Query 000262
Match_columns 1768
No_of_seqs 312 out of 370
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 01:48:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000262.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000262hhsearch_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 1.1E-56 2.3E-61 518.2 12.0 317 1389-1762 1-317 (319)
2 PF08214 KAT11: Histone acetyl 100.0 5.7E-55 1.2E-59 513.5 15.9 279 1189-1477 8-344 (346)
3 smart00551 ZnF_TAZ TAZ zinc fi 99.7 2.4E-17 5.1E-22 157.7 7.8 74 1654-1731 2-79 (79)
4 smart00551 ZnF_TAZ TAZ zinc fi 99.7 8.8E-17 1.9E-21 153.8 5.3 77 701-777 3-79 (79)
5 PF02135 zf-TAZ: TAZ zinc fing 99.4 6E-14 1.3E-18 133.1 1.6 73 704-776 2-75 (75)
6 PF02135 zf-TAZ: TAZ zinc fing 99.3 1.1E-12 2.4E-17 124.5 3.4 69 1658-1730 2-75 (75)
7 cd02337 ZZ_CBP Zinc finger, ZZ 98.9 7.8E-10 1.7E-14 94.0 2.6 41 1593-1638 1-41 (41)
8 PF00569 ZZ: Zinc finger, ZZ t 98.8 1.4E-09 3.1E-14 94.6 1.2 44 1591-1635 3-46 (46)
9 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.6 4E-08 8.6E-13 86.4 3.1 46 1593-1638 1-48 (48)
10 smart00291 ZnF_ZZ Zinc-binding 98.5 1.1E-07 2.3E-12 82.2 3.4 42 1590-1633 2-43 (44)
11 cd02344 ZZ_HERC2 Zinc finger, 98.4 1.2E-07 2.7E-12 82.2 3.1 43 1593-1636 1-43 (45)
12 cd02340 ZZ_NBR1_like Zinc fing 98.4 1.4E-07 3.1E-12 81.1 3.0 42 1593-1637 1-42 (43)
13 cd02345 ZZ_dah Zinc finger, ZZ 98.3 2.6E-07 5.7E-12 81.6 3.0 42 1594-1636 2-47 (49)
14 cd02339 ZZ_Mind_bomb Zinc fing 98.3 3.3E-07 7.1E-12 79.7 3.2 42 1594-1636 2-43 (45)
15 cd02249 ZZ Zinc finger, ZZ typ 98.3 5.1E-07 1.1E-11 78.7 3.1 42 1593-1636 1-44 (46)
16 cd02335 ZZ_ADA2 Zinc finger, Z 98.3 5.9E-07 1.3E-11 79.4 3.3 33 1593-1625 1-33 (49)
17 cd02334 ZZ_dystrophin Zinc fin 98.2 8.4E-07 1.8E-11 78.5 3.0 33 1593-1625 1-33 (49)
18 cd02338 ZZ_PCMF_like Zinc fing 98.1 2.1E-06 4.5E-11 76.0 2.6 33 1593-1625 1-33 (49)
19 PF06001 DUF902: Domain of Unk 98.1 8.7E-07 1.9E-11 74.8 0.0 35 1017-1051 6-41 (42)
20 cd02342 ZZ_UBA_plant Zinc fing 98.0 2.1E-06 4.6E-11 73.4 2.2 35 1593-1627 1-35 (43)
21 cd02343 ZZ_EF Zinc finger, ZZ 98.0 4E-06 8.8E-11 73.7 3.3 42 1594-1636 2-46 (48)
22 KOG4582 Uncharacterized conser 97.6 3E-05 6.5E-10 91.1 2.9 45 1592-1637 152-196 (278)
23 cd02336 ZZ_RSC8 Zinc finger, Z 96.9 0.00056 1.2E-08 59.9 2.6 37 1593-1631 1-37 (45)
24 KOG1280 Uncharacterized conser 96.8 0.00053 1.2E-08 80.8 1.7 47 1591-1637 7-56 (381)
25 PF00569 ZZ: Zinc finger, ZZ t 96.4 0.002 4.4E-08 56.5 2.2 38 1465-1506 1-38 (46)
26 cd02334 ZZ_dystrophin Zinc fin 96.1 0.0028 6E-08 56.6 1.8 34 1470-1507 2-35 (49)
27 cd02342 ZZ_UBA_plant Zinc fing 96.1 0.0028 6.2E-08 54.8 1.7 35 1470-1508 2-36 (43)
28 cd02344 ZZ_HERC2 Zinc finger, 96.1 0.0029 6.4E-08 55.5 1.8 32 1470-1505 2-33 (45)
29 cd02338 ZZ_PCMF_like Zinc fing 96.1 0.0031 6.7E-08 56.1 1.8 34 1470-1507 2-35 (49)
30 KOG0457 Histone acetyltransfer 96.0 0.0028 6E-08 77.2 1.6 35 1591-1625 13-47 (438)
31 cd02339 ZZ_Mind_bomb Zinc fing 95.8 0.0056 1.2E-07 53.7 2.1 32 1470-1505 2-33 (45)
32 cd02249 ZZ Zinc finger, ZZ typ 95.5 0.0077 1.7E-07 52.8 1.9 34 1469-1507 1-34 (46)
33 KOG4286 Dystrophin-like protei 95.5 0.0056 1.2E-07 77.9 1.3 49 1590-1638 601-652 (966)
34 cd02341 ZZ_ZZZ3 Zinc finger, Z 95.4 0.0077 1.7E-07 53.6 1.8 35 1469-1507 1-37 (48)
35 cd02345 ZZ_dah Zinc finger, ZZ 95.4 0.0082 1.8E-07 53.5 1.7 33 1470-1506 2-34 (49)
36 PF02172 KIX: KIX domain; Int 95.2 0.05 1.1E-06 53.5 6.8 55 67-121 12-67 (81)
37 cd02335 ZZ_ADA2 Zinc finger, Z 95.2 0.011 2.4E-07 52.6 2.0 34 1469-1506 1-34 (49)
38 cd02340 ZZ_NBR1_like Zinc fing 94.9 0.014 3E-07 50.9 1.6 32 1470-1506 2-33 (43)
39 COG5087 RTT109 Uncharacterized 94.7 0.43 9.2E-06 55.7 13.4 127 1212-1355 25-156 (349)
40 KOG4534 Uncharacterized conser 94.7 0.43 9.2E-06 55.7 13.4 127 1212-1355 25-156 (349)
41 PF00628 PHD: PHD-finger; Int 94.6 0.005 1.1E-07 54.4 -1.8 41 1092-1132 9-49 (51)
42 smart00291 ZnF_ZZ Zinc-binding 94.5 0.02 4.2E-07 49.9 1.7 34 1468-1506 4-37 (44)
43 KOG0956 PHD finger protein AF1 94.0 0.018 3.9E-07 72.9 0.7 88 1017-1118 8-95 (900)
44 COG5114 Histone acetyltransfer 94.0 0.021 4.6E-07 66.9 1.1 34 1592-1625 5-38 (432)
45 cd02337 ZZ_CBP Zinc finger, ZZ 94.0 0.023 5.1E-07 49.0 1.0 32 1469-1506 1-32 (41)
46 cd02343 ZZ_EF Zinc finger, ZZ 93.7 0.04 8.8E-07 49.1 2.0 34 1470-1508 2-35 (48)
47 smart00249 PHD PHD zinc finger 93.5 0.053 1.1E-06 45.9 2.4 38 1093-1131 10-47 (47)
48 KOG4582 Uncharacterized conser 93.4 0.037 8E-07 65.6 1.8 34 1469-1506 153-186 (278)
49 KOG1280 Uncharacterized conser 92.1 0.14 3.1E-06 61.2 4.3 88 1468-1564 8-104 (381)
50 KOG3598 Thyroid hormone recept 90.2 0.1 2.3E-06 70.3 0.8 8 151-158 1845-1852(2220)
51 PF07649 C1_3: C1-like domain; 86.8 0.31 6.7E-06 39.2 1.1 28 1594-1622 2-29 (30)
52 KOG4274 Positive cofactor 2 (P 82.7 3.3 7.2E-05 52.7 7.7 57 68-136 10-66 (742)
53 KOG1778 CREB binding protein/P 79.5 1.8 3.8E-05 52.7 4.0 65 722-788 231-299 (319)
54 KOG3598 Thyroid hormone recept 79.4 0.94 2E-05 61.9 1.8 9 415-423 2067-2075(2220)
55 PF07227 DUF1423: Protein of u 78.9 1.7 3.7E-05 54.4 3.6 42 1093-1134 142-192 (446)
56 PF09606 Med15: ARC105 or Med1 68.4 3.5 7.7E-05 55.4 3.0 53 73-134 3-56 (799)
57 KOG4369 RTK signaling protein 67.6 6.5 0.00014 53.5 5.0 26 150-175 1400-1425(2131)
58 KOG4369 RTK signaling protein 67.6 6.1 0.00013 53.7 4.7 32 345-376 1742-1774(2131)
59 KOG4323 Polycomb-like PHD Zn-f 67.0 1.9 4E-05 54.5 0.1 38 1096-1133 184-223 (464)
60 KOG0957 PHD finger protein [Ge 62.6 3.2 7E-05 52.0 0.9 89 1014-1120 119-217 (707)
61 PF03107 C1_2: C1 domain; Int 62.0 4.9 0.00011 32.6 1.6 28 1594-1622 2-29 (30)
62 KOG4786 Ubinuclein, nuclear pr 61.5 64 0.0014 42.7 11.7 64 327-397 972-1041(1136)
63 COG5141 PHD zinc finger-contai 61.0 2.9 6.2E-05 52.4 0.1 87 1015-1118 194-280 (669)
64 KOG4301 Beta-dystrobrevin [Cyt 59.3 5.8 0.00013 48.0 2.2 45 1581-1625 229-273 (434)
65 COG2888 Predicted Zn-ribbon RN 56.9 9 0.0002 36.0 2.5 28 1031-1066 9-36 (61)
66 KOG4286 Dystrophin-like protei 47.5 9.4 0.0002 50.3 1.5 39 1468-1510 603-641 (966)
67 KOG0457 Histone acetyltransfer 40.0 16 0.00034 45.9 1.8 37 1468-1508 14-50 (438)
68 KOG1844 PHD Zn-finger proteins 39.5 14 0.00031 47.3 1.5 39 1094-1135 98-136 (508)
69 KOG0955 PHD finger protein BR1 36.3 21 0.00046 49.6 2.3 76 1014-1118 219-306 (1051)
70 PF07496 zf-CW: CW-type Zinc F 35.9 14 0.0003 33.5 0.3 34 1095-1130 1-34 (50)
71 PF00412 LIM: LIM domain; Int 32.9 32 0.0007 30.9 2.2 39 1023-1066 18-56 (58)
72 PF13831 PHD_2: PHD-finger; PD 31.9 9.2 0.0002 32.5 -1.3 33 1096-1131 3-35 (36)
73 KOG4592 Uncharacterized conser 30.2 1.4E+02 0.0031 39.3 7.8 42 350-395 48-89 (728)
74 KOG0336 ATP-dependent RNA heli 29.1 43 0.00094 42.0 3.1 33 1315-1350 164-197 (629)
75 KOG2462 C2H2-type Zn-finger pr 27.4 32 0.00069 41.2 1.5 37 1098-1134 188-224 (279)
