Query 011853
Match_columns 476
No_of_seqs 382 out of 1733
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 05:57:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1677 CCCH-type Zn-finger pr 99.9 2.8E-25 6.1E-30 225.8 19.4 277 10-370 46-332 (332)
2 KOG1677 CCCH-type Zn-finger pr 99.5 1.7E-13 3.6E-18 139.7 13.6 83 33-117 121-204 (332)
3 KOG1040 Polyadenylation factor 99.4 5.6E-13 1.2E-17 136.2 7.0 66 305-374 159-225 (325)
4 KOG1040 Polyadenylation factor 99.2 8E-12 1.7E-16 127.8 6.5 98 31-161 30-130 (325)
5 KOG1492 C3H1-type Zn-finger pr 99.2 1.3E-11 2.9E-16 119.4 4.4 80 42-160 204-283 (377)
6 KOG2494 C3H1-type Zn-finger pr 99.1 4.4E-11 9.5E-16 121.0 6.3 218 90-381 37-260 (331)
7 KOG1492 C3H1-type Zn-finger pr 99.1 4.9E-11 1.1E-15 115.5 3.7 54 88-161 204-257 (377)
8 COG5084 YTH1 Cleavage and poly 98.6 3.3E-07 7.1E-12 92.5 12.8 87 43-161 73-159 (285)
9 COG5063 CTH1 CCCH-type Zn-fing 98.6 5.4E-08 1.2E-12 97.9 5.5 103 45-161 231-339 (351)
10 COG5063 CTH1 CCCH-type Zn-fing 98.5 4.7E-07 1E-11 91.2 9.6 197 43-383 114-347 (351)
11 KOG4791 Uncharacterized conser 98.5 1E-07 2.2E-12 100.5 4.5 86 45-166 4-90 (667)
12 COG5084 YTH1 Cleavage and poly 98.5 1.9E-07 4.1E-12 94.3 5.6 87 43-162 103-191 (285)
13 KOG2494 C3H1-type Zn-finger pr 98.3 3E-07 6.4E-12 93.6 3.8 102 44-161 37-154 (331)
14 PF00642 zf-CCCH: Zinc finger 98.3 1.5E-07 3.2E-12 62.9 0.6 26 42-67 1-26 (27)
15 PF00642 zf-CCCH: Zinc finger 98.2 2.2E-07 4.8E-12 62.0 0.1 27 88-114 1-27 (27)
16 KOG2333 Uncharacterized conser 98.1 1.3E-06 2.8E-11 93.0 1.5 59 304-372 76-136 (614)
17 KOG1595 CCCH-type Zn-finger pr 97.8 4.1E-05 8.9E-10 82.5 7.5 91 54-166 207-297 (528)
18 KOG4791 Uncharacterized conser 97.8 9.5E-06 2E-10 86.0 2.6 53 90-161 3-55 (667)
19 smart00356 ZnF_C3H1 zinc finge 97.7 2.9E-05 6.4E-10 50.8 2.5 26 88-114 2-27 (27)
20 smart00356 ZnF_C3H1 zinc finge 97.7 3.2E-05 7E-10 50.6 2.5 26 42-68 2-27 (27)
21 KOG1763 Uncharacterized conser 97.4 3.4E-05 7.4E-10 77.8 0.2 76 88-164 90-194 (343)
22 KOG1763 Uncharacterized conser 97.4 3.1E-05 6.7E-10 78.1 -1.1 79 37-116 85-192 (343)
23 KOG2333 Uncharacterized conser 97.0 0.00022 4.8E-09 76.4 0.9 63 89-161 75-141 (614)
24 KOG1595 CCCH-type Zn-finger pr 96.9 0.00043 9.3E-09 74.8 1.9 59 45-118 237-295 (528)
25 COG5252 Uncharacterized conser 96.7 0.00026 5.6E-09 69.7 -1.7 79 37-116 78-177 (299)
26 KOG2185 Predicted RNA-processi 96.2 0.0027 5.8E-08 66.9 2.3 56 58-115 98-164 (486)
27 KOG2185 Predicted RNA-processi 96.1 0.0036 7.8E-08 65.9 2.5 32 130-162 134-165 (486)
28 COG5252 Uncharacterized conser 96.0 0.0014 2.9E-08 64.7 -0.6 75 88-163 83-178 (299)
29 KOG3702 Nuclear polyadenylated 95.8 0.014 3.1E-07 64.7 6.1 101 45-165 545-650 (681)
30 PF14608 zf-CCCH_2: Zinc finge 95.8 0.0053 1.2E-07 37.9 1.6 19 92-113 1-19 (19)
