Query 016862
Match_columns 381
No_of_seqs 187 out of 323
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 03:28:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016862hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1595 CCCH-type Zn-finger pr 100.0 7.1E-67 1.5E-71 531.5 19.7 333 1-353 97-462 (528)
2 KOG1677 CCCH-type Zn-finger pr 99.3 2.4E-12 5.1E-17 124.0 6.1 92 106-197 96-208 (332)
3 KOG1677 CCCH-type Zn-finger pr 98.6 3.4E-08 7.4E-13 95.4 3.5 71 92-163 124-206 (332)
4 COG5063 CTH1 CCCH-type Zn-fing 98.5 7.6E-08 1.6E-12 95.2 3.2 66 133-198 226-306 (351)
5 KOG1595 CCCH-type Zn-finger pr 98.4 2.2E-06 4.8E-11 89.7 12.8 66 94-166 230-299 (528)
6 COG5063 CTH1 CCCH-type Zn-fing 98.0 6.5E-06 1.4E-10 81.9 4.4 109 84-193 212-341 (351)
7 PF00642 zf-CCCH: Zinc finger 97.9 2.3E-06 4.9E-11 56.4 -0.7 25 133-157 1-26 (27)
8 smart00356 ZnF_C3H1 zinc finge 97.6 3.5E-05 7.6E-10 49.1 2.4 25 133-157 2-26 (27)
9 KOG2494 C3H1-type Zn-finger pr 97.6 1.4E-05 3E-10 79.8 0.6 59 135-195 37-98 (331)
10 KOG1040 Polyadenylation factor 96.9 0.00072 1.6E-08 67.8 3.5 50 134-190 76-129 (325)
11 PF00642 zf-CCCH: Zinc finger 96.6 0.00049 1.1E-08 45.3 -0.1 23 168-190 1-27 (27)
12 KOG1492 C3H1-type Zn-finger pr 96.5 0.0015 3.2E-08 63.7 2.2 65 106-189 216-282 (377)
13 KOG1040 Polyadenylation factor 95.9 0.0067 1.4E-07 61.0 3.6 78 97-191 74-158 (325)
14 KOG2494 C3H1-type Zn-finger pr 95.3 0.011 2.3E-07 59.7 2.5 52 105-162 45-97 (331)
15 smart00356 ZnF_C3H1 zinc finge 95.2 0.016 3.5E-07 36.7 2.2 24 167-190 1-27 (27)
16 KOG4791 Uncharacterized conser 94.1 0.031 6.6E-07 59.3 2.4 75 107-197 13-91 (667)
17 KOG1492 C3H1-type Zn-finger pr 93.5 0.092 2E-06 51.5 4.4 86 99-195 232-339 (377)
18 KOG3702 Nuclear polyadenylated 93.3 0.11 2.4E-06 56.6 5.0 88 100-191 544-646 (681)
19 COG5084 YTH1 Cleavage and poly 93.1 0.8 1.7E-05 45.7 10.3 80 98-192 102-191 (285)
20 COG5084 YTH1 Cleavage and poly 92.4 0.12 2.5E-06 51.6 3.4 62 113-190 91-158 (285)
21 PF14608 zf-CCCH_2: Zinc finge 91.4 0.14 3.1E-06 31.6 1.8 11 146-156 8-18 (19)
22 KOG2333 Uncharacterized conser 90.5 0.16 3.5E-06 54.3 2.3 59 134-194 75-144 (614)
23 COG5152 Uncharacterized conser 90.0 0.13 2.9E-06 49.5 1.1 32 129-160 135-167 (259)
24 KOG2185 Predicted RNA-processi 89.1 0.22 4.7E-06 52.1 1.9 25 134-158 139-163 (486)
25 KOG2333 Uncharacterized conser 87.8 0.26 5.6E-06 52.7 1.5 59 99-160 75-142 (614)
26 PF14608 zf-CCCH_2: Zinc finge 87.4 0.43 9.3E-06 29.4 1.7 18 172-189 1-19 (19)
27 KOG1813 Predicted E3 ubiquitin 87.0 0.26 5.7E-06 49.5 1.0 31 130-160 181-212 (313)
28 KOG3702 Nuclear polyadenylated 84.7 1.5 3.3E-05 48.2 5.3 82 96-191 581-666 (681)
29 COG5252 Uncharacterized conser 84.3 0.22 4.8E-06 49.1 -1.0 60 133-192 83-177 (299)
30 COG5252 Uncharacterized conser 84.1 0.13 2.7E-06 50.7 -2.7 62 99-160 84-177 (299)
31 KOG2185 Predicted RNA-processi 82.9 0.67 1.4E-05 48.6 1.7 38 159-196 129-173 (486)
32 KOG1763 Uncharacterized conser 82.9 0.29 6.2E-06 49.4 -0.9 30 133-162 90-119 (343)
33 KOG1763 Uncharacterized conser 75.0 0.5 1.1E-05 47.8 -1.9 31 99-130 91-124 (343)
34 KOG0153 Predicted RNA-binding 72.8 2.2 4.7E-05 44.1 1.9 37 123-159 149-185 (377)
35 KOG4791 Uncharacterized conser 57.7 3.6 7.9E-05 44.3 0.2 54 135-194 3-58 (667)
36 KOG1039 Predicted E3 ubiquitin 48.4 6.6 0.00014 40.3 0.3 24 136-159 9-32 (344)
37 PF10650 zf-C3H1: Putative zin 34.6 25 0.00054 23.2 1.3 19 137-156 2-21 (23)
38 KOG2202 U2 snRNP splicing fact 28.5 28 0.00061 34.7 1.2 24 135-158 152-175 (260)
No 1
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=7.1e-67 Score=531.49 Aligned_cols=333 Identities=44% Similarity=0.729 Sum_probs=258.3
Q ss_pred CCcCCC-CCCCCCcccCCCCCCCCCCCCCccCCCCccCCCCCCCCCCC-------CC--CChHHHHHHHH--hhCCCCCC
Q 016862 1 MMLGEA-HRPNPTILVPPWPQLPDDPTADNIFSPHSLNSNANGSPEYS-------NL--YHIPETYAALH--RYLPSNDP 68 (381)
Q Consensus 1 mm~~e~-~~~~~~~~~ppw~~~~~~~~~~~~~~~~~~~~~~~~~~d~~-------~~--~~~~~~~~~l~--~~Lp~n~~ 68 (381)
||||++ +..++++|||+|+.+. .. .|+.|+..++.. +- ....+++..|+ .+|+.++.