76 KOG1973 Chromatin remodeling p 26.7 30 0.00064 41.6 1.2 35 1096-1134 231-268 (274)
77 KOG4301 Beta-dystrobrevin [Cyt 25.8 23 0.00049 43.3 -0.0 47 1446-1504 226-272 (434)
78 KOG4552 Vitamin-D-receptor int 25.7 92 0.002 36.0 4.6 71 317-395 164-238 (272)
79 TIGR00515 accD acetyl-CoA carb 25.6 23 0.0005 42.8 0.0 60 1231-1322 108-167 (285)
80 PF07500 TFIIS_M: Transcriptio 24.5 1.2E+02 0.0027 31.6 5.1 50 68-120 4-54 (115)
81 PF11498 Activator_LAG-3: Tran 23.3 27 0.00059 42.7 0.0 16 122-137 75-90 (468)
82 cd02336 ZZ_RSC8 Zinc finger, Z 22.3 53 0.0012 29.5 1.6 33 1470-1507 2-34 (45)
83 KOG1701 Focal adhesion adaptor 22.2 29 0.00062 43.6 -0.1 121 1459-1624 270-429 (468)
84 CHL00174 accD acetyl-CoA carbo 22.1 31 0.00067 42.0 0.1 58 1231-1320 121-178 (296)
85 TIGR03046 PS_II_psbV2 photosys 21.6 1E+02 0.0022 34.5 3.9 39 1321-1359 110-148 (155)
86 COG2956 Predicted N-acetylgluc 21.3 41 0.00089 41.4 0.9 28 1588-1616 350-377 (389)
87 TIGR03826 YvyF flagellar opero 21.0 7.2 0.00016 42.3 -4.8 26 1589-1625 78-103 (137)
No 1
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=100.00 E-value=1.1e-56 Score=518.22 Aligned_cols=317 Identities=38% Similarity=0.670 Sum_probs=278.6
Q ss_pred cccCCCccHHHHHHHHHHHhhcccccccccccchhhhHHHHHhcCCCCCCCCcchhHHHHHHhhhccccCccceeeeecc
Q 000262 1389 YFDGDYWPGAAEDLIYQIRQDEDGKKQNKGITKKTITKRALKASGQTDLSGNASKDLLLMHKLGETICPMKEDFIMVHLQ 1468 (1768)
Q Consensus 1389 yF~gd~Wp~~~E~ii~~l~~e~~~~k~~k~~~kk~~~kr~~k~~g~~~~~~~~~kd~~lm~klg~~i~~~Ke~F~v~~Lq 1468 (1768)
||+||+ +||.|..+.++- ++-.++ .| .+...++.++...|+++ +|.+++++|++++++
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 466666 777777766551 111111 14 44556677888999999 899999999999999
Q ss_pred ccccccccccccCceeeeecccccccccccchhhhHHHhhcccccCCCCCccccccccccccCCCCCCCCCCCccccCcc
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKREDRERHPVNSREVHILEEVPVTDVPADTKDKDEILESEF 1548 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~~~~~~~hp~~~~~~h~L~~v~v~~vp~~t~D~D~~i~sef 1548 (1768)
+ |++.++.+++|+|..| +++++|++||.+. -+.|+.+.++.|.|.++.+..||..+.|+|++++|++
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 4678999999999999889999999999999999999
Q ss_pred cccHHHHHHHhhhCCCCcchhhhcccchhhHHHhhcCCCCCcccccccccccCCCCCCceeccCCCCCccchhhhccCCC
Q 000262 1549 FDTRQAFLSLCQGNHYQYDTLRRAKHSSMMVLYHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGG 1628 (1768)
Q Consensus 1549 fdtR~aFL~lcq~nHyQFDsLRRAKhSSMMvLyhLHn~~~~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~ 1628 (1768)
||+|++||.||+.+||+|++||||||||||++||||+++.+.|+++|+.|+.++. .+|||++|+|||+|..||.++.
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 CCCCCCCcCCCCCcchhhhhHHHHHHHHHHHHHHHHHHHHhccCCCCCCCChhhHHHHHHHHhhhhcccccCCCChhHHH
Q 000262 1629 IDHPHKLTNHPSTADRDAQNKEARQLRVLQLRKMLDLLVHASQCRSPHCQYPNCRKVKGLFRHGIQCKTRASGGCVLCKK 1708 (1768)
Q Consensus 1629 ~~H~Hkl~~~p~~~~~~~~~~~arq~r~~qL~~~m~~L~HA~~C~~a~C~~~~C~kmK~l~~H~~~C~~R~~ggC~~Ckr 1708 (1768)
|+|+++..++.. ++...+..|+..|.+ ++++|.++.|.+||+||+|++.|+.| |||++|++
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 999999888722 233445556666665 58999999999999999999999999 99999999
Q ss_pred HHHHHHHHHhhcCCCCCCCCCchhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 000262 1709 MWYLLQLHARACKESECHVPRCRDLKEHLRRLQQQSDTRRRQAVMEMMRQRAAE 1762 (1768)
Q Consensus 1709 ~w~Ll~~HAk~C~~~~C~VP~C~~iK~~~~~~q~q~d~rrr~~v~~~~r~r~~~ 1762 (1768)
||+|++|||++|++..|+||+|++||+++++++++.+++|+.+++.+|+.+.+.
T Consensus 264 m~~L~~lha~~c~~~~C~vP~c~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (319)
T KOG1778|consen 264 LWQLLELHARHCDDSKCKVPLCRNLKQKLEKQQKQADERRWKLLVRRVAGTKAD 317 (319)
T ss_pred HHHHHHHHHHHcccccCCCCCCccHHHHHHHHHhhhhhHHHHHHHHHHHhhhcc
Confidence 999999999999999999999999999999999999999988887777776654
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=5.7e-55 Score=513.51 Aligned_cols=279 Identities=43% Similarity=0.702 Sum_probs=220.1
Q ss_pred CCCCCcceEEEEEeccchhhhhhHHHHHhhhhcCCCCcccceeEEEEEEEEeCCeEEEEEEEEEeecCCCCCCCCCceEE
Q 000262 1189 EVPGAEALVIRVVSSVDKKLEVKQRFLEIFQEENYPTEFPYKSKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVY 1268 (1768)
Q Consensus 1189 ev~~a~~l~IRvVss~~k~~~vk~~f~~~f~e~~yp~~f~YrsK~I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vy 1268 (1768)
.+|+++.++||+|++.+++++++..|...|.+..||.+|+|+.|+|+|||++||+|||||+|+||||+..|+.||++|||
T Consensus 8 ~lp~~~~~~ir~v~S~~~~~~~~~~~~~~~~~~~~~~~~~y~~r~~~~fq~~~g~dv~~f~m~v~eY~~~~~~~~~~~v~ 87 (346)
T PF08214_consen 8 VLPKDEEFTIRHVSSPPKKCEVLFSFPPKFAEKGYPPEFTYKSRHFFVFQEIDGVDVLFFAMEVQEYGTICPAPNQRWVY 87 (346)
T ss_dssp CSCTT-EEEEEEEEEEEEEEE--TCHHHCTTTTTS-CCEEEEEEEEEEEEECTTEEEEEEEEEEEEEECCCSTCCCCEEE
T ss_pred hCCCCceEEEEEEEcCCEEccccccCCcccccccCCCCceeEEEEEEEEEEeCCccEEEEEEEEEEecCCCCCCCceEEE
Confidence 48999999999999999999999999999988789999999999999999999999999999999999999999999999
Q ss_pred EEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcCCcEEEEEeCCCCCCCCeeeccCCCCCCCCC-----hhH
Q 000262 1269 LSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIWACPPLKGEDYILYCHPEIQKTPK-----SDK 1343 (1768)
Q Consensus 1269 IsYLDSV~yf~P~~~~~~G~~lRt~VYheIL~~Yl~y~k~~GF~~ahIWAcPP~~GDDYIF~~HP~~Qk~p~-----~~~ 1343 (1768)
|+|||||.||+|. .+||.+||++|++||+|++.+||.++|||||||.+|||||| |..|++|+ .++
T Consensus 88 IsylDSv~y~~~~-------~~r~~~~~~~ll~Yl~~~~~~g~~~~~~~a~~pr~~dqYlF---P~s~k~p~KhvL~~~~ 157 (346)
T PF08214_consen 88 ISYLDSVGYFKPS-------PSRTRVYHEILLSYLDYARPRGYTKAHIWACFPRAGDQYLF---PNSQKNPKKHVLDDDR 157 (346)
T ss_dssp EEEEEE-S--SSG-------GGHHHHHHHHHHHHHHCCHCHCHHCCEEEEEEE-CCS-SSS---TTCGGSTTS----HHH
T ss_pred EEECcccCCCCcc-------cccHHHHHHHHHHHHHHhhccCCcEEEEEEecCCCCCCeEc---CCcccCCccccccchH
Confidence 9999999999995 68999999999999999999999999999999999999999 88888888 999
Q ss_pred HHHHHHHHHHHHH-------hcCeEeechhhhhh--hhccccccc------------cccCccccCcccCCCccHHHHHH
Q 000262 1344 LREWYLAMLRKAA-------KENIVVDLTNLYDH--FFVSTGECR------------AKVTAARLPYFDGDYWPGAAEDL 1402 (1768)
Q Consensus 1344 L~~WY~~mL~kg~-------~egiV~~~~n~yd~--~f~~~~~~~------------~~~~~~~LPyF~gd~Wp~~~E~i 1402 (1768)
|++||.+||++|+ +++||+...++|+. |+....... ....++.||||+||+||+.||++
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 433322100 01267889999999999999999
Q ss_pred HHH-------HHhhcccc--ccc--------------------ccccchhhhHHHHHhcCCC---CCCCCcchhHHHHHH
Q 000262 1403 IYQ-------IRQDEDGK--KQN--------------------KGITKKTITKRALKASGQT---DLSGNASKDLLLMHK 1450 (1768)
Q Consensus 1403 i~~-------l~~e~~~~--k~~--------------------k~~~kk~~~kr~~k~~g~~---~~~~~~~kd~~lm~k 1450 (1768)
+++ |+++.++. ++. +...++...|..+++.+.. +.++.......+|++
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 223344455689999
Q ss_pred hhhccccCccceeeeeccccccccccc
Q 000262 1451 LGETICPMKEDFIMVHLQHACNHCCIL 1477 (1768)
Q Consensus 1451 lg~~i~~~Ke~F~v~~Lq~~C~~C~~~ 1477 (1768)
|+++|+++||+||+|+|+..|++|+..
