Query 000748
Match_columns 1303
No_of_seqs 248 out of 305
Neff 4.1
Searched_HMMs 46136
Date Mon Apr 1 22:58:02 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000748.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000748hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08214 KAT11: Histone acetyl 100.0 8.3E-50 1.8E-54 451.2 15.5 210 742-962 8-252 (346)
2 KOG1778 CREB binding protein/P 100.0 2E-47 4.3E-52 425.9 10.8 225 1006-1277 74-298 (319)
3 smart00551 ZnF_TAZ TAZ zinc fi 99.7 7.8E-18 1.7E-22 155.9 7.9 76 1185-1265 2-79 (79)
4 smart00551 ZnF_TAZ TAZ zinc fi 99.5 2E-15 4.3E-20 140.0 2.5 70 218-287 2-79 (79)
5 PF02135 zf-TAZ: TAZ zinc fing 99.3 3.1E-13 6.8E-18 123.3 2.8 72 1189-1264 2-75 (75)
6 PF02135 zf-TAZ: TAZ zinc fing 99.2 1.6E-12 3.4E-17 118.7 -0.5 65 222-286 2-75 (75)
7 cd02337 ZZ_CBP Zinc finger, ZZ 99.0 2E-10 4.3E-15 94.9 2.1 41 1107-1152 1-41 (41)
8 PF00569 ZZ: Zinc finger, ZZ t 98.8 1.2E-09 2.7E-14 91.9 1.7 44 1105-1149 3-46 (46)
9 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.4 1.4E-07 3E-12 80.7 2.8 45 1107-1151 1-47 (48)
10 smart00291 ZnF_ZZ Zinc-binding 98.4 2.1E-07 4.6E-12 77.8 2.9 35 1104-1139 2-36 (44)
11 cd02344 ZZ_HERC2 Zinc finger, 98.3 2.2E-07 4.7E-12 78.6 2.4 42 1107-1151 1-44 (45)
12 cd02249 ZZ Zinc finger, ZZ typ 98.3 4.9E-07 1.1E-11 76.2 2.5 43 1107-1151 1-45 (46)
13 cd02345 ZZ_dah Zinc finger, ZZ 98.3 5E-07 1.1E-11 77.4 2.6 42 1108-1150 2-47 (49)
14 PF06001 DUF902: Domain of Unk 98.3 1.9E-07 4.1E-12 77.3 0.0 36 569-604 6-42 (42)
15 cd02340 ZZ_NBR1_like Zinc fing 98.2 6.9E-07 1.5E-11 74.7 2.5 41 1108-1151 2-42 (43)
16 cd02339 ZZ_Mind_bomb Zinc fing 98.1 1.4E-06 3.1E-11 73.7 2.6 43 1108-1151 2-44 (45)
17 cd02335 ZZ_ADA2 Zinc finger, Z 98.1 1.8E-06 3.8E-11 73.9 2.8 33 1107-1139 1-33 (49)
18 cd02334 ZZ_dystrophin Zinc fin 97.9 4.7E-06 1E-10 71.8 2.5 32 1108-1139 2-33 (49)
19 cd02338 ZZ_PCMF_like Zinc fing 97.9 6.1E-06 1.3E-10 70.8 2.2 32 1108-1139 2-33 (49)
20 cd02342 ZZ_UBA_plant Zinc fing 97.9 5.9E-06 1.3E-10 69.3 1.9 34 1108-1141 2-35 (43)
21 cd02343 ZZ_EF Zinc finger, ZZ 97.8 1.3E-05 2.8E-10 68.9 2.7 41 1108-1150 2-46 (48)
22 KOG4582 Uncharacterized conser 97.6 3.1E-05 6.6E-10 87.5 2.1 46 1107-1154 153-199 (278)
23 cd02336 ZZ_RSC8 Zinc finger, Z 96.9 0.0006 1.3E-08 58.1 2.3 32 1107-1139 1-32 (45)
24 KOG1280 Uncharacterized conser 96.3 0.0014 3E-08 75.4 1.3 48 1106-1153 8-58 (381)
25 PF00628 PHD: PHD-finger; Int 95.0 0.0037 8.1E-08 53.0 -1.5 42 645-686 9-50 (51)
26 KOG0457 Histone acetyltransfer 94.7 0.012 2.6E-07 69.7 1.3 35 1105-1139 13-47 (438)
27 COG5087 RTT109 Uncharacterized 94.5 0.64 1.4E-05 53.0 13.7 100 796-908 54-156 (349)
28 KOG4534 Uncharacterized conser 94.5 0.64 1.4E-05 53.0 13.7 100 796-908 54-156 (349)
29 smart00249 PHD PHD zinc finger 93.9 0.042 9.1E-07 44.4 2.4 38 646-684 10-47 (47)
30 COG5114 Histone acetyltransfer 92.0 0.12 2.7E-06 59.3 3.4 35 1105-1139 4-38 (432)
31 KOG4286 Dystrophin-like protei 89.1 0.16 3.4E-06 63.7 1.0 62 1091-1152 588-652 (966)
32 KOG0956 PHD finger protein AF1 88.5 0.16 3.4E-06 63.2 0.5 88 569-671 8-95 (900)
33 PF07649 C1_3: C1-like domain; 86.4 0.3 6.6E-06 38.0 0.9 28 1108-1136 2-29 (30)
34 PF07227 DUF1423: Protein of u 77.2 2.5 5.4E-05 51.3 4.2 39 649-687 145-192 (446)
35 KOG4323 Polycomb-like PHD Zn-f 66.6 2 4.4E-05 52.4 0.3 38 650-687 185-224 (464)
36 PF03107 C1_2: C1 domain; Int 64.5 3.6 7.9E-05 32.3 1.2 28 1108-1136 2-29 (30)
37 KOG4301 Beta-dystrobrevin [Cyt 63.8 10 0.00022 45.0 5.0 47 1093-1139 227-273 (434)
38 PF13831 PHD_2: PHD-finger; PD 54.3 2.9 6.3E-05 34.4 -0.9 33 649-684 3-35 (36)
39 COG5141 PHD zinc finger-contai 52.0 9.5 0.00021 46.8 2.4 81 567-671 194-280 (669)
40 KOG1778 CREB binding protein/P 51.9 12 0.00027 44.0 3.3 129 1112-1257 60-191 (319)
41 KOG1844 PHD Zn-finger proteins 48.3 8.3 0.00018 47.1 1.2 39 647-688 98-136 (508)
42 KOG0957 PHD finger protein [Ge 46.0 12 0.00026 46.1 2.0 92 565-674 118-218 (707)
43 KOG1973 Chromatin remodeling p 43.9 17 0.00037 41.8 2.8 35 649-687 231-268 (274)
44 COG2888 Predicted Zn-ribbon RN 38.6 22 0.00048 32.8 2.0 28 583-619 9-36 (61)
45 PF07496 zf-CW: CW-type Zinc F 34.9 16 0.00034 32.0 0.5 34 648-683 1-34 (50)
46 PF00412 LIM: LIM domain; Int 34.1 37 0.0008 29.2 2.7 39 575-619 18-56 (58)
47 PF00150 Cellulase: Cellulase 33.5 1.9E+02 0.0041 31.7 8.7 55 851-916 22-79 (281)
48 COG2956 Predicted N-acetylgluc 30.7 25 0.00054 41.9 1.4 43 1086-1129 334-376 (389)
49 PF02318 FYVE_2: FYVE-type zin 24.5 1.2E+02 0.0025 30.8 4.7 52 564-620 52-104 (118)
50 KOG0336 ATP-dependent RNA heli 22.6 38 0.00082 41.5 1.0 34 868-904 164-198 (629)
51 PRK06266 transcription initiat 22.6 96 0.0021 33.9 3.9 55 647-728 114-168 (178)
52 KOG0955 PHD finger protein BR1 22.0 58 0.0013 44.0 2.6 89 565-671 218-306 (1051)
53 smart00642 Aamy Alpha-amylase 21.0 2.2E+02 0.0048 30.4 6.2 63 852-916 21-87 (166)
54 TIGR00373 conserved hypothetic 20.6 76 0.0016 33.9 2.6 33 645-686 104-136 (158)
No 1
>PF08214 KAT11: Histone acetylation protein; InterPro: IPR013178 Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal RTT109 protein, which is required for H3K56 acetylation. In Schizosaccharomyces pombe (Fission yeast) loss of RTT109 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin []. RTT109 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast []. This family also incorporates the p300/CBP histone acetyltransferase domain which has different catalytic properties and cofactor regulation to RTT109 []. This entry also contains CREB-binding proteins; these acetylate histones, giving a specific tag for transcriptional activation. They also acetylate non-histone proteins, like NCOA3 coactivator. They bind specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes [, ]. ; PDB: 3CZ7_A 2RIM_A 3Q66_C 2ZFN_A 3QM0_A 3Q68_C 3Q35_A 3Q33_A 3BIY_A.
