Query 000411
Match_columns 1553
No_of_seqs 242 out of 277
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:40:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000411hhsearch_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 7E-57 1.5E-61 519.1 14.7 280 1189-1478 8-345 (346)
2 smart00551 ZnF_TAZ TAZ zinc fi 99.7 2.6E-17 5.6E-22 155.3 5.4 77 701-777 3-79 (79)
3 PF02135 zf-TAZ: TAZ zinc fing 99.5 1.6E-14 3.5E-19 134.5 2.0 73 704-776 2-75 (75)
4 KOG1778 CREB binding protein/P 98.7 1.8E-09 4E-14 124.9 0.0 121 1389-1544 1-121 (319)
5 smart00551 ZnF_TAZ TAZ zinc fi 98.6 8.5E-08 1.8E-12 91.3 6.1 66 733-798 10-79 (79)
6 PF06001 DUF902: Domain of Unk 98.1 6.1E-07 1.3E-11 75.4 0.0 35 1017-1051 6-41 (42)
7 PF02135 zf-TAZ: TAZ zinc fing 98.1 2.1E-06 4.7E-11 80.4 3.3 63 733-795 6-73 (75)
8 PF00569 ZZ: Zinc finger, ZZ t 97.4 9.5E-05 2E-09 63.9 2.5 38 1465-1506 1-38 (46)
9 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.3 0.00011 2.4E-09 64.3 2.1 46 1469-1528 1-48 (48)
10 cd02344 ZZ_HERC2 Zinc finger, 97.1 0.00019 4.2E-09 62.1 1.6 32 1470-1505 2-33 (45)
11 cd02342 ZZ_UBA_plant Zinc fing 97.1 0.00024 5.1E-09 60.8 1.9 35 1470-1508 2-36 (43)
12 cd02338 ZZ_PCMF_like Zinc fing 96.9 0.00045 9.7E-09 60.6 1.8 34 1470-1507 2-35 (49)
13 cd02335 ZZ_ADA2 Zinc finger, Z 96.9 0.00056 1.2E-08 59.9 2.1 34 1469-1506 1-34 (49)
14 cd02249 ZZ Zinc finger, ZZ typ 96.9 0.00054 1.2E-08 59.1 1.9 34 1469-1507 1-34 (46)
15 cd02345 ZZ_dah Zinc finger, ZZ 96.8 0.00061 1.3E-08 59.8 1.8 32 1470-1506 2-34 (49)
16 cd02337 ZZ_CBP Zinc finger, ZZ 96.8 0.00044 9.5E-09 58.8 0.8 33 1469-1507 1-33 (41)
17 cd02334 ZZ_dystrophin Zinc fin 96.5 0.0012 2.6E-08 58.2 1.9 34 1470-1507 2-35 (49)
18 cd02339 ZZ_Mind_bomb Zinc fing 96.5 0.0012 2.6E-08 57.2 1.8 32 1470-1505 2-33 (45)
19 smart00291 ZnF_ZZ Zinc-binding 96.5 0.0014 3E-08 56.2 1.9 36 1466-1506 2-37 (44)
20 cd02340 ZZ_NBR1_like Zinc fing 96.3 0.0019 4.2E-08 55.4 1.6 32 1470-1506 2-33 (43)
21 PF02172 KIX: KIX domain; Int 95.5 0.043 9.3E-07 53.4 7.1 54 68-121 13-67 (81)
22 KOG4582 Uncharacterized conser 95.4 0.0066 1.4E-07 70.5 1.7 34 1469-1506 153-186 (278)
23 COG5087 RTT109 Uncharacterized 95.3 0.24 5.3E-06 57.1 13.3 127 1212-1355 25-156 (349)
24 KOG4534 Uncharacterized conser 95.3 0.24 5.3E-06 57.1 13.3 127 1212-1355 25-156 (349)
25 PF00628 PHD: PHD-finger; Int 94.9 0.0043 9.4E-08 53.8 -1.4 41 1092-1132 9-49 (51)
26 KOG0956 PHD finger protein AF1 94.7 0.011 2.4E-07 73.9 0.7 88 1017-1118 8-95 (900)
27 smart00249 PHD PHD zinc finger 94.2 0.033 7.2E-07 46.1 2.4 38 1093-1131 10-47 (47)
28 cd02343 ZZ_EF Zinc finger, ZZ 93.3 0.047 1E-06 48.3 1.8 33 1470-1507 2-34 (48)
29 KOG1778 CREB binding protein/P 92.5 0.12 2.5E-06 61.4 4.1 51 745-795 231-283 (319)
30 KOG4274 Positive cofactor 2 (P 82.8 3.5 7.5E-05 51.9 7.9 57 68-136 10-66 (742)
31 KOG1280 Uncharacterized conser 80.8 1 2.2E-05 53.7 2.5 38 1466-1507 6-43 (381)
32 KOG4323 Polycomb-like PHD Zn-f 74.5 1 2.2E-05 55.8 0.1 38 1096-1133 184-223 (464)
33 cd02336 ZZ_RSC8 Zinc finger, Z 72.9 2.5 5.3E-05 37.3 2.0 34 1469-1507 1-34 (45)
34 COG2888 Predicted Zn-ribbon RN 66.9 4.7 0.0001 37.6 2.5 50 1031-1133 9-58 (61)
35 KOG0957 PHD finger protein [Ge 66.7 2.4 5.2E-05 52.5 0.9 89 1014-1120 119-217 (707)
36 PF09606 Med15: ARC105 or Med1 65.1 4.7 0.0001 53.4 3.1 52 73-133 3-55 (799)
37 COG5141 PHD zinc finger-contai 64.8 2.2 4.8E-05 52.8 0.1 87 1015-1118 194-280 (669)
38 KOG4786 Ubinuclein, nuclear pr 57.3 94 0.002 40.9 11.9 23 327-351 972-994 (1136)
39 KOG4286 Dystrophin-like protei 56.2 5.8 0.00013 51.5 1.6 37 1468-1508 603-639 (966)
40 KOG0457 Histone acetyltransfer 54.0 5.5 0.00012 49.1 0.9 36 1468-1507 14-49 (438)
41 KOG1844 PHD Zn-finger proteins 47.8 8.9 0.00019 48.0 1.4 40 1094-1136 98-137 (508)
42 KOG3598 Thyroid hormone recept 44.5 34 0.00073 47.7 5.7 70 123-198 1857-1933(2220)
43 KOG4369 RTK signaling protein 44.4 17 0.00036 49.5 3.0 25 150-174 1400-1424(2131)
44 KOG0955 PHD finger protein BR1 42.0 15 0.00033 50.2 2.2 77 1013-1118 218-306 (1051)
45 PF07649 C1_3: C1-like domain; 40.5 16 0.00034 29.2 1.3 29 1470-1503 2-30 (30)
46 PF07496 zf-CW: CW-type Zinc F 40.5 11 0.00023 33.7 0.4 34 1095-1130 1-34 (50)
47 PF07227 DUF1423: Protein of u 39.8 18 0.00039 45.1 2.3 42 1093-1134 142-192 (446)
48 PF13831 PHD_2: PHD-finger; PD 38.9 6.2 0.00013 33.2 -1.3 33 1096-1131 3-35 (36)
49 PF00412 LIM: LIM domain; Int 36.9 26 0.00056 30.9 2.2 39 1023-1066 18-56 (58)
50 COG5114 Histone acetyltransfer 35.9 14 0.0003 44.1 0.5 36 1468-1507 5-40 (432)
51 TIGR00515 accD acetyl-CoA carb 33.6 14 0.0003 43.9 -0.0 60 1230-1321 107-166 (285)
52 KOG2462 C2H2-type Zn-finger pr 33.5 22 0.00047 42.0 1.5 37 1098-1134 188-224 (279)
53 KOG1973 Chromatin remodeling p 33.4 20 0.00042 42.3 1.2 35 1096-1134 231-268 (274)
54 KOG0336 ATP-dependent RNA heli 32.8 36 0.00078 42.3 3.2 33 1315-1350 164-197 (629)
55 KOG4301 Beta-dystrobrevin [Cyt 31.6 15 0.00032 44.3 -0.2 48 1445-1504 225-272 (434)
56 CHL00174 accD acetyl-CoA carbo 28.6 20 0.00043 42.9 0.1 58 1231-1320 121-178 (296)
57 PLN03086 PRLI-interacting fact 28.5 82 0.0018 40.9 5.5 63 713-775 424-511 (567)
58 PRK06266 transcription initiat 27.8 51 0.0011 36.7 3.1 53 1092-1170 112-164 (178)
59 TIGR00373 conserved hypothetic 27.2 41 0.00089 36.7 2.2 34 1091-1133 103-136 (158)
60 TIGR03046 PS_II_psbV2 photosys 25.4 79 0.0017 34.8 3.9 39 1321-1359 110-148 (155)
61 PF00150 Cellulase: Cellulase 23.9 1.7E+02 0.0037 32.9 6.5 55 1298-1363 22-79 (281)
62 PF07500 TFIIS_M: Transcriptio 23.7 1.3E+02 0.0029 30.7 5.0 50 68-120 4-54 (115)
63 PF00643 zf-B_box: B-box zinc 23.5 60 0.0013 27.3 2.1 31 1469-1507 4-34 (42)
64 KOG4552 Vitamin-D-receptor int 22.5 1.2E+02 0.0025 34.9 4.6 71 317-395 164-238 (272)
65 smart00531 TFIIE Transcription 22.4 67 0.0015 34.4 2.7 39 1092-1134 94-132 (147)
66 PF00583 Acetyltransf_1: Acety 22.3 5.9E+02 0.013 23.0 10.3 67 1240-1321 3-69 (83)
67 PF12773 DZR: Double zinc ribb 21.7 39 0.00085 29.5 0.7 35 1468-1502 12-49 (50)
68 smart00661 RPOL9 RNA polymeras 21.4 53 0.0011 28.7 1.4 20 1470-1489 2-26 (52)
69 KOG1280 Uncharacterized conser 21.3 31 0.00067 41.9 -0.0 35 1033-1069 10-44 (381)
70 smart00642 Aamy Alpha-amylase 21.0 2.5E+02 0.0054 30.8 6.7 70 1299-1370 21-94 (166)
71 COG1779 C4-type Zn-finger prot 20.1 17 0.00037 41.2 -2.4 56 1244-1317 2-57 (201)
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=7e-57 Score=519.09 Aligned_cols=280 Identities=43% Similarity=0.694 Sum_probs=220.7
Q ss_pred CCCCCccEEEEEEeccchhhhhhHHHHHhhhhcCCCCccccceEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEE