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=2.4e-17 Score=157.71 Aligned_cols=74 Identities=47% Similarity=1.027 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHHhccCCC--CCCCChhhHHHHHHHHhhhhcccc--cCCCChhHHHHHHHHHHHHhhcCCCCCCCCC
Q 000262 1654 LRVLQLRKMLDLLVHASQCRS--PHCQYPNCRKVKGLFRHGIQCKTR--ASGGCVLCKKMWYLLQLHARACKESECHVPR 1729 (1768)
Q Consensus 1654 ~r~~qL~~~m~~L~HA~~C~~--a~C~~~~C~kmK~l~~H~~~C~~R--~~ggC~~Ckr~w~Ll~~HAk~C~~~~C~VP~ 1729 (1768)
.+|.+|+++|++|+||+.|+. ++|.+++|.+||.||+|++.|+.| ..+||..||+||+ |+++|++.+|+||+
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 467899999999999999976 899999999999999999999999 7899999999999 99999999999999
Q ss_pred ch
Q 000262 1730 CR 1731 (1768)
Q Consensus 1730 C~ 1731 (1768)
|+
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=8.8e-17 Score=153.83 Aligned_cols=77 Identities=52% Similarity=1.032 Sum_probs=74.4
Q ss_pred hHhhhhchhhhhhhccccCCCCCCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchhh
Q 000262 701 QFRNQQRWLLFLRHARRCAAPEGKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVPV 777 (1768)
Q Consensus 701 ~~~~qqrwLl~L~HA~~C~~~~g~C~~~~C~~~k~lL~H~~~C~~~~C~~~~C~ssr~ll~H~k~C~~~~CpvC~PV 777 (1768)
.+..+|+||+||+||.+|..+++.|..++|.+||.||+||.+|+.++|.+++|.++|.||.||+.|++.+||||.||
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 46789999999999999999999999999999999999999999999999999999999999999999999999885
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=99.40 E-value=6e-14 Score=133.12 Aligned_cols=73 Identities=41% Similarity=0.957 Sum_probs=68.9
Q ss_pred hhhchhhhhhhccccCCCC-CCCCCCCchhHHHHHhcccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchh
Q 000262 704 NQQRWLLFLRHARRCAAPE-GKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVP 776 (1768)
Q Consensus 704 ~qqrwLl~L~HA~~C~~~~-g~C~~~~C~~~k~lL~H~~~C~~~~C~~~~C~ssr~ll~H~k~C~~~~CpvC~P 776 (1768)
.+++||+||+||..|..++ +.|..++|..||.||.|+..|..+.|.+++|..+|.||.||+.|++.+|+||.+
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 4789999999999999988 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=99.30 E-value=1.1e-12 Score=124.54 Aligned_cols=69 Identities=49% Similarity=1.058 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHhccCCC---CCCCChhhHHHHHHHHhhhhccccc--CCCChhHHHHHHHHHHHHhhcCCCCCCCCCc
Q 000262 1658 QLRKMLDLLVHASQCRS---PHCQYPNCRKVKGLFRHGIQCKTRA--SGGCVLCKKMWYLLQLHARACKESECHVPRC 1730 (1768)
Q Consensus 1658 qL~~~m~~L~HA~~C~~---a~C~~~~C~kmK~l~~H~~~C~~R~--~ggC~~Ckr~w~Ll~~HAk~C~~~~C~VP~C 1730 (1768)
+|++.|++|.||..|+. +.|.++.|.+||.||.|+..|..+. .++|..||+||. |++.|++.+|+||+|
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 68899999999999998 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=98.89 E-value=7.8e-10 Score=94.00 Aligned_cols=41 Identities=44% Similarity=1.125 Sum_probs=35.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcCC
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTNH 1638 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl~~~ 1638 (1768)
|+||.|...+ +.||||.+|+|||||..||.+ ..|+|+|+++
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 4699999864
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=98.79 E-value=1.4e-09 Score=94.57 Aligned_cols=44 Identities=43% Similarity=0.955 Sum_probs=34.5
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCC
Q 000262 1591 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKL 1635 (1768)
Q Consensus 1591 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl 1635 (1768)
..++|+.|..+...|.||||.+|+|||||.+||.+ |.+.|.|+|
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=98.55 E-value=4e-08 Score=86.38 Aligned_cols=46 Identities=26% Similarity=0.686 Sum_probs=38.4
Q ss_pred ccccccccCCCCCCceeccCCC--CCccchhhhccCCCCCCCCCCcCC
Q 000262 1593 TTCNICHLDIETGQGWRCEVCP--DYDVCNACYQKDGGIDHPHKLTNH 1638 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~--DfDLC~~CY~k~g~~~H~Hkl~~~ 1638 (1768)
|+|+.|..+..+|.||||.+|+ |||||.+||.+...|...|.|.++
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=98.47 E-value=1.1e-07 Score=82.22 Aligned_cols=42 Identities=36% Similarity=0.918 Sum_probs=34.6
Q ss_pred cccccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCC
Q 000262 1590 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPH 1633 (1768)
Q Consensus 1590 ~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~H 1633 (1768)
.+.++|+.|.. ..++.||||.+|+|||||.+||.+ |.+.+.|
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 456789999999999999999988 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=82.20 Aligned_cols=43 Identities=26% Similarity=0.770 Sum_probs=35.5
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCc
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLT 1636 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl~ 1636 (1768)
++|+.|......|.||+|.+|+|||||..||.+.. |.-.|.+.
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 48999999888889999999999999999999833 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=98.42 E-value=1.4e-07 Score=81.14 Aligned_cols=42 Identities=36% Similarity=0.853 Sum_probs=34.8
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcC
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1637 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl~~ 1637 (1768)
++|+.|+..| .|.||+|.+|+|||||.+||.+. +| ..|+|.+
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=98.34 E-value=2.6e-07 Score=81.61 Aligned_cols=42 Identities=36% Similarity=0.890 Sum_probs=33.8
Q ss_pred ccccccc-CCCCCCceeccCCCCCccchhhhccC---CCCCCCCCCc
Q 000262 1594 TCNICHL-DIETGQGWRCEVCPDYDVCNACYQKD---GGIDHPHKLT 1636 (1768)
Q Consensus 1594 tCn~C~~-~I~t~~rwhC~vC~DfDLC~~CY~k~---g~~~H~Hkl~ 1636 (1768)
+|+.|.+ +|. |.||+|.+|+|||||..||.+. ++|.-.|+|.
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=98.33 E-value=3.3e-07 Score=79.70 Aligned_cols=42 Identities=33% Similarity=0.962 Sum_probs=35.8
Q ss_pred cccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCc
Q 000262 1594 TCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLT 1636 (1768)
Q Consensus 1594 tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl~ 1636 (1768)
.|+.|+.....|.||+|.+|+|||||..||.. +.|...|++.
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=98.27 E-value=5.1e-07 Score=78.66 Aligned_cols=42 Identities=38% Similarity=0.909 Sum_probs=34.2
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCC--CCCCc
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDH--PHKLT 1636 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H--~Hkl~ 1636 (1768)
++|+.|..+|. |.||+|.+|+|||||..||.+.. ..| .|.+.
T Consensus 1 ~~C~~C~~~i~-g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~ 44 (46)
T cd02249 1 YSCDGCLKPIV-GVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFT 44 (46)
T ss_pred CCCcCCCCCCc-CCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEe
Confidence 57999999776 58999999999999999999842 344 56654
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=98.26 E-value=5.9e-07 Score=79.37 Aligned_cols=33 Identities=33% Similarity=0.952 Sum_probs=31.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
++|+.|.+++..|.||+|.+|+|||||.+||..