Probab=100.00 E-value=8.3e-50 Score=451.18 Aligned_cols=210 Identities=44% Similarity=0.793 Sum_probs=181.1
Q ss_pred CCCCCCCeEEEEEeecchhhhhhHhHHHhhhhCCCCCcccceeEEEEEEEEeCCeEEEEEEEEeeecCCCCCCCCcceEE
Q 000748 742 EVPTAEDLVVRVVLSVDKKLKVKQQFLDIFHEANYPTEFPYRLKVILLFQKIEGVDVCLFGMYVQEFGSECSHPNQRCVY 821 (1303)
Q Consensus 742 ev~~Ae~l~IRVVsSvdK~~eVk~~f~~~F~~~~yp~efpYrsKaI~vFQkIDGVDVcfF~MyVQEYgs~c~~PN~rrVy 821 (1303)
.+|+++.++||+|+|++++++++..|...|.+..||.+++|+.|+|+|||++||+|||||+|+||||+..|+.||++|||
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 37889999999999999999999999999987779999999999999999999999999999999999999999999999
Q ss_pred EEeccccccccccccccccccchhHHHHHHHHHHHHHHHhcCCcEEEEEeCCCCCCCCeeeccCCCCCCCCC-----hhH
Q 000748 822 ISYLDSVKYFRPETETAAGKTLRTFVYHEILIGYLEYSKKRGFATCYIWACPPVKGEDYILYCHPEMQKTPK-----SDK 896 (1303)
Q Consensus 822 IsYLDSV~YFrP~~~~~sGe~lRT~VYhEILi~Yl~Yak~~GF~~aHIWAcPP~kGDDYIF~cHP~~Qk~pk-----~~r 896 (1303)
|+|||||.||+|. .+||.+||++|++||+|++.+||.++|||||||.+|||||| |..|++|+ .++
T Consensus 88 IsylDSv~y~~~~-------~~r~~~~~~~ll~Yl~~~~~~g~~~~~~~a~~pr~~dqYlF---P~s~k~p~KhvL~~~~ 157 (346)
T PF08214_consen 88 ISYLDSVGYFKPS-------PSRTRVYHEILLSYLDYARPRGYTKAHIWACFPRAGDQYLF---PNSQKNPKKHVLDDDR 157 (346)
T ss_dssp EEEEEE-S--SSG-------GGHHHHHHHHHHHHHHCCHCHCHHCCEEEEEEE-CCS-SSS---TTCGGSTTS----HHH
T ss_pred EEECcccCCCCcc-------cccHHHHHHHHHHHHHHhhccCCcEEEEEEecCCCCCCeEc---CCcccCCccccccchH
Confidence 9999999999996 68999999999999999999999999999999999999999 88888888 999
Q ss_pred HHHHHHHHHHHHH-------hcCcEeeehhhhhh--hccCCCCCCc--------------CCcCccCcccCCCccHHHHH
Q 000748 897 LRQWYRSMLRKAA-------EEKIVVGISNLYDQ--FFIPTGQHSK--------------VTAARLPYFDGDYWSGAAEG 953 (1303)
Q Consensus 897 L~~WY~~mL~kgk-------~eGIV~~~~n~yd~--~f~~~~e~~k--------------~~a~~LPYFeGd~Wp~~~E~ 953 (1303)
|++||.+||++|+ +.+||+...++|+. |+.. ..... ..+..||||+||+||+.||+
T Consensus 158 L~~Wy~~~L~~~~~~~~~~~~~~~vvpg~d~~~~~~~~~~-~~~~~~W~~g~~~~~~~~~~~~~~iP~FpdDpk~rfle~ 236 (346)
T PF08214_consen 158 LLKWYKKMLDKAKEESFKNAKAYLVVPGSDLYETRKYLPN-TPDSNSWTYGHPFSQIKSDPAACLIPYFPDDPKPRFLEE 236 (346)
T ss_dssp HHHHHHHHHHHHHHHHB-TTCCCCE-CCCEHHHHHHHHTC-CCCTTTEEES-ST-SSSTSBGGGCSB--TT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhhhcccccccceEecCccHHHhhhhccc-cccccccccccccccccccCccccCCcCCCchHHHHHHH
Confidence 9999999999999 99999999999986 3332 22222 26778999999999999999
Q ss_pred HHHH-------HHhhc
Q 000748 954 VIKS-------IEQER 962 (1303)
Q Consensus 954 iike-------i~qE~ 962 (1303)
++++ |+++.
T Consensus 237 l~~e~~~~~~s~~~fw 252 (346)
T PF08214_consen 237 LIEEGRWKKVSLDQFW 252 (346)
T ss_dssp HHHTT-TTT-BHHHHH
T ss_pred HHHhhhhccccHHHHH
Confidence 9999 77754
No 2
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=100.00 E-value=2e-47 Score=425.92 Aligned_cols=225 Identities=31% Similarity=0.562 Sum_probs=199.9
Q ss_pred cccceeecccchhhhhhcCCCcccccccccccccccccccCCCCCCCCCCcccccccccChHHHHHHHhhcCCccchhhh
Q 000748 1006 QFLFFLSCCRCHDAERNLNGEDIHTLNGKEKHALNKVMVDDVPCHTRDKDVIIDNTSFENRNAFLSFCQKNYYQFDTLRR 1085 (1303)
Q Consensus 1006 q~knF~ic~~c~~~e~~l~~~~~hp~~~k~~~~l~~v~i~~~p~~t~D~D~~i~se~~d~R~aFL~lCq~nh~QFdsLRR 1085 (1303)
..++++++++|+.+. .++|+.+.+++|.++.+.+.++|..+.|+|++++|++|++|++||.+|+.+||||++|||
T Consensus 74 ~c~~~~~~~~~l~~~-----~ek~e~~~~~ihll~~~~~~~v~~~~~d~~~~~~~~~~~~r~~flvl~~~~~~~~~~lr~ 148 (319)
T KOG1778|consen 74 PCKAVNVFIRFLYSS-----LEKHEMVFFDIHLLALSHVYVVPQPKADCDPILECGLFDKRNVFLVLQLAEHCDFSDLRR 148 (319)
T ss_pred cccccchhhhhhccc-----hhhhHHHHHHHHHHhhhhhhhccCccccCCccccchhhhhHHHHHHHHHHHhcccchHHH
Confidence 347889999998766 467888889999999888889999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhcccccccccccccccccCcccCCccccCCCCCCccchhhhhccCCcccccccccccccCCCCCcchHH
Q 000748 1086 AKYSSMMILHHLHNSSMLTAESICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKLTQRSSAVDGGTESREA 1165 (1303)
Q Consensus 1086 AK~SSMmmLyhLHNp~~~~fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm~~~~~~~d~g~~~~~~ 1165 (1303)
|+|||||++|+||+++++.|+|+|+.|+.+++++ |||++|+|||+|.+||.+.. |.|+|+.+++..+
T Consensus 149 a~hss~~~~~~~H~~t~~~~~~~c~~c~~~~~~~--~~c~~~~d~d~~~~~~~k~~---h~h~~~~~~~~~~-------- 215 (319)
T KOG1778|consen 149 AKHSSIMLLFDLHLQTEKWFAYTCPICKLEVLTA--WHCEVCPDYDRCRACEEKPL---HPHLYEAMESCTD-------- 215 (319)
T ss_pred HHHHHHHHHHHHHhcccCceeeecCccccccccc--cccccCCchhhhhcccCCCC---CCcchhccccccc--------
Confidence 9999999999999999999999999999999555 99999999999999999965 9999999887321
Q ss_pred HHHHHHhCCCCCccccchhhHHHHHHHHHHHHHHhhcCCCCCCCCCCchhhHHHHHHHHHhhhcccccCCCCcchHHHHH
Q 000748 1166 QTKALQAGRNPDTYIHSQVNLTLQKTQLMNLLQHASQCSLTKSKGCSYPKCLQMKTLFYHARSCNVRTAGGCQHCRKIWL 1245 (1303)
Q Consensus 1166 q~~~~~~~r~P~~~~~~qes~~~qLqr~me~LvHA~~C~~~~~a~C~~p~C~kMK~L~~H~~~Ck~R~~GGC~~CKrmw~ 1245 (1303)
... .++.++.+|.+ + +++|.++.|.+||+||+|++.|+.| |||++|++||+
T Consensus 216 -~~~------------~~~~~~~~i~~-----------~---~~~C~~~~C~~~k~lirH~~~Ck~R--~gC~iCk~m~~ 266 (319)
T KOG1778|consen 216 -GCA------------TIGPRNKSINR-----------R---DANCSYPSCNGLKRLIRHFRGCKLR--GGCPICKRLWQ 266 (319)
T ss_pred -ccc------------cccchhhhhcc-----------C---CCCCCCchhHHHHHHHHHHHHHHhc--cCCchHHHHHH
Confidence 111 12223355554 3 7999999999999999999999999 99999999999
Q ss_pred HHHHHhhcCCCCCCCCCCchhHHHHHHHhhhh
Q 000748 1246 LLTMHSRRCKELDCRVPRCKDLKQWNAEAVVG 1277 (1303)
Q Consensus 1246 Ll~lHAk~C~e~~C~VP~C~~iK~~~qe~~~~ 1277 (1303)
|++|||++|+++.|+||+|++||++++++...