Q 000411 1189 EVPGAEALVIRVVSSVDKKLEVKQRFLEIFQEENYPTEFPYKSKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVY 1268 (1553)
Q Consensus 1189 evp~a~~l~VRvVss~dK~~~Vk~~f~~~F~e~~yp~efpYrsKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~Vy 1268 (1553)
.+|+++.++||+|++.+++++++..|...|.++.||.+|+|+.|+|+|||++||+|||||+|+||||+..|+.||++|||
T Consensus 8 ~lp~~~~~~ir~v~S~~~~~~~~~~~~~~~~~~~~~~~~~y~~r~~~~fq~~~g~dv~~f~m~v~eY~~~~~~~~~~~v~ 87 (346)
T PF08214_consen 8 VLPKDEEFTIRHVSSPPKKCEVLFSFPPKFAEKGYPPEFTYKSRHFFVFQEIDGVDVLFFAMEVQEYGTICPAPNQRWVY 87 (346)
T ss_dssp CSCTT-EEEEEEEEEEEEEEE--TCHHHCTTTTTS-CCEEEEEEEEEEEEECTTEEEEEEEEEEEEEECCCSTCCCCEEE
T ss_pred hCCCCceEEEEEEEcCCEEccccccCCcccccccCCCCceeEEEEEEEEEEeCCccEEEEEEEEEEecCCCCCCCceEEE
Confidence 48999999999999999999999999999988789999999999999999999999999999999999999999999999
Q ss_pred EEecccccccccccccccccchhhHHHHHHHHHHHHHHHhcCCcEEEEEeCCCCCCCCeeeccCCCCCCCCC-----hhH
Q 000411 1269 LSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIWACPPLKGEDYILYCHPEIQKTPK-----SDK 1343 (1553)
Q Consensus 1269 IsYLDSV~YfrP~~~~~~Ge~lRT~VYhEILi~Yl~Yak~~GF~~ahIWAcPP~kGDDYIF~cHP~~Qk~pk-----~~r 1343 (1553)
|+|||||.||+|. .+||.|||++||+||+|++.+||.++|||||||.+|||||| |..|++|+ .++
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 58999999999999999999999999999999999999999 88888888 999
Q ss_pred HHHHHHHHHHHHH-------hcCeEeeecchhhh--hcccccccc------------cccCccccCcccCCCCchHHHHH
Q 000411 1344 LREWYLAMLRKAA-------KENIVVDLTNLYDH--FFVSTGECR------------AKVTAARLPYFDGDYWPGAAEDL 1402 (1553)
Q Consensus 1344 L~~WY~~mL~ka~-------~eGIV~~~~n~yd~--~f~~~~e~k------------~~~~a~~LPYFeGd~Wp~~~E~i 1402 (1553)
|++||.+||++|+ +++||+...|+|+. |+....... ....++.||||+||+||+.||++
T Consensus 158 L~~Wy~~~L~~~~~~~~~~~~~~~vvpg~d~~~~~~~~~~~~~~~~W~~g~~~~~~~~~~~~~~iP~FpdDpk~rfle~l 237 (346)
T PF08214_consen 158 LLKWYKKMLDKAKEESFKNAKAYLVVPGSDLYETRKYLPNTPDSNSWTYGHPFSQIKSDPAACLIPYFPDDPKPRFLEEL 237 (346)
T ss_dssp HHHHHHHHHHHHHHHHB-TTCCCCE-CCCEHHHHHHHHTCCCCTTTEEES-ST-SSSTSBGGGCSB--TT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhcccccccceEecCccHHHhhhhccccccccccccccccccccccCccccCCcCCCchHHHHHHHH
Confidence 9999999999999 99999999999987 333221100 11267889999999999999999
Q ss_pred HHH-------HHhccccccc----------------------cccccchhhhHHHhhhcCCCCC---CCCcchhHHHHHH
Q 000411 1403 IYQ-------IRQDEDGKKQ----------------------NKGITKKTITKRALKASGQTDL---SGNASKDLLLMHK 1450 (1553)
Q Consensus 1403 i~~-------l~~e~~~~k~----------------------~k~~~kK~~~kr~~k~~g~~~~---~~~~skd~~lm~K 1450 (1553)
+++ |+++.++... .+....|...|...+..+..+. ++..+....+|++
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 8876654211 0111122223333333332222 2334455689999
Q ss_pred HhhhccCCccceeeehhhhcccccccce
Q 000411 1451 LGETICPMKEDFIMVHLQHACNHCCILM 1478 (1553)
Q Consensus 1451 lg~~i~~~kedf~vvhLq~~C~~C~~~i 1478 (1553)
|+++|.++||+|++|+|+++|++|+..+
T Consensus 318 l~~~~~~~k~~~~~v~~~~~~~~~~~~~ 345 (346)
T PF08214_consen 318 LYETMEKHKEDFFVVRLKHQCTACSKPR 345 (346)
T ss_dssp HHHHHCHTGGGEEEEESSBGGG--SS-H
T ss_pred HHHHhcccccccEEEEEecccccccccC
Confidence 9999999999999999999999998753
No 2
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=99.68 E-value=2.6e-17 Score=155.28 Aligned_cols=77 Identities=52% Similarity=1.032 Sum_probs=73.8
Q ss_pred HHhhhhhhhhhhhhccccCCCCCCCCCCCchhHHHHHhhccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchHH
Q 000411 701 QFRNQQRWLLFLRHARRCAAPEGKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVPV 777 (1553)
Q Consensus 701 ~~~~qqrwLllL~HA~kC~~~~g~C~~~~C~~mK~lL~Hm~~C~~~~C~~~~C~sSR~Ll~H~k~C~~~~CpvC~pv 777 (1553)
.+..+++||+||+||.+|..+++.|..++|.+||.||+||.+|+.++|.+++|.++|+||.||+.|++.+||||.++
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 46678999999999999999999999999999999999999999999999999999999999999999999999864
No 3
>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=99.46 E-value=1.6e-14 Score=134.46 Aligned_cols=73 Identities=41% Similarity=0.957 Sum_probs=68.6
Q ss_pred hhhhhhhhhhhccccCCCC-CCCCCCCchhHHHHHhhccccCCCCCCCCCccchHHHHHHhhccCCCCCCCchH
Q 000411 704 NQQRWLLFLRHARRCAAPE-GKCQDVNCITVQKLWRHMDNCTSSQCPYPRCHHSKILIHHHKHCRDPSCPVCVP 776 (1553)
Q Consensus 704 ~qqrwLllL~HA~kC~~~~-g~C~~~~C~~mK~lL~Hm~~C~~~~C~~~~C~sSR~Ll~H~k~C~~~~CpvC~p 776 (1553)
.+++||+||+||..|..++ +.|..++|..||.||.|+..|..+.|.+++|..+|.||.||+.|++.+|+||.+
T Consensus 2 ~~~~~L~~L~Ha~~C~~~~~~~C~~~~C~~~K~ll~H~~~C~~~~C~~~~C~~~k~ll~H~~~C~~~~C~vc~C 75 (75)
T PF02135_consen 2 QLQRWLELLLHASSCRDPEHPNCSLPHCRKMKKLLKHMRTCRNRDCPVPGCQSCKRLLSHARSCKDSDCPVCFC 75 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHCTT-SSTTHHHHHHHHHHHCCSSSCCSSCCTHHHHHHHHHHHHHHTSTTSSSHHH
T ss_pred HHHHHHHHHHHHhHCcCCCCCCCCCcccHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcCCCCCCCCCCC
Confidence 4689999999999999988 899999999999999999999997799999999999999999999999999974
No 4
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=98.73 E-value=1.8e-09 Score=124.93 Aligned_cols=121 Identities=25% Similarity=0.272 Sum_probs=103.9
Q ss_pred cccCCCCchHHHHHHHHHHhccccccccccccchhhhHHHhhhcCCCCCCCCcchhHHHHHHHhhhccCCccceeeehhh
Q 000411 1389 YFDGDYWPGAAEDLIYQIRQDEDGKKQNKGITKKTITKRALKASGQTDLSGNASKDLLLMHKLGETICPMKEDFIMVHLQ 1468 (1553)
Q Consensus 1389 YFeGd~Wp~~~E~ii~~l~~e~~~~k~~k~~~kK~~~kr~~k~~g~~~~~~~~skd~~lm~Klg~~i~~~kedf~vvhLq 1468 (1553)
||+||+ +||.|..+.++ .++-+++. | .+...++.+|...|+++ +|.|++++|++++++
T Consensus 1 ~~~~~~----~ed~~~~~~~~------~~~~~~~~---------~-~~~~~~~~~~~~~~~s~--~l~~~~~~~~~~~~~ 58 (319)
T KOG1778|consen 1 YPIPDP----AEDLLSQMTQE------VSGDTRPT---------G-DVEIVTDVKDLIPAHSL--VLGPASPVFKKVLKQ 58 (319)
T ss_pred CCCCcH----HHHHHHhhhhh------cccccCCc---------c-chhhhhhhhhhhHHHHh--cccccchHHHHHHhh
Confidence 577887 88888888776 11212221 5 55667888999999999 999999999999999
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHHhhcccccCcCCCCcceeeeecccccccccccccCceee
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKKREDRERHPVNSREVHILEELPMCLLIRKIKMRFSKV 1544 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~~~~~~~~~~~~~~~~h~~~~~~v~~~p~~t~~~~~~~ 1544 (1553)
+ |++.++.+++|+|..| +++.+|++||.++ .|+|+.+.+++|.|.++.+..||..+.|.|.-+
T Consensus 59 ~----~~~~~~~~~~~~~~~c----~~~~~~~~~l~~~-----~ek~e~~~~~ihll~~~~~~~v~~~~~d~~~~~ 121 (319)
T KOG1778|consen 59 P----CRKSLVKGNKILGVPC----KAVNVFIRFLYSS-----LEKHEMVFFDIHLLALSHVYVVPQPKADCDPIL 121 (319)
T ss_pred h----cchhhhhcceeecccc----cccchhhhhhccc-----hhhhHHHHHHHHHHhhhhhhhccCccccCCccc
Confidence 9 9999999999999999 9999999999998 588999999999999999999999999987643
No 5
>smart00551 ZnF_TAZ TAZ zinc finger, present in p300 and CBP.