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 589999999999999999999999999999988
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=8.4e-07 Score=78.49 Aligned_cols=33 Identities=39% Similarity=0.933 Sum_probs=30.6
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
++|+.|+.....|.||+|.+|+|||||..||.+
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
>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=98.07 E-value=2.1e-06 Score=76.02 Aligned_cols=33 Identities=36% Similarity=1.002 Sum_probs=28.7
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
.+|+.|......|.||+|.+|+|||||.+||.+
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 19
>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=98.05 E-value=8.7e-07 Score=74.83 Aligned_cols=35 Identities=34% Similarity=0.640 Sum_probs=0.4
Q ss_pred cccccCcceeccCCcccccCC-CceecCCCeeeeec
Q 000262 1017 CQLCAVEKLTFEPPPIYCSPC-GTRIKRNAMYYTMG 1051 (1768)
Q Consensus 1017 C~~C~~~~l~F~p~~l~C~~c-~cRI~r~~~Yy~~~ 1051 (1768)
-++||+++|.|.|++|+|+|. .|.|+||+.||+++
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 379999999999999999986 59999999999985
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=98.05 E-value=2.1e-06 Score=73.37 Aligned_cols=35 Identities=31% Similarity=0.767 Sum_probs=31.8
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCC
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDG 1627 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g 1627 (1768)
.+|..|...-..|.||+|.+|+|||||..||.+-+
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=4e-06 Score=73.71 Aligned_cols=42 Identities=26% Similarity=0.732 Sum_probs=33.1
Q ss_pred cccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCc
Q 000262 1594 TCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLT 1636 (1768)
Q Consensus 1594 tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k---~g~~~H~Hkl~ 1636 (1768)
.|+.|...+ .+.||+|..|+|||||.+||.+ -++|...|+|.
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=3e-05 Score=91.10 Aligned_cols=45 Identities=29% Similarity=0.748 Sum_probs=36.6
Q ss_pred cccccccccCCCCCCceeccCCCCCccchhhhccCCCCCCCCCCcC
Q 000262 1592 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDHPHKLTN 1637 (1768)
Q Consensus 1592 ~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H~Hkl~~ 1637 (1768)
..-|++|......|.||+|++|+|||||..||.+.+ +.=+|.|..
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=96.93 E-value=0.00056 Score=59.87 Aligned_cols=37 Identities=27% Similarity=0.606 Sum_probs=32.0
Q ss_pred ccccccccCCCCCCceeccCCCCCccchhhhccCCCCCC
Q 000262 1593 TTCNICHLDIETGQGWRCEVCPDYDVCNACYQKDGGIDH 1631 (1768)
Q Consensus 1593 ~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k~g~~~H 1631 (1768)
|.|+.|..|+.+ .||||..+.|||||..||.+ |....
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=96.78 E-value=0.00053 Score=80.83 Aligned_cols=47 Identities=28% Similarity=0.588 Sum_probs=40.7
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCcC
Q 000262 1591 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTN 1637 (1768)
Q Consensus 1591 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k---~g~~~H~Hkl~~ 1637 (1768)
-.+.|..|...--++.||+|..|-|||||.+||.. .+.|.|.|+|.-
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 445778888753
No 25
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=96.37 E-value=0.002 Score=56.52 Aligned_cols=38 Identities=29% Similarity=0.783 Sum_probs=29.9
Q ss_pred eeccccccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1465 VHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1465 ~~Lq~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
+|-...|+.|....+.|.||.|..| .+|+||+.||...
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 4566789999997778899999999 9999999999874
No 26
>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=96.11 E-value=0.0028 Score=56.57 Aligned_cols=34 Identities=35% Similarity=0.877 Sum_probs=30.8
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHHh
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~ 1507 (1768)
.|+.|.+..+.|.||+|..| .+|+||+.||....
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 99999999998753
No 27
>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=96.11 E-value=0.0028 Score=54.78 Aligned_cols=35 Identities=26% Similarity=0.708 Sum_probs=31.6
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHHhh
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1508 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~ 1508 (1768)
.|+.|...-+.|.||+|..| .+|+||+.||....+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C----~dyDLC~~C~~~~~n 36 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVK----EDYDLCTICFSRMGN 36 (43)
T ss_pred CCCCCCCCcccccceEeCCC----CCCccHHHHhhhhcC
Confidence 59999998899999999999 999999999977543
No 28
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=96.09 E-value=0.0029 Score=55.48 Aligned_cols=32 Identities=31% Similarity=1.144 Sum_probs=29.9
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHH
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~ 1505 (1768)
.|+.|....+.|.||+|..| .+|+||+.||..
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 999999999977
No 29
>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=96.06 E-value=0.0031 Score=56.15 Aligned_cols=34 Identities=26% Similarity=0.816 Sum_probs=29.6
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHHh
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~ 1507 (1768)
.|+.|.+..+.|.||+|..| .+|.||+.||....
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 69999965556999999999 99999999998653
No 30
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.00 E-value=0.0028 Score=77.17 Aligned_cols=35 Identities=34% Similarity=0.852 Sum_probs=32.9
Q ss_pred ccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1591 FVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1591 f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
--|.|+.|..+|..-.+.+|.+|||||||..|+..
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 46799999999999999999999999999999987
No 31
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=95.77 E-value=0.0056 Score=53.74 Aligned_cols=32 Identities=31% Similarity=0.937 Sum_probs=30.0
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHH
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~ 1505 (1768)
.|+.|.+..+.|.||+|..| .+|+||+.|+..
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 32
>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=95.48 E-value=0.0077 Score=52.82 Aligned_cols=34 Identities=32% Similarity=0.873 Sum_probs=29.5
Q ss_pred ccccccccccccCceeeeecccccccccccchhhhHHHh
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~ 1507 (1768)
+.|+.|...| .|.||.|.+| .+|.||.+||....
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 99999999998764
No 33
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.45 E-value=0.0056 Score=77.85 Aligned_cols=49 Identities=22% Similarity=0.447 Sum_probs=40.3
Q ss_pred cccccccccccCCCCCCceeccCCCCCccchhhhcc---CCCCCCCCCCcCC
Q 000262 1590 AFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK---DGGIDHPHKLTNH 1638 (1768)
Q Consensus 1590 ~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k---~g~~~H~Hkl~~~ 1638 (1768)
+....||.|+..-.-|.||+|.+|-+||||.+||-. -|+|.-+|+|...
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 3446666777654
No 34
>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=95.44 E-value=0.0077 Score=53.60 Aligned_cols=35 Identities=31% Similarity=0.909 Sum_probs=30.2
Q ss_pred ccccccccccccCceeeeeccccccc--ccccchhhhHHHh
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNK--NFQLCDKCFEAEK 1507 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~--~f~lC~~Cy~~e~ 1507 (1768)
+.|+.|....+.|.||.|..| . +|.||+.||....
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C----~~~d~DlC~~C~~~~~ 37 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSEC----DDGDFDLCQDCVVKGE 37 (48)
T ss_pred CCCCCCCCCccccceEECCCC----CCCCCccCHHHHhCcC
Confidence 369999996666999999999 8 9999999998753
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=95.35 E-value=0.0082 Score=53.54 Aligned_cols=33 Identities=30% Similarity=0.881 Sum_probs=28.7
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
.|+.|.+.-+.|.||.|..| .+|.||..||...
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 59999994444899999999 9999999999865
No 36
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=95.22 E-value=0.05 Score=53.50 Aligned_cols=55 Identities=11% Similarity=0.429 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHhhcc-CCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc
Q 000262 67 LRARGFMRDRIFGMLLHRQ-TQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM 121 (1768)
Q Consensus 67 ~~~R~~m~~ri~~~l~~r~-~~~~~~~~~~r~~~lakRLEe~l~k~a~tK~~Y~n~ 121 (1768)
..||..|++||+..|+-.. |.+..+.--..|-+-||.+|.-+|.+|.|++|||.+
T Consensus 12 ~~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~l~~yarkvE~~~fe~A~sreeYY~l 67 (81)
T PF02172_consen 12 PDLRNHLVHKLVQAIFPTPDPNAMNDPRMKNLIEYARKVEKDMFETAQSREEYYHL 67 (81)
T ss_dssp HHHHHHHHHHHHHHHS-SSSCCCCCSHHHHHHHHHHHHHHHHHHHC-SSHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence 3689999999999998662 334444444567788999999999999999999998
No 37
>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=95.18 E-value=0.011 Score=52.61 Aligned_cols=34 Identities=32% Similarity=0.804 Sum_probs=31.4
Q ss_pred ccccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
+.|+.|.+.++.|.||+|.+| .+|.||..||...
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 38
>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=94.88 E-value=0.014 Score=50.86 Aligned_cols=32 Identities=28% Similarity=0.762 Sum_probs=28.6
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
.|+.|.+ .+.|.||.|.+| .+|+||+.||...
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 5899999 557799999999 9999999999864
No 39
>COG5087 RTT109 Uncharacterized conserved protein [Function unknown]
Probab=94.74 E-value=0.43 Score=55.71 Aligned_cols=127 Identities=20% Similarity=0.338 Sum_probs=87.4
Q ss_pred HHHHHhhhhcCCCCcccce-eEE-EEEEEEeCCeEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccch
Q 000262 1212 QRFLEIFQEENYPTEFPYK-SKV-VLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEA 1289 (1768)
Q Consensus 1212 ~~f~~~f~e~~yp~~f~Yr-sK~-I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~G~~ 1289 (1768)
..+...|...+-...|++- .|- .+||- .+++||+|-+|-|..+ ..++|||+=-||--|-. .|..
T Consensus 25 ~~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gvs 90 (349)
T COG5087 25 RHMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGVS 90 (349)
T ss_pred HhhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------cccc
Confidence 3444444444444444443 333 33443 6899999999999554 35899999999999974 2456
Q ss_pred hhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000262 1290 LRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1768)
Q Consensus 1290 lRt~VYheIL~~Yl~y~k~~GF~~a-hIWAcPP~~GDDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~kg 1355 (1768)
-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
T Consensus 91 ~~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T COG5087 91 RGTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred ccchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 7899999988887665555555444 5677664 56999765443 34899999999999777643
No 40
>KOG4534 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.74 E-value=0.43 Score=55.71 Aligned_cols=127 Identities=20% Similarity=0.338 Sum_probs=87.4
Q ss_pred HHHHHhhhhcCCCCcccce-eEE-EEEEEEeCCeEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccch
Q 000262 1212 QRFLEIFQEENYPTEFPYK-SKV-VLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEA 1289 (1768)
Q Consensus 1212 ~~f~~~f~e~~yp~~f~Yr-sK~-I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~G~~ 1289 (1768)
..+...|...+-...|++- .|- .+||- .+++||+|-+|-|..+ ..++|||+=-||--|-. .|..