T Consensus 267 L~~lha~~c~~~~C~vP~c~~~k~~~~~~~~~ 298 (319)
T KOG1778|consen 267 LLELHARHCDDSKCKVPLCRNLKQKLEKQQKQ 298 (319)
T ss_pred HHHHHHHHcccccCCCCCCccHHHHHHHHHhh
Confidence 99999999999999999999999998777543
No 3
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.72 E-value=7.8e-18 Score=155.90 Aligned_cols=76 Identities=38% Similarity=0.861 Sum_probs=70.9
Q ss_pred hHHHHHHHHHHHHHHhhcCCCCCCCCCCchhhHHHHHHHHHhhhcccc--cCCCCcchHHHHHHHHHHhhcCCCCCCCCC
Q 000748 1185 NLTLQKTQLMNLLQHASQCSLTKSKGCSYPKCLQMKTLFYHARSCNVR--TAGGCQHCRKIWLLLTMHSRRCKELDCRVP 1262 (1303)
Q Consensus 1185 s~~~qLqr~me~LvHA~~C~~~~~a~C~~p~C~kMK~L~~H~~~Ck~R--~~GGC~~CKrmw~Ll~lHAk~C~e~~C~VP 1262 (1303)
.+|.+|+++|++|+||++|+.. +++|.+++|.+||.||+|+++|+.+ ..+||..||+||+ ||++|++.+|+||
T Consensus 2 ~~~~~lq~~l~~L~Ha~~C~~~-~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~----H~k~C~~~~C~Vc 76 (79)
T smart00551 2 TRYKQLQRWLELLVHARRCKAR-EAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQ----HSKHCKDSNCPVC 76 (79)
T ss_pred cHHHHHHHHHHHHHHHHhCCCC-CCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHH----HHHhcCCCCCCCC
Confidence 3579999999999999999833 3899999999999999999999999 7899999999999 9999999999999
Q ss_pred Cch
Q 000748 1263 RCK 1265 (1303)
Q Consensus 1263 ~C~ 1265 (1303)
+|+
T Consensus 77 ~c~ 79 (79)
T smart00551 77 KCV 79 (79)
T ss_pred CCC
Confidence 995
No 4
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.54 E-value=2e-15 Score=140.00 Aligned_cols=70 Identities=17% Similarity=0.330 Sum_probs=67.0
Q ss_pred hhhhhhhhHHHHhhcccccccCCCCCCCcccc-----ccccccccCCcc---cccchhhhhhhcccCCCCCCccchhh
Q 000748 218 SCLYLENRILHAYINYKSSMVANGGSIVSFVN-----YLHSTICNIHWC---GCERFCILLSHFDGCHSAECHICGPV 287 (1303)
Q Consensus 218 ~~l~~qqrwLl~l~HA~~C~~p~g~C~~~~C~-----~~Hm~~C~~~~C---~C~ssr~lLsH~k~C~~~~CpVC~PV 287 (1303)
..+.++||||+||+||.+|+.+++.|..++|. |.||..|+.+.| +|.++|.|++||++|++++||||.|+
T Consensus 2 ~~~~~lq~~l~~L~Ha~~C~~~~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~H~k~C~~~~C~Vc~c~ 79 (79)
T smart00551 2 TRYKQLQRWLELLVHARRCKAREAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQHSKHCKDSNCPVCKCV 79 (79)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 35778999999999999999999999999999 999999999999 99999999999999999999999986
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=99.35 E-value=3.1e-13 Score=123.29 Aligned_cols=72 Identities=42% Similarity=0.867 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHhhcCCCCCCCCCCchhhHHHHHHHHHhhhccccc--CCCCcchHHHHHHHHHHhhcCCCCCCCCCCc
Q 000748 1189 QKTQLMNLLQHASQCSLTKSKGCSYPKCLQMKTLFYHARSCNVRT--AGGCQHCRKIWLLLTMHSRRCKELDCRVPRC 1264 (1303)
Q Consensus 1189 qLqr~me~LvHA~~C~~~~~a~C~~p~C~kMK~L~~H~~~Ck~R~--~GGC~~CKrmw~Ll~lHAk~C~e~~C~VP~C 1264 (1303)
+|++.|++|.||..|+.+..+.|.++.|.+||.||.|+..|..+. .++|..||+||. |++.|++.+|+||+|
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 689999999999999921118999999999999999999999887 788999999888 999999999999987
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=99.21 E-value=1.6e-12 Score=118.69 Aligned_cols=65 Identities=23% Similarity=0.416 Sum_probs=60.8
Q ss_pred hhhhHHHHhhcccccccCC-CCCCCcccc-----ccccccccCCcc---cccchhhhhhhcccCCCCCCccchh
Q 000748 222 LENRILHAYINYKSSMVAN-GGSIVSFVN-----YLHSTICNIHWC---GCERFCILLSHFDGCHSAECHICGP 286 (1303)
Q Consensus 222 ~qqrwLl~l~HA~~C~~p~-g~C~~~~C~-----~~Hm~~C~~~~C---~C~ssr~lLsH~k~C~~~~CpVC~P 286 (1303)
.+||||.||+||.+|+.++ +.|..++|. |.|+..|.++.| +|.++|.|++||++|++.+|+||.+
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 5789999999999999987 899999999 999999998878 9999999999999999999999975
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=98.97 E-value=2e-10 Score=94.91 Aligned_cols=41 Identities=27% Similarity=0.906 Sum_probs=36.2
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhccCCcccccccccc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKLTQR 1152 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm~~~ 1152 (1303)
||||.|...+ +.||||.+|+|||||..||.+ ..|+|+|+++
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 6899998854 378999999999999999998 4699999874
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=98.82 E-value=1.2e-09 Score=91.90 Aligned_cols=44 Identities=30% Similarity=0.842 Sum_probs=34.9
Q ss_pred ccccccccccCcccCCccccCCCCCCccchhhhhccCCccccccc
Q 000748 1105 AESICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKL 1149 (1303)
Q Consensus 1105 fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm 1149 (1303)
..++|+.|+.+..+|.||||.+|+|||||.+||.+ |...|.|+|
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 56899999998888999999999999999999987 667889987
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=98.41 E-value=1.4e-07 Score=80.72 Aligned_cols=45 Identities=20% Similarity=0.550 Sum_probs=36.5
Q ss_pred ccccccccCcccCCccccCCCC--CCccchhhhhccCCccccccccc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCP--QFEVCTACYQEKGNSLHIHKLTQ 1151 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~--DfDLC~~CY~k~G~~~H~Hkm~~ 1151 (1303)
|+|++|...-.+|.||||.+|+ |||||..||.+.......|+|++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~ 47 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGESHQEDHWLVK 47 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcCCCCCCCceee
Confidence 6899999966669999999999 99999999998322233577765
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=98.37 E-value=2.1e-07 Score=77.78 Aligned_cols=35 Identities=23% Similarity=0.881 Sum_probs=31.9
Q ss_pred cccccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1104 TAESICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1104 ~fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
.+.++|+.|+. ..++.||||.+|+|||||..||.+
T Consensus 2 ~~~~~C~~C~~-~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 2 HHSYSCDTCGK-PIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred CCCcCCCCCCC-CCcCCEEECCCCCCccchHHHHhC
Confidence 46789999999 557899999999999999999997
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=98.35 E-value=2.2e-07 Score=78.60 Aligned_cols=42 Identities=21% Similarity=0.701 Sum_probs=35.5
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhccCCccc--cccccc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLH--IHKLTQ 1151 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H--~Hkm~~ 1151 (1303)
.+|+.|+.....|.||+|.+|+|||||..||.+. .| .|.+.+
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~---~H~~~H~F~r 44 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKTR---KHNTRHTFGR 44 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCCC---CcCCCCceee
Confidence 3799999988889999999999999999999984 35 566543
No 12
>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=98.26 E-value=4.9e-07 Score=76.17 Aligned_cols=43 Identities=30% Similarity=0.706 Sum_probs=35.5
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhccCCccc--cccccc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLH--IHKLTQ 1151 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H--~Hkm~~ 1151 (1303)
|+|+.|++.|. |.+|||.+|+|||||..||.+.- ..| .|+|+.