T Consensus 97 ~~~g~s~~~~e~~~hL~~~k~~~-~~----------tda~g~~~~~v~~~~~~~~~~~~r~~~~~l~e~~~~~~~~~~e~ 165 (528)
T KOG1595|consen 97 AVLGRSVGDTERTYHLRYYKTLP-CV----------TDARGNCVKNVLHCAFAHGPNDLRPPVEDLLELQGGSGLPDDEP 165 (528)
T ss_pred hhcccccCCcceeEecccccccc-Cc----------cccCCCcccCcccccccCCccccccHHHHHHhcccccCccCCCc
Confidence 799995 6777999999999988 32 355666554431 11 34567777777 77888887
Q ss_pred CCCCCCCCCC--CC---CCCCCCccccCceEeeccceeccCCCCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCcc
Q 016862 69 DLDSDSDMSG--LD---PDSPVDAYSCDHFRMYEFKVRKCARGRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFRK 143 (381)
Q Consensus 69 ~~~~d~~~~~--~~---~~~~v~~Ys~DeFrm~~FKTr~C~rg~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frk 143 (381)
+++.+.+... +. |++. ++|++||||||.||||+|+|++||||++|||||++||+|||||++|+|+.++||+|+|
T Consensus 166 ~~~~~~~~~~y~~Dp~~pdi~-~~ys~DeFrMy~fKir~C~R~~shDwteCPf~HpgEkARRRDPRkyhYs~tpCPefrk 244 (528)
T KOG1595|consen 166 EVESKLDVTEYPEDPSWPDIN-GIYSSDEFRMYSFKIRRCSRPRSHDWTECPFAHPGEKARRRDPRKYHYSSTPCPEFRK 244 (528)
T ss_pred ccccccccccccCCCCccccc-ccccccceEEEeeeecccCCccCCCcccCCccCCCcccccCCcccccccCccCccccc
Confidence 6644411110 11 3444 8999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCcCcchhhcCcCCccCcCCCCCCCCCCcccCCCCCCcccCCCCCC-CCCCCCCCCC---CCCc-CCCCC
Q 016862 144 GSCKKGDACEFAHGVFECWLHPARYRTQPCKDGGGCKRRVCFFAHTPDQLRILPQQ-SPRSASASDS---PSCA-KTLPF 218 (381)
Q Consensus 144 G~C~~Gd~C~FAHg~~El~~HP~~YKTk~Ck~~g~C~r~~C~FAH~~~ELR~~p~~-sP~s~~s~dg---sPl~-~~~~~ 218 (381)
|.|++||.|+||||+||+|+||.+|||++|+++|+|+|.+|||||.++|||.++.. .+....+.+. +|.. ....+
T Consensus 245 G~C~rGD~CEyaHgvfEcwLHPa~YRT~~CkDg~~C~RrvCfFAH~~eqLR~l~~s~~s~~~~sp~~s~~sp~~~~~~~~ 324 (528)
T KOG1595|consen 245 GSCERGDSCEYAHGVFECWLHPARYRTRKCKDGGYCPRRVCFFAHSPEQLRPLPPSTGSDRPSSPSSSSASPMMASLRSL 324 (528)
T ss_pred CCCCCCCccccccceehhhcCHHHhccccccCCCCCccceEeeecChHHhcccCCCCCCCCCCCcccccCCCCccccccC
Confidence 99999999999999999999999999999999999999999999999999999851 1111111111 2322 22333
Q ss_pred CCCCCCCCCCCCCCCCCCCC---CCcccccCcchHHHHHHhhhc-cccCccccCC-CccccccCCCCCCCCCCCCCCCCC
Q 016862 219 LSSPESASPPPSPRTESPMS---HSLSRSLGTSSINEMMASFRN-LQLGKVKSLP-SSWNIQVGGVGGSPGYGSPRGSML 293 (381)
Q Consensus 219 ~~sP~s~sPp~sp~~~s~~~---~~~~~~~~~~~~~e~~~s~r~-l~~~~~~s~p-~~~~~~~~~~~~~~~~gSpr~s~l 293 (381)
..+|+..+||+||...+.++ .-...+....+++...+.++. .+|....++. +.|+.++...+-..+||+|.+++|
T Consensus 325 ~~s~~~~~~p~sp~~~~~~~~~~~~~s~~~~~~~~~~p~~~~~~~Srl~s~~~a~~i~~~~~~~~~~l~~~f~s~~sssl 404 (528)
T KOG1595|consen 325 PFSPSPGSPPLSPSANGVSSPIASGGSRSLNSNSPSSPAAPLRSFSRLSSSLSAADISMSSPMNLGNLSELFSSPDSSSL 404 (528)
T ss_pred CCCCCCCCCCCCccccccccccccccccccCCCCCCCccccccccccccccccccccccccccccccchhhhcCcccccc
Confidence 44666678888886665444 333455666788999999999 9999888755 477777754322348999999999
Q ss_pred CCccccCCCCCCCCCCCCCCCCCCCccccccc-cccccchhh---hhcchhhHHHHHHH--hhhcc
Q 016862 294 RPGFCSLPSTPTRTPTRPGIGYPDIFNTCWEE-EEEEPVMER---VESGRDLRAKMFER--LSKEN 353 (381)
Q Consensus 294 r~g~~SLp~tpt~~~~~~~~~~~d~~~~~wd~-~eEep~meR---VESGr~lRak~~er--Lsken 353 (381)
.+.|.+|+++||.+..... =+ |.. +|++++|++ |+++|.||+.++++ ||.+.
T Consensus 405 ~~~~~~~~~~~tsP~~~~~----~~----~~~~~e~s~~~~~~~~~~~~r~l~~~l~~~~~~s~~~ 462 (528)
T KOG1595|consen 405 NPQLQVLSSAPTSPVFTDT----AS----FGSSVESSPAMEGRSQVMSSRELRASLKRSSTLSDKP 462 (528)
T ss_pred chhhhhcccCCcCCcCCcc----cc----cccccccchhhhcccccccchhhhhhhcccccccccc
Confidence 9999999988887632211 13 655 799999999 99999999999999 99993
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.30 E-value=2.4e-12 Score=124.00 Aligned_cols=92 Identities=37% Similarity=0.674 Sum_probs=72.3
Q ss_pred CCCCCCCCCCCCCCcccccCCCC---C----CCCccCCCCcCCcc-CCCCC-CCCCCCCcCcchhh--------cCcCCc
Q 016862 106 GRSHDWTECPYAHPGEKARRRDP---R----KYHYSGTACPDFRK-GSCKK-GDACEFAHGVFECW--------LHPARY 168 (381)
Q Consensus 106 g~chd~t~CpFAH~~Ek~RRRdP---~----~~~Yst~lCP~frk-G~C~~-Gd~C~FAHg~~El~--------~HP~~Y 168 (381)
+.|-....|+|.|+..+.+.+.. . .-.|++.+|..|++ |.|++ |++|+|+|+..|++ ..+.+|
T Consensus 96 ~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~~~~~~~~~~~~ 175 (332)
T KOG1677|consen 96 GVCGYGSSCRYNHPDLRLRPRPVRRSRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPSSENQVGNPPKY 175 (332)
T ss_pred CCCCCCCCCCccCcccccccCCccccccccCcccccCCcceeeecCccccccCchhhhcCCcccccccccchhhcCCCCC
Confidence 33555559999999522222221 1 12478999999985 89999 99999999999988 247799
Q ss_pred cCcCCCCC---CCCCC-cccCCCCCCcccCCCC
Q 016862 169 RTQPCKDG---GGCKR-RVCFFAHTPDQLRILP 197 (381)
Q Consensus 169 KTk~Ck~~---g~C~r-~~C~FAH~~~ELR~~p 197 (381)
||++|..| |.|++ .+|.|+|+..+++...