T Consensus 25 ~~~~~l~g~sk~~k~~~~s~~~hlfllf~----q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gvs 90 (349)
T KOG4534|consen 25 RHMESLCGRSKLGKQAFVSNGRHLFLLFN----QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGVS 90 (349)
T ss_pred HhhhhhcCcccccccccccCcceEEEEee----cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------cccc
Confidence 3444444444444444443 333 33443 6899999999999554 35899999999999974 2456
Q ss_pred hhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000262 1290 LRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1768)
Q Consensus 1290 lRt~VYheIL~~Yl~y~k~~GF~~a-hIWAcPP~~GDDYIF~~HP~~--Qk~p~~~~L~~WY~~mL~kg 1355 (1768)
-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
T Consensus 91 ~~t~ii~~filsId~iRKq~a~~v~iclFs~p~---sqYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T KOG4534|consen 91 RGTKIILEFILSIDKIRKQLAPGVCICLFSVPR---SQYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred ccchhhhhhhhhhhhhhhccCCceEEEEEeccc---cceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 7899999988887665555555444 5677664 56999765443 34899999999999777643
No 41
>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=94.59 E-value=0.005 Score=54.37 Aligned_cols=41 Identities=29% Similarity=0.734 Sum_probs=31.2
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCc
Q 000262 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCY 1132 (1768)
Q Consensus 1092 ~~~E~~v~C~~C~~~~HqiCaLfn~~~~~~~~a~f~C~~C~ 1132 (1768)
...+.+|.|+.|++|+|..|.-............|+|+.|.
T Consensus 9 ~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 9 DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 45778999999999999999977644222113479999985
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=94.50 E-value=0.02 Score=49.93 Aligned_cols=34 Identities=29% Similarity=0.841 Sum_probs=30.0
Q ss_pred cccccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1468 q~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
...|..|.. .+.|.||.|..| .+|.||..||...
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 9999999999763
No 43
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=94.00 E-value=0.018 Score=72.88 Aligned_cols=88 Identities=26% Similarity=0.489 Sum_probs=58.3
Q ss_pred cccccCcceeccCCcccccCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCCccc
Q 000262 1017 CQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEEW 1096 (1768)
Q Consensus 1017 C~~C~~~~l~F~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~kCf~~~~~~~i~~~~~~~~K~~~~kkkNd~~~~E~ 1096 (1768)
|-+|-.|+=.-|-|-+||.|-.|.+.-..-.|..-.-.+--|||-||-..-+.-.|.-+-.+. |+.-.||. |
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~-kdGALKkT-D------ 79 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPH-KDGALKKT-D------ 79 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccC-cccceecc-c------
Confidence 557778888999999999998888888888887544233469999998765432221111111 11111111 1
Q ss_pred ceeccccccccccccccccccc
Q 000262 1097 WVQCDKCEAWQHQICALFNGRR 1118 (1768)
Q Consensus 1097 ~v~C~~C~~~~HqiCaLfn~~~ 1118 (1768)
=+.|-|.|||||.++.
T Consensus 80 ------n~GWAHVVCALYIPEV 95 (900)
T KOG0956|consen 80 ------NGGWAHVVCALYIPEV 95 (900)
T ss_pred ------CCCceEEEEEeeccce
Confidence 1689999999998765
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.00 E-value=0.021 Score=66.91 Aligned_cols=34 Identities=29% Similarity=0.856 Sum_probs=32.2
Q ss_pred cccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1592 VTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1592 ~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
-+-|+.|..++....+-+|..|++||||..|+..
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 45
>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=93.95 E-value=0.023 Score=49.01 Aligned_cols=32 Identities=28% Similarity=0.862 Sum_probs=27.2
Q ss_pred ccccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
+.|..|.. + .|.||.|..| .+|+||+.||...
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 4699999999 9999999999773
No 46
>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=93.68 E-value=0.04 Score=49.13 Aligned_cols=34 Identities=32% Similarity=0.777 Sum_probs=29.8
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHHhh
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1508 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~ 1508 (1768)
.|+.|.+. +.|.||+|.+| .+|+||..||.....
T Consensus 2 ~CdgC~~~-~~~~RykCl~C----~d~DlC~~Cf~~g~~ 35 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQC----TDMDLCKTCFLGGVK 35 (48)
T ss_pred CCCCCCCc-CCCceEECCCC----CCchhHHHHHhCCcc
Confidence 59999985 57899999999 999999999988653
No 47
>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 KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=93.38 E-value=0.037 Score=65.65 Aligned_cols=34 Identities=26% Similarity=0.826 Sum_probs=31.4
Q ss_pred ccccccccccccCceeeeecccccccccccchhhhHHH
Q 000262 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1768)
Q Consensus 1469 ~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e 1506 (1768)
..|+.|....+.|.||+|++| .+|+||++|+...
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 689999997888899999999 9999999999774
No 49
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=92.13 E-value=0.14 Score=61.18 Aligned_cols=88 Identities=23% Similarity=0.452 Sum_probs=58.4
Q ss_pred cccccccccccccCceeeeecccccccccccchhhhHHHhhcc-cccCCCCCccccccccccccCCC----CCCCCCCCc
Q 000262 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKRE-DRERHPVNSREVHILEEVPVTDV----PADTKDKDE 1542 (1768)
Q Consensus 1468 q~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~~~-~~~~hp~~~~~~h~L~~v~v~~v----p~~t~D~D~ 1542 (1768)
...|+.|.+.-+.++||+|..| .+|+||..||+...... ..+-||+- -+|.+++++-. |-...+++
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C----~DyDlC~sCyen~~tt~~H~~dHPmq----cil~~~dfeL~f~Ge~i~~y~~q- 78 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRC----SDYDLCFSCYENGATTPIHDEDHPMQ----CILSRVDFELYFGGEPISHYDPQ- 78 (381)
T ss_pred CceeccccccceeeeeeEeeee----cchhHHHHHhhcCCCCcccCCCCcee----EEeeccceeeEecCccccccccc-
Confidence 3589999999999999999999 99999999998864322 12235542 34555554422 22233333
Q ss_pred cccCcccc----cHHHHHHHhhhCCC
Q 000262 1543 ILESEFFD----TRQAFLSLCQGNHY 1564 (1768)
Q Consensus 1543 ~i~seffd----tR~aFL~lcq~nHy 1564 (1768)
-.+|.... |=..|+.++...|.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCc
Confidence 67777655 33567777666663
No 50
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=90.20 E-value=0.1 Score=70.34 Aligned_cols=8 Identities=13% Similarity=0.115 Sum_probs=3.7
Q ss_pred CCCccccc
Q 000262 151 SSSIGTMI 158 (1768)
Q Consensus 151 ss~~gtmi 158 (1768)
+|++|..|
T Consensus 1845 ~~p~~~~~ 1852 (2220)
T KOG3598|consen 1845 ASPKDDVT 1852 (2220)
T ss_pred CCCCCCCC
Confidence 44455444
No 51
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=86.78 E-value=0.31 Score=39.18 Aligned_cols=28 Identities=36% Similarity=0.973 Sum_probs=13.2
Q ss_pred cccccccCCCCCCceeccCCCCCccchhh
Q 000262 1594 TCNICHLDIETGQGWRCEVCPDYDVCNAC 1622 (1768)
Q Consensus 1594 tCn~C~~~I~t~~rwhC~vC~DfDLC~~C 1622 (1768)
+|+.|...+..+..|+|..| ||+|...|
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 52
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=82.66 E-value=3.3 Score=52.65 Aligned_cols=57 Identities=25% Similarity=0.358 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCcchHHHHHHHHHhcCC
Q 000262 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNMDTLEARLSYLIKGRP 136 (1768)
Q Consensus 68 ~~R~~m~~ri~~~l~~r~~~~~~~~~~~r~~~lakRLEe~l~k~a~tK~~Y~n~~tle~rL~~~i~~~~ 136 (1768)
+.|...+.||-. ++.|..+..+ .=||-.|+-+|+|+.||+|||.+ -.+|-..++-+.
T Consensus 10 kFRq~vIsried-~l~~n~q~~~--------k~a~~mE~hVF~K~~tkDEYl~l---vAkli~h~~d~s 66 (742)
T KOG4274|consen 10 KFRQHVISRIED-ELRKNGQAHS--------KSAKDMESHVFLKAKTKDEYLSL---VAKLIIHFRDIS 66 (742)
T ss_pred HHHHHHHHHhhh-hhhhhhhccC--------cchHHHHHHHHHhhhhHHHHHHH---HHHHHHHHHhhh
Confidence 568899999755 6677766654 45899999999999999999975 344444444443
No 53
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=79.50 E-value=1.8 Score=52.67 Aligned_cols=65 Identities=32% Similarity=0.768 Sum_probs=55.4
Q ss_pred CCCCCCCCchhHHHHHhcccccCCC-CCCCCCccchHHHHHHh-hccCCCCCCC--chhhhHHHHHHHHHh
Q 000262 722 EGKCQDVNCITVQKLWRHMDNCTSS-QCPYPRCHHSKILIHHH-KHCRDPSCPV--CVPVKNYLQQQKERA 788 (1768)
Q Consensus 722 ~g~C~~~~C~~~k~lL~H~~~C~~~-~C~~~~C~ssr~ll~H~-k~C~~~~Cpv--C~PVr~~v~k~~qqa 788 (1768)
...|..+.|..++.|++|...|+.. .| +.|....+|+.=| +.|.+..|+| |-.+|.-+++..+++
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 4798888888655 9999999999 999999998766543
No 54
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=79.43 E-value=0.94 Score=61.93 Aligned_cols=9 Identities=11% Similarity=-0.186 Sum_probs=3.6
Q ss_pred Ccccccccc
Q 000262 415 NSGSLQSMP 423 (1768)
Q Consensus 415 ~s~nl~s~s 423 (1768)
-.+|-|+-+
T Consensus 2067 ~~m~py~~p 2075 (2220)
T KOG3598|consen 2067 PLMNPYGGP 2075 (2220)
T ss_pred hhcccccCC
Confidence 334444433
No 55
>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=78.90 E-value=1.7 Score=54.40 Aligned_cols=42 Identities=31% Similarity=0.680 Sum_probs=31.7
Q ss_pred CcccceecccccccccccccccccccC-----CC----CCCcccCCCCchh
Q 000262 1093 TEEWWVQCDKCEAWQHQICALFNGRRN-----DG----GQAEYTCPNCYIT 1134 (1768)
Q Consensus 1093 ~~E~~v~C~~C~~~~HqiCaLfn~~~~-----~~----~~a~f~C~~C~~~ 1134 (1768)
..=-||.|+.|+-|-|--|||-...+- .+ -+..|.|..|...