T Consensus 1 ~~C~~C~~~i~-g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~ 45 (46)
T cd02249 1 YSCDGCLKPIV-GVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTE 45 (46)
T ss_pred CCCcCCCCCCc-CCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeE
Confidence 57999999764 68999999999999999999742 356 577764
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=98.25 E-value=5e-07 Score=77.45 Aligned_cols=42 Identities=29% Similarity=0.820 Sum_probs=34.1
Q ss_pred ccccccc-CcccCCccccCCCCCCccchhhhhccC-Cccc--ccccc
Q 000748 1108 ICCLCRK-DTVIDQCWQCETCPQFEVCTACYQEKG-NSLH--IHKLT 1150 (1303)
Q Consensus 1108 tCn~C~~-~iet~~~whC~vC~DfDLC~~CY~k~G-~~~H--~Hkm~ 1150 (1303)
+|+.|.+ +|. |.||+|.+|+|||||..||.... ...| .|+|.
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 776 89999999999999999999731 1245 66664
No 14
>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=98.25 E-value=1.9e-07 Score=77.31 Aligned_cols=36 Identities=31% Similarity=0.551 Sum_probs=0.4
Q ss_pred cccccCccceecCCcccccCC-CccccCCCeeeecCC
Q 000748 569 CQLCQAEKLLLAPTPIYCSYC-GADIKRYVIYYSTPE 604 (1303)
Q Consensus 569 C~lC~~~kL~F~p~~lyC~~c-~cRIkr~a~Yy~~~~ 604 (1303)
-++||+++|.|.|++|||+|. .|.|+||+.||++++
T Consensus 6 lGyCCgrk~~f~p~~L~C~Gk~lCtI~Rd~~Y~~Y~n 42 (42)
T PF06001_consen 6 LGYCCGRKLVFTPQVLYCYGKQLCTIPRDAVYYSYQN 42 (42)
T ss_dssp H------------------------------------
T ss_pred cCcccCCceEecCceEEecCCceeeeecCCEEEEeeC
Confidence 479999999999999999987 699999999999864
No 15
>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=98.21 E-value=6.9e-07 Score=74.75 Aligned_cols=41 Identities=22% Similarity=0.686 Sum_probs=34.5
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhccCCccccccccc
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKLTQ 1151 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm~~ 1151 (1303)
+|+.|+..| +|.||+|.+|+|||||..||...+ . ..|+|.+
T Consensus 2 ~Cd~C~~~i-~G~ry~C~~C~d~dLC~~C~~~~~-H-~~H~f~~ 42 (43)
T cd02340 2 ICDGCQGPI-VGVRYKCLVCPDYDLCESCEAKGV-H-PEHAMLK 42 (43)
T ss_pred CCCCCCCcC-cCCeEECCCCCCccchHHhhCcCC-C-CCCCEEe
Confidence 799999954 789999999999999999999842 2 3788764
No 16
>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=98.12 E-value=1.4e-06 Score=73.70 Aligned_cols=43 Identities=35% Similarity=0.968 Sum_probs=35.4
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhccCCccccccccc
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKLTQ 1151 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm~~ 1151 (1303)
.|+.|+.....|.||+|.+|+|||||..||.... ....|+|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~~-H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGDK-HDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCCC-CCCCCCEEe
Confidence 6999998888899999999999999999999632 233677653
No 17
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.10 E-value=1.8e-06 Score=73.92 Aligned_cols=33 Identities=30% Similarity=0.846 Sum_probs=31.6
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
|+|+.|.+++..+.||+|.+|+|||||..||..
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 589999999999999999999999999999997
No 18
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=97.94 E-value=4.7e-06 Score=71.76 Aligned_cols=32 Identities=19% Similarity=0.816 Sum_probs=30.1
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
+|+.|+....+|.||+|.+|+|||||..||.+
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~ 33 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFS 33 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhC
Confidence 79999998778999999999999999999987
No 19
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=97.89 E-value=6.1e-06 Score=70.80 Aligned_cols=32 Identities=25% Similarity=0.838 Sum_probs=28.4
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
+|+.|+....+|.||+|.+|+|||||.+||.+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~ 33 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDS 33 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhC
Confidence 69999954444999999999999999999997
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=97.88 E-value=5.9e-06 Score=69.28 Aligned_cols=34 Identities=18% Similarity=0.557 Sum_probs=31.3
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhccC
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKG 1141 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G 1141 (1303)
+|..|...=..|.||+|.+|+|||||..||.+.|
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 7999998878899999999999999999999854
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=97.80 E-value=1.3e-05 Score=68.86 Aligned_cols=41 Identities=20% Similarity=0.567 Sum_probs=32.8
Q ss_pred cccccccCcccCCccccCCCCCCccchhhhhccCCc----ccccccc
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNS----LHIHKLT 1150 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~----~H~Hkm~ 1150 (1303)
.|+.|... .++.||+|.+|+|||||..||.. |.. ...|||.
T Consensus 2 ~CdgC~~~-~~~~RykCl~C~d~DlC~~Cf~~-g~~~~~H~~~Hpm~ 46 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQCTDMDLCKTCFLG-GVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCc-CCCceEECCCCCCchhHHHHHhC-CccCCCCCCCCCcc
Confidence 59999995 57889999999999999999987 333 3356654
No 22
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.56 E-value=3.1e-05 Score=87.47 Aligned_cols=46 Identities=22% Similarity=0.679 Sum_probs=38.8
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhccCCccc-ccccccccc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLH-IHKLTQRSS 1154 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H-~Hkm~~~~~ 1154 (1303)
..|.+|.+....|.||+|.+|+|||||..||.+.+ .| .|.|.++..