T Consensus 176 kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~~~~ 208 (332)
T KOG1677|consen 176 KTKLCPKFQKTGLCKYGSRCRFIHGEPEDRASN 208 (332)
T ss_pred CCcCCCccccCCCCCCCCcCeecCCCccccccc
Confidence 99999999 89996 8999999999998754
No 3
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.57 E-value=3.4e-08 Score=95.39 Aligned_cols=71 Identities=31% Similarity=0.545 Sum_probs=57.4
Q ss_pred ceEeeccceeccCC----CCCCC-CCCCCCCCCcccccC------CCCCCCCccCCCCcCCcc-CCCCCCCCCCCCcCcc
Q 016862 92 HFRMYEFKVRKCAR----GRSHD-WTECPYAHPGEKARR------RDPRKYHYSGTACPDFRK-GSCKKGDACEFAHGVF 159 (381)
Q Consensus 92 eFrm~~FKTr~C~r----g~chd-~t~CpFAH~~Ek~RR------RdP~~~~Yst~lCP~frk-G~C~~Gd~C~FAHg~~ 159 (381)
+..-..|||..|-. +.|.+ +.+|-|+|..|. .| ..-+..+|+|++|+.|.+ |.|++|.+|.|+|+..
T Consensus 124 ~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e-~r~~~~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 124 ERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEE-LRLPSSENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEP 202 (332)
T ss_pred ccCcccccCCcceeeecCccccccCchhhhcCCccc-ccccccchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCc
Confidence 34456799999984 77999 999999999765 44 222346799999999997 9999999999999988
Q ss_pred hhhc
Q 016862 160 ECWL 163 (381)
Q Consensus 160 El~~ 163 (381)
|...
T Consensus 203 ~~~~ 206 (332)
T KOG1677|consen 203 EDRA 206 (332)
T ss_pred cccc
Confidence 7663
No 4
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.48 E-value=7.6e-08 Score=95.24 Aligned_cols=66 Identities=35% Similarity=0.672 Sum_probs=57.3
Q ss_pred ccC--CCCcCCc-cCCCCC---CCCCCCC---cCcchhhcC--cCCccCcCCCCC---CCCCC-cccCCCCCCcccCCCC
Q 016862 133 YSG--TACPDFR-KGSCKK---GDACEFA---HGVFECWLH--PARYRTQPCKDG---GGCKR-RVCFFAHTPDQLRILP 197 (381)
Q Consensus 133 Yst--~lCP~fr-kG~C~~---Gd~C~FA---Hg~~El~~H--P~~YKTk~Ck~~---g~C~r-~~C~FAH~~~ELR~~p 197 (381)
|++ .+|..|. +|.|++ |++|+|| ||.-|+... -..|||++|+.| |+|++ .+|.|+|+.+++.-++
T Consensus 226 ~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~~ 305 (351)
T COG5063 226 YKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEMY 305 (351)
T ss_pred hcCCHHHhhccCcCCCCccccccccccccccccccccccccccccccccCCccchhhcccCccccccccccCChhhcccc
Confidence 677 7999986 799999 9999999 998876544 467999999999 89996 8999999999988776
Q ss_pred C
Q 016862 198 Q 198 (381)
Q Consensus 198 ~ 198 (381)
.
T Consensus 306 ~ 306 (351)
T COG5063 306 E 306 (351)
T ss_pred c
Confidence 5
No 5
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.44 E-value=2.2e-06 Score=89.67 Aligned_cols=66 Identities=30% Similarity=0.554 Sum_probs=55.6
Q ss_pred EeeccceeccCC---CCCCCCCCCCCCCCc-ccccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcchhhcCcC
Q 016862 94 RMYEFKVRKCAR---GRSHDWTECPYAHPG-EKARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVFECWLHPA 166 (381)
Q Consensus 94 rm~~FKTr~C~r---g~chd~t~CpFAH~~-Ek~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~El~~HP~ 166 (381)
|.|.|.-..||- |.|+.|+.|-|||.. |-| =.|. +|+|++|++- |.|++ --|-|||..+||+.++.
T Consensus 230 RkyhYs~tpCPefrkG~C~rGD~CEyaHgvfEcw--LHPa--~YRT~~CkDg--~~C~R-rvCfFAH~~eqLR~l~~ 299 (528)
T KOG1595|consen 230 RKYHYSSTPCPEFRKGSCERGDSCEYAHGVFECW--LHPA--RYRTRKCKDG--GYCPR-RVCFFAHSPEQLRPLPP 299 (528)
T ss_pred ccccccCccCcccccCCCCCCCccccccceehhh--cCHH--HhccccccCC--CCCcc-ceEeeecChHHhcccCC
Confidence 689999999995 779999999999985 333 3444 5789999998 78999 89999999999987763
No 6
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=97.97 E-value=6.5e-06 Score=81.86 Aligned_cols=109 Identities=20% Similarity=0.347 Sum_probs=83.1
Q ss_pred CCCccccCceEeeccce--eccCC----CCCCC---CCCCCCC---CCcccccCCCCCCCCccCCCCcCCcc-CCCCCCC
Q 016862 84 PVDAYSCDHFRMYEFKV--RKCAR----GRSHD---WTECPYA---HPGEKARRRDPRKYHYSGTACPDFRK-GSCKKGD 150 (381)
Q Consensus 84 ~v~~Ys~DeFrm~~FKT--r~C~r----g~chd---~t~CpFA---H~~Ek~RRRdP~~~~Yst~lCP~frk-G~C~~Gd 150 (381)
.+.+|...+--|.-+|| ..|.- |.|.. +..|.|+ |.. +...-.=.+..|+|++|-+|.+ |.|++|.
T Consensus 212 ~~~~~~~~e~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGl-N~l~~k~k~~~frTePcinwe~sGyc~yg~ 290 (351)
T COG5063 212 DELIYQKQEQNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGL-NELKSKKKKQNFRTEPCINWEKSGYCPYGL 290 (351)
T ss_pred hhhhhhhhhccchhhcCCHHHhhccCcCCCCcccccccccccccccccc-ccccccccccccccCCccchhhcccCcccc
Confidence 34566667778889999 89963 77888 8899999 874 3333333445699999999997 8999999
Q ss_pred CCCCCcCcchhh---cCc-CCccCcCCCCC---CCCCC-cccCCCCCCccc
Q 016862 151 ACEFAHGVFECW---LHP-ARYRTQPCKDG---GGCKR-RVCFFAHTPDQL 193 (381)
Q Consensus 151 ~C~FAHg~~El~---~HP-~~YKTk~Ck~~---g~C~r-~~C~FAH~~~EL 193 (381)
+|.|+||..+.. .|+ +.|+...|+.+ |.|+. ..|.|-|...-+
T Consensus 291 Rc~F~hgd~~~ie~~~~~~~~y~~~~crt~~~~g~~p~g~~~c~~~dkkn~ 341 (351)
T COG5063 291 RCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPSGGAVCKSFDKKNL 341 (351)
T ss_pred ccccccCChhhccccccccccccccccccccccCccCCCCchhhccccchh
Confidence 999999986654 444 57999999998 78984 557777765433
No 7
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=97.86 E-value=2.3e-06 Score=56.42 Aligned_cols=25 Identities=48% Similarity=1.069 Sum_probs=20.1
Q ss_pred ccCCCCcCCcc-CCCCCCCCCCCCcC
Q 016862 133 YSGTACPDFRK-GSCKKGDACEFAHG 157 (381)
Q Consensus 133 Yst~lCP~frk-G~C~~Gd~C~FAHg 157 (381)
|++++|++|.+ |.|++|++|.|+|+
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred CccccChhhccCCccCCCCCcCccCC
Confidence 67899999987 99999999999997
No 8
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.65 E-value=3.5e-05 Score=49.11 Aligned_cols=25 Identities=44% Similarity=0.999 Sum_probs=23.1
Q ss_pred ccCCCCcCCccCCCCCCCCCCCCcC
Q 016862 133 YSGTACPDFRKGSCKKGDACEFAHG 157 (381)
Q Consensus 133 Yst~lCP~frkG~C~~Gd~C~FAHg 157 (381)
|++.+|+.|.+|.|++|++|.|+|.