T Consensus 142 n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 142 NTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred CCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 344699999999999999999865431 11 1457999999753
No 56
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=68.39 E-value=3.5 Score=55.38 Aligned_cols=53 Identities=19% Similarity=0.365 Sum_probs=33.0
Q ss_pred HHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc-chHHHHHHHHHhc
Q 000262 73 MRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM-DTLEARLSYLIKG 134 (1768)
Q Consensus 73 m~~ri~~~l~~r~~~~~~~~~~~r~~~lakRLEe~l~k~a~tK~~Y~n~-~tle~rL~~~i~~ 134 (1768)
.+.||=+ .++|...+++ .=||-+|+-+|.||.||||||++ .-|--|+...-+.
T Consensus 3 vi~~ie~-a~~~~~~~~~--------k~a~emE~hvF~Ka~tkdEYl~~varli~h~r~~~~~ 56 (799)
T PF09606_consen 3 VISKIEE-AMRKNGQNTP--------KSAREMENHVFQKAKTKDEYLSLVARLILHIRDMSKK 56 (799)
T ss_dssp HHHHHHH-HHHHH----S--------S-HHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHH-HHHHhCCCCC--------CCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhhhc
Confidence 4556544 4455655543 34788999999999999999997 6666666555533
No 57
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=67.57 E-value=6.5 Score=53.49 Aligned_cols=26 Identities=35% Similarity=0.416 Sum_probs=14.6
Q ss_pred CCCCccccccCCCCCCCCCcceEEee
Q 000262 150 SSSSIGTMIPTPGMSHCGNSSLMVTS 175 (1768)
Q Consensus 150 sss~~gtmiptpg~~~~~n~~~~~~~ 175 (1768)
+-+.+|-||=-|+.+.-.|+++..++
T Consensus 1400 a~~~I~~~i~Dpdv~~~~~ssi~~as 1425 (2131)
T KOG4369|consen 1400 ATSPIGLPIIDPDVSSPSSSSIPLAS 1425 (2131)
T ss_pred hhccccceeecCCcCccccccchhhh
Confidence 45566666666665555555554443
No 58
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=67.57 E-value=6.1 Score=53.73 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=12.3
Q ss_pred eeccCCCCCCccccccccCCCC-CccccccCCC
Q 000262 345 LLINEPGTSEGYLTGTQYANSP-KPLQHHFDHQ 376 (1768)
Q Consensus 345 ~min~pg~s~gy~~~~~y~~s~-k~~Qq~~~~q 376 (1768)
++.+--|+....-++++-..++ ...|+.|-.|
T Consensus 1742 ~~~~~~ga~ss~n~s~s~n~~~~e~~q~~~~sq 1774 (2131)
T KOG4369|consen 1742 QFLPQLGANSSLNNSNSKNDSSNEWGQNEFISQ 1774 (2131)
T ss_pred hhcccccccccccCCCCCchhhhhhhccchhhh
Confidence 3444445332222333223333 3334444454
No 59
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=67.04 E-value=1.9 Score=54.46 Aligned_cols=38 Identities=32% Similarity=0.605 Sum_probs=27.0
Q ss_pred cceeccccccccccccccccccc--CCCCCCcccCCCCch
Q 000262 1096 WWVQCDKCEAWQHQICALFNGRR--NDGGQAEYTCPNCYI 1133 (1768)
Q Consensus 1096 ~~v~C~~C~~~~HqiCaLfn~~~--~~~~~a~f~C~~C~~ 1133 (1768)
-+|+|++|+.|||+-|.--.-.. ..+..-+|.|..|..
T Consensus 184 rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 184 RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 36999999999999998432111 012246899999975
No 60
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=62.57 E-value=3.2 Score=52.00 Aligned_cols=89 Identities=19% Similarity=0.370 Sum_probs=54.4
Q ss_pred CcccccccCcceeccCCcccccCCCceecCCCeeeeecC----------CccceeeccccccccCCCceeecCchhhHHH
Q 000262 1014 ENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGA----------GDTRHYFCIKCYNEARGDTIVVDGTTIAKAR 1083 (1768)
Q Consensus 1014 ~~~C~~C~~~~l~F~p~~l~C~~c~cRI~r~~~Yy~~~~----------~~~~~~~C~kCf~~~~~~~i~~~~~~~~K~~ 1083 (1768)
-+.|.+|-+++..=.---+.|..||..+..| .|..-+ ..+.-|||..|--......-+|. + .|..
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~CGi~VHEg--CYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElC--P-n~~G 193 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDKCGINVHEG--CYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELC--P-NRFG 193 (707)
T ss_pred ceEEEEeecCccccccceeeccccCceeccc--ccccccccccCCCCccCCCCchhhhhHhcCCCCCccccC--C-CcCC
Confidence 3478899888876666778899988776655 454321 12457999999776432111110 0 0111
Q ss_pred HHHhhcCCCCcccceecccccccccccccccccccCC
Q 000262 1084 LEKKKNDEETEEWWVQCDKCEAWQHQICALFNGRRND 1120 (1768)
Q Consensus 1084 ~~kkkNd~~~~E~~v~C~~C~~~~HqiCaLfn~~~~~ 1120 (1768)
.-|. ..=|||+|-|||||....+-
T Consensus 194 ifKe-------------tDigrWvH~iCALYvpGVaf 217 (707)
T KOG0957|consen 194 IFKE-------------TDIGRWVHAICALYVPGVAF 217 (707)
T ss_pred cccc-------------cchhhHHHHHHHhhcCcccc
Confidence 0011 13479999999999887653
No 61
>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=61.98 E-value=4.9 Score=32.57 Aligned_cols=28 Identities=21% Similarity=0.648 Sum_probs=23.7
Q ss_pred cccccccCCCCCCceeccCCCCCccchhh
Q 000262 1594 TCNICHLDIETGQGWRCEVCPDYDVCNAC 1622 (1768)
Q Consensus 1594 tCn~C~~~I~t~~rwhC~vC~DfDLC~~C 1622 (1768)
.|..|.+.++...+|+|..|. |+|...|
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 62
>KOG4786 consensus Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription; Signal transduction mechanisms]
Probab=61.51 E-value=64 Score=42.71 Aligned_cols=64 Identities=17% Similarity=0.154 Sum_probs=31.1
Q ss_pred cCCCCCcccCCccccccceeccCCC------CCCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCCCCCcc
Q 000262 327 YGFSNGALNGGLGMIGNNLLINEPG------TSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADSYGTGN 397 (1768)
Q Consensus 327 ~g~s~~s~nggmg~~g~~~min~pg------~s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~~g~~~ 397 (1768)
-|-+++...||-| |.|.+.|.|| .+.+-....+++.|..-+| + .+.+|.-.|-.++-..+|++.
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 6667777777 1122233344454432111 1 233344456555555555443
No 63
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=60.96 E-value=2.9 Score=52.38 Aligned_cols=87 Identities=21% Similarity=0.386 Sum_probs=45.9
Q ss_pred cccccccCcceeccCCcccccCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCCc
Q 000262 1015 NSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETE 1094 (1768)
Q Consensus 1015 ~~C~~C~~~~l~F~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~kCf~~~~~~~i~~~~~~~~K~~~~kkkNd~~~~ 1094 (1768)
..|..|.+-.-.=.-.-.||.|| -|--....|...--..-.++|-+|.=... .|.-...-.+.+.--|.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC--~i~VHq~CYGI~f~peG~WlCrkCi~~~~--~i~~C~fCps~dGaFkq------- 262 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGC--EICVHQSCYGIQFLPEGFWLCRKCIYGEY--QIRCCSFCPSSDGAFKQ------- 262 (669)
T ss_pred hhhHhccccccCCcceEEEecCc--chhhhhhcccceecCcchhhhhhhccccc--ceeEEEeccCCCCceee-------
Confidence 35666655433333445679876 46667777775432223688999865421 11100000000000000
Q ss_pred ccceeccccccccccccccccccc
Q 000262 1095 EWWVQCDKCEAWQHQICALFNGRR 1118 (1768)
Q Consensus 1095 E~~v~C~~C~~~~HqiCaLfn~~~ 1118 (1768)
..=|||-|-|||+|++..
T Consensus 263 ------T~dgrW~H~iCA~~~pel 280 (669)
T COG5141 263 ------TSDGRWGHVICAMFNPEL 280 (669)
T ss_pred ------ccCCchHhHhHHHhcchh
Confidence 123899999999999754
No 64
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=59.34 E-value=5.8 Score=48.04 Aligned_cols=45 Identities=22% Similarity=0.637 Sum_probs=37.3
Q ss_pred HhhcCCCCCcccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1581 YHLHNPTAPAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1581 yhLHn~~~~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
+-|-+.+...--+.|+.|..+-..|.||+|.-|-.|.||+.|+=+
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 334455444455789999999999999999999999999999977
No 65
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=56.87 E-value=9 Score=36.04 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=20.9
Q ss_pred cccccCCCceecCCCeeeeecCCccceeeccccccc
Q 000262 1031 PIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 1066 (1768)
Q Consensus 1031 ~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~kCf~~ 1066 (1768)
+-.|..|+..|.+++.|= ...|..|=++
T Consensus 9 ~~~CtSCg~~i~p~e~~v--------~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGETAV--------KFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCcee--------EeeCCCCCce
Confidence 678999999998887662 3568877554
No 66
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=47.45 E-value=9.4 Score=50.27 Aligned_cols=39 Identities=26% Similarity=0.508 Sum_probs=34.8
Q ss_pred cccccccccccccCceeeeecccccccccccchhhhHHHhhcc
Q 000262 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKRE 1510 (1768)
Q Consensus 1468 q~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~~~ 1510 (1768)
+.+|..|++.-+.|.||.|..| .|+.||..|+.......