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~--~h~~H~~lR~~t 199 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNE--HHAAHAMLRLHT 199 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCC--CCcccceeeccc
Confidence 68999999888899999999999999999999731 23 788877443
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=96.87 E-value=0.0006 Score=58.09 Aligned_cols=32 Identities=25% Similarity=0.697 Sum_probs=29.9
Q ss_pred ccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1107 SICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1107 ~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
|.|+.|..++. +.||||..+.|||||..||.+
T Consensus 1 y~C~~Cg~D~t-~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 1 YHCFTCGNDCT-RVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred CcccCCCCccC-ceEEEecCCCccccChHHHhC
Confidence 67999999995 689999999999999999997
No 24
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=96.33 E-value=0.0014 Score=75.35 Aligned_cols=48 Identities=19% Similarity=0.473 Sum_probs=40.2
Q ss_pred cccccccccCcccCCccccCCCCCCccchhhhhccC---Cccccccccccc
Q 000748 1106 ESICCLCRKDTVIDQCWQCETCPQFEVCTACYQEKG---NSLHIHKLTQRS 1153 (1303)
Q Consensus 1106 v~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~G---~~~H~Hkm~~~~ 1153 (1303)
...|..|...--++.||+|..|.|||||..||+.+- ...|.|||.=+-
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil 58 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCIL 58 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEe
Confidence 457999999999999999999999999999999842 235788986543
No 25
>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=94.97 E-value=0.0037 Score=52.99 Aligned_cols=42 Identities=29% Similarity=0.710 Sum_probs=31.2
Q ss_pred cccccceecccccCcccccccccccccCCCCCcccccCCCcc
Q 000748 645 AIEEAWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPKCRL 686 (1303)
Q Consensus 645 ~~~EpwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~C~~ 686 (1303)
...+.+|+|+.|++|+|..|.-............|+|+.|..
T Consensus 9 ~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 9 DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 456789999999999999999776442221123799999863
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.74 E-value=0.012 Score=69.69 Aligned_cols=35 Identities=26% Similarity=0.700 Sum_probs=32.6
Q ss_pred ccccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1105 AESICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1105 fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
--|.|++|..+|....+.+|.+|||||||..|...
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 56889999999998888999999999999999986
No 27
>COG5087 RTT109 Uncharacterized conserved protein [Function unknown]
Probab=94.49 E-value=0.64 Score=52.98 Aligned_cols=100 Identities=19% Similarity=0.361 Sum_probs=78.4
Q ss_pred eEEEEEEEEeeecCCCCCCCCcceEEEEeccccccccccccccccccchhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCC
Q 000748 796 VDVCLFGMYVQEFGSECSHPNQRCVYISYLDSVKYFRPETETAAGKTLRTFVYHEILIGYLEYSKKRGFATC-YIWACPP 874 (1303)
Q Consensus 796 VDVcfF~MyVQEYgs~c~~PN~rrVyIsYLDSV~YFrP~~~~~sGe~lRT~VYhEILi~Yl~Yak~~GF~~a-HIWAcPP 874 (1303)
..++||||-+|-|..+ ..++|||+=-||--|-. .|...||.++-|+|++-.---|+.|=.-+ -+++-|-
T Consensus 54 q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gvs~~t~ii~~filsId~iRKq~a~~v~iclFs~p~ 123 (349)
T COG5087 54 QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGVSRGTKIILEFILSIDKIRKQLAPGVCICLFSVPR 123 (349)
T ss_pred cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------ccccccchhhhhhhhhhhhhhhccCCceEEEEEeccc
Confidence 6899999999999554 35799999999999964 34567899999999998876666665555 6788775
Q ss_pred CCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000748 875 VKGEDYILYCHPEM--QKTPKSDKLRQWYRSMLRKA 908 (1303)
Q Consensus 875 ~kGDDYIF~cHP~~--Qk~pk~~rL~~WY~~mL~kg 908 (1303)
. .|||..--.+ ..++++..|.+|...+|+--
T Consensus 124 s---qYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T COG5087 124 S---QYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred c---ceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 4 5999765443 33899999999999877654
No 28
>KOG4534 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.49 E-value=0.64 Score=52.98 Aligned_cols=100 Identities=19% Similarity=0.361 Sum_probs=78.4
Q ss_pred eEEEEEEEEeeecCCCCCCCCcceEEEEeccccccccccccccccccchhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCC
Q 000748 796 VDVCLFGMYVQEFGSECSHPNQRCVYISYLDSVKYFRPETETAAGKTLRTFVYHEILIGYLEYSKKRGFATC-YIWACPP 874 (1303)
Q Consensus 796 VDVcfF~MyVQEYgs~c~~PN~rrVyIsYLDSV~YFrP~~~~~sGe~lRT~VYhEILi~Yl~Yak~~GF~~a-HIWAcPP 874 (1303)
..++||||-+|-|..+ ..++|||+=-||--|-. .|...||.++-|+|++-.---|+.|=.-+ -+++-|-
T Consensus 54 q~~~~fgme~~vyEad----ae~~vfVskaDttGygn------~gvs~~t~ii~~filsId~iRKq~a~~v~iclFs~p~ 123 (349)
T KOG4534|consen 54 QETLLFGMELQVYEAD----AENRVFVSKADTTGYGN------RGVSRGTKIILEFILSIDKIRKQLAPGVCICLFSVPR 123 (349)
T ss_pred cceEEEEEEEEEEecC----ceeEEEEEecccCCcCc------ccccccchhhhhhhhhhhhhhhccCCceEEEEEeccc
Confidence 6899999999999554 35799999999999964 34567899999999998876666665555 6788775
Q ss_pred CCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000748 875 VKGEDYILYCHPEM--QKTPKSDKLRQWYRSMLRKA 908 (1303)
Q Consensus 875 ~kGDDYIF~cHP~~--Qk~pk~~rL~~WY~~mL~kg 908 (1303)
. .|||..--.+ ..++++..|.+|...+|+--
T Consensus 124 s---qYlFp~Ss~N~~Khiln~~eLl~wW~~i~~~~ 156 (349)
T KOG4534|consen 124 S---QYLFPGSSRNREKHILNPGELLEWWIFILEVF 156 (349)
T ss_pred c---ceecCCccccccccccChHHHHHHHHHHHHHH
Confidence 4 5999765443 33899999999999877654
No 29
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=91.97 E-value=0.12 Score=59.35 Aligned_cols=35 Identities=23% Similarity=0.677 Sum_probs=32.3
Q ss_pred ccccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1105 AESICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1105 fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
.-+-|++|..++....+-+|..||+||||..|+..
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~ 38 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVN 38 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhc
Confidence 34679999999999999999999999999999987
No 31
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=89.12 E-value=0.16 Score=63.74 Aligned_cols=62 Identities=11% Similarity=0.378 Sum_probs=44.7
Q ss_pred HHHHHHhcccccccccccccccccCcccCCccccCCCCCCccchhhhhcc---CCcccccccccc
Q 000748 1091 MMILHHLHNSSMLTAESICCLCRKDTVIDQCWQCETCPQFEVCTACYQEK---GNSLHIHKLTQR 1152 (1303)
Q Consensus 1091 MmmLyhLHNp~~~~fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k~---G~~~H~Hkm~~~ 1152 (1303)
++||+-+---..-+-...||+|+.-=.-|.||+|.+|=+||||.+|+-.- |+..-.|||...
T Consensus 588 L~vlhRv~~aE~~kH~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey 652 (966)
T KOG4286|consen 588 LPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEY 652 (966)
T ss_pred HHHHHHHHHHHHHHhhhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceee
Confidence 44444444434445567899999988889999999999999999999762 112225888654
No 32
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=88.49 E-value=0.16 Score=63.18 Aligned_cols=88 Identities=23% Similarity=0.486 Sum_probs=59.1
Q ss_pred cccccCccceecCCcccccCCCccccCCCeeeecCCCCccceEEecccccccCCCceeccCccchHHhHHHhhcCccccc
Q 000748 569 CQLCQAEKLLLAPTPIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQSRGGKISLYGISFSKAKMYKRKNDEAIEE 648 (1303)
Q Consensus 569 C~lC~~~kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~~~~~~I~~~~~~i~K~~~~KkkNde~~~E 648 (1303)
|..|..|+=.=|-|-+||.|-.|.+.-++-.|.... -.+--|||-||-...+.-.|.-+--+.+--.|+| -|+
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvq-VPtGpWfCrKCesqeraarvrCeLCP~kdGALKk--TDn---- 80 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQ-VPTGPWFCRKCESQERAARVRCELCPHKDGALKK--TDN---- 80 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEe-cCCCchhhhhhhhhhhhccceeecccCcccceec--ccC----
Confidence 556888988889999999987788888888887764 3455899999987765443322111111011111 122
Q ss_pred cceecccccCccccccccccccc
Q 000748 649 AWVLCDKCQGWQHQICALYNNKR 671 (1303)
Q Consensus 649 pwVeC~~C~r~~HqiCaLfn~~~ 671 (1303)
+.|-|.|||||.+..