Probab=98.57 E-value=8.5e-08 Score=91.32 Aligned_cols=66 Identities=26% Similarity=0.578 Sum_probs=61.5
Q ss_pred HHHHHhhccccCC--CCCCCCCccchHHHHHHhhccCCCCCCC--chHHHHHHHHHHHhcCCCCCCCCcc
Q 000411 733 VQKLWRHMDNCTS--SQCPYPRCHHSKILIHHHKHCRDPSCPV--CVPVKNYLQQQKERARPKTDSCLPS 798 (1553)
Q Consensus 733 mK~lL~Hm~~C~~--~~C~~~~C~sSR~Ll~H~k~C~~~~Cpv--C~pvR~~i~~~~q~~~~~~~~c~p~ 798 (1553)
.-++|.|+.+|+. ..|.+++|...+.|+.|+..|++.+|++ |...|+++.|++.|.+..||||.++
T Consensus 10 ~l~~L~Ha~~C~~~~~~C~~~~C~~~k~L~~H~~~C~~~~C~~~~C~~ck~~~~H~k~C~~~~C~Vc~c~ 79 (79)
T smart00551 10 WLELLVHARRCKAREAKCQYPNCKTMKKLLRHMDSCKVRKCKYGYCASCKQLWQHSKHCKDSNCPVCKCV 79 (79)
T ss_pred HHHHHHHHHhCCCCCCCCCCchhHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 3489999999998 6999999999999999999999999977 9999999999999999999999764
No 6
>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=98.10 E-value=6.1e-07 Score=75.41 Aligned_cols=35 Identities=34% Similarity=0.640 Sum_probs=0.4
Q ss_pred cccccCcceeccCCcccccCC-CceecCCCeeeeec
Q 000411 1017 CQLCAVEKLTFEPPPIYCSPC-GTRIKRNAMYYTMG 1051 (1553)
Q Consensus 1017 C~~C~~~kL~F~p~~lyC~~c-~cRI~r~~~Yy~~~ 1051 (1553)
-++||+++|.|.|++|||+|. .|.|+||+.||+++
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 479999999999999999986 59999999999985
No 7
>PF02135 zf-TAZ: TAZ zinc finger; InterPro: IPR000197 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. TAZ (Transcription Adaptor putative Zinc finger) domains are zinc-containing domains found in the homologous transcriptional co-activators CREB-binding protein (CBP) and the P300. CBP and P300 are histone acetyltransferases (2.3.1.48 from EC) that catalyse the reversible acetylation of all four histones in nucleosomes, acting to regulate transcription via chromatin remodelling. These large nuclear proteins interact with numerous transcription factors and viral oncoproteins, including p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1, and are involved in cell growth, differentiation and apoptosis []. Both CBP and P300 have two copies of the TAZ domain, one in the N-terminal region, the other in the C-terminal region. The TAZ1 domain of CBP and P300 forms a complex with CITED2 (CBP/P300-interacting transactivator with ED-rich tail), inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration []. Adaptation to hypoxia is mediated by transactivation of hypoxia-responsive genes by hypoxia-inducible factor-1 (HIF-1) in complex with the CBP and p300 transcriptional coactivators []. The TAZ domain adopts an all-alpha fold with zinc-binding sites in the loops connecting the helices. The TAZ1 domain in P300 and the TAZ2 (CH3) domain in CBP have each been shown to have four amphipathic helices, organised by three zinc-binding clusters with HCCC-type coordination [, , ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003712 transcription cofactor activity, 0004402 histone acetyltransferase activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1P4Q_B 1L3E_B 2KJE_A 1WO3_A 1WO4_A 1WO5_A 1LIQ_A 3P57_P 2K8F_A 3IO2_A ....
Probab=98.09 E-value=2.1e-06 Score=80.43 Aligned_cols=63 Identities=29% Similarity=0.712 Sum_probs=57.8
Q ss_pred HHHHHhhccccCC---CCCCCCCccchHHHHHHhhccCCCCCCC--chHHHHHHHHHHHhcCCCCCCC
Q 000411 733 VQKLWRHMDNCTS---SQCPYPRCHHSKILIHHHKHCRDPSCPV--CVPVKNYLQQQKERARPKTDSC 795 (1553)
Q Consensus 733 mK~lL~Hm~~C~~---~~C~~~~C~sSR~Ll~H~k~C~~~~Cpv--C~pvR~~i~~~~q~~~~~~~~c 795 (1553)
.-++|.|+..|.. +.|.+++|...|.||.|...|.+.+|++ |...|.++.|++.|.+..|++|
T Consensus 6 ~L~~L~Ha~~C~~~~~~~C~~~~C~~~K~ll~H~~~C~~~~C~~~~C~~~k~ll~H~~~C~~~~C~vc 73 (75)
T PF02135_consen 6 WLELLLHASSCRDPEHPNCSLPHCRKMKKLLKHMRTCRNRDCPVPGCQSCKRLLSHARSCKDSDCPVC 73 (75)
T ss_dssp HHHHHHHHHHHHHHHCTT-SSTTHHHHHHHHHHHCCSSSCCSSCCTHHHHHHHHHHHHHHTSTTSSSH
T ss_pred HHHHHHHHhHCcCCCCCCCCCcccHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhcCCCCCCCCC
Confidence 3479999999999 8999999999999999999999999876 9999999999999998889886
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=97.39 E-value=9.5e-05 Score=63.88 Aligned_cols=38 Identities=29% Similarity=0.783 Sum_probs=30.3
Q ss_pred ehhhhcccccccceecCceEEeccccccccCcccchhhhHHH
Q 000411 1465 VHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1465 vhLq~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
+|-.+.|..|+...+.|.||.|.+| .+|+||+.||...
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 4677899999997778999999999 9999999999874
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=97.32 E-value=0.00011 Score=64.33 Aligned_cols=46 Identities=33% Similarity=0.812 Sum_probs=36.2
Q ss_pred hcccccccceecCceEEecccccccc--CcccchhhhHHHhhcccccCcCCCCcceeeeecc
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNK--NFQLCDKCFEAEKKREDRERHPVNSREVHILEEL 1528 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~--~f~LCd~C~~~e~~~~~~~~~~~~~~~~h~~~~~ 1528 (1553)
|.|..|....+.|.||.|.+| . +|+||+.||.... .|. ..|.|.++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C----~~~d~DlC~~C~~~~~------~H~----~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSEC----DDGDFDLCQDCVVKGE------SHQ----EDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCC----CCCCCccCHHHHhCcC------CCC----CCCceeeC
Confidence 579999995556999999999 8 9999999997543 333 56766653
No 10
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.13 E-value=0.00019 Score=62.12 Aligned_cols=32 Identities=31% Similarity=1.144 Sum_probs=30.1
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHH
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~ 1505 (1553)
.|..|....+.|.||.|.+| .+|+||+.||..
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 69999998888999999999 999999999987
No 11
>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=97.12 E-value=0.00024 Score=60.84 Aligned_cols=35 Identities=26% Similarity=0.708 Sum_probs=32.0
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHHHhh
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1508 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~~ 1508 (1553)
.|..|+...+-|.||.|..| .+|+||+.||...-+
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 69999999999999999999 999999999987553
No 12
>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=96.90 E-value=0.00045 Score=60.64 Aligned_cols=34 Identities=26% Similarity=0.816 Sum_probs=29.0
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
.|+.|....+.|.||.|.+| .+|+||+.||....
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 69999954444999999999 99999999998653
No 13
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=96.86 E-value=0.00056 Score=59.89 Aligned_cols=34 Identities=32% Similarity=0.804 Sum_probs=31.4
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHH
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
+.|..|...+..|.||.|.+| .+|+||..|+...
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 469999999999999999999 9999999999754
No 14
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=96.86 E-value=0.00054 Score=59.12 Aligned_cols=34 Identities=32% Similarity=0.873 Sum_probs=29.7
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
+.|..|...| .|.||.|.+| .+|+||..||....
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 4699999965 5799999999 99999999998654
No 15
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=96.79 E-value=0.00061 Score=59.83 Aligned_cols=32 Identities=28% Similarity=0.875 Sum_probs=28.8
Q ss_pred ccccccc-ceecCceEEeccccccccCcccchhhhHHH
Q 000411 1470 ACNHCCI-LMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1470 ~C~~C~~-~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
.|..|.. .|+ |.||.|.+| .+|+||..||...
T Consensus 2 ~C~~C~~~~i~-g~R~~C~~C----~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDIS-GIRFPCQVC----RDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCce-EeeEECCCC----CCcCchHHHHhCC
Confidence 6999999 665 999999999 9999999999854
No 16
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=96.78 E-value=0.00044 Score=58.79 Aligned_cols=33 Identities=30% Similarity=0.888 Sum_probs=28.5
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
|+|..|.. ++ |.||.|..| .+||||+.|+....
T Consensus 1 y~C~~C~~-~~-~~r~~C~~C----~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKH-HV-ETRWHCTVC----EDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCC-cC-CCceECCCC----cchhhHHHHhCCCC
Confidence 57999988 43 799999999 99999999997743
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=96.55 E-value=0.0012 Score=58.20 Aligned_cols=34 Identities=35% Similarity=0.877 Sum_probs=30.8
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
.|..|+...+.|.||.|-+| .+|+||+.||....
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 69999988778999999999 99999999997754
No 18
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=96.54 E-value=0.0012 Score=57.22 Aligned_cols=32 Identities=31% Similarity=0.937 Sum_probs=30.1
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHH
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEA 1505 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~ 1505 (1553)
.|..|.+..+.|.||.|.+| .+|+||+.|+..
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 59999998999999999999 999999999984
No 19
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=96.50 E-value=0.0014 Score=56.20 Aligned_cols=36 Identities=31% Similarity=0.832 Sum_probs=31.2
Q ss_pred hhhhcccccccceecCceEEeccccccccCcccchhhhHHH
Q 000411 1466 HLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1466 hLq~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
|-.+.|..|.. .+.|.||.|..| .+|+||..||...