T Consensus 2 ~k~~~C~~~~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 2 YKTELCKFFKRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCCCcCcCccCCCCCCCCCcCCCCc
Confidence 5688999999999999999999997
No 9
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=97.64 E-value=1.4e-05 Score=79.82 Aligned_cols=59 Identities=34% Similarity=0.798 Sum_probs=46.4
Q ss_pred CCCCcCCccCCCCCCCC-CCCCcCcchhhcCcCCccCcCCCCC--CCCCCcccCCCCCCcccCC
Q 016862 135 GTACPDFRKGSCKKGDA-CEFAHGVFECWLHPARYRTQPCKDG--GGCKRRVCFFAHTPDQLRI 195 (381)
Q Consensus 135 t~lCP~frkG~C~~Gd~-C~FAHg~~El~~HP~~YKTk~Ck~~--g~C~r~~C~FAH~~~ELR~ 195 (381)
-+.|++|.+|.|.+||. |+|+|--.-+ +-..-+-..|.++ |.|.|..|.|+|.+.+++.
T Consensus 37 ~eVCReF~rn~C~R~d~~CkfaHP~~~~--~V~~g~v~aC~Ds~kgrCsR~nCkylHpp~hlkd 98 (331)
T KOG2494|consen 37 LEVCREFLRNTCSRGDRECKFAHPPKNC--QVSNGRVIACFDSQKGRCSRENCKYLHPPQHLKD 98 (331)
T ss_pred HHHHHHHHhccccCCCccccccCCCCCC--CccCCeEEEEeccccCccCcccceecCCChhhhh
Confidence 36899999999999998 9999975422 2223445579998 8899999999999988874
No 10
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=96.91 E-value=0.00072 Score=67.83 Aligned_cols=50 Identities=34% Similarity=0.755 Sum_probs=26.7
Q ss_pred cCCCCcCCccCCCCCCCCCCCCcCcchhhcCcCCccCcCCCCC---CCCCC-cccCCCCCC
Q 016862 134 SGTACPDFRKGSCKKGDACEFAHGVFECWLHPARYRTQPCKDG---GGCKR-RVCFFAHTP 190 (381)
Q Consensus 134 st~lCP~frkG~C~~Gd~C~FAHg~~El~~HP~~YKTk~Ck~~---g~C~r-~~C~FAH~~ 190 (381)
+.+.|+.|..|.|+.||.|.|+|-. + +-|...|..| +.|.+ ..|.|.|+.
T Consensus 76 ~~~vcK~~l~glC~kgD~C~Flhe~-~------~~k~rec~ff~~~g~c~~~~~c~y~h~d 129 (325)
T KOG1040|consen 76 GKVVCKHWLRGLCKKGDQCEFLHEY-D------LTKMRECKFFSLFGECTNGKDCPYLHGD 129 (325)
T ss_pred CceeehhhhhhhhhccCcCcchhhh-h------hcccccccccccccccccccCCcccCCC
Confidence 3556666666666666666666653 1 2233345444 45554 455555554
No 11
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=96.61 E-value=0.00049 Score=45.33 Aligned_cols=23 Identities=39% Similarity=0.724 Sum_probs=17.8
Q ss_pred ccCcCCCCC---CCCCC-cccCCCCCC
Q 016862 168 YRTQPCKDG---GGCKR-RVCFFAHTP 190 (381)
Q Consensus 168 YKTk~Ck~~---g~C~r-~~C~FAH~~ 190 (381)
|||++|+.| |.|++ ..|.|+|++
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred CccccChhhccCCccCCCCCcCccCCC
Confidence 799999998 89996 899999974
No 12
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=96.48 E-value=0.0015 Score=63.72 Aligned_cols=65 Identities=28% Similarity=0.682 Sum_probs=52.9
Q ss_pred CCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcchhhcCcCCccCcCCCCC--CCCCCcc
Q 016862 106 GRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVFECWLHPARYRTQPCKDG--GGCKRRV 183 (381)
Q Consensus 106 g~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~El~~HP~~YKTk~Ck~~--g~C~r~~ 183 (381)
|.|-.+..|-|.|-..+ .+.||.|..|.|.+.+.|...|...- .+--.|+.| |.|..+.
T Consensus 216 gicgkgaacrfvheptr------------kticpkflngrcnkaedcnlsheldp-------rripacryfllgkcnnpn 276 (377)
T KOG1492|consen 216 GICGKGAACRFVHEPTR------------KTICPKFLNGRCNKAEDCNLSHELDP-------RRIPACRYFLLGKCNNPN 276 (377)
T ss_pred CcccCCceeeeeccccc------------cccChHHhcCccCchhcCCcccccCc-------cccchhhhhhhccCCCCC
Confidence 56888999999995321 47999999999999999999998532 233469998 9999999
Q ss_pred cCCCCC
Q 016862 184 CFFAHT 189 (381)
Q Consensus 184 C~FAH~ 189 (381)
|+|.|-
T Consensus 277 cryvhi 282 (377)
T KOG1492|consen 277 CRYVHI 282 (377)
T ss_pred ceEEEE
Confidence 999884
No 13
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=95.91 E-value=0.0067 Score=61.03 Aligned_cols=78 Identities=23% Similarity=0.451 Sum_probs=56.4
Q ss_pred ccceeccCC---CCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCc-cCCCCCCCCCCCCcCcchhhcCcCCccCcC
Q 016862 97 EFKVRKCAR---GRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFR-KGSCKKGDACEFAHGVFECWLHPARYRTQP 172 (381)
Q Consensus 97 ~FKTr~C~r---g~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~fr-kG~C~~Gd~C~FAHg~~El~~HP~~YKTk~ 172 (381)
.+++..|.. +.|..++.|.|.|-.+ ..+ .-.|..|. .|.|.+|.+|.|-|+..| -+-+.
T Consensus 74 ~~~~~vcK~~l~glC~kgD~C~Flhe~~--~~k--------~rec~ff~~~g~c~~~~~c~y~h~dpq-------t~~k~ 136 (325)
T KOG1040|consen 74 SRGKVVCKHWLRGLCKKGDQCEFLHEYD--LTK--------MRECKFFSLFGECTNGKDCPYLHGDPQ-------TAIKK 136 (325)
T ss_pred cCCceeehhhhhhhhhccCcCcchhhhh--hcc--------cccccccccccccccccCCcccCCChh-------hhhhc
Confidence 577888885 7799999999999641 122 22455555 578999999999999752 34456
Q ss_pred CCCC--CCCCC-cccCCCCCCc
Q 016862 173 CKDG--GGCKR-RVCFFAHTPD 191 (381)
Q Consensus 173 Ck~~--g~C~r-~~C~FAH~~~ 191 (381)
|+.+ |.|+. ..|.+.|-..
