK--GEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKENIVV 1244 (1650)
Q Consensus 1180 ILi~Yl~y~k~~GF~~ahiWAcP-P~~--GdDYIF~~HP~~Qk~p~~~~L~~WY~~mL~ka~~egiV~ 1244 (1650)
+...+|+.++..||.++.|+... ... ..+| .-.+...+.+.++|+.|.+.||.+
T Consensus 22 ~~~~~~~~~~~~G~n~VRi~v~~~~~~~~~~~~-----------~~~~~~~~~ld~~v~~a~~~gi~v 78 (281)
T PF00150_consen 22 ITEADFDQLKALGFNTVRIPVGWEAYQEPNPGY-----------NYDETYLARLDRIVDAAQAYGIYV 78 (281)
T ss_dssp SHHHHHHHHHHTTESEEEEEEESTSTSTTSTTT-----------SBTHHHHHHHHHHHHHHHHTT-EE
T ss_pred CHHHHHHHHHHCCCCEEEeCCCHHHhcCCCCCc-----------cccHHHHHHHHHHHHHHHhCCCeE
Confidence 45689999999999999999984 111 1122 223456677899999999999877
No 73
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=29.67 E-value=39 Score=42.29 Aligned_cols=115 Identities=20% Similarity=0.423 Sum_probs=0.0
Q ss_pred ccceeEeeccccCcccccccccCc-------------eeeeecccc--cccccc------chhhhhHHHhh---------
Q 000333 1341 KEDFIMVHLQHACNHCCILMVSGS-------------RHVCEQCTK--LNKNFQ------LCDKCFEAEKK--------- 1390 (1650)
Q Consensus 1341 Ke~f~v~~Lq~~C~~C~~~iv~~~-------------rw~c~~c~~--~~k~f~------lC~~Cy~~e~~--------- 1390 (1650)
+|++|. .|.+|++-|+... -|+|.+|.+ .++.|+ +||.||..-..
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 ------cccccCCCCCccccccc----cccccCCCCCCCCCCCccccCcccccHHHHHHHhhhCCCCcchhhhcccchhh
Q 000333 1391 ------REDRERHPVNSREVHIL----EEVPVTDVPADTKDKDEILESEFFDTRQAFLSLCQGNHYQYDTLRRAKHSSMM 1460 (1650)
Q Consensus 1391 ------~~~~~~hp~~~~~~h~l----~~~~v~~vp~~t~D~D~~i~seffdtR~~FL~lcq~nHyQFDsLRRAKhSSMM 1460 (1650)
.-.+.+|| +.| ..--+++||. |-|-+-.+-|=
T Consensus 345 ~d~iLrA~GkayHp------~CF~Cv~C~r~ldgipF-tvd~~n~v~Cv------------------------------- 386 (468)
T KOG1701|consen 345 MDRILRALGKAYHP------GCFTCVVCARCLDGIPF-TVDSQNNVYCV------------------------------- 386 (468)
T ss_pred HHHHHHhcccccCC------CceEEEEeccccCCccc-cccCCCceeee-------------------------------
Q ss_pred HHHhhcCCCCCcccccccccccCCCCCCceecc-----CCCCCccchhhhc
Q 000333 1461 VLYHLHNPTAPAFVTTCNICHLDIETGQGWRCE-----VCPDYDVCNACYQ 1506 (1650)
Q Consensus 1461 vLyhLHn~~~~~f~~tCn~C~~~I~t~~rwhC~-----vC~DfDLC~~Cy~ 1506 (1650)
.---++|.-.|+.|...|.. +-=|+ ||-|-|.-.+||+
T Consensus 387 ------~dfh~kfAPrCs~C~~PI~P--~~G~~etvRvvamdr~fHv~CY~ 429 (468)
T KOG1701|consen 387 ------PDFHKKFAPRCSVCGNPILP--RDGKDETVRVVAMDRDFHVNCYK 429 (468)
T ss_pred ------hhhhhhcCcchhhccCCccC--CCCCcceEEEEEcccccccccee
No 74
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=28.66 E-value=76 Score=36.36 Aligned_cols=72 Identities=24% Similarity=0.224 Sum_probs=40.1
Q ss_pred CCCCCccccc----cCCCCCcccCCccccccceeccCCCCCCCcccccccCCCCCccccccCCCCCcccCCCCCCCCCCC
Q 000333 199 GMRSGLQHKS----YGFSNGALNGGLGMIGNNLLINEPGTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADS 274 (1650)