T Consensus 81 --------~GWAHVVCALYIPEV 95 (900)
T KOG0956|consen 81 --------GGWAHVVCALYIPEV 95 (900)
T ss_pred --------CCceEEEEEeeccce
Confidence 689999999998754
No 33
>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=86.44 E-value=0.3 Score=38.04 Aligned_cols=28 Identities=25% Similarity=0.685 Sum_probs=13.0
Q ss_pred cccccccCcccCCccccCCCCCCccchhh
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTAC 1136 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~C 1136 (1303)
+|+.|+..+..+..|+|..| ||+|...|
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 69999999988778999999 99999887
No 34
>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=77.19 E-value=2.5 Score=51.32 Aligned_cols=39 Identities=33% Similarity=0.813 Sum_probs=30.7
Q ss_pred cceecccccCcccccccccccccCCC----C-----CcccccCCCccc
Q 000748 649 AWVLCDKCQGWQHQICALYNNKRDTE----G-----KAEYICPKCRLK 687 (1303)
Q Consensus 649 pwVeC~~C~r~~HqiCaLfn~~~~~~----~-----~s~FiCp~C~~~ 687 (1303)
-||.|+.|+.|-|--|||-...+-+| | +..|-|..|...
T Consensus 145 ~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 145 SWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred eEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 59999999999999999976644221 1 457999999863
No 35
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=66.61 E-value=2 Score=52.40 Aligned_cols=38 Identities=32% Similarity=0.681 Sum_probs=26.4
Q ss_pred ceecccccCcccccccccccccC--CCCCcccccCCCccc
Q 000748 650 WVLCDKCQGWQHQICALYNNKRD--TEGKAEYICPKCRLK 687 (1303)
Q Consensus 650 wVeC~~C~r~~HqiCaLfn~~~~--~~~~s~FiCp~C~~~ 687 (1303)
+|+|++|+.||||-|.--.-..- .+-.-+|.|..|...
T Consensus 185 mlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 185 MLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred eeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 79999999999999983211110 011357999999853
No 36
>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=64.47 E-value=3.6 Score=32.32 Aligned_cols=28 Identities=25% Similarity=0.670 Sum_probs=23.2
Q ss_pred cccccccCcccCCccccCCCCCCccchhh
Q 000748 1108 ICCLCRKDTVIDQCWQCETCPQFEVCTAC 1136 (1303)
Q Consensus 1108 tCn~C~~~iet~~~whC~vC~DfDLC~~C 1136 (1303)
.|.+|.+.+.....|+|+.|. |+|...|
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 599998887644399999998 9998877
No 37
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=63.76 E-value=10 Score=44.96 Aligned_cols=47 Identities=19% Similarity=0.710 Sum_probs=39.9
Q ss_pred HHHHhcccccccccccccccccCcccCCccccCCCCCCccchhhhhc
Q 000748 1093 ILHHLHNSSMLTAESICCLCRKDTVIDQCWQCETCPQFEVCTACYQE 1139 (1303)
Q Consensus 1093 mLyhLHNp~~~~fv~tCn~C~~~iet~~~whC~vC~DfDLC~~CY~k 1139 (1303)
+|+-|-+.+.----..|+.|..+--+|.+|+|.-|-.|.||..|.=+
T Consensus 227 Lmhrla~v~nv~hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwr 273 (434)
T KOG4301|consen 227 LMHRLATVENVFHPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWR 273 (434)
T ss_pred HHHHHHhhcccCCCccCcceecccccchhhhHhhcCCccccchhhcc
Confidence 45666666665556689999999999999999999999999999876
No 38
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=54.33 E-value=2.9 Score=34.41 Aligned_cols=33 Identities=24% Similarity=0.681 Sum_probs=17.0
Q ss_pred cceecccccCcccccccccccccCCCCCcccccCCC
Q 000748 649 AWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPKC 684 (1303)
Q Consensus 649 pwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~C 684 (1303)
++++|+.|+-.+|+.|.=-.... ....+.|..|
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 68999999999999998443321 2335888766
No 39
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=52.04 E-value=9.5 Score=46.84 Aligned_cols=81 Identities=19% Similarity=0.353 Sum_probs=46.2
Q ss_pred cccccccCccceecCCcccccCCCccccCCCeeeecCCCCccceEEecccccccCCCcee------ccCccchHHhHHHh
Q 000748 567 NSCQLCQAEKLLLAPTPIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQSRGGKIS------LYGISFSKAKMYKR 640 (1303)
Q Consensus 567 ~~C~lC~~~kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~~~~~~I~------~~~~~i~K~~~~Kk 640 (1303)
..|..|.+-.-.=.-.-.+|.|| -|--++.-|...- -..-.++|-+|-=... ..++ .+|.. . .
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC--~i~VHq~CYGI~f-~peG~WlCrkCi~~~~-~i~~C~fCps~dGaF------k-q 262 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGC--EICVHQSCYGIQF-LPEGFWLCRKCIYGEY-QIRCCSFCPSSDGAF------K-Q 262 (669)
T ss_pred hhhHhccccccCCcceEEEecCc--chhhhhhccccee-cCcchhhhhhhccccc-ceeEEEeccCCCCce------e-e
Confidence 46666666443333556789876 4666667776652 2233778888864421 1110 12210 0 0
Q ss_pred hcCccccccceecccccCccccccccccccc
Q 000748 641 KNDEAIEEAWVLCDKCQGWQHQICALYNNKR 671 (1303)
Q Consensus 641 kNde~~~EpwVeC~~C~r~~HqiCaLfn~~~ 671 (1303)
..=|||-|-|||+|++..
T Consensus 263 -------------T~dgrW~H~iCA~~~pel 280 (669)
T COG5141 263 -------------TSDGRWGHVICAMFNPEL 280 (669)
T ss_pred -------------ccCCchHhHhHHHhcchh
Confidence 122899999999999754
No 40
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=51.88 E-value=12 Score=44.05 Aligned_cols=129 Identities=19% Similarity=0.169 Sum_probs=75.5
Q ss_pred cccCcccCCccccCCCCCCccchhhhhccCCcccccccccccccCCCCCcchHHHHH-HHHhCCCCCccccchhhHHHHH
Q 000748 1112 CRKDTVIDQCWQCETCPQFEVCTACYQEKGNSLHIHKLTQRSSAVDGGTESREAQTK-ALQAGRNPDTYIHSQVNLTLQK 1190 (1303)
Q Consensus 1112 C~~~iet~~~whC~vC~DfDLC~~CY~k~G~~~H~Hkm~~~~~~~d~g~~~~~~q~~-~~~~~r~P~~~~~~qes~~~qL 1190 (1303)
|...+.+++.|.|.-|..+.+|+.||.-. .|.|+|+....-+-.. ++.. ..+..+.|. ...++....=
T Consensus 60 ~~~~~~~~~~~~~~~c~~~~~~~~~l~~~---~ek~e~~~~~ihll~~-----~~~~~v~~~~~d~~---~~~~~~~~~~ 128 (319)
T KOG1778|consen 60 CRKSLVKGNKILGVPCKAVNVFIRFLYSS---LEKHEMVFFDIHLLAL-----SHVYVVPQPKADCD---PILECGLFDK 128 (319)
T ss_pred cchhhhhcceeecccccccchhhhhhccc---hhhhHHHHHHHHHHhh-----hhhhhccCccccCC---ccccchhhhh
Confidence 66677789999999999999999999873 7888886532111000 0000 000000000 0111222223
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCchhhHHHHHHHHHhh--hcccccCCCCcchHHHHHHHHHHhhcCCCC
Q 000748 1191 TQLMNLLQHASQCSLTKSKGCSYPKCLQMKTLFYHAR--SCNVRTAGGCQHCRKIWLLLTMHSRRCKEL 1257 (1303)
Q Consensus 1191 qr~me~LvHA~~C~~~~~a~C~~p~C~kMK~L~~H~~--~Ck~R~~GGC~~CKrmw~Ll~lHAk~C~e~ 1257 (1303)
+.+...|.|+-.|.. ..-|...+|.-|..+-.|.. .|. .--|++|+.-. +...|-..|.+-
T Consensus 129 r~~flvl~~~~~~~~--~~lr~a~hss~~~~~~~H~~t~~~~---~~~c~~c~~~~-~~~~~c~~~~d~ 191 (319)
T KOG1778|consen 129 RNVFLVLQLAEHCDF--SDLRRAKHSSIMLLFDLHLQTEKWF---AYTCPICKLEV-LTAWHCEVCPDY 191 (319)
T ss_pred HHHHHHHHHHHhccc--chHHHHHHHHHHHHHHHHhcccCce---eeecCcccccc-ccccccccCCch
Confidence 346667777777773 45577777777777777765 333 33688887766 666666666653
No 41
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=48.28 E-value=8.3 Score=47.10 Aligned_cols=39 Identities=31% Similarity=0.762 Sum_probs=32.4
Q ss_pred cccceecccccCcccccccccccccCCCCCcccccCCCcccc
Q 000748 647 EEAWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPKCRLKE 688 (1303)
Q Consensus 647 ~EpwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~C~~~e 688 (1303)
..-.++|+.|++|.|.+|..+.+... ...|.|..|..+.