31 PF14608 zf-CCCH_2: Zinc finge 95.8 0.0057 1.2E-07 37.8 1.6 19 138-159 1-19 (19)
32 COG5152 Uncharacterized conser 95.1 0.007 1.5E-07 58.5 0.6 30 43-72 140-169 (259)
33 COG5152 Uncharacterized conser 94.1 0.019 4.1E-07 55.6 0.8 27 89-115 140-166 (259)
34 KOG3702 Nuclear polyadenylated 91.2 0.54 1.2E-05 52.7 7.2 44 89-162 624-667 (681)
35 KOG1813 Predicted E3 ubiquitin 91.1 0.068 1.5E-06 54.6 0.2 29 43-71 185-213 (313)
36 KOG1039 Predicted E3 ubiquitin 88.9 0.15 3.3E-06 53.4 0.7 24 91-115 9-32 (344)
37 KOG2202 U2 snRNP splicing fact 88.3 0.17 3.7E-06 50.8 0.5 29 87-116 149-177 (260)
38 KOG1813 Predicted E3 ubiquitin 88.2 0.15 3.2E-06 52.2 0.1 26 90-115 186-211 (313)
39 KOG1039 Predicted E3 ubiquitin 87.4 0.21 4.7E-06 52.3 0.7 25 137-162 9-33 (344)
40 PF10650 zf-C3H1: Putative zin 83.2 0.76 1.6E-05 29.9 1.5 23 91-114 1-23 (23)
41 PF10650 zf-C3H1: Putative zin 81.1 0.99 2.2E-05 29.4 1.4 23 137-160 1-23 (23)
42 KOG2202 U2 snRNP splicing fact 69.2 1.9 4.2E-05 43.4 0.7 29 40-69 148-176 (260)
43 KOG0153 Predicted RNA-binding 69.1 2.8 6E-05 44.1 1.8 30 86-116 157-186 (377)
44 KOG0153 Predicted RNA-binding 65.3 3.9 8.4E-05 43.0 2.0 28 135-163 160-187 (377)
45 KOG2135 Proteins containing th 24.2 31 0.00067 37.9 0.6 38 34-71 202-239 (526)
46 KOG2135 Proteins containing th 20.7 56 0.0012 36.0 1.7 35 298-332 206-240 (526)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.93 E-value=2.8e-25 Score=225.85 Aligned_cols=277 Identities=38% Similarity=0.732 Sum_probs=184.8
Q ss_pred CCCCCCCCCCCCCCCCCCccccCC------CCCCCCCCCCCcCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCC
Q 011853 10 GSQSDPSPEWTAPGTETGPEGLGV------GAESYPERPDEADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGE 83 (476)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~e~~~------~~~~yp~Rpgt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~ 83 (476)
...++...+|.............+ ....|++++...+|.+|.+++.|.++..|+|+|+..+.+.....+.....
T Consensus 46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~ 125 (332)
T KOG1677|consen 46 STRSDNSKQPSELAAEDSSPGTELEQLRTPGSSPYPERSGEGDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVRRSRGER 125 (332)
T ss_pred CcccccccCcccccccccCcccccchhcccccCcCCCCCCccccccccccCCCCCCCCCCccCcccccccCCcccccccc
Confidence 345666777776533233322222 34569999998999999999999999999999997444332221234458
Q ss_pred CCCCCCCcCcccccccCCCCC-CCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCCC
Q 011853 84 FPERVGQPVCQYYMRTGTCKY-GASCKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQPA 162 (476)
Q Consensus 84 ~Per~ktp~C~~flrtG~Ck~-G~~CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~~ 162 (476)
.|++.++++|++|.++|.|+| |++|+|+|...+.+... .++..+++.+.++++|.+|+++|.|+||.+|+|.|+...