T Consensus 2 ~~~~~C~~C~~-~i~g~ry~C~~C----~d~dlC~~Cf~~~ 37 (44)
T smart00291 2 HHSYSCDTCGK-PIVGVRYHCLVC----PDYDLCQSCFAKG 37 (44)
T ss_pred CCCcCCCCCCC-CCcCCEEECCCC----CCccchHHHHhCc
Confidence 34568999999 667999999999 9999999999753
No 20
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=96.28 E-value=0.0019 Score=55.41 Aligned_cols=32 Identities=28% Similarity=0.762 Sum_probs=28.7
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHHH
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
.|..|+. .+.|.||.|.+| .+|+||+.||...
T Consensus 2 ~Cd~C~~-~i~G~ry~C~~C----~d~dLC~~C~~~~ 33 (43)
T cd02340 2 ICDGCQG-PIVGVRYKCLVC----PDYDLCESCEAKG 33 (43)
T ss_pred CCCCCCC-cCcCCeEECCCC----CCccchHHhhCcC
Confidence 5999999 558899999999 9999999999754
No 21
>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=95.47 E-value=0.043 Score=53.36 Aligned_cols=54 Identities=11% Similarity=0.451 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHhhcc-CCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc
Q 000411 68 RARGFMRDRIFGMLLHRQ-TQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM 121 (1553)
Q Consensus 68 ~~R~~m~~rI~~~l~qR~-~~p~~~~~k~kl~dlakRLEe~lfk~a~tKeeY~n~ 121 (1553)
.+|..|++||+..|+-.. |.+..+.--..|-+-||++|.-+|++|.|++|||.+
T Consensus 13 ~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~l~~yarkvE~~~fe~A~sreeYY~l 67 (81)
T PF02172_consen 13 DLRNHLVHKLVQAIFPTPDPNAMNDPRMKNLIEYARKVEKDMFETAQSREEYYHL 67 (81)
T ss_dssp HHHHHHHHHHHHHHS-SSSCCCCCSHHHHHHHHHHHHHHHHHHHC-SSHHHHHHH
T ss_pred HHHHHHHHHHHHhhCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence 579999999999998662 334444444567788999999999999999999998
No 22
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.42 E-value=0.0066 Score=70.48 Aligned_cols=34 Identities=26% Similarity=0.826 Sum_probs=31.8
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHH
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAE 1506 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e 1506 (1553)
..|+.|....+.|.||.|++| .+||||++|+...
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 789999998889999999999 9999999999764
No 23
>COG5087 RTT109 Uncharacterized conserved protein [Function unknown]
Probab=95.29 E-value=0.24 Score=57.09 Aligned_cols=127 Identities=20% Similarity=0.338 Sum_probs=87.6
Q ss_pred HHHHHhhhhcCCCCccccc-eEE-EEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccc
Q 000411 1212 QRFLEIFQEENYPTEFPYK-SKV-VLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEA 1289 (1553)
Q Consensus 1212 ~~f~~~F~e~~yp~efpYr-sKa-I~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~ 1289 (1553)
..+...|...+-...|++- .|- .+||- .+++||+|-+|-|..+ ..++|||+=-||--|-. .|..
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 3444445444444444443 333 33443 6799999999999654 35899999999999974 2456
Q ss_pred hhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000411 1290 LRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1553)
Q Consensus 1290 lRT~VYhEILi~Yl~Yak~~GF~~a-hIWAcPP~kGDDYIF~cHP~~--Qk~pk~~rL~~WY~~mL~ka 1355 (1553)
-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
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 7899999988887665555555544 6677664 56999755433 34899999999999777643
No 24
>KOG4534 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.29 E-value=0.24 Score=57.09 Aligned_cols=127 Identities=20% Similarity=0.338 Sum_probs=87.6
Q ss_pred HHHHHhhhhcCCCCccccc-eEE-EEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccc
Q 000411 1212 QRFLEIFQEENYPTEFPYK-SKV-VLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEA 1289 (1553)
Q Consensus 1212 ~~f~~~F~e~~yp~efpYr-sKa-I~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~ 1289 (1553)
..+...|...+-...|++- .|- .+||- .+++||+|-+|-|..+ ..++|||+=-||--|-. .|..
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 3444445444444444443 333 33443 6799999999999654 35899999999999974 2456
Q ss_pred hhhHHHHHHHHHHHHHHHhcCCcEE-EEEeCCCCCCCCeeeccCCCC--CCCCChhHHHHHHHHHHHHH
Q 000411 1290 LRTFVYHEILIGYLEYCKLRGFTSC-YIWACPPLKGEDYILYCHPEI--QKTPKSDKLREWYLAMLRKA 1355 (1553)
Q Consensus 1290 lRT~VYhEILi~Yl~Yak~~GF~~a-hIWAcPP~kGDDYIF~cHP~~--Qk~pk~~rL~~WY~~mL~ka 1355 (1553)
-||.++-|+|++-.---|+.|=.-+ -+++-|- ..|||..--.. ..+++...|.+|+..+|+--
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 7899999988887665555555544 6677664 56999755433 34899999999999777643
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=94.87 E-value=0.0043 Score=53.79 Aligned_cols=41 Identities=29% Similarity=0.734 Sum_probs=31.2
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCc
Q 000411 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCY 1132 (1553)
Q Consensus 1092 ~~~E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~ 1132 (1553)
.+.+.+|.|+.|++|+|..|.-............|+|+.|.
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 26
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=94.65 E-value=0.011 Score=73.88 Aligned_cols=88 Identities=25% Similarity=0.505 Sum_probs=58.2
Q ss_pred cccccCcceeccCCcccccCCCceecCCCeeeeecCCccceEeccccccccCCCceeecCchhhHHHHHHhhcCCCCccc
Q 000411 1017 CQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEEW 1096 (1553)
Q Consensus 1017 C~~C~~~kL~F~p~~lyC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~~~g~~i~~~~~~i~K~~~~KkkNd~~~~E~ 1096 (1553)
|-.|-.|+=.-|-|-.||.|..|.+.-..-+|..-.-.+--|||-||-...+.-.|.-+-.+.+--.|+|. |
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGALKkT--D------ 79 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGALKKT--D------ 79 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccceecc--c------
Confidence 55777888899999999999888898888888654433346999999876443222111111111111111 1
Q ss_pred ceeccccccccccccccccccc
Q 000411 1097 WVQCDKCEAWQHQICALFNGRR 1118 (1553)
Q Consensus 1097 wVeC~~C~r~~HqiCaLfn~~~ 1118 (1553)
=+.|-|.|||||.++.
T Consensus 80 ------n~GWAHVVCALYIPEV 95 (900)
T KOG0956|consen 80 ------NGGWAHVVCALYIPEV 95 (900)
T ss_pred ------CCCceEEEEEeeccce
Confidence 1689999999998764
No 27
>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 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=93.32 E-value=0.047 Score=48.34 Aligned_cols=33 Identities=30% Similarity=0.769 Sum_probs=29.3
Q ss_pred cccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
.|+.|... +.|-||.|-+| .+|+||..|+....
T Consensus 2 ~CdgC~~~-~~~~RykCl~C----~d~DlC~~Cf~~g~ 34 (48)
T cd02343 2 SCDGCDEI-APWHRYRCLQC----TDMDLCKTCFLGGV 34 (48)
T ss_pred CCCCCCCc-CCCceEECCCC----CCchhHHHHHhCCc
Confidence 59999985 57899999999 99999999998755
No 29
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=92.47 E-value=0.12 Score=61.45 Aligned_cols=51 Identities=27% Similarity=0.655 Sum_probs=41.5
Q ss_pred CCCCCCCCccchHHHHHHhhccCCC-CCCCchHHHHHHHHH-HHhcCCCCCCC
Q 000411 745 SSQCPYPRCHHSKILIHHHKHCRDP-SCPVCVPVKNYLQQQ-KERARPKTDSC 795 (1553)
Q Consensus 745 ~~~C~~~~C~sSR~Ll~H~k~C~~~-~CpvC~pvR~~i~~~-~q~~~~~~~~c 795 (1553)
...|.|+.|..++.|+.|+..|+.. .|++|-..+.++.=+ ++|.+..|+|.
T Consensus 231 ~~~C~~~~C~~~k~lirH~~~Ck~R~gC~iCk~m~~L~~lha~~c~~~~C~vP 283 (319)
T KOG1778|consen 231 DANCSYPSCNGLKRLIRHFRGCKLRGGCPICKRLWQLLELHARHCDDSKCKVP 283 (319)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHcccccCCCC
Confidence 4588888999999999999999885 899998888888544 58887778774
No 30
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=82.76 E-value=3.5 Score=51.91 Aligned_cols=57 Identities=25% Similarity=0.358 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCchhHHHHHHHHHhhCC
Q 000411 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNMDTLEARLSYLIKGRP 136 (1553)
Q Consensus 68 ~~R~~m~~rI~~~l~qR~~~p~~~~~k~kl~dlakRLEe~lfk~a~tKeeY~n~~tlesrLq~~ik~~~ 136 (1553)
+.|...+.||-. ++.|.....+ .=||-.|+-+|+|++||+|||.+ -.+|=..+|-+.
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 568899999865 5566666544 45899999999999999999975 345555555444
No 31
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=80.78 E-value=1 Score=53.68 Aligned_cols=38 Identities=26% Similarity=0.665 Sum_probs=34.1
Q ss_pred hhhhcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1466 HLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1466 hLq~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
|=.-.|.-|.+.-..+.||.|=.| .+||||..||+..-
T Consensus 6 He~v~CdgC~k~~~t~rrYkCL~C----~DyDlC~sCyen~~ 43 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTFRRYKCLRC----SDYDLCFSCYENGA 43 (381)
T ss_pred cCCceeccccccceeeeeeEeeee----cchhHHHHHhhcCC
Confidence 334589999999999999999999 99999999998874
No 32
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=74.53 E-value=1 Score=55.85 Aligned_cols=38 Identities=32% Similarity=0.605 Sum_probs=27.1
Q ss_pred cceeccccccccccccccccccc--CCCCCCcccCCCCch
Q 000411 1096 WWVQCDKCEAWQHQICALFNGRR--NDGGQAEYTCPNCYI 1133 (1553)
Q Consensus 1096 ~wVeC~~C~r~~HqiCaLfn~~~--~~~~~a~FiC~~C~~ 1133 (1553)
-+|+|++|+.|||+-|.--.-.. ..+..-+|.|..|..