T Consensus 137 c~~~~~g~c~~g~~c~~~h~~~ 158 (325)
T KOG1040|consen 137 CKWYKEGFCRGGPSCKKRHERK 158 (325)
T ss_pred cchhhhccCCCcchhhhhhhcc
Confidence 7777 77874 7888888766
No 14
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=95.28 E-value=0.011 Score=59.66 Aligned_cols=52 Identities=25% Similarity=0.478 Sum_probs=39.4
Q ss_pred CCCCCCCCC-CCCCCCcccccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcchhh
Q 016862 105 RGRSHDWTE-CPYAHPGEKARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVFECW 162 (381)
Q Consensus 105 rg~chd~t~-CpFAH~~Ek~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~El~ 162 (381)
|+.|.++++ |-|||+-+ ++..-+=+-..|=++.||.|.+ ++|+|.|...++.
T Consensus 45 rn~C~R~d~~CkfaHP~~-----~~~V~~g~v~aC~Ds~kgrCsR-~nCkylHpp~hlk 97 (331)
T KOG2494|consen 45 RNTCSRGDRECKFAHPPK-----NCQVSNGRVIACFDSQKGRCSR-ENCKYLHPPQHLK 97 (331)
T ss_pred hccccCCCccccccCCCC-----CCCccCCeEEEEeccccCccCc-ccceecCCChhhh
Confidence 466766776 99999953 3444444456999999999998 6799999986654
No 15
>smart00356 ZnF_C3H1 zinc finger.
Probab=95.17 E-value=0.016 Score=36.71 Aligned_cols=24 Identities=42% Similarity=0.707 Sum_probs=20.6
Q ss_pred CccCcCCCCC--CCCCC-cccCCCCCC
Q 016862 167 RYRTQPCKDG--GGCKR-RVCFFAHTP 190 (381)
Q Consensus 167 ~YKTk~Ck~~--g~C~r-~~C~FAH~~ 190 (381)
.|||.+|+.| |.|.+ ..|.|.|..
T Consensus 1 ~~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 1 KYKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 4799999998 88995 789999973
No 16
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.07 E-value=0.031 Score=59.28 Aligned_cols=75 Identities=25% Similarity=0.531 Sum_probs=56.4
Q ss_pred CCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCccC-CCCCCCCCCCCcCcchhhcCcCCccCcCCCCC--CC-CCCc
Q 016862 107 RSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFRKG-SCKKGDACEFAHGVFECWLHPARYRTQPCKDG--GG-CKRR 182 (381)
Q Consensus 107 ~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frkG-~C~~Gd~C~FAHg~~El~~HP~~YKTk~Ck~~--g~-C~r~ 182 (381)
.|...+.|+|.|. |.++-- -+-|.+|..+ .|++ .|.|-|+.+-+. ..-.+|..| ++ |.+.
T Consensus 13 ~cKk~d~c~~rh~-E~al~n--------~t~C~~w~~~~~C~k--~C~YRHSe~~~k-----r~e~~CYwe~~p~gC~k~ 76 (667)
T KOG4791|consen 13 TCKKGDSCPFRHC-EAALGN--------ETVCTLWQEGRCCRK--VCRYRHSEIDKK-----RSEIPCYWENQPTGCQKL 76 (667)
T ss_pred hhhccCcCcchhh-HHHhcC--------cchhhhhhhcCcccc--cccchhhHHhhh-----cCcccceeecCCCccCCC
Confidence 4677899999998 665211 4789999976 4553 999999976654 455789988 44 9999
Q ss_pred ccCCCCCCcccCCCC
Q 016862 183 VCFFAHTPDQLRILP 197 (381)
Q Consensus 183 ~C~FAH~~~ELR~~p 197 (381)
.|-|-|+.-.|..+-
T Consensus 77 ~CgfRH~~pPLkg~l 91 (667)
T KOG4791|consen 77 NCGFRHNRPPLKGVL 91 (667)
T ss_pred ccccccCCCchhhhc
Confidence 999999865555443
No 17
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=93.52 E-value=0.092 Score=51.53 Aligned_cols=86 Identities=27% Similarity=0.586 Sum_probs=50.6
Q ss_pred ceeccCC---CCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcchhh----cCcCCc---
Q 016862 99 KVRKCAR---GRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVFECW----LHPARY--- 168 (381)
Q Consensus 99 KTr~C~r---g~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~El~----~HP~~Y--- 168 (381)
+-..||+ |+|..-..|...|-. +-||-| .|+.|.-|.|.. -+|.|.|--.--- +.-..|
T Consensus 232 rkticpkflngrcnkaedcnlshel--dprrip--------acryfllgkcnn-pncryvhihysenapicfefakygfc 300 (377)
T KOG1492|consen 232 RKTICPKFLNGRCNKAEDCNLSHEL--DPRRIP--------ACRYFLLGKCNN-PNCRYVHIHYSENAPICFEFAKYGFC 300 (377)
T ss_pred ccccChHHhcCccCchhcCCccccc--Cccccc--------hhhhhhhccCCC-CCceEEEEeecCCCceeeeehhccee
Confidence 3457886 889999999999964 456655 355555555543 3555554310000 000000
Q ss_pred ------c---CcCCCCC---CCCCCcccCCCCCCcccCC
Q 016862 169 ------R---TQPCKDG---GGCKRRVCFFAHTPDQLRI 195 (381)
Q Consensus 169 ------K---Tk~Ck~~---g~C~r~~C~FAH~~~ELR~ 195 (381)
| --.|.++ |.|..+.|.+.|+.-..-+
T Consensus 301 elgtscknqhilqctdyamfgscnnpqcslyhgavsadv 339 (377)
T KOG1492|consen 301 ELGTSCKNQHILQCTDYAMFGSCNNPQCSLYHGAVSADV 339 (377)
T ss_pred ccccccccceeeeecchhhhcCCCCCcceeecceeccCC
Confidence 1 1147776 8999999999999654433
No 18
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=93.34 E-value=0.11 Score=56.61 Aligned_cols=88 Identities=24% Similarity=0.536 Sum_probs=48.0
Q ss_pred eeccCCCC-CCCCCCCCCCCCcccc-cCCCCCCCCccCCCCcCCccCCCCCCC-----CCCCCcCcchh--hcC--cCCc
Q 016862 100 VRKCARGR-SHDWTECPYAHPGEKA-RRRDPRKYHYSGTACPDFRKGSCKKGD-----ACEFAHGVFEC--WLH--PARY 168 (381)
Q Consensus 100 Tr~C~rg~-chd~t~CpFAH~~Ek~-RRRdP~~~~Yst~lCP~frkG~C~~Gd-----~C~FAHg~~El--~~H--P~~Y 168 (381)
+.+|.++- |. ...|-|+|+.-.. ----|.+-. ...|-.-. -+|+.|. .|.|.|+-.-. .+. |..+
T Consensus 544 l~~Cky~~~Ct-~a~Ce~~HPtaa~~~~s~p~k~f--a~~~~ks~-p~Ck~~~kCtasDC~~sH~~~~~pvq~t~ip~~~ 619 (681)
T KOG3702|consen 544 LTRCKYGPACT-SAECEFAHPTAAENAKSLPNKKF--ASKCLKSH-PGCKFGKKCTASDCNYSHAGRRIPVQPTRIPPPF 619 (681)
T ss_pred eccccCCCcCC-chhhhhcCCcchhhhhccccccc--cccceecc-cccccccccccccCcccccCCCCCCccccCCCCC
Confidence 45677754 44 7889999984110 011121100 11111111 1355543 67899985432 111 2222
Q ss_pred ----cCcCCCCCCCCCCcccCCCCCCc
Q 016862 169 ----RTQPCKDGGGCKRRVCFFAHTPD 191 (381)
Q Consensus 169 ----KTk~Ck~~g~C~r~~C~FAH~~~ 191 (381)
-+.+|+.+++|....|.|.|-..