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 55689999999999999998877553 4579999999754
No 42
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=46.03 E-value=12 Score=46.11 Aligned_cols=92 Identities=21% Similarity=0.456 Sum_probs=54.9
Q ss_pred CCcccccccCccceecCCcccccCCCccccCCCeeeecCC---------CCccceEEecccccccCCCceeccCccchHH
Q 000748 565 SDNSCQLCQAEKLLLAPTPIYCSYCGADIKRYVIYYSTPE---------ENGMRHCFCKSCYKQSRGGKISLYGISFSKA 635 (1303)
Q Consensus 565 ~e~~C~lC~~~kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~---------eg~~~~~~C~kCF~~~~~~~I~~~~~~i~K~ 635 (1303)
..+.|..|-+++..=.---+.|..||..+.. -.|..-+ +.++.-+||..|--..-...-.|- + .|.
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~CGi~VHE--gCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElC--P-n~~ 192 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDKCGINVHE--GCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELC--P-NRF 192 (707)
T ss_pred cceEEEEeecCccccccceeeccccCceecc--cccccccccccCCCCccCCCCchhhhhHhcCCCCCccccC--C-CcC
Confidence 4458999999997777778899988754444 4444331 134578999999654321111110 0 000
Q ss_pred hHHHhhcCccccccceecccccCcccccccccccccCCC
Q 000748 636 KMYKRKNDEAIEEAWVLCDKCQGWQHQICALYNNKRDTE 674 (1303)
Q Consensus 636 ~~~KkkNde~~~EpwVeC~~C~r~~HqiCaLfn~~~~~~ 674 (1303)
...|. ..=|||+|-|||||....+-+
T Consensus 193 GifKe-------------tDigrWvH~iCALYvpGVafg 218 (707)
T KOG0957|consen 193 GIFKE-------------TDIGRWVHAICALYVPGVAFG 218 (707)
T ss_pred Ccccc-------------cchhhHHHHHHHhhcCccccc
Confidence 11111 124799999999998876543
No 43
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=43.94 E-value=17 Score=41.83 Aligned_cols=35 Identities=31% Similarity=0.907 Sum_probs=25.6
Q ss_pred cceeccc--cc-CcccccccccccccCCCCCcccccCCCccc
Q 000748 649 AWVLCDK--CQ-GWQHQICALYNNKRDTEGKAEYICPKCRLK 687 (1303)
Q Consensus 649 pwVeC~~--C~-r~~HqiCaLfn~~~~~~~~s~FiCp~C~~~ 687 (1303)
.+|.||- |. .|||-.|+=.... + .-..-|+.|...
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 3678877 99 9999999944321 1 234899999865
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=38.60 E-value=22 Score=32.83 Aligned_cols=28 Identities=25% Similarity=0.514 Sum_probs=18.9
Q ss_pred cccccCCCccccCCCeeeecCCCCccceEEecccccc
Q 000748 583 PIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQ 619 (1303)
Q Consensus 583 ~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~ 619 (1303)
+-.|..|+..|.++..|= ...|..|=++
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 667888888887766652 3347777544
No 45
>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=34.88 E-value=16 Score=32.02 Aligned_cols=34 Identities=24% Similarity=0.647 Sum_probs=14.9
Q ss_pred ccceecccccCcccccccccccccCCCCCcccccCC
Q 000748 648 EAWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPK 683 (1303)
Q Consensus 648 EpwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~ 683 (1303)
+-||||+.|++|=.-. .-+....... ...|.|..
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 3233211111 23788843
No 46
>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=34.07 E-value=37 Score=29.19 Aligned_cols=39 Identities=26% Similarity=0.645 Sum_probs=31.0
Q ss_pred ccceecCCcccccCCCccccCCCeeeecCCCCccceEEecccccc
Q 000748 575 EKLLLAPTPIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQ 619 (1303)
Q Consensus 575 ~kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~ 619 (1303)
....|++.=+.|..|+..|..+. ||...+ ..||..||.+
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 44679999999999999998887 555543 7899999965
No 47
>PF00150 Cellulase: Cellulase (glycosyl hydrolase family 5); InterPro: IPR001547 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 5 GH5 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); beta-mannanase (3.2.1.78 from EC); exo-1,3-glucanase (3.2.1.58 from EC); endo-1,6-glucanase (3.2.1.75 from EC); xylanase (3.2.1.8 from EC); endoglycoceramidase (3.2.1.123 from EC). The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A [] or as the glycosyl hydrolases family 5 []. One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved [] in the catalytic mechanism.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3NDY_A 3NDZ_B 1LF1_A 1TVP_B 1TVN_A 3AYR_A 3AYS_A 1QI0_A 1W3K_A 1OCQ_A ....
Probab=33.48 E-value=1.9e+02 Score=31.74 Aligned_cols=55 Identities=18% Similarity=0.079 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhcCCcEEEEEeCCC-CC--CCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcCcEee
Q 000748 851 ILIGYLEYSKKRGFATCYIWACPP-VK--GEDYILYCHPEMQKTPKSDKLRQWYRSMLRKAAEEKIVVG 916 (1303)
Q Consensus 851 ILi~Yl~Yak~~GF~~aHIWAcPP-~k--GDDYIF~cHP~~Qk~pk~~rL~~WY~~mL~kgk~eGIV~~ 916 (1303)
+...+|+.++..||.++.|+.... .. ..+| .-.....+.+.++|+.|.+.||.+=
T Consensus 22 ~~~~~~~~~~~~G~n~VRi~v~~~~~~~~~~~~-----------~~~~~~~~~ld~~v~~a~~~gi~vi 79 (281)
T PF00150_consen 22 ITEADFDQLKALGFNTVRIPVGWEAYQEPNPGY-----------NYDETYLARLDRIVDAAQAYGIYVI 79 (281)
T ss_dssp SHHHHHHHHHHTTESEEEEEEESTSTSTTSTTT-----------SBTHHHHHHHHHHHHHHHHTT-EEE
T ss_pred CHHHHHHHHHHCCCCEEEeCCCHHHhcCCCCCc-----------cccHHHHHHHHHHHHHHHhCCCeEE
Confidence 456999999999999999999841 11 1111 2234567778999999999999874
No 48
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=30.72 E-value=25 Score=41.93 Aligned_cols=43 Identities=19% Similarity=0.327 Sum_probs=31.0
Q ss_pred hhchhHHHHHHhcccccccccccccccccCcccCCccccCCCCC
Q 000748 1086 AKYSSMMILHHLHNSSMLTAESICCLCRKDTVIDQCWQCETCPQ 1129 (1303)
Q Consensus 1086 AK~SSMmmLyhLHNp~~~~fv~tCn~C~~~iet~~~whC~vC~D 1129 (1303)
+|-|-++|=.-+--+-..+..|+|.+|.=..-+ ..|||..|-.