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 36999999999999998322111 012257899999974
No 33
>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=72.86 E-value=2.5 Score=37.25 Aligned_cols=34 Identities=21% Similarity=0.470 Sum_probs=29.4
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
|.|..|..-+. .-|++|-.+ ++++||..||....
T Consensus 1 y~C~~Cg~D~t-~vryh~~~~----~~~dLC~~CF~~G~ 34 (45)
T cd02336 1 YHCFTCGNDCT-RVRYHNLKA----KKYDLCPSCYQEGR 34 (45)
T ss_pred CcccCCCCccC-ceEEEecCC----CccccChHHHhCcC
Confidence 57999999875 689999999 89999999997654
No 34
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=66.91 E-value=4.7 Score=37.60 Aligned_cols=50 Identities=28% Similarity=0.711 Sum_probs=37.1
Q ss_pred cccccCCCceecCCCeeeeecCCccceEeccccccccCCCceeecCchhhHHHHHHhhcCCCCcccceeccccccccccc
Q 000411 1031 PIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETEEWWVQCDKCEAWQHQI 1110 (1553)
Q Consensus 1031 ~lyC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~~~g~~i~~~~~~i~K~~~~KkkNd~~~~E~wVeC~~C~r~~Hqi 1110 (1553)
+-.|..|+..|.+++.|= ...|..|=++ .+.+|.+|.+.
T Consensus 9 ~~~CtSCg~~i~p~e~~v--------~F~CPnCGe~-----------------------------~I~Rc~~CRk~---- 47 (61)
T COG2888 9 PPVCTSCGREIAPGETAV--------KFPCPNCGEV-----------------------------EIYRCAKCRKL---- 47 (61)
T ss_pred CceeccCCCEeccCCcee--------EeeCCCCCce-----------------------------eeehhhhHHHc----
Confidence 678999999998888763 3568888653 35778887653
Q ss_pred ccccccccCCCCCCcccCCCCch
Q 000411 1111 CALFNGRRNDGGQAEYTCPNCYI 1133 (1553)
Q Consensus 1111 CaLfn~~~~~~~~a~FiC~~C~~ 1133 (1553)
-..|+||+|.-
T Consensus 48 ------------g~~Y~Cp~CGF 58 (61)
T COG2888 48 ------------GNPYRCPKCGF 58 (61)
T ss_pred ------------CCceECCCcCc
Confidence 25799999974
No 35
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=66.69 E-value=2.4 Score=52.51 Aligned_cols=89 Identities=19% Similarity=0.330 Sum_probs=54.1
Q ss_pred CcccccccCcceeccCCcccccCCCceecCCCeeeeecC----------CccceEeccccccccCCCceeecCchhhHHH
Q 000411 1014 ENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGA----------GDTRHYFCIKCYNEARGDTIVVDGTTIAKAR 1083 (1553)
Q Consensus 1014 e~sC~~C~~~kL~F~p~~lyC~~c~cRI~r~~~Yy~~~~----------g~~~~~~C~kCf~~~~g~~i~~~~~~i~K~~ 1083 (1553)
-+-|..|-+++..=.---+.|..||..+..| .|..-+ ..+.-|||..|--......-+|.
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~CGi~VHEg--CYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElC-------- 188 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDKCGINVHEG--CYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELC-------- 188 (707)
T ss_pred ceEEEEeecCccccccceeeccccCceeccc--ccccccccccCCCCccCCCCchhhhhHhcCCCCCccccC--------
Confidence 3478889888877667778999887666665 554321 12457999999765432111111
Q ss_pred HHHhhcCCCCcccceecccccccccccccccccccCC
Q 000411 1084 LEKKKNDEETEEWWVQCDKCEAWQHQICALFNGRRND 1120 (1553)
Q Consensus 1084 ~~KkkNd~~~~E~wVeC~~C~r~~HqiCaLfn~~~~~ 1120 (1553)
-|.- .+++=..=+||+|-|||||....+-
T Consensus 189 ----Pn~~----GifKetDigrWvH~iCALYvpGVaf 217 (707)
T KOG0957|consen 189 ----PNRF----GIFKETDIGRWVHAICALYVPGVAF 217 (707)
T ss_pred ----CCcC----CcccccchhhHHHHHHHhhcCcccc
Confidence 0100 0011113479999999999877653
No 36
>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=65.05 E-value=4.7 Score=53.37 Aligned_cols=52 Identities=19% Similarity=0.379 Sum_probs=32.1
Q ss_pred HHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhcCChhhhcCc-hhHHHHHHHHHh
Q 000411 73 MRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAASTKEDYMNM-DTLEARLSYLIK 133 (1553)
Q Consensus 73 m~~rI~~~l~qR~~~p~~~~~k~kl~dlakRLEe~lfk~a~tKeeY~n~-~tlesrLq~~ik 133 (1553)
.+.||=+ .++|...+++ .=||-+|+-+|.||+||||||++ +-|--|+...-+
T Consensus 3 vi~~ie~-a~~~~~~~~~--------k~a~emE~hvF~Ka~tkdEYl~~varli~h~r~~~~ 55 (799)
T PF09606_consen 3 VISKIEE-AMRKNGQNTP--------KSAREMENHVFQKAKTKDEYLSLVARLILHIRDMSK 55 (799)
T ss_dssp HHHHHHH-HHHHH----S--------S-HHHHHHHHHHH-SSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HHHHhCCCCC--------CCHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhhh
Confidence 4556544 4455555543 34788999999999999999997 555555555443
No 37
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=64.81 E-value=2.2 Score=52.76 Aligned_cols=87 Identities=21% Similarity=0.386 Sum_probs=45.9
Q ss_pred cccccccCcceeccCCcccccCCCceecCCCeeeeecCCccceEeccccccccCCCceeecCchhhHHHHHHhhcCCCCc
Q 000411 1015 NSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEETE 1094 (1553)
Q Consensus 1015 ~sC~~C~~~kL~F~p~~lyC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~~~g~~i~~~~~~i~K~~~~KkkNd~~~~ 1094 (1553)
..|..|.+-.-.=.-.-.||.|| -|--....|...--..-.++|-+|.=... .|.-.....+.+.--|.
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 36666665433333455678876 56677777765431222688999965311 11100000000000000
Q ss_pred ccceeccccccccccccccccccc
Q 000411 1095 EWWVQCDKCEAWQHQICALFNGRR 1118 (1553)
Q Consensus 1095 E~wVeC~~C~r~~HqiCaLfn~~~ 1118 (1553)
..=|||-|-|||+|++..
T Consensus 263 ------T~dgrW~H~iCA~~~pel 280 (669)
T COG5141 263 ------TSDGRWGHVICAMFNPEL 280 (669)
T ss_pred ------ccCCchHhHhHHHhcchh
Confidence 122899999999999754
No 38
>KOG4786 consensus Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription; Signal transduction mechanisms]
Probab=57.27 E-value=94 Score=40.92 Aligned_cols=23 Identities=26% Similarity=0.222 Sum_probs=14.5
Q ss_pred cCCCCCccCCCccccccceeccCCC
Q 000411 327 YGFSNGALNGGLGMIGNNLLINEPG 351 (1553)
Q Consensus 327 ~g~s~~s~nggmG~~Gnn~min~Pg 351 (1553)
-|-+++...||-| |.|.+.|.||
T Consensus 972 ~~~P~~~sS~~s~--GV~~~~~~~~ 994 (1136)
T KOG4786|consen 972 HQNPQIATSSSSG--GVNQFYNNGG 994 (1136)
T ss_pred CCCCCccccCCch--hHHHHhcCCC
Confidence 4556666655544 6677777777
No 39
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=56.19 E-value=5.8 Score=51.48 Aligned_cols=37 Identities=27% Similarity=0.530 Sum_probs=33.5
Q ss_pred hhcccccccceecCceEEeccccccccCcccchhhhHHHhh
Q 000411 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEKK 1508 (1553)
Q Consensus 1468 q~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~~ 1508 (1553)
+..|..|+.+.+-|-||.|-+| -|++||..|+-..-+
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~----fn~dlCq~CF~sgra 639 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKH----FNYDICQSCFFSGRA 639 (966)
T ss_pred hhhcchhhhCccceeeeeehhh----cChhHHhhHhhhccc
Confidence 4689999999999999999999 999999999977653
No 40
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=53.99 E-value=5.5 Score=49.07 Aligned_cols=36 Identities=28% Similarity=0.770 Sum_probs=31.7
Q ss_pred hhcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1468 q~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
.|.|+.|..-|-.-.|-.|-+| .+|+||-.|+...-
T Consensus 14 ky~C~~C~~dit~~i~ikCaeC----p~fdLCl~CFs~Ga 49 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAEC----PDFDLCLQCFSVGA 49 (438)
T ss_pred CCCCccHhHHhccceEEEeecC----CCcchhHHHHhccc
Confidence 5889999988877777999999 99999999998754
No 41
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=47.82 E-value=8.9 Score=47.99 Aligned_cols=40 Identities=33% Similarity=0.682 Sum_probs=33.1
Q ss_pred cccceecccccccccccccccccccCCCCCCcccCCCCchhhh
Q 000411 1094 EEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITEV 1136 (1553)
Q Consensus 1094 ~E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~~~ 1136 (1553)
..-.++|+.|++|.|.+|..+.+... ...|.|..|.....
T Consensus 98 ~g~~i~c~~c~~Wqh~~C~g~~~~~~---p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 98 EGLMIQCDWCGRWQHKICCGSFKSTK---PDKYVCEICTPRNK 137 (508)
T ss_pred CceeeCCcccCcccCceeeeecCCCC---chhceeeeeccccc
Confidence 66789999999999999999877542 46899999987643
No 42
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=44.54 E-value=34 Score=47.71 Aligned_cols=70 Identities=19% Similarity=0.126 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhhCCCCCccccccccccCCCCccccccCC-C------CCCCCCcceeEEeecccccccccCCCccccccc
Q 000411 123 TLEARLSYLIKGRPGNNHNQRHQQLVNSSSSIGTMIPTP-G------MSHCGNSSLMVTSSVDSSMIAASGCNTIAPTTV 195 (1553)
Q Consensus 123 tlesrLq~~ik~~~~~~~nqq~~~~~~sSs~~gtmiptP-g------~s~~~ns~~~~~~~~~~~~~~~s~~~~~~~~~~ 195 (1553)
.+++|-..+...+-+-..|.-|-.+ |.+-+-|+==|.| | .--++|.+..-+-+ .++. |...++||+.