T Consensus 126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~--~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~ 203 (332)
T KOG1677|consen 126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS--SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPE 203 (332)
T ss_pred CcccccCCcceeeecCccccccCchhhhcCCcccccccc--cchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcc
Confidence 899999999999999999999 99999999998774222 346678889999999999999999999999999999875
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCC-CCCCCCcccccCCccccCCCCCCCCc
Q 011853 163 GVPAPTPSPAPQVAAVPTPVPAPALYPPLQSPSVPSAQQYGVVVARPPLLHGS-YVQGPYGPVLVSPSMFSLQGWSPYAT 241 (476)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~~~~~r~~~~p~s-~~~~~y~p~~~~~g~vp~~~w~~y~~ 241 (476)
....... . + .+.. .+..++|+....|+.+.... .++.+|.+..++++++| .|.
T Consensus 204 ~~~~~~~----------------~-~-~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p--~~~---- 257 (332)
T KOG1677|consen 204 DRASNRH----------------P-Y-PVSR--NPQPQSYGLTASRSSLLNQQSKLQQPFAPSGLSESVLP--RSS---- 257 (332)
T ss_pred ccccccC----------------C-c-cccc--cccccccchhhcchhhccccccccccccccccccccCc--CCc----
Confidence 4432110 0 1 1111 33445565444444443222 33334444334555555 110
Q ss_pred CCCCCCCCCCCCccCCCcccccccccCCCCCCCCCCccccCCCCCCCC--CCCCCCCCCCCCCCcccccccccCCCCCCC
Q 011853 242 SLNPISSPGTGTQSSVGSSSIYGITQLSASAPAYTGTYQSLPSSVGPS--SSSQKEHPFPERPGQQECQYYMKTGDCKFG 319 (476)
Q Consensus 242 ~~~p~~s~~~~~~~~~~~~~~yg~~~~~~~~~~~~~~~~~~~s~~~P~--~~~~k~~~~p~rp~~~~C~yy~k~G~Ck~G 319 (476)
++.+.....+ .. ....+. ....+++.+++++.+++|.+ |++|
T Consensus 258 ------------~~~~~~~~~~------~~------------~~~~~~~~~~~~~~~~~~~~p~~~~~~~-~~~~----- 301 (332)
T KOG1677|consen 258 ------------QQNLLPQGLR------SS------------SSSHPSGSQENVNENGFRARPEQPECRS-MKSG----- 301 (332)
T ss_pred ------------cccccccccc------cc------------cccccccchhccccccCcCCCCCCccch-hccc-----
Confidence 0000000000 00 000011 12345677899999999999 9988
Q ss_pred CCCCCCCCCCccCCCCCcccCCCCCCCCCCCccCccccccCCCCCCCCCCC
Q 011853 320 SSCRFHHPRELIVPKMDVTLSPFGLPLRPGAAPCTHYVQRGVCKFGPACKF 370 (476)
Q Consensus 320 ~~Ckf~Hp~~~~~~~~~~~l~~~g~p~Rpg~~~C~~y~~~G~Ck~G~~Crf 370 (476)
.++. +++|++...|.+|..+|+|+||..|+|
T Consensus 302 --------~~~l------------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 332 (332)
T KOG1677|consen 302 --------ENRL------------LPLRPGPGACTLFSRYGSCKFGPLCKF 332 (332)
T ss_pred --------cccc------------cCCCCCcccccccccccccCCCCcCCC
Confidence 1111 789999999999999999999999997
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.50 E-value=1.7e-13 Score=139.72 Aligned_cols=83 Identities=28% Similarity=0.626 Sum_probs=70.0
Q ss_pred CCCCCCCCCCCCcCCcchhccCCCCC-CCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCC
Q 011853 33 VGAESYPERPDEADCIHYVRTGFCAY-GSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYH 111 (476)
Q Consensus 33 ~~~~~yp~Rpgt~~C~~f~rtG~C~~-Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~ 111 (476)
......|++.++++|.+|.++|.|+| |++|+|+|..++.+... ......++.++|+++|.+|+++|.|+||.+|+|+
T Consensus 121 ~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~--~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~ 198 (332)
T KOG1677|consen 121 SRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS--SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFI 198 (332)
T ss_pred cccccCcccccCCcceeeecCccccccCchhhhcCCcccccccc--cchhhcCCCCCCCcCCCccccCCCCCCCCcCeec
Confidence 35678899999999999999999999 99999999999875211 0111256678999999999999999999999999
Q ss_pred CCCCCC
Q 011853 112 HPRQGA 117 (476)
Q Consensus 112 H~~~~~ 117 (476)
|...+.