Q Consensus 199 gm~sg~q~~s----~g~s~~s~nggmg~~g~~~min~pg~s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~ 274 (1650)
-||+|+.-++ .|-|..+.||||-.--...||+.-|+.++-.. -+--|.++|++|.-|- ..|.|.-..+
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 4777777654 55666677788664322226666665543222 2344678888777432 3454544444
Q ss_pred CCCc
Q 000333 275 YGTG 278 (1650)
Q Consensus 275 ~g~~ 278 (1650)
+.+-
T Consensus 236 ~~s~ 239 (272)
T KOG4552|consen 236 SSSP 239 (272)
T ss_pred CCCC
Confidence 4443
No 75
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=27.77 E-value=20 Score=43.47 Aligned_cols=46 Identities=39% Similarity=0.871 Sum_probs=36.0
Q ss_pred HHHHHhhhccccCccceeEeeccccCcccccccccCceeeeeccccccccccchhhhh
Q 000333 1328 LLMHKLGETICPMKEDFIMVHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCF 1385 (1650)
Q Consensus 1328 ~lm~kl~~~i~~~Ke~f~v~~Lq~~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy 1385 (1650)
.||++|+. + |. |. ---.|++|...-+-|.|+.|..| -++++|..|+
T Consensus 226 pLmhrla~-v----~n--v~-hpv~cs~c~srs~~gfry~cq~C----~nyqlcq~cf 271 (434)
T KOG4301|consen 226 PLMHRLAT-V----EN--VF-HPVECSYCRSRSMMGFRYRCQQC----HNYQLCQQCF 271 (434)
T ss_pred HHHHHHHh-h----cc--cC-CCccCcceecccccchhhhHhhc----CCccccchhh
Confidence 58888842 2 22 11 12479999999999999999999 9999999995
No 76
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=27.35 E-value=28 Score=41.47 Aligned_cols=35 Identities=26% Similarity=0.802 Sum_probs=26.1
Q ss_pred cceeccc--cc-ccccccccccccccCCCCCCcccCCCCchh
Q 000333 978 WWVQCDK--CE-AWQHQICALFNGRRNDGGQAEYTCPNCYIT 1016 (1650)
Q Consensus 978 ~~v~C~~--C~-r~~HqiCaLfn~~~~~~~~~~f~C~~C~~~ 1016 (1650)
++|.||- |. .|||-.|+=.... + .....|+.|...
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 4688887 99 9999999954422 1 234899999865
No 77
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.47 E-value=34 Score=40.75 Aligned_cols=36 Identities=22% Similarity=0.501 Sum_probs=23.4
Q ss_pred eecccccccccccccccccccCCCCCCcccCCCCch
Q 000333 980 VQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYI 1015 (1650)
Q Consensus 980 v~C~~C~r~~HqiCaLfn~~~~~~~~~~f~C~~C~~ 1015 (1650)
-+|..||+.|++-=-|---.|...||++|.|+.|.+
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~k 223 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGK 223 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccc
Confidence 567777777766555543334455677888888865
No 78
>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=25.75 E-value=41 Score=29.91 Aligned_cols=33 Identities=21% Similarity=0.507 Sum_probs=27.4
Q ss_pred cCcccccccccCceeeeeccccccccccchhhhhHHHh
Q 000333 1352 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1389 (1650)
Q Consensus 1352 ~C~~C~~~iv~~~rw~c~~c~~~~k~f~lC~~Cy~~e~ 1389 (1650)
.|..|..... ..|+.|..+ +++.||..||....