T Consensus 620 ~~~ti~~~CrY~pnCrnm~C~F~HPk~ 646 (681)
T KOG3702|consen 620 PGGTIRGLCRYRPNCRNMQCKFYHPKT 646 (681)
T ss_pred CCCCccccceeccCcCCccccccCCcc
Confidence 25668888999999999999743
No 19
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=93.11 E-value=0.8 Score=45.73 Aligned_cols=80 Identities=29% Similarity=0.553 Sum_probs=50.5
Q ss_pred cceeccCC---CCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCC-ccCCCCCCCCCCCCcCcchhhcCcCCccCcCC
Q 016862 98 FKVRKCAR---GRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDF-RKGSCKKGDACEFAHGVFECWLHPARYRTQPC 173 (381)
Q Consensus 98 FKTr~C~r---g~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~f-rkG~C~~Gd~C~FAHg~~El~~HP~~YKTk~C 173 (381)
.....|.. +.|.....|.|.|.. .+|+ + .+..|..| .+|.|..|..|.|.|.. |+. +-..|
T Consensus 102 ~s~V~c~~~~~g~c~s~~~c~~lh~~--d~~~-s-----~~~~c~~Fs~~G~cs~g~~c~~~h~d------p~~-~~~~~ 166 (285)
T COG5084 102 SSSVVCKFFLRGLCKSGFSCEFLHEY--DLRS-S-----QGPPCRSFSLKGSCSSGPSCGYSHID------PDS-FAGNC 166 (285)
T ss_pred cCCcccchhccccCcCCCccccccCC--Cccc-c-----cCCCcccccccceeccCCCCCccccC------ccc-ccccc
Confidence 44445553 556667788888864 2222 2 26788888 57888888888888885 211 11224
Q ss_pred CCC-----CCCCC-cccCCCCCCcc
Q 016862 174 KDG-----GGCKR-RVCFFAHTPDQ 192 (381)
Q Consensus 174 k~~-----g~C~r-~~C~FAH~~~E 192 (381)
..+ +.|+. ..|.|-|+..-
T Consensus 167 ~~~~~~~~~f~p~g~~c~~~H~~~~ 191 (285)
T COG5084 167 DQYSGATYGFCPLGASCKFSHTLKR 191 (285)
T ss_pred cccCcccccccCCCCcccccccccc
Confidence 443 56774 78888888763
No 20
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=92.44 E-value=0.12 Score=51.56 Aligned_cols=62 Identities=32% Similarity=0.636 Sum_probs=50.5
Q ss_pred CCCCCCCcccccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcchhhcCcCCcc--CcCCCCC---CCCCC-cccCC
Q 016862 113 ECPYAHPGEKARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVFECWLHPARYR--TQPCKDG---GGCKR-RVCFF 186 (381)
Q Consensus 113 ~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~El~~HP~~YK--Tk~Ck~~---g~C~r-~~C~F 186 (381)
.|++-|- + | +.|+...|+.|..|.|+.|+.|.|+|+.. +-+ +-.|+.| |.|.. ..|.+
T Consensus 91 s~~~~~~--~-----~--~~~s~V~c~~~~~g~c~s~~~c~~lh~~d-------~~~s~~~~c~~Fs~~G~cs~g~~c~~ 154 (285)
T COG5084 91 STPNNHV--N-----P--VLSSSVVCKFFLRGLCKSGFSCEFLHEYD-------LRSSQGPPCRSFSLKGSCSSGPSCGY 154 (285)
T ss_pred cCCcccc--C-----c--cccCCcccchhccccCcCCCccccccCCC-------cccccCCCcccccccceeccCCCCCc
Confidence 6777774 2 1 15778999999999999999999999953 333 6679998 89995 89999
Q ss_pred CCCC
Q 016862 187 AHTP 190 (381)
Q Consensus 187 AH~~ 190 (381)
.|..
T Consensus 155 ~h~d 158 (285)
T COG5084 155 SHID 158 (285)
T ss_pred cccC
Confidence 9996
No 21
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=91.43 E-value=0.14 Score=31.56 Aligned_cols=11 Identities=55% Similarity=1.467 Sum_probs=6.7
Q ss_pred CCCCCCCCCCc
Q 016862 146 CKKGDACEFAH 156 (381)
Q Consensus 146 C~~Gd~C~FAH 156 (381)
|++|++|.|.|
T Consensus 8 C~~~~~C~f~H 18 (19)
T PF14608_consen 8 CTNGDNCPFSH 18 (19)
T ss_pred CCCCCcCccCC
Confidence 66666666655
No 22
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=90.50 E-value=0.16 Score=54.27 Aligned_cols=59 Identities=27% Similarity=0.503 Sum_probs=40.3
Q ss_pred cCCCCcCCccC---CCCCCCCCCCCcCcchhhcC--cCCccCcCCCCC---CCCCC-cccCCC--CCCcccC
Q 016862 134 SGTACPDFRKG---SCKKGDACEFAHGVFECWLH--PARYRTQPCKDG---GGCKR-RVCFFA--HTPDQLR 194 (381)
Q Consensus 134 st~lCP~frkG---~C~~Gd~C~FAHg~~El~~H--P~~YKTk~Ck~~---g~C~r-~~C~FA--H~~~ELR 194 (381)
...|||....| .|.+||+|.|.|.+.-.+.. |+.= -.|.-| |.|++ -.|+|+ |-..+-+
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Dig--~~Cp~f~s~G~Cp~G~~CRFl~aHld~~g~ 144 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDIG--PSCPVFESLGFCPYGFKCRFLGAHLDIEGN 144 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCcccC--CccceeeccccCCccceeehhhcccCcccc
Confidence 46799998865 79999999999998654432 1111 237766 88996 679995 5544444
No 23
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=90.01 E-value=0.13 Score=49.48 Aligned_cols=32 Identities=28% Similarity=0.694 Sum_probs=27.7
Q ss_pred CCCCccCCCCcCCc-cCCCCCCCCCCCCcCcch
Q 016862 129 RKYHYSGTACPDFR-KGSCKKGDACEFAHGVFE 160 (381)
Q Consensus 129 ~~~~Yst~lCP~fr-kG~C~~Gd~C~FAHg~~E 160 (381)
..+.|.+..|.+|+ +|.|-|||.|.|.|....
T Consensus 135 ~viD~qpdVCKdyk~TGYCGYGDsCKflH~R~D 167 (259)
T COG5152 135 EVIDTQPDVCKDYKETGYCGYGDSCKFLHDRSD 167 (259)
T ss_pred ceeecCcccccchhhcccccCCchhhhhhhhhh
Confidence 34668899999998 699999999999999763
No 24
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=89.07 E-value=0.22 Score=52.10 Aligned_cols=25 Identities=40% Similarity=0.962 Sum_probs=23.4
Q ss_pred cCCCCcCCccCCCCCCCCCCCCcCc
Q 016862 134 SGTACPDFRKGSCKKGDACEFAHGV 158 (381)
Q Consensus 134 st~lCP~frkG~C~~Gd~C~FAHg~ 158 (381)
+.++|++|..|.|+.|.+|.|.||.