T Consensus 199 H~~~~~ 204 (332)
T KOG1677|consen 199 HGEPED 204 (332)
T ss_pred CCCccc
Confidence 998865
No 3
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.38 E-value=5.6e-13 Score=136.25 Aligned_cols=66 Identities=21% Similarity=0.127 Sum_probs=40.2
Q ss_pred ccccccccCCCCCCCCC-CCCCCCCCccCCCCCcccCCCCCCCCCCCccCccccccCCCCCCCCCCCCCCC
Q 011853 305 QECQYYMKTGDCKFGSS-CRFHHPRELIVPKMDVTLSPFGLPLRPGAAPCTHYVQRGVCKFGPACKFDHPM 374 (476)
Q Consensus 305 ~~C~yy~k~G~Ck~G~~-Ckf~Hp~~~~~~~~~~~l~~~g~p~Rpg~~~C~~y~~~G~Ck~G~~Crf~Hp~ 374 (476)
+.|..|+ .|.|..|.+ |.+.|+.-.....- .+..-.-+.|.++.++.+| -...|.....|++.+.-
T Consensus 159 ~~c~~y~-~gfC~~g~q~c~~~hp~~~~~~~~--~~~~q~~~~~~~~~~~~~~-~~~~~~k~~~~~~~~~~ 225 (325)
T KOG1040|consen 159 VLCPPYN-AGFCPKGPQRCDMLHPEFQQPPFH--QGSVQHPPQRQSQQPGKIS-GEEKIHKLLQDKQLPQQ 225 (325)
T ss_pred cCCCchh-hhhccCCCCcccccCCCCCCChhh--ccccCCCCCCCCcCccccc-cccccchhhhhhhhhHH
Confidence 5667777 688888877 88888543222110 0111122455667777777 56677777778887754
No 4
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.24 E-value=8e-12 Score=127.85 Aligned_cols=98 Identities=24% Similarity=0.593 Sum_probs=75.2
Q ss_pred cCCCCCCCC--CCCCCcCCcchhcc-CCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCC
Q 011853 31 LGVGAESYP--ERPDEADCIHYVRT-GFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGAS 107 (476)
Q Consensus 31 ~~~~~~~yp--~Rpgt~~C~~f~rt-G~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~ 107 (476)
.++....+. .+-+...|.++.+. -.|.+|..|.+.|...+ ...+..+|+||++ |.|++|+.