T Consensus 2 ~C~~Cg~D~t-~vryh~~~~----~~~dLC~~CF~~G~ 34 (45)
T cd02336 2 HCFTCGNDCT-RVRYHNLKA----KKYDLCPSCYQEGR 34 (45)
T ss_pred cccCCCCccC-ceEEEecCC----CccccChHHHhCcC
Confidence 5888888875 589999988 89999999997643
No 79
>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=23.46 E-value=89 Score=34.63 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=33.2
Q ss_pred CCCCCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcC
Q 000333 1203 PLKGEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKEN 1241 (1650)
Q Consensus 1203 P~~GdDYIF~~HP~~Qk~p~~~~L~~WY~~mL~ka~~eg 1241 (1650)
+.+|+||+|.+||.....++.++|..=..=+|+.|++.+
T Consensus 110 s~kG~~~~~~~~mp~~~~LsdeEL~aIAaYLl~qa~~~~ 148 (155)
T TIGR03046 110 SYDGSEESYGCRPVPEDWMDDEEVENLAAFILRAAQKAP 148 (155)
T ss_pred ccCcccccccccCCcccCCCHHHHHHHHHHHHHhhhhcC
Confidence 568999999999999999999999877777777776654
No 80
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=23.43 E-value=34 Score=41.70 Aligned_cols=28 Identities=21% Similarity=0.565 Sum_probs=22.3
Q ss_pred CCcccccccccccCCCCCCceeccCCCCC
Q 000333 1470 APAFVTTCNICHLDIETGQGWRCEVCPDY 1498 (1650)
Q Consensus 1470 ~~~f~~tCn~C~~~I~t~~rwhC~vC~Df 1498 (1650)
...+.|.|.+|.=..-+ -.|||..|-.+
T Consensus 350 ~~~~~YRC~~CGF~a~~-l~W~CPsC~~W 377 (389)
T COG2956 350 RRKPRYRCQNCGFTAHT-LYWHCPSCRAW 377 (389)
T ss_pred hhcCCceecccCCccee-eeeeCCCcccc
Confidence 34678999999987776 58999999554
No 81
>KOG4592 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.97 E-value=1.6e+02 Score=38.72 Aligned_cols=41 Identities=17% Similarity=0.245 Sum_probs=21.4
Q ss_pred CCCCCcccccccCCCCCccccccCCCCCcccCCCCCCCCCCCCCC
Q 000333 233 GTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADSYGT 277 (1650)
Q Consensus 233 g~s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~~g~ 277 (1650)
|..-.|.|..+-+.|..|- +++ .+..+-+.||.+++..+.+
T Consensus 49 g~dfDF~np~ssass~~~~--~~N--~~~~~ar~i~~a~~El~~~ 89 (728)
T KOG4592|consen 49 GGDFDFANPLSSASSSSPA--PLN--APFRQARHIGDADLELNIS 89 (728)
T ss_pred cCCccCCCccccCccCCCC--CcC--ccccccccccccccccccc
Confidence 3333566665555554422 222 2344556677777766665
No 82
>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=22.29 E-value=28 Score=41.76 Aligned_cols=60 Identities=13% Similarity=0.019 Sum_probs=44.0
Q ss_pred eEEEEEEEEeCCeEEEEEEEEeeecCCCCCCCCCceEEEEecccccccccccccccccchhHHHHHHHHHHHHHHHHhcC
Q 000333 1113 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1192 (1650)
Q Consensus 1113 sK~I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~g~~~Rt~VYheILi~Yl~y~k~~G 1192 (1650)
.=+|.-|=+|+|..|.++++--.-+|- .+ +.+..|=+...+++|-+.|
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 468999999999999988884333321 11 2355666778899999999
Q ss_pred CcEEEEEeCCCC
Q 000333 1193 FTSCYIWACPPL 1204 (1650)
Q Consensus 1193 F~~ahiWAcPP~ 1204 (1650)
.=-+.|.+.+=.
T Consensus 156 lPlV~l~dSgGa 167 (285)
T TIGR00515 156 CPLIIFSASGGA 167 (285)
T ss_pred CCEEEEEcCCCc
Confidence 999999887753
No 83
>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=22.27 E-value=6.6 Score=42.31 Aligned_cols=26 Identities=27% Similarity=0.772 Sum_probs=21.1
Q ss_pred CcccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000333 1471 PAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1507 (1650)
Q Consensus 1471 ~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~Cy~k 1507 (1650)
+...+.|-.|...|.+| -+|.+|..+
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 35579999999999997 367888866
No 84
>smart00642 Aamy Alpha-amylase domain.
Probab=21.32 E-value=2.3e+02 Score=31.35 Aligned_cols=65 Identities=23% Similarity=0.228 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcCCcEEEEEeCCCCCCCC---eeeccCCCCCCCCChh-HHHHHHHHHHHHHHhcCeEeecc
Q 000333 1181 LIGYLEYCKLRGFTSCYIWACPPLKGED---YILYCHPEIQKTPKSD-KLREWYLAMLRKAAKENIVVDLT 1247 (1650)
Q Consensus 1181 Li~Yl~y~k~~GF~~ahiWAcPP~~GdD---YIF~~HP~~Qk~p~~~-~L~~WY~~mL~ka~~egiV~~~~ 1247 (1650)
|+.-|+|.+.+||+. ||..|+.+... .-..-.|.+-..+++. .=.+=+++|+++|.+.||-+=+.
T Consensus 21 i~~~l~yl~~lG~~~--I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vilD 89 (166)
T smart00642 21 IIEKLDYLKDLGVTA--IWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVILD 89 (166)
T ss_pred HHHHHHHHHHCCCCE--EEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEEE
Confidence 567789999999986 56688865432 1011122222222210 01355788999999998765433
Done!