T Consensus 139 sMkpC~ffLeg~CRF~enCRfSHG~ 163 (486)
T KOG2185|consen 139 SMKPCKFFLEGRCRFGENCRFSHGL 163 (486)
T ss_pred hhccchHhhccccccCcccccccCc
Confidence 5679999999999999999999995
No 25
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=87.76 E-value=0.26 Score=52.72 Aligned_cols=59 Identities=29% Similarity=0.544 Sum_probs=43.4
Q ss_pred ceeccCC---C---CCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCCcc-CCCCCCCCCCCC--cCcch
Q 016862 99 KVRKCAR---G---RSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDFRK-GSCKKGDACEFA--HGVFE 160 (381)
Q Consensus 99 KTr~C~r---g---~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~frk-G~C~~Gd~C~FA--Hg~~E 160 (381)
+.++||. + .|..+++|-|-|..+--.-..+..+ ...||-|.. |.|++|-+|.|+ |-..|
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Di---g~~Cp~f~s~G~Cp~G~~CRFl~aHld~~ 142 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDI---GPSCPVFESLGFCPYGFKCRFLGAHLDIE 142 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCccc---CCccceeeccccCCccceeehhhcccCcc
Confidence 7899996 2 4899999999998764333333222 468999985 899999999996 54443
No 26
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=87.35 E-value=0.43 Score=29.43 Aligned_cols=18 Identities=44% Similarity=0.995 Sum_probs=15.4
Q ss_pred CCCCCCCCCCc-ccCCCCC
Q 016862 172 PCKDGGGCKRR-VCFFAHT 189 (381)
Q Consensus 172 ~Ck~~g~C~r~-~C~FAH~ 189 (381)
+|+.|.+|... .|.|+|.
T Consensus 1 ~Ck~~~~C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPNCTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCCCCCCCcCccCCc
Confidence 58988889975 9999993
No 27
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.00 E-value=0.26 Score=49.53 Aligned_cols=31 Identities=32% Similarity=0.853 Sum_probs=27.3
Q ss_pred CCCccCCCCcCCc-cCCCCCCCCCCCCcCcch
Q 016862 130 KYHYSGTACPDFR-KGSCKKGDACEFAHGVFE 160 (381)
Q Consensus 130 ~~~Yst~lCP~fr-kG~C~~Gd~C~FAHg~~E 160 (381)
++-|.+..|.+|+ +|.|-+||+|.|.|...-
T Consensus 181 ~~d~qpDicKdykeTgycg~gdSckFlh~r~D 212 (313)
T KOG1813|consen 181 RIDYQPDICKDYKETGYCGYGDSCKFLHDRSD 212 (313)
T ss_pred eeecCchhhhhhHhhCcccccchhhhhhhhhh
Confidence 4668899999998 699999999999998753
No 28
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=84.66 E-value=1.5 Score=48.16 Aligned_cols=82 Identities=24% Similarity=0.488 Sum_probs=52.5
Q ss_pred eccceeccCCCCCCCCCCCCCCCCcccccCCCCCCCCccCCCCcCC---ccCCCCCCCCCCCCcCcchhhcCcCCccCcC
Q 016862 96 YEFKVRKCARGRSHDWTECPYAHPGEKARRRDPRKYHYSGTACPDF---RKGSCKKGDACEFAHGVFECWLHPARYRTQP 172 (381)
Q Consensus 96 ~~FKTr~C~rg~chd~t~CpFAH~~Ek~RRRdP~~~~Yst~lCP~f---rkG~C~~Gd~C~FAHg~~El~~HP~~YKTk~ 172 (381)
..|-...|..+..---..|+|.|.+ |+.|-. |++..|+.= ..+-|+|+-+|.---= .+||| +.
T Consensus 581 ~~ks~p~Ck~~~kCtasDC~~sH~~----~~~pvq--~t~ip~~~~~~ti~~~CrY~pnCrnm~C---~F~HP-----k~ 646 (681)
T KOG3702|consen 581 CLKSHPGCKFGKKCTASDCNYSHAG----RRIPVQ--PTRIPPPFPGGTIRGLCRYRPNCRNMQC---KFYHP-----KT 646 (681)
T ss_pred ceecccccccccccccccCcccccC----CCCCCc--cccCCCCCCCCCccccceeccCcCCccc---cccCC-----cc
Confidence 3444556666543334679999985 555554 556666653 1367777776632111 23555 67
Q ss_pred CCCCCCCC-CcccCCCCCCc
Q 016862 173 CKDGGGCK-RRVCFFAHTPD 191 (381)
Q Consensus 173 Ck~~g~C~-r~~C~FAH~~~ 191 (381)
|+...+|. +..|.|+|-.-
T Consensus 647 cRf~~~c~~~~sc~fYh~r~ 666 (681)
T KOG3702|consen 647 CRFNTNCPNNPSCTFYHERP 666 (681)
T ss_pred ccccccCCCCcccccccCCc
Confidence 99999999 68999999743
No 29
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=84.34 E-value=0.22 Score=49.05 Aligned_cols=60 Identities=35% Similarity=0.636 Sum_probs=45.1
Q ss_pred ccCCCCcCCccCCCCCCCCCCCCcCcchhhcC--cCCc-------------------cCcCCCCC---------C---CC
Q 016862 133 YSGTACPDFRKGSCKKGDACEFAHGVFECWLH--PARY-------------------RTQPCKDG---------G---GC 179 (381)
Q Consensus 133 Yst~lCP~frkG~C~~Gd~C~FAHg~~El~~H--P~~Y-------------------KTk~Ck~~---------g---~C 179 (381)
-++..|-.|..+.|..|+.|.|+|+..|.+-. |++| -.+.|+.| | .|
T Consensus 83 pK~~vcalF~~~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~C 162 (299)
T COG5252 83 PKTVVCALFLNKTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWTC 162 (299)
T ss_pred chhHHHHHhccCccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceeeC
Confidence 46789999999999999999999998887633 4444 22347765 1 59
Q ss_pred CC--cccCCCCCCcc
Q 016862 180 KR--RVCFFAHTPDQ 192 (381)
Q Consensus 180 ~r--~~C~FAH~~~E 192 (381)
+. ..|-|.|..-+
T Consensus 163 Png~~~C~y~H~Lp~ 177 (299)
T COG5252 163 PNGNMRCSYIHKLPD 177 (299)
T ss_pred CCCCceeeeeeccCc
Confidence 85 58999998655
No 30
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=84.13 E-value=0.13 Score=50.70 Aligned_cols=62 Identities=29% Similarity=0.597 Sum_probs=42.9
Q ss_pred ceeccCC---CCCCCCCCCCCCCCcccccC-CCCCCCCc-----------------cCCCCcCCcc----C------CCC
Q 016862 99 KVRKCAR---GRSHDWTECPYAHPGEKARR-RDPRKYHY-----------------SGTACPDFRK----G------SCK 147 (381)
Q Consensus 99 KTr~C~r---g~chd~t~CpFAH~~Ek~RR-RdP~~~~Y-----------------st~lCP~frk----G------~C~ 147 (381)
|+..|.. +.|.+++.|-|+|.-|..|| ..|.+|.- .-..|..|.. | .|+
T Consensus 84 K~~vcalF~~~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~CP 163 (299)
T COG5252 84 KTVVCALFLNKTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWTCP 163 (299)
T ss_pred hhHHHHHhccCccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceeeCC
Confidence 6667765 45788999999999766544 23333220 1237888862 3 899
Q ss_pred CC-CCCCCCcCcch
Q 016862 148 KG-DACEFAHGVFE 160 (381)
Q Consensus 148 ~G-d~C~FAHg~~E 160 (381)
+| +.|.|-|...+
T Consensus 164 ng~~~C~y~H~Lp~ 177 (299)
T COG5252 164 NGNMRCSYIHKLPD 177 (299)
T ss_pred CCCceeeeeeccCc
Confidence 97 79999999766
No 31
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=82.89 E-value=0.67 Score=48.64 Aligned_cols=38 Identities=34% Similarity=0.587 Sum_probs=30.5
Q ss_pred chhhcCcCCccCcCCCCC--CCCC-CcccCCCCCCc----ccCCC
Q 016862 159 FECWLHPARYRTQPCKDG--GGCK-RRVCFFAHTPD----QLRIL 196 (381)
Q Consensus 159 ~El~~HP~~YKTk~Ck~~--g~C~-r~~C~FAH~~~----ELR~~ 196 (381)
-=+++||+---.++|++| |.|+ +..|+|.||.. .||..