T Consensus 1857 ~hhp~~~~~~~~ln~~~~~~g~~tq-nq~l~pgg~r~dp~g~~~~~~~~~pt~p~~~~~n~--~~~t---~~a~~~p~s~ 1930 (2220)
T KOG3598|consen 1857 EHHPRASDAAAALNAPETNKGMDTQ-NQKLAPGGRRPDPRGRRKRNSGARPTGPRAKRANS--RADT---AQAAAAPTSW 1930 (2220)
T ss_pred hcCCCchhhHHhccCCCCCCCcccC-CCCCCCCCCCCCCCCccccccccCCCCCcccccch--hhhh---hhhhcCCccc
Confidence 3455555555555544444444333 2222223333333 2 22233444443333 2222 5556677777
Q ss_pred ccC
Q 000411 196 NSG 198 (1553)
Q Consensus 196 n~~ 198 (1553)
|+.
T Consensus 1931 ~a~ 1933 (2220)
T KOG3598|consen 1931 NAP 1933 (2220)
T ss_pred ccc
Confidence 764
No 43
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=44.40 E-value=17 Score=49.45 Aligned_cols=25 Identities=32% Similarity=0.404 Sum_probs=12.7
Q ss_pred CCCCccccccCCCCCCCCCcceeEE
Q 000411 150 SSSSIGTMIPTPGMSHCGNSSLMVT 174 (1553)
Q Consensus 150 sSs~~gtmiptPg~s~~~ns~~~~~ 174 (1553)
+-+.||.||=-|+.+.-.|+++..+
T Consensus 1400 a~~~I~~~i~Dpdv~~~~~ssi~~a 1424 (2131)
T KOG4369|consen 1400 ATSPIGLPIIDPDVSSPSSSSIPLA 1424 (2131)
T ss_pred hhccccceeecCCcCccccccchhh
Confidence 4455666665555444444444333
No 44
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=42.04 E-value=15 Score=50.15 Aligned_cols=77 Identities=18% Similarity=0.554 Sum_probs=50.2
Q ss_pred CCcccccccCcceeccCCcccccCCCceecCCCeeeeecCCccceEeccccccccCCCceeecCchhhHHHHHHhhcCCC
Q 000411 1013 SENSCQLCAVEKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARGDTIVVDGTTIAKARLEKKKNDEE 1092 (1553)
Q Consensus 1013 ~e~sC~~C~~~kL~F~p~~lyC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~~~g~~i~~~~~~i~K~~~~KkkNd~~ 1092 (1553)
....|..|...+-.=.-.-+||.+| .|--....|..+---.-.+.|-.|--.-.+.
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~C--nl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~---------------------- 273 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGC--NLAVHQECYGIPFIPEGQWLCRRCLQSPQRP---------------------- 273 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCC--cchhhhhccCCCCCCCCcEeehhhccCcCcc----------------------
Confidence 3457888877666655667899986 4556666776332112258899997653321
Q ss_pred Ccccceecccc------------ccccccccccccccc
Q 000411 1093 TEEWWVQCDKC------------EAWQHQICALFNGRR 1118 (1553)
Q Consensus 1093 ~~E~wVeC~~C------------~r~~HqiCaLfn~~~ 1118 (1553)
|.|.-| |+|.|.+||++.+..
T Consensus 274 -----v~c~~cp~~~gAFkqt~dgrw~Hv~caiwipev 306 (1051)
T KOG0955|consen 274 -----VRCLLCPSKGGAFKQTDDGRWAHVVCAIWIPEV 306 (1051)
T ss_pred -----cceEeccCCCCcceeccCCceeeeehhhccccc
Confidence 333333 899999999997654
No 45
>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=40.52 E-value=16 Score=29.21 Aligned_cols=29 Identities=28% Similarity=0.737 Sum_probs=13.0
Q ss_pred cccccccceecCceEEeccccccccCcccchhhh
Q 000411 1470 ACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCF 1503 (1553)
Q Consensus 1470 ~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~ 1503 (1553)
.|..|+..+..+-.+.|..| +|.|...|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-----df~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-----DFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT----------HHHH
T ss_pred cCCcCCCcCCCCceEECccC-----CCccChhcC
Confidence 58999999977788999999 899988873
No 46
>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=40.48 E-value=11 Score=33.70 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=15.2
Q ss_pred ccceecccccccccccccccccccCCCCCCcccCCC
Q 000411 1095 EWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPN 1130 (1553)
Q Consensus 1095 E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~ 1130 (1553)
+-||+|+.|++|=.-- .-+...+... ...|.|..
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 3599999999997555 3333322112 33798844
No 47
>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=39.76 E-value=18 Score=45.12 Aligned_cols=42 Identities=31% Similarity=0.680 Sum_probs=31.9
Q ss_pred CcccceecccccccccccccccccccC-----CC----CCCcccCCCCchh
Q 000411 1093 TEEWWVQCDKCEAWQHQICALFNGRRN-----DG----GQAEYTCPNCYIT 1134 (1553)
Q Consensus 1093 ~~E~wVeC~~C~r~~HqiCaLfn~~~~-----~~----~~a~FiC~~C~~~ 1134 (1553)
..=-||.|+.|+.|-|--|||-...+- .+ -+..|.|..|...
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 345799999999999999999865431 11 1458999999853
No 48
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=38.94 E-value=6.2 Score=33.19 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=17.0
Q ss_pred cceecccccccccccccccccccCCCCCCcccCCCC
Q 000411 1096 WWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNC 1131 (1553)
Q Consensus 1096 ~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C 1131 (1553)
+++.|+.|+-.+|+.|.=..... ....+.|..|
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 49
>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=36.94 E-value=26 Score=30.88 Aligned_cols=39 Identities=23% Similarity=0.675 Sum_probs=31.0
Q ss_pred cceeccCCcccccCCCceecCCCeeeeecCCccceEeccccccc
Q 000411 1023 EKLTFEPPPIYCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNE 1066 (1553)
Q Consensus 1023 ~kL~F~p~~lyC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~ 1066 (1553)
.+..|.+.=+.|..|+..|..+. ||.... ..||..||.+
T Consensus 18 ~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~----~~~C~~c~~~ 56 (58)
T PF00412_consen 18 MGKFWHPECFKCSKCGKPLNDGD-FYEKDG----KPYCKDCYQK 56 (58)
T ss_dssp TTEEEETTTSBETTTTCBTTTSS-EEEETT----EEEEHHHHHH
T ss_pred CCcEEEccccccCCCCCccCCCe-eEeECC----EEECHHHHhh
Confidence 35679999999999999998888 555432 6899999975
No 50
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=35.87 E-value=14 Score=44.10 Aligned_cols=36 Identities=25% Similarity=0.598 Sum_probs=31.9
Q ss_pred hhcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1468 QHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1468 q~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
.+.|.+|-.-|..-.+-.|..| ..|+||-.|+...-
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC----~~~DLC~pCF~~g~ 40 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNEC----PAVDLCLPCFVNGI 40 (432)
T ss_pred eeeehHHHHhhhcceeeeeecc----cccceehhhhhccc
Confidence 4679999999989999999999 99999999997543
No 51
>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=33.55 E-value=14 Score=43.91 Aligned_cols=60 Identities=15% Similarity=0.043 Sum_probs=43.9
Q ss_pred ceEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccchhhHHHHHHHHHHHHHHHhc
Q 000411 1230 KSKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLR 1309 (1553)
Q Consensus 1230 rsKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYhEILi~Yl~Yak~~ 1309 (1553)
..=+|.-|=+|||..|.++++--.-.|- .+ +.+..|=+...+++|-+.
T Consensus 107 ~d~vVtG~g~I~G~~V~v~a~D~~f~gG-------------------------------Sm-g~~~geKi~r~~e~A~~~ 154 (285)
T TIGR00515 107 KDAVVTGKGTLYGMPIVVAVFDFAFMGG-------------------------------SM-GSVVGEKFVRAIEKALED 154 (285)
T ss_pred CCcEEEEEEEECCEEEEEEEEeccccCC-------------------------------Cc-cHHHHHHHHHHHHHHHHc
Confidence 3467999999999999988883333321 11 124556677889999999
Q ss_pred CCcEEEEEeCCC
Q 000411 1310 GFTSCYIWACPP 1321 (1553)
Q Consensus 1310 GF~~ahIWAcPP 1321 (1553)
|.=-+.|.+.+=
T Consensus 155 ~lPlV~l~dSgG 166 (285)
T TIGR00515 155 NCPLIIFSASGG 166 (285)
T ss_pred CCCEEEEEcCCC
Confidence 999999988775
No 52
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=33.50 E-value=22 Score=42.05 Aligned_cols=37 Identities=22% Similarity=0.493 Sum_probs=25.2
Q ss_pred eecccccccccccccccccccCCCCCCcccCCCCchh
Q 000411 1098 VQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1553)
Q Consensus 1098 VeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~ 1134 (1553)
-+|..||+.|++-=-|---.|...||++|.|+.|.+.
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kA 224 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKA 224 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccch
Confidence 5688888887766555443444556788888888753
No 53
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=33.38 E-value=20 Score=42.27 Aligned_cols=35 Identities=26% Similarity=0.802 Sum_probs=26.1
Q ss_pred cceeccc--cc-ccccccccccccccCCCCCCcccCCCCchh
Q 000411 1096 WWVQCDK--CE-AWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1553)
Q Consensus 1096 ~wVeC~~--C~-r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~ 1134 (1553)
++|.||- |. .|||-.|+=.... + .-...|+.|...
T Consensus 231 ~Mi~CDn~~C~~eWFH~~CVGL~~~--P--kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 231 KMIGCDNPGCPIEWFHFTCVGLKTK--P--KGKWYCPRCKAE 268 (274)
T ss_pred cccccCCCCCCcceEEEeccccccC--C--CCcccchhhhhh
Confidence 4688888 99 9999999954422 1 235899999765
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=32.83 E-value=36 Score=42.29 Aligned_cols=33 Identities=27% Similarity=0.679 Sum_probs=27.5
Q ss_pred EEEe-CCCCCCCCeeeccCCCCCCCCChhHHHHHHHH
Q 000411 1315 YIWA-CPPLKGEDYILYCHPEIQKTPKSDKLREWYLA 1350 (1553)
Q Consensus 1315 hIWA-cPP~kGDDYIF~cHP~~Qk~pk~~rL~~WY~~ 1350 (1553)
.=|| |||.+-+ ||.-|..++.+....|++||..