T Consensus 30 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~vcK~~l~-glC~kgD~ 93 (325)
T KOG1040|consen 30 PGASLAPFRVRDESGRATCEFNESREKPCERGPICPKSHNDVS---------------DSRGKVVCKHWLR-GLCKKGDQ 93 (325)
T ss_pred ccccccccccccccccchhcccccCCCCccCCCCCccccCCcc---------------ccCCceeehhhhh-hhhhccCc
Confidence 344333443 33346889988631 47889999999998653 1136789999999 99999999
Q ss_pred CCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCC
Q 011853 108 CKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQP 161 (476)
Q Consensus 108 CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~ 161 (476)
|-|+|..+.. +.++|.||..+|.|.++.+|.|.|..+
T Consensus 94 C~Flhe~~~~-----------------k~rec~ff~~~g~c~~~~~c~y~h~dp 130 (325)
T KOG1040|consen 94 CEFLHEYDLT-----------------KMRECKFFSLFGECTNGKDCPYLHGDP 130 (325)
T ss_pred Ccchhhhhhc-----------------ccccccccccccccccccCCcccCCCh
Confidence 9999987532 335899999999999999999999884
No 5
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=99.18 E-value=1.3e-11 Score=119.39 Aligned_cols=80 Identities=26% Similarity=0.752 Sum_probs=60.9
Q ss_pred CCCcCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCC
Q 011853 42 PDEADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVS 121 (476)
Q Consensus 42 pgt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~ 121 (476)
|....|+||..+|.|.+|..|+|.|...+. .+|..|+. |.|.+.+.|...|..+..
T Consensus 204 psavycryynangicgkgaacrfvheptrk-------------------ticpkfln-grcnkaedcnlsheldpr---- 259 (377)
T KOG1492|consen 204 PSAVYCRYYNANGICGKGAACRFVHEPTRK-------------------TICPKFLN-GRCNKAEDCNLSHELDPR---- 259 (377)
T ss_pred CceeEEEEecCCCcccCCceeeeecccccc-------------------ccChHHhc-CccCchhcCCcccccCcc----
Confidence 345668888888888888888888875542 36888888 888888888888877643
Q ss_pred ccccCCCCCCCCCCccccccccccccCCCCCCCccCCCC
Q 011853 122 NVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQ 160 (476)
Q Consensus 122 ~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~ 160 (476)
.-+.|+||+- |.|. ..+|||.|..
T Consensus 260 -------------ripacryfll-gkcn-npncryvhih 283 (377)
T KOG1492|consen 260 -------------RIPACRYFLL-GKCN-NPNCRYVHIH 283 (377)
T ss_pred -------------ccchhhhhhh-ccCC-CCCceEEEEe
Confidence 1247888887 8886 6788888865
No 6
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=99.15 E-value=4.4e-11 Score=120.96 Aligned_cols=218 Identities=20% Similarity=0.380 Sum_probs=116.6
Q ss_pred CcCcccccccCCCCCCCC-CCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCCCCCCCCC
Q 011853 90 QPVCQYYMRTGTCKYGAS-CKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQPAGVPAPT 168 (476)
Q Consensus 90 tp~C~~flrtG~Ck~G~~-CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~~~~~~~~ 168 (476)
-.+||.|+| |.|++|++ |||.|+..... |+.+ +-..|..|+| |.|. .++|||.|+....+....
T Consensus 37 ~eVCReF~r-n~C~R~d~~CkfaHP~~~~~----V~~g--------~v~aC~Ds~k-grCs-R~nCkylHpp~hlkdql~ 101 (331)
T KOG2494|consen 37 LEVCREFLR-NTCSRGDRECKFAHPPKNCQ----VSNG--------RVIACFDSQK-GRCS-RENCKYLHPPQHLKDQLK 101 (331)
T ss_pred HHHHHHHHh-ccccCCCccccccCCCCCCC----ccCC--------eEEEEecccc-CccC-cccceecCCChhhhhhhh
Confidence 358999999 99999999 99999987432 2111 2257999999 9998 577999999887766543
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCccccc---CCccccCCCCCCCCcCCC-
Q 011853 169 PSPAPQVAAVPTPVPAPALYPPLQSPSVPSAQQYGVVVARPPLLHGSYVQGPYGPVLV---SPSMFSLQGWSPYATSLN- 244 (476)
Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~~~~~r~~~~p~s~~~~~y~p~~~---~~g~vp~~~w~~y~~~~~- 244 (476)
.. .+...+++...-+++..+.+. ||-.+.+ .|++- --+-++.-.+++|+.++.