T Consensus 334 ~k~sL~~lr~mvge~l~~~~~YRC~~CGF~a~~-l~W~CPsC~~ 376 (389)
T COG2956 334 AKESLDLLRDMVGEQLRRKPRYRCQNCGFTAHT-LYWHCPSCRA 376 (389)
T ss_pred hhhhHHHHHHHHHHHHhhcCCceecccCCccee-eeeeCCCccc
Confidence 676655554445555667899999999976554 3799999943
No 49
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=24.53 E-value=1.2e+02 Score=30.85 Aligned_cols=52 Identities=23% Similarity=0.446 Sum_probs=32.2
Q ss_pred cCCcccccccCc-cceecCCcccccCCCccccCCCeeeecCCCCccceEEeccccccc
Q 000748 564 LSDNSCQLCQAE-KLLLAPTPIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQS 620 (1303)
Q Consensus 564 ~~e~~C~lC~~~-kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~~ 620 (1303)
.++..|.+|+.. .+.+ .+...|..|..+|=+.-..|... ...+.|.-|+...
T Consensus 52 ~~~~~C~~C~~~fg~l~-~~~~~C~~C~~~VC~~C~~~~~~----~~~WlC~vC~k~r 104 (118)
T PF02318_consen 52 YGERHCARCGKPFGFLF-NRGRVCVDCKHRVCKKCGVYSKK----EPIWLCKVCQKQR 104 (118)
T ss_dssp HCCSB-TTTS-BCSCTS-TTCEEETTTTEEEETTSEEETSS----SCCEEEHHHHHHH
T ss_pred cCCcchhhhCCcccccC-CCCCcCCcCCccccCccCCcCCC----CCCEEChhhHHHH
Confidence 477899999875 2333 44588888765554444444322 3577899999873
No 50
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=22.64 E-value=38 Score=41.48 Aligned_cols=34 Identities=24% Similarity=0.678 Sum_probs=27.9
Q ss_pred EEEe-CCCCCCCCeeeccCCCCCCCCChhHHHHHHHHH
Q 000748 868 YIWA-CPPVKGEDYILYCHPEMQKTPKSDKLRQWYRSM 904 (1303)
Q Consensus 868 HIWA-cPP~kGDDYIF~cHP~~Qk~pk~~rL~~WY~~m 904 (1303)
.=|| |||.+-+ ||.-|..++.+++.+|++||..-
T Consensus 164 ~kW~~lpPi~kn---fYke~~e~s~ls~~q~~~~r~en 198 (629)
T KOG0336|consen 164 FKWAKLPPIKKN---FYKESNETSNLSKEQLQEWRKEN 198 (629)
T ss_pred cccccCCchhhh---hhhcCchhccCCHHHHHHHHHcC
Confidence 3487 4887776 77789999999999999999753
No 51
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.63 E-value=96 Score=33.87 Aligned_cols=55 Identities=20% Similarity=0.461 Sum_probs=35.1
Q ss_pred cccceecccccCcccccccccccccCCCCCcccccCCCcccccccccccccccccccccCCCCCchhhHHHHHHHHHHHH
Q 000748 647 EEAWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPKCRLKEIETGDHLLLAESTFFAAKDLPSTMLSDHLEQRLFTRIQ 726 (1303)
Q Consensus 647 ~EpwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~C~~~e~~~g~~~plp~~~~~~AkdLP~T~LS~fIE~RLn~~L~ 726 (1303)
...+..|..|+..|=.-=|+ +..|+||.|... + .....+.+.+.|++++.. |+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~---------~~~F~Cp~Cg~~---------L--------~~~dn~~~~~~l~~~I~~-l~ 166 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAM---------EYGFRCPQCGEM---------L--------EEYDNSELIKELKEQIKE-LE 166 (178)
T ss_pred CCCEEECCCCCcEEeHHHHh---------hcCCcCCCCCCC---------C--------eecccHHHHHHHHHHHHH-HH
Confidence 34689999999888433232 135999999853 1 112355667778888753 44
Q ss_pred HH
Q 000748 727 EE 728 (1303)
Q Consensus 727 ~e 728 (1303)
++
T Consensus 167 ~~ 168 (178)
T PRK06266 167 EE 168 (178)
T ss_pred HH
Confidence 43
No 52
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=22.03 E-value=58 Score=44.03 Aligned_cols=89 Identities=18% Similarity=0.397 Sum_probs=50.3
Q ss_pred CCcccccccCccceecCCcccccCCCccccCCCeeeecCCCCccceEEecccccccCCCceeccCccchHHhHHHhhcCc
Q 000748 565 SDNSCQLCQAEKLLLAPTPIYCSYCGADIKRYVIYYSTPEENGMRHCFCKSCYKQSRGGKISLYGISFSKAKMYKRKNDE 644 (1303)
Q Consensus 565 ~e~~C~lC~~~kL~F~p~~lyC~~c~cRIkr~a~Yy~~~~eg~~~~~~C~kCF~~~~~~~I~~~~~~i~K~~~~KkkNde 644 (1303)
....|..|....-.=.-.-+||.+|+ |--+..-|.-+- --+-.+.|-.|--... ..|...-- .++.- ..|.+|
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~Cn--l~VHq~Cygi~~-ipeg~WlCr~Cl~s~~-~~v~c~~c-p~~~g-AFkqt~- 290 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGCN--LAVHQECYGIPF-IPEGQWLCRRCLQSPQ-RPVRCLLC-PSKGG-AFKQTD- 290 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCCc--chhhhhccCCCC-CCCCcEeehhhccCcC-cccceEec-cCCCC-cceecc-
Confidence 34578899887776667788999774 444455555321 1123778999976632 21211000 00000 011112
Q ss_pred cccccceecccccCccccccccccccc
Q 000748 645 AIEEAWVLCDKCQGWQHQICALYNNKR 671 (1303)
Q Consensus 645 ~~~EpwVeC~~C~r~~HqiCaLfn~~~ 671 (1303)
=|+|-|.+||++.+..
T Consensus 291 -----------dgrw~Hv~caiwipev 306 (1051)
T KOG0955|consen 291 -----------DGRWAHVVCAIWIPEV 306 (1051)
T ss_pred -----------CCceeeeehhhccccc
Confidence 2899999999987654
No 53
>smart00642 Aamy Alpha-amylase domain.
Probab=21.04 E-value=2.2e+02 Score=30.43 Aligned_cols=63 Identities=19% Similarity=0.212 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCCcEEEEEeCCCCCCCCe---eeccCCCCCCCCChh-HHHHHHHHHHHHHHhcCcEee
Q 000748 852 LIGYLEYSKKRGFATCYIWACPPVKGEDY---ILYCHPEMQKTPKSD-KLRQWYRSMLRKAAEEKIVVG 916 (1303)
Q Consensus 852 Li~Yl~Yak~~GF~~aHIWAcPP~kGDDY---IF~cHP~~Qk~pk~~-rL~~WY~~mL~kgk~eGIV~~ 916 (1303)
|+.-|+|.+.+||+. ||..|+.+...- -..-.|.+-..+++. .=.+=++.|++++.+.||-+=
T Consensus 21 i~~~l~yl~~lG~~~--I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vi 87 (166)
T smart00642 21 IIEKLDYLKDLGVTA--IWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVI 87 (166)
T ss_pred HHHHHHHHHHCCCCE--EEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEE
Confidence 567789999999986 566888554421 011122222222210 013557789999999987654
No 54
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.58 E-value=76 Score=33.88 Aligned_cols=33 Identities=15% Similarity=0.374 Sum_probs=23.6
Q ss_pred cccccceecccccCcccccccccccccCCCCCcccccCCCcc
Q 000748 645 AIEEAWVLCDKCQGWQHQICALYNNKRDTEGKAEYICPKCRL 686 (1303)
Q Consensus 645 ~~~EpwVeC~~C~r~~HqiCaLfn~~~~~~~~s~FiCp~C~~ 686 (1303)
+....+..|..|+..|=.-=|+- ..|+||.|..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~ 136 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGA 136 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCC
Confidence 34457899999998884433332 2499999985
Done!