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 4487 5888776 7788999999999999999953
No 55
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=31.57 E-value=15 Score=44.31 Aligned_cols=48 Identities=40% Similarity=0.742 Sum_probs=36.2
Q ss_pred HHHHHHHhhhccCCccceeeehhhhcccccccceecCceEEeccccccccCcccchhhhH
Q 000411 1445 LLLMHKLGETICPMKEDFIMVHLQHACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFE 1504 (1553)
Q Consensus 1445 ~~lm~Klg~~i~~~kedf~vvhLq~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~ 1504 (1553)
..||++|.-. . = |.=--.|.+|+---.-|-|+.|..| -+++||..|+=
T Consensus 225 lpLmhrla~v-~------n-v~hpv~cs~c~srs~~gfry~cq~C----~nyqlcq~cfw 272 (434)
T KOG4301|consen 225 LPLMHRLATV-E------N-VFHPVECSYCRSRSMMGFRYRCQQC----HNYQLCQQCFW 272 (434)
T ss_pred HHHHHHHHhh-c------c-cCCCccCcceecccccchhhhHhhc----CCccccchhhc
Confidence 3678877532 1 0 1112479999998888999999999 99999999973
No 56
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.64 E-value=20 Score=42.92 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=41.0
Q ss_pred eEEEEEEEEeCCEEEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccchhhHHHHHHHHHHHHHHHhcC
Q 000411 1231 SKVVLLFQKIEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRG 1310 (1553)
Q Consensus 1231 sKaI~vFQkiDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYhEILi~Yl~Yak~~G 1310 (1553)
.=+|.-+=+|||.+|++++| +|.- -|..+ +.|..|=|.-=+++|.+.|
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 35688899999999998877 5421 11122 2356666777789999999
Q ss_pred CcEEEEEeCC
Q 000411 1311 FTSCYIWACP 1320 (1553)
Q Consensus 1311 F~~ahIWAcP 1320 (1553)
-=-+.|.+..
T Consensus 169 lPlV~l~~SG 178 (296)
T CHL00174 169 LPLIIVCASG 178 (296)
T ss_pred CCEEEEECCC
Confidence 8888777765
No 57
>PLN03086 PRLI-interacting factor K; Provisional
Probab=28.51 E-value=82 Score=40.92 Aligned_cols=63 Identities=21% Similarity=0.463 Sum_probs=31.4
Q ss_pred hhccccCCCCCCCCC------------------CCch---hHHHHHhhccccCCC-CCCCCCccchHHHHHHhh-ccC--
Q 000411 713 RHARRCAAPEGKCQD------------------VNCI---TVQKLWRHMDNCTSS-QCPYPRCHHSKILIHHHK-HCR-- 767 (1553)
Q Consensus 713 ~HA~kC~~~~g~C~~------------------~~C~---~mK~lL~Hm~~C~~~-~C~~~~C~sSR~Ll~H~k-~C~-- 767 (1553)
+|-..|..-.-.|.. ++|. ....+-+|+..|..+ .|+-........|..|.. .|.
T Consensus 424 lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~CpCg~~~~R~~L~~H~~thCp~K 503 (567)
T PLN03086 424 LHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCPCGVVLEKEQMVQHQASTCPLR 503 (567)
T ss_pred HHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccchHHHHHHHHhcCCCccCCCCCCcchhHHHhhhhccCCCC
Confidence 677777776656653 2331 234566677666543 554001122244445533 463
Q ss_pred CCCCCCch
Q 000411 768 DPSCPVCV 775 (1553)
Q Consensus 768 ~~~CpvC~ 775 (1553)
.-.|++|.
T Consensus 504 pi~C~fC~ 511 (567)
T PLN03086 504 LITCRFCG 511 (567)
T ss_pred ceeCCCCC
Confidence 24566665
No 58
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.81 E-value=51 Score=36.71 Aligned_cols=53 Identities=17% Similarity=0.382 Sum_probs=33.8
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCchhhhccccccCCCcccccccCCCCCCcchHHHHHHHHH
Q 000411 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYITEVERGERKPLPQSAVLGAKDLPRTILSDHIEHRLFR 1170 (1553)
Q Consensus 1092 ~~~E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~~~~~~~r~p~p~~~~~~AkdLP~T~LS~fiE~rLn~ 1170 (1553)
+....++.|..|++.|=.-=|+ +..|+||.|... +. .+..+.+...|++++..
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~---------~~~F~Cp~Cg~~---------L~--------~~dn~~~~~~l~~~I~~ 164 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAM---------EYGFRCPQCGEM---------LE--------EYDNSELIKELKEQIKE 164 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHh---------hcCCcCCCCCCC---------Ce--------ecccHHHHHHHHHHHHH
Confidence 3445789999999888433222 246999999753 10 12345666777777754
No 59
>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=27.24 E-value=41 Score=36.65 Aligned_cols=34 Identities=24% Similarity=0.393 Sum_probs=24.3
Q ss_pred CCCcccceecccccccccccccccccccCCCCCCcccCCCCch
Q 000411 1091 EETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYI 1133 (1553)
Q Consensus 1091 ~~~~E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~ 1133 (1553)
.+....++-|..|+..|=.-=|+ +..|+||.|..
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~---------~~~F~Cp~Cg~ 136 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAM---------ELNFTCPRCGA 136 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHH---------HcCCcCCCCCC
Confidence 34556889999999888433333 23699999975
No 60
>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=25.38 E-value=79 Score=34.84 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=32.8
Q ss_pred CCCCCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcC
Q 000411 1321 PLKGEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKEN 1359 (1553)
Q Consensus 1321 P~kGDDYIF~cHP~~Qk~pk~~rL~~WY~~mL~ka~~eG 1359 (1553)
+.+|+||+|.|||.....++.+.|..=..=+|+.|++.+
T Consensus 110 s~kG~~~~~~~~mp~~~~LsdeEL~aIAaYLl~qa~~~~ 148 (155)
T TIGR03046 110 SYDGSEESYGCRPVPEDWMDDEEVENLAAFILRAAQKAP 148 (155)
T ss_pred ccCcccccccccCCcccCCCHHHHHHHHHHHHHhhhhcC
Confidence 568999999999999999999998777777777776654
No 61
>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=23.86 E-value=1.7e+02 Score=32.94 Aligned_cols=55 Identities=16% Similarity=0.075 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhcCCcEEEEEeCC-CCC--CCCeeeccCCCCCCCCChhHHHHHHHHHHHHHHhcCeEee
Q 000411 1298 ILIGYLEYCKLRGFTSCYIWACP-PLK--GEDYILYCHPEIQKTPKSDKLREWYLAMLRKAAKENIVVD 1363 (1553)
Q Consensus 1298 ILi~Yl~Yak~~GF~~ahIWAcP-P~k--GDDYIF~cHP~~Qk~pk~~rL~~WY~~mL~ka~~eGIV~~ 1363 (1553)
+...+|+.++..||..+.|+... ... ..+| .-.+...+.+.++|+.|.+.||.+=
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 46799999999999999999984 111 1122 2234566778999999999998773
No 62
>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=23.70 E-value=1.3e+02 Score=30.74 Aligned_cols=50 Identities=26% Similarity=0.420 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHhhccCCCCCHHHHHhHHHHHHHHHHHHhhhc-CChhhhcC
Q 000411 68 RARGFMRDRIFGMLLHRQTQTIDETQRTKFKDISKRLEEGLFKAA-STKEDYMN 120 (1553)
Q Consensus 68 ~~R~~m~~rI~~~l~qR~~~p~~~~~k~kl~dlakRLEe~lfk~a-~tKeeY~n 120 (1553)
.+|..+++.++..|......+. --..+..||..+|+.||... .++.+|..
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 4788888888888877754411 13467899999999999998 45566654
No 63
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=23.51 E-value=60 Score=27.28 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=22.5
Q ss_pred hcccccccceecCceEEeccccccccCcccchhhhHHHh
Q 000411 1469 HACNHCCILMVSGSRHVCEQCTKLNKNFQLCDKCFEAEK 1507 (1553)
Q Consensus 1469 ~~C~~C~~~ivsg~rw~c~~C~~~~~~f~LCd~C~~~e~ 1507 (1553)
..|..|... ..+|+|..| +.-||..|.....
T Consensus 4 ~~C~~H~~~---~~~~~C~~C-----~~~~C~~C~~~~H 34 (42)
T PF00643_consen 4 PKCPEHPEE---PLSLFCEDC-----NEPLCSECTVSGH 34 (42)
T ss_dssp SB-SSTTTS---BEEEEETTT-----TEEEEHHHHHTST
T ss_pred ccCccCCcc---ceEEEecCC-----CCccCccCCCCCC
Confidence 356777664 248999999 5589999997654
No 64
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=22.50 E-value=1.2e+02 Score=34.94 Aligned_cols=71 Identities=24% Similarity=0.235 Sum_probs=36.9
Q ss_pred CCCCCCCccc----cCCCCCccCCCccccccceeccCCCCCCccccccccCCCCCccccccCCCCCcccCCCCCCCCCCC
Q 000411 317 GMRSGLQHKS----YGFSNGALNGGLGMIGNNLLINEPGTSEGYLTGTQYANSPKPLQHHFDHQRPMVQGDGYGGSNADS 392 (1553)
Q Consensus 317 gm~sg~qq~s----~g~s~~s~nggmG~~Gnn~min~Pg~segy~n~~~y~~spk~~Qq~f~~qrs~~q~~~Yg~sn~d~ 392 (1553)
-||+|++-++ .|-|..+.||||-.--...||+.-++.++-.. -+--|.++|++|.-|- ..|.|.-..+
T Consensus 164 EmR~GLlGk~~~~in~ps~s~~Ngg~P~~~~~tl~gsA~tg~~sga---gg~~P~~~q~Q~~Wq~-----~~~~m~m~~p 235 (272)
T KOG4552|consen 164 EMRAGLLGKQRPLINSPSASSSNGGAPIRTVGTLIGSAPTGDFSGA---GGDEPPPIQQQVLWQN-----SPYNMVMQSP 235 (272)
T ss_pred HHhccCccccccccCCCCcCCCCCCCCchhhccccccCCCCCcccc---CCCCCchhhhhccccC-----CcchhhccCC
Confidence 3566665533 44556666777654222226666655543222 2345778888877432 3344444444
Q ss_pred CCC
Q 000411 393 YGT 395 (1553)
Q Consensus 393 ~gs 395 (1553)
+.+
T Consensus 236 ~~s 238 (272)
T KOG4552|consen 236 SSS 238 (272)
T ss_pred CCC
Confidence 443
No 65
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.43 E-value=67 Score=34.44 Aligned_cols=39 Identities=26% Similarity=0.428 Sum_probs=24.9
Q ss_pred CCcccceecccccccccccccccccccCCCCCCcccCCCCchh
Q 000411 1092 ETEEWWVQCDKCEAWQHQICALFNGRRNDGGQAEYTCPNCYIT 1134 (1553)
Q Consensus 1092 ~~~E~wVeC~~C~r~~HqiCaLfn~~~~~~~~a~FiC~~C~~~ 1134 (1553)
+.....+.|..|+..|=.-=++... + .+..|+||.|...