T Consensus 129 RVlfl~PTh~sMkpC~ffLeg~CRF~enCRfSHG~~V~lsslr~y 173 (486)
T KOG2185|consen 129 RVLFLTPTHESMKPCKFFLEGRCRFGENCRFSHGLDVPLSSLRNY 173 (486)
T ss_pred EEEeecCcchhhccchHhhccccccCcccccccCcccchhhcccC
Confidence 335678888899999999 9999 57899999974 56643
No 32
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=82.87 E-value=0.29 Score=49.45 Aligned_cols=30 Identities=33% Similarity=0.774 Sum_probs=25.8
Q ss_pred ccCCCCcCCccCCCCCCCCCCCCcCcchhh
Q 016862 133 YSGTACPDFRKGSCKKGDACEFAHGVFECW 162 (381)
Q Consensus 133 Yst~lCP~frkG~C~~Gd~C~FAHg~~El~ 162 (381)
=++.+|-.|..|.|..|+.|.|+|...+.+
T Consensus 90 PKSvvCafFk~g~C~KG~kCKFsHdl~~~~ 119 (343)
T KOG1763|consen 90 PKSVVCAFFKQGTCTKGDKCKFSHDLAVER 119 (343)
T ss_pred chHHHHHHHhccCCCCCCcccccchHHHhh
Confidence 357899999999999999999999975544
No 33
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=74.95 E-value=0.5 Score=47.78 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=20.2
Q ss_pred ceeccCC---CCCCCCCCCCCCCCcccccCCCCCC
Q 016862 99 KVRKCAR---GRSHDWTECPYAHPGEKARRRDPRK 130 (381)
Q Consensus 99 KTr~C~r---g~chd~t~CpFAH~~Ek~RRRdP~~ 130 (381)
|+..|.. +.|..++.|-|+|..+. .|+.+.+
T Consensus 91 KSvvCafFk~g~C~KG~kCKFsHdl~~-~~k~eK~ 124 (343)
T KOG1763|consen 91 KSVVCAFFKQGTCTKGDKCKFSHDLAV-ERKKEKI 124 (343)
T ss_pred hHHHHHHHhccCCCCCCcccccchHHH-hhhccch
Confidence 4455654 56777899999998543 3544443
No 34
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=72.76 E-value=2.2 Score=44.06 Aligned_cols=37 Identities=30% Similarity=0.577 Sum_probs=31.2
Q ss_pred ccCCCCCCCCccCCCCcCCccCCCCCCCCCCCCcCcc
Q 016862 123 ARRRDPRKYHYSGTACPDFRKGSCKKGDACEFAHGVF 159 (381)
Q Consensus 123 ~RRRdP~~~~Yst~lCP~frkG~C~~Gd~C~FAHg~~ 159 (381)
..||.|..-.-.+..|..|.+|.|++|+.|.|-|...
T Consensus 149 l~rt~p~ykrn~p~Icsf~v~geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 149 LQRTTPYYKRNRPHICSFFVKGECKRGAECPYRHEKP 185 (377)
T ss_pred HhccCccccCCCCccccceeeccccccccccccccCC
Confidence 4577776666678899999999999999999999854
No 35
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.68 E-value=3.6 Score=44.28 Aligned_cols=54 Identities=33% Similarity=0.619 Sum_probs=40.2
Q ss_pred CCCCcCCccCCCCCCCCCCCCcCcchhhcCcCCccCcCCCCC--CCCCCcccCCCCCCcccC
Q 016862 135 GTACPDFRKGSCKKGDACEFAHGVFECWLHPARYRTQPCKDG--GGCKRRVCFFAHTPDQLR 194 (381)
Q Consensus 135 t~lCP~frkG~C~~Gd~C~FAHg~~El~~HP~~YKTk~Ck~~--g~C~r~~C~FAH~~~ELR 194 (381)
...|..|....|+.+|.|.|.|...-+ ---.-|..| +.|-+..|.|-|+.-.+.
T Consensus 3 ~~dcyff~ys~cKk~d~c~~rh~E~al------~n~t~C~~w~~~~~C~k~C~YRHSe~~~k 58 (667)
T KOG4791|consen 3 GEDCYFFFYSTCKKGDSCPFRHCEAAL------GNETVCTLWQEGRCCRKVCRYRHSEIDKK 58 (667)
T ss_pred cccchhhhhhhhhccCcCcchhhHHHh------cCcchhhhhhhcCcccccccchhhHHhhh
Confidence 456888888899999999999985322 122358888 555566999999986654
No 36
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.36 E-value=6.6 Score=40.28 Aligned_cols=24 Identities=42% Similarity=0.944 Sum_probs=23.1
Q ss_pred CCCcCCccCCCCCCCCCCCCcCcc
Q 016862 136 TACPDFRKGSCKKGDACEFAHGVF 159 (381)
Q Consensus 136 ~lCP~frkG~C~~Gd~C~FAHg~~ 159 (381)
+.|..|.+|.|++|+.|.|.|...
T Consensus 9 tic~~~~~g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQKGNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhcccccccccceeeeeccCc
Confidence 899999999999999999999986
No 37
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=34.56 E-value=25 Score=23.19 Aligned_cols=19 Identities=42% Similarity=0.954 Sum_probs=10.4
Q ss_pred CCcCCccC-CCCCCCCCCCCc
Q 016862 137 ACPDFRKG-SCKKGDACEFAH 156 (381)
Q Consensus 137 lCP~frkG-~C~~Gd~C~FAH 156 (381)
+|+.-..| .|.. +.|.|-|
T Consensus 2 lC~yEl~Gg~Cnd-~~C~~QH 21 (23)
T PF10650_consen 2 LCPYELTGGVCND-PDCEFQH 21 (23)
T ss_pred CCccccCCCeeCC-CCCCccc
Confidence 45555554 5543 4666665
No 38
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=28.53 E-value=28 Score=34.71 Aligned_cols=24 Identities=33% Similarity=0.862 Sum_probs=20.9
Q ss_pred CCCCcCCccCCCCCCCCCCCCcCc
Q 016862 135 GTACPDFRKGSCKKGDACEFAHGV 158 (381)
Q Consensus 135 t~lCP~frkG~C~~Gd~C~FAHg~ 158 (381)
-..|..|..+.|.+|..|.|-|-.
T Consensus 152 ea~C~~~e~~~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 152 EAICGQFERTECSRGGACNFMHVK 175 (260)
T ss_pred hhhhcccccccCCCCCcCcchhhh
Confidence 457888988999999999999974
Done!