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~----fn~dlCq~CF~sgraak 641 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKH----FNYDICQSCFFSGRAAK 641 (966)
T ss_pred hhhcchhhhCccceeeeeehhh----cChhHHhhHhhhccccc
Confidence 5699999999999999999999 99999999998865544
No 67
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=39.99 E-value=16 Score=45.92 Aligned_cols=37 Identities=27% Similarity=0.760 Sum_probs=32.1
Q ss_pred cccccccccccccCceeeeecccccccccccchhhhHHHhh
Q 000262 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1508 (1768)
Q Consensus 1468 q~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~~ 1508 (1768)
.+.|.-|...|-.--|.+|.+| .+|.||-.|+.....
T Consensus 14 ky~C~~C~~dit~~i~ikCaeC----p~fdLCl~CFs~GaE 50 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAEC----PDFDLCLQCFSVGAE 50 (438)
T ss_pred CCCCccHhHHhccceEEEeecC----CCcchhHHHHhcccc
Confidence 4689999988877777999999 999999999988653
No 68
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=39.47 E-value=14 Score=47.33 Aligned_cols=39 Identities=33% Similarity=0.714 Sum_probs=32.4
Q ss_pred cccceecccccccccccccccccccCCCCCCcccCCCCchhh
Q 000262 1094 EEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITE 1135 (1768)
Q Consensus 1094 ~E~~v~C~~C~~~~HqiCaLfn~~~~~~~~a~f~C~~C~~~~ 1135 (1768)
..-.++|+.|++|.|.+|..+.+... ...|.|..|....
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 56789999999999999999877542 4579999998753
No 69
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=36.27 E-value=21 Score=49.61 Aligned_cols=76 Identities=18% Similarity=0.560 Sum_probs=50.5
Q ss_pred CcccccccCcceeccCCcccccCCCceecCCCeeeeecCCccceeeccccccccCCCceeecCchhhHHHHHHhhcCCCC
Q 000262 1014 ENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEET 1093 (1768)
Q Consensus 1014 ~~~C~~C~~~~l~F~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~kCf~~~~~~~i~~~~~~~~K~~~~kkkNd~~~ 1093 (1768)
...|.+|...+-.=.-.-+||.+| .|--+...|..+--.+-.+.|-.|--.-.+.
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~C--nl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~----------------------- 273 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGC--NLAVHQECYGIPFIPEGQWLCRRCLQSPQRP----------------------- 273 (1051)
T ss_pred CccceeecccccCCCceEEEcCCC--cchhhhhccCCCCCCCCcEeehhhccCcCcc-----------------------
Confidence 457888887666655667899987 4556777777332122258899997653321
Q ss_pred cccceecccc------------ccccccccccccccc
Q 000262 1094 EEWWVQCDKC------------EAWQHQICALFNGRR 1118 (1768)
Q Consensus 1094 ~E~~v~C~~C------------~~~~HqiCaLfn~~~ 1118 (1768)
|.|.-| |+|.|.+||++.+..
T Consensus 274 ----v~c~~cp~~~gAFkqt~dgrw~Hv~caiwipev 306 (1051)
T KOG0955|consen 274 ----VRCLLCPSKGGAFKQTDDGRWAHVVCAIWIPEV 306 (1051)
T ss_pred ----cceEeccCCCCcceeccCCceeeeehhhccccc
Confidence 233333 899999999998755
No 70
>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=35.87 E-value=14 Score=33.46 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=15.0
Q ss_pred ccceecccccccccccccccccccCCCCCCcccCCC
Q 000262 1095 EWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPN 1130 (1768)
Q Consensus 1095 E~~v~C~~C~~~~HqiCaLfn~~~~~~~~a~f~C~~ 1130 (1768)
+-||+|+.|++|=.-- .-+...+... ...|.|..
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 3233221112 23788844
No 71
>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=32.89 E-value=32 Score=30.86 Aligned_cols=39 Identities=23% Similarity=0.675 Sum_probs=30.8
Q ss_pred cceeccCCcccccCCCceecCCCeeeeecCCccceeeccccccc
Q 000262 1023 EKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 1066 (1768)
Q Consensus 1023 ~~l~F~p~~l~C~~c~cRI~r~~~Yy~~~~~~~~~~~C~kCf~~ 1066 (1768)
....|.+.=+.|..|+..|..+. ||.... ..||..||.+
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 35679999999999999998887 555432 6899999975
No 72
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=31.92 E-value=9.2 Score=32.51 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=16.9
Q ss_pred cceecccccccccccccccccccCCCCCCcccCCCC
Q 000262 1096 WWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNC 1131 (1768)
Q Consensus 1096 ~~v~C~~C~~~~HqiCaLfn~~~~~~~~a~f~C~~C 1131 (1768)
+++.|+.|+-.+|+.|.=..... ....+.|..|
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 68999999999999997544322 1235888766
No 73
>KOG4592 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.23 E-value=1.4e+02 Score=39.34 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=22.1
Q ss_pred CCCCCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCCCCC
Q 000262 350 PGTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADSYGT 395 (1768)
Q Consensus 350 pg~s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~~g~ 395 (1768)
.|..-.|.|..+-+.|..|- +++ .+..+-+.||.+++..+.+
T Consensus 48 ~g~dfDF~np~ssass~~~~--~~N--~~~~~ar~i~~a~~El~~~ 89 (728)
T KOG4592|consen 48 SGGDFDFANPLSSASSSSPA--PLN--APFRQARHIGDADLELNIS 89 (728)
T ss_pred ccCCccCCCccccCccCCCC--CcC--ccccccccccccccccccc
Confidence 33334566665555554422 222 2344556677777776665
No 74
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=29.12 E-value=43 Score=42.05 Aligned_cols=33 Identities=27% Similarity=0.679 Sum_probs=27.8
Q ss_pred EEEe-CCCCCCCCeeeccCCCCCCCCChhHHHHHHHH
Q 000262 1315 YIWA-CPPLKGEDYILYCHPEIQKTPKSDKLREWYLA 1350 (1768)
Q Consensus 1315 hIWA-cPP~~GDDYIF~~HP~~Qk~p~~~~L~~WY~~ 1350 (1768)
.=|| |||.+-+ ||.-|..++.++..+|++||..
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 7788999999999999999974
No 75
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=27.37 E-value=32 Score=41.23 Aligned_cols=37 Identities=22% Similarity=0.493 Sum_probs=24.1
Q ss_pred eecccccccccccccccccccCCCCCCcccCCCCchh
Q 000262 1098 VQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1768)
Q Consensus 1098 v~C~~C~~~~HqiCaLfn~~~~~~~~a~f~C~~C~~~ 1134 (1768)
-+|..||+.|++-=-|---.|...||++|.|+.|.+.
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kA 224 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKA 224 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccch
Confidence 5677888777765555433344456788888888653
No 76
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=26.73 E-value=30 Score=41.60 Aligned_cols=35 Identities=26% Similarity=0.802 Sum_probs=26.1
Q ss_pred cceeccc--cc-ccccccccccccccCCCCCCcccCCCCchh
Q 000262 1096 WWVQCDK--CE-AWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1768)
Q Consensus 1096 ~~v~C~~--C~-~~~HqiCaLfn~~~~~~~~a~f~C~~C~~~ 1134 (1768)
++|.||- |. .|||-.|+=.... + .-...||.|...
T Consensus 231 ~Mi~CDn~~C~~eWFH~~CVGL~~~--P--kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 231 KMIGCDNPGCPIEWFHFTCVGLKTK--P--KGKWYCPRCKAE 268 (274)
T ss_pred cccccCCCCCCcceEEEeccccccC--C--CCcccchhhhhh
Confidence 4688888 99 9999999954432 1 234899999865
No 77
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=25.76 E-value=23 Score=43.27 Aligned_cols=47 Identities=40% Similarity=0.849 Sum_probs=36.3
Q ss_pred HHHHHhhhccccCccceeeeeccccccccccccccCceeeeecccccccccccchhhhH
Q 000262 1446 LLMHKLGETICPMKEDFIMVHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFE 1504 (1768)
Q Consensus 1446 ~lm~klg~~i~~~Ke~F~v~~Lq~~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~ 1504 (1768)
.||++|+ +++ . |.| --.|++|...-+-|.|+.|..| -++++|..|+=
T Consensus 226 pLmhrla-~v~----n--v~h-pv~cs~c~srs~~gfry~cq~C----~nyqlcq~cfw 272 (434)
T KOG4301|consen 226 PLMHRLA-TVE----N--VFH-PVECSYCRSRSMMGFRYRCQQC----HNYQLCQQCFW 272 (434)
T ss_pred HHHHHHH-hhc----c--cCC-CccCcceecccccchhhhHhhc----CCccccchhhc
Confidence 5888874 222 1 212 2479999999999999999999 99999999953
No 78
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=25.66 E-value=92 Score=36.00 Aligned_cols=71 Identities=24% Similarity=0.249 Sum_probs=36.8
Q ss_pred CCCCCccccc----cCCCCCcccCCccccccceeccCCCCCCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCC
Q 000262 317 GMRSGLQHKS----YGFSNGALNGGLGMIGNNLLINEPGTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADS 392 (1768)
Q Consensus 317 gm~sg~q~~s----~g~s~~s~nggmg~~g~~~min~pg~s~gy~~~~~y~~s~k~~Qq~~~~qrs~~q~~~yg~sn~~~ 392 (1768)
-||+|+.-++ .|-|..+.||||-.--...||+.-|+.++ +-+ -+--|.++|++|.-|- ..|.|.-..+
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 EMRAGLLGKQRPLINSPSASSSNGGAPIRTVGTLIGSAPTGDF-SGA--GGDEPPPIQQQVLWQN-----SPYNMVMQSP 235 (272)
T ss_pred HHhccCccccccccCCCCcCCCCCCCCchhhccccccCCCCCc-ccc--CCCCCchhhhhccccC-----CcchhhccCC
Confidence 3555555533 44556666777654222226666665543 222 2344678888877432 3444544444
Q ss_pred CCC
Q 000262 393 YGT 395 (1768)
Q Consensus 393 ~g~ 395 (1768)
+.+
T Consensus 236 ~~s 238 (272)
T KOG4552|consen 236 SSS 238 (272)
T ss_pred CCC
Confidence 444
No 79
>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=25.57 E-value=23 Score=42.80 Aligned_cols=60 Identities=13% Similarity=0.019 Sum_probs=44.0
Q ss_pred eEEEEEEEEeCCeEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcC
Q 000262 1231 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1310 (1768)
Q Consensus 1231 sK~I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~G~~lRt~VYheIL~~Yl~y~k~~G 1310 (1768)
.=+|.-|=+|+|..|.++++--.-+|- .+ +.+..|=+...+++|-+.|
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 000262 1311 FTSCYIWACPPL 1322 (1768)
Q Consensus 1311 F~~ahIWAcPP~ 1322 (1768)
.=-+.|.+.+=.