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~---d-~~~~f~Cp~Cg~~ 132 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLL---D-MDGTFTCPRCGEE 132 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhc---C-CCCcEECCCCCCE
Confidence 3445799999999887532222221 1 1345999999854
No 66
>PF00583 Acetyltransf_1: Acetyltransferase (GNAT) family; InterPro: IPR000182 The N-acetyltransferases (NAT) (EC 2.3.1.-) are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling. The Gcn5-related N-acetyltransferases (GNAT) catalyze the transfer of the acetyl from the CoA donor to a primary amine of the acceptor. The GNAT proteins share a domain composed of four conserved sequence motifs A-D [, ]. This GNAT domain is named after yeast GCN5 (from General Control Nonrepressed) and related histone acetyltransferases (HATs) like Hat1 and PCAF. HATs acetylate lysine residues of amino terminal histone tails, resulting in transcription activation. Another category of GNAT, the aminoglycoside N-acetyltransferases, confer antibiotic resistance by catalyzing the acetylation of amino groups in aminoglycoside antibiotics []. GNAT proteins can also have anabolic and catabolic functions in both prokaryotes and eukaryotes [, , , , ]. The acetyltransferase/GNAT domain forms a structurally conserved fold of 6 to 7 beta strands (B) and 4 helices (H) in the topology B1-H1-H2-B2-B3-B4-H3-B5-H4-B6, followed by a C-terminal strand which may be from the same monomer or contributed by another [, ]. Motifs D (B2-B3), A (B4-H3) and B (B5-H4) are collectively called the HAT core [, , ], while the N-terminal motif C (B1-H1) is less conserved. Some proteins known to contain a GNAT domain: Yeast GCN5 and Hat1, which are histone acetyltransferases (EC 2.3.1.48). Human PCAF, a histone acetyltransferase. Mammalian serotonin N-acetyltransferase (SNAT) or arylalkylamine NAT (AANAT), which acetylates serotonin into a circadian neurohormone that may participate in light-dark rhythms, and human mood and behavior. Mammalian glucosamine 6-phosphate N-acetyltransferase (GNA1) (EC 2.3.1.4). Escherichia coli rimI and rimJ, which acetylate the N-terminal alanine of ribosomal proteins S18 and S5, respectively (EC 2.3.1.128). Mycobacterium tuberculosis aminoglycoside 2'-N-acetyltransferase (aac), which acetylates the 2' hydroxyl or amino group of a broad spectrum of aminoglycoside antibiotics. Bacillus subtilis bltD and paiA, which acetylate spermine and spermidine. This entry represents the entire GNAT domain.; GO: 0008080 N-acetyltransferase activity, 0008152 metabolic process; PDB: 3T9Y_A 2R7H_B 2OZH_A 1Y9W_B 1VKC_B 2OH1_C 3R9E_B 3R9G_B 3R9F_A 3R96_A ....
Probab=22.27 E-value=5.9e+02 Score=23.03 Aligned_cols=67 Identities=16% Similarity=0.186 Sum_probs=45.3
Q ss_pred eCCEEEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccchhhHHHHHHHHHHHHHHHhcCCcEEEEEeC
Q 000411 1240 IEGVEVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIWAC 1319 (1553)
Q Consensus 1240 iDGVDV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYhEILi~Yl~Yak~~GF~~ahIWAc 1319 (1553)
.||.=|-+..........+. .+..+|.=|=.-+-|| +..+...+|....++|++.|+..+.+++-
T Consensus 3 ~~~~ivg~~~~~~~~~~~~~----~~~~~i~~~~v~~~~r-----------~~Gig~~L~~~~~~~~~~~g~~~i~~~~~ 67 (83)
T PF00583_consen 3 EDGQIVGFASLRPPPEPFDH----GNHAYIHRLAVDPEYR-----------GQGIGSKLLQAAEEWARKRGIKRIYLDVS 67 (83)
T ss_dssp ETTEEEEEEEEEEEETTTTT----TTEEEEEEEEECGGGT-----------TSSHHHHHHHHHHHHHHHTTESEEEEEEE
T ss_pred CCCEEEEEEEEEECCCcccc----CCEEEEEEEEEcHHHh-----------hCCCchhhhhhhhhhHHhcCccEEEEEEe
Confidence 35555555555555544311 3566766555545554 34578889999999999999999999987
Q ss_pred CC
Q 000411 1320 PP 1321 (1553)
Q Consensus 1320 PP 1321 (1553)
+.
T Consensus 68 ~~ 69 (83)
T PF00583_consen 68 PD 69 (83)
T ss_dssp TT
T ss_pred CC
Confidence 65
No 67
>PF12773 DZR: Double zinc ribbon
Probab=21.73 E-value=39 Score=29.48 Aligned_cols=35 Identities=29% Similarity=0.767 Sum_probs=26.8
Q ss_pred hhccccccccee--cCceEEeccccccc-cCcccchhh
Q 000411 1468 QHACNHCCILMV--SGSRHVCEQCTKLN-KNFQLCDKC 1502 (1553)
Q Consensus 1468 q~~C~~C~~~iv--sg~rw~c~~C~~~~-~~f~LCd~C 1502 (1553)
..+|.+|+..+. ....++|..|.+.+ .+...|..|
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 357889998887 67778899997754 677777776
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.40 E-value=53 Score=28.73 Aligned_cols=20 Identities=30% Similarity=0.938 Sum_probs=15.5
Q ss_pred cccccccceecC-----ceEEeccc
Q 000411 1470 ACNHCCILMVSG-----SRHVCEQC 1489 (1553)
Q Consensus 1470 ~C~~C~~~ivsg-----~rw~c~~C 1489 (1553)
+|..|+..+.-. .||+|..|
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~C 26 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKC 26 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcC
Confidence 699998866432 48999999
No 69
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=21.30 E-value=31 Score=41.88 Aligned_cols=35 Identities=23% Similarity=0.562 Sum_probs=18.1
Q ss_pred cccCCCceecCCCeeeeecCCccceEeccccccccCC
Q 000411 1033 YCSPCGTRIKRNAMYYTMGAGDTRHYFCIKCYNEARG 1069 (1553)
Q Consensus 1033 yC~~c~cRI~r~~~Yy~~~~g~~~~~~C~kCf~~~~g 1069 (1553)
-|.||+.+==++-.|-+..=.| |-.|..||+....
T Consensus 10 ~CdgC~k~~~t~rrYkCL~C~D--yDlC~sCyen~~t 44 (381)
T KOG1280|consen 10 SCDGCGKTAFTFRRYKCLRCSD--YDLCFSCYENGAT 44 (381)
T ss_pred eeccccccceeeeeeEeeeecc--hhHHHHHhhcCCC
Confidence 3555544333333333322112 5689999997543
No 70
>smart00642 Aamy Alpha-amylase domain.
Probab=21.02 E-value=2.5e+02 Score=30.78 Aligned_cols=70 Identities=23% Similarity=0.246 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCcEEEEEeCCCCCCCC---eeeccCCCCCCCCChh-HHHHHHHHHHHHHHhcCeEeeecchhhh
Q 000411 1299 LIGYLEYCKLRGFTSCYIWACPPLKGED---YILYCHPEIQKTPKSD-KLREWYLAMLRKAAKENIVVDLTNLYDH 1370 (1553)
Q Consensus 1299 Li~Yl~Yak~~GF~~ahIWAcPP~kGDD---YIF~cHP~~Qk~pk~~-rL~~WY~~mL~ka~~eGIV~~~~n~yd~ 1370 (1553)
|+.-|+|.+..||+. ||..|+.+... .-..-.|.+-..+++. .=.+=+++|+++|.+.||-+=+--...|
T Consensus 21 i~~~l~yl~~lG~~~--I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vilD~V~NH 94 (166)
T smart00642 21 IIEKLDYLKDLGVTA--IWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVILDVVINH 94 (166)
T ss_pred HHHHHHHHHHCCCCE--EEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEEEECCCC
Confidence 567799999999986 56688865332 1011122222111110 0124578899999999876644433333
No 71
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=20.13 E-value=17 Score=41.15 Aligned_cols=56 Identities=21% Similarity=0.226 Sum_probs=44.2
Q ss_pred EEEEEEEEEeecCCCCCCCCCceEEEEecccccccccccccccccchhhHHHHHHHHHHHHHHHhcCCcEEEEE
Q 000411 1244 EVCLFGMYVQEFGSECQFPNQRRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKLRGFTSCYIW 1317 (1553)
Q Consensus 1244 DV~fF~MyVQEYgs~c~~PN~r~VyIsYLDSV~YfrP~~~~~~Ge~lRT~VYhEILi~Yl~Yak~~GF~~ahIW 1317 (1553)
+|--|-+-++|..-+||....-..++.||+.+|||..- +-|.-+|++.||.+.-+.
T Consensus 2 ~~~~~~~~~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V------------------~i~t~~C~~CgYR~~DV~ 57 (201)
T COG1779 2 EVDMFPKEEFETRIDCPVCGGTLKAHMYLYDIPYFGEV------------------LISTGVCERCGYRSTDVK 57 (201)
T ss_pred CcccccceeeeeeecCCcccceeeEEEeeecCCccceE------------------EEEEEEccccCCccccee
Confidence 44556677888888999988877899999999999752 344567999999987665
Done!