T Consensus 156 lPlV~l~dSgGa 167 (285)
T TIGR00515 156 CPLIIFSASGGA 167 (285)
T ss_pred CCEEEEEcCCCc
Confidence 999998887753
No 80
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=24.49 E-value=1.2e+02 Score=31.57 Aligned_cols=50 Identities=26% Similarity=0.420 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhc-CChhhhcC
Q 000262 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAA-STKEDYMN 120 (1768)
Q Consensus 68 ~~R~~m~~ri~~~l~~r~~~~~~~~~~~r~~~lakRLEe~l~k~a-~tK~~Y~n 120 (1768)
.+|..+++.++.-|......+. --..+..||..+|+.||... .++.+|..
T Consensus 4 ~~R~k~~~~L~~~l~~~~~~~~---~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~ 54 (115)
T PF07500_consen 4 KVRDKARKLLYKALQKRSDEQD---DPEDAKELAKEIEEALFDKFGSTSKKYKQ 54 (115)
T ss_dssp HHHHHHHHHHHHHHHHCCCCCC---CTCCHHHHHHHHHHHHHHHHTSTSHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCcccc---chhHHHHHHHHHHHHHHHHHccCcHHHHH
Confidence 5788889888888877754411 13367899999999999998 35566654
No 81
>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=23.27 E-value=27 Score=42.68 Aligned_cols=16 Identities=13% Similarity=0.036 Sum_probs=8.5
Q ss_pred chHHHHHHHHHhcCCC
Q 000262 122 DTLEARLSYLIKGRPG 137 (1768)
Q Consensus 122 ~tle~rL~~~i~~~~~ 137 (1768)
+.|..|+..--+|-.+
T Consensus 75 a~Lf~RfTEdeeRKr~ 90 (468)
T PF11498_consen 75 AELFTRFTEDEERKRA 90 (468)
T ss_dssp HHTHHHHHHHHHHHHH
T ss_pred HHHHHhhchHHHHHHH
Confidence 4556666555444444
No 82
>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=22.26 E-value=53 Score=29.46 Aligned_cols=33 Identities=21% Similarity=0.507 Sum_probs=27.4
Q ss_pred cccccccccccCceeeeecccccccccccchhhhHHHh
Q 000262 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1768)
Q Consensus 1470 ~C~~C~~~iv~~~rw~c~~c~~~~~~f~lC~~Cy~~e~ 1507 (1768)
.|..|..... ..|+.|..+ +++.||..||....
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 589999888 78999999997753
No 83
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=22.18 E-value=29 Score=43.65 Aligned_cols=121 Identities=20% Similarity=0.436 Sum_probs=0.0
Q ss_pred ccceeeeeccccccccccccccCc-------------eeeeecccc--cccccc------cchhhhHHHhhcccccCCCC
Q 000262 1459 KEDFIMVHLQHACNHCCILMVSGS-------------RHVCEQCTK--LNKNFQ------LCDKCFEAEKKREDRERHPV 1517 (1768)
Q Consensus 1459 Ke~F~v~~Lq~~C~~C~~~iv~~~-------------rw~c~~c~~--~~~~f~------lC~~Cy~~e~~~~~~~~hp~ 1517 (1768)
+|++|. .|..|++-|+... -|+|.+|.+ .++.|+ +||.||..-...=..=-|++
T Consensus 270 ~~~~~~-----iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I 344 (468)
T KOG1701|consen 270 VEDYFG-----ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPI 344 (468)
T ss_pred hhhhhh-----hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHH
Q ss_pred Ccccccccccc-------------ccCCCCCCCCCCCccccCcccccHHHHHHHhhhCCCCcchhhhcccchhhHHHhhc
Q 000262 1518 NSREVHILEEV-------------PVTDVPADTKDKDEILESEFFDTRQAFLSLCQGNHYQYDTLRRAKHSSMMVLYHLH 1584 (1768)
Q Consensus 1518 ~~~~~h~L~~v-------------~v~~vp~~t~D~D~~i~seffdtR~aFL~lcq~nHyQFDsLRRAKhSSMMvLyhLH 1584 (1768)
..+-..++-.+ -+++||. |-|-+-.+-|=
T Consensus 345 ~d~iLrA~GkayHp~CF~Cv~C~r~ldgipF-tvd~~n~v~Cv------------------------------------- 386 (468)
T KOG1701|consen 345 MDRILRALGKAYHPGCFTCVVCARCLDGIPF-TVDSQNNVYCV------------------------------------- 386 (468)
T ss_pred HHHHHHhcccccCCCceEEEEeccccCCccc-cccCCCceeee-------------------------------------
Q ss_pred CCCCCcccccccccccCCCCCCceecc-----CCCCCccchhhhc
Q 000262 1585 NPTAPAFVTTCNICHLDIETGQGWRCE-----VCPDYDVCNACYQ 1624 (1768)
Q Consensus 1585 n~~~~~f~~tCn~C~~~I~t~~rwhC~-----vC~DfDLC~~CY~ 1624 (1768)
.---.+|.-.|+.|...|.. +==|+ ||-|-|.-.+||+
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 84
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.13 E-value=31 Score=41.99 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=40.9
Q ss_pred eEEEEEEEEeCCeEEEEEEEEEeecCCCCCCCCCceEEEEeccccccccccccccccchhhhHHHHHHHHHHHHHHHhcC
Q 000262 1231 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1310 (1768)
Q Consensus 1231 sK~I~vFQkidGvDV~fF~M~VqEYgs~c~~pn~r~vyIsYLDSV~yf~P~~~~~~G~~lRt~VYheIL~~Yl~y~k~~G 1310 (1768)
.=+|.-+=+|||.+|++++| +|.- -|..+ +.|..|-|.-=+++|.+.|
T Consensus 121 dgVVtG~G~I~Gr~v~v~a~---Dftf----------------------------~gGSm-G~v~geKi~ra~e~A~~~r 168 (296)
T CHL00174 121 DAVQTGIGQLNGIPVALGVM---DFQF----------------------------MGGSM-GSVVGEKITRLIEYATNES 168 (296)
T ss_pred ccEEEEEEEECCEEEEEEEE---CCcc----------------------------cccCc-CHHHHHHHHHHHHHHHHcC
Confidence 35788899999999998877 4421 11122 2366666677789999999
Q ss_pred CcEEEEEeCC
Q 000262 1311 FTSCYIWACP 1320 (1768)
Q Consensus 1311 F~~ahIWAcP 1320 (1768)
-=-+.|.+..
T Consensus 169 lPlV~l~~SG 178 (296)
T CHL00174 169 LPLIIVCASG 178 (296)
T ss_pred CCEEEEECCC
Confidence 8888777765
No 85
>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=21.61 E-value=1e+02 Score=34.50 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=32.9
Q ss_pred CCCCCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcC
Q 000262 1321 PLKGEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKEN 1359 (1768)
Q Consensus 1321 P~~GDDYIF~~HP~~Qk~p~~~~L~~WY~~mL~kg~~eg 1359 (1768)
+.+|+||+|.+||.....++.+.|..=..=+|+.|++.+
T Consensus 110 s~kG~~~~~~~~mp~~~~LsdeEL~aIAaYLl~qa~~~~ 148 (155)
T TIGR03046 110 SYDGSEESYGCRPVPEDWMDDEEVENLAAFILRAAQKAP 148 (155)
T ss_pred ccCcccccccccCCcccCCCHHHHHHHHHHHHHhhhhcC
Confidence 568999999999999999999999877777777776554
No 86
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=21.27 E-value=41 Score=41.39 Aligned_cols=28 Identities=21% Similarity=0.565 Sum_probs=22.2
Q ss_pred CCcccccccccccCCCCCCceeccCCCCC
Q 000262 1588 APAFVTTCNICHLDIETGQGWRCEVCPDY 1616 (1768)
Q Consensus 1588 ~~~f~~tCn~C~~~I~t~~rwhC~vC~Df 1616 (1768)
...+.|.|.+|.=..-+ -.|||..|-.+
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 34678999999977766 58999999554
No 87
>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=20.98 E-value=7.2 Score=42.32 Aligned_cols=26 Identities=27% Similarity=0.772 Sum_probs=21.2
Q ss_pred CcccccccccccCCCCCCceeccCCCCCccchhhhcc
Q 000262 1589 PAFVTTCNICHLDIETGQGWRCEVCPDYDVCNACYQK 1625 (1768)
Q Consensus 1589 ~~f~~tCn~C~~~I~t~~rwhC~vC~DfDLC~~CY~k 1625 (1768)
+...+.|-.|...|.+| -+|.+|..+
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 378888866
Done!