T Consensus 102 in-----------grn~l~lq~~~aA~~~q~~~~----------~g~Pi~~--v~~f~~~~~~~g~~~~s~~~y~~~~Pg 158 (331)
T KOG2494|consen 102 IN-----------GRNNLILQKTAAAMLAQQMQG----------PGTPICS--VPMFATGPCLGGNTACSYWPYLPPVPG 158 (331)
T ss_pred hc-----------ccccHHHHHHHHhhhcccccC----------CCccccc--cccccccccccCCCccccccccCCCCC
Confidence 20 111122222111222223232 1111111 11110 012233445555555330
Q ss_pred CCCCCCCCCccCCCcccccccccCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCCCCC-CC
Q 011853 245 PISSPGTGTQSSVGSSSIYGITQLSASAPAYTGTYQSLPSSVGPSSSSQKEHPFPERPGQQECQYYMKTGDCKFGSS-CR 323 (476)
Q Consensus 245 p~~s~~~~~~~~~~~~~~yg~~~~~~~~~~~~~~~~~~~s~~~P~~~~~k~~~~p~rp~~~~C~yy~k~G~Ck~G~~-Ck 323 (476)
.....+ .+....+|. ...+.+..|... -+......+..++|+- . .|.|..++. |+
T Consensus 159 ~~vp~~-----~~p~~~~~~---------------~g~p~v~~~~~~--~~~k~~r~~~~e~~~~-~-~gn~~r~e~d~~ 214 (331)
T KOG2494|consen 159 GLVPAD-----GLPTTPVFV---------------PGGPGVPGPGLV--GGQKLLRSDRLEVCRE-Q-RGNCRRGEQDAQ 214 (331)
T ss_pred CCCCCc-----CCCCCcccc---------------CCCCcccccccc--cccccccCCCCCCCcc-c-ccccccchhHHH
Confidence 000000 011112221 111212222221 1122223344677887 3 699999875 99
Q ss_pred CCCCCCccCCCCCcccCCCCCCCCCCCccCccccccCCCCCCCCCCCCCCCCCCCCCC
Q 011853 324 FHHPRELIVPKMDVTLSPFGLPLRPGAAPCTHYVQRGVCKFGPACKFDHPMGMLSYSP 381 (476)
Q Consensus 324 f~Hp~~~~~~~~~~~l~~~g~p~Rpg~~~C~~y~~~G~Ck~G~~Crf~Hp~~~~~~~~ 381 (476)
|.|+.+.+....+... ...|..| .+|.|.- ++||+.|......++.
T Consensus 215 f~~~~k~~~~~s~~~t----------~~~~~~~-t~~~~~~-en~~~~~~~~h~~~~~ 260 (331)
T KOG2494|consen 215 FAHPAKSIMIDSNDNT----------VEVCLRY-TKGRCET-ENCKYFHAPAHDQASA 260 (331)
T ss_pred HhhhhhhhhcccCCCc----------chhcccc-ccceech-hcccccCchHHHHHHH
Confidence 9998876643332211 2358888 7899984 7899999876654433
No 7
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=99.09 E-value=4.9e-11 Score=115.51 Aligned_cols=54 Identities=24% Similarity=0.679 Sum_probs=47.2
Q ss_pred CCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCC
Q 011853 88 VGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQP 161 (476)
Q Consensus 88 ~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~ 161 (476)
+...-|+||..+|.|-+|..|+|.|..... .+|.-|+. |.|...++|.+.|..+
T Consensus 204 psavycryynangicgkgaacrfvheptrk-------------------ticpkfln-grcnkaedcnlsheld 257 (377)
T KOG1492|consen 204 PSAVYCRYYNANGICGKGAACRFVHEPTRK-------------------TICPKFLN-GRCNKAEDCNLSHELD 257 (377)
T ss_pred CceeEEEEecCCCcccCCceeeeecccccc-------------------ccChHHhc-CccCchhcCCcccccC
Confidence 356689999999999999999999977643 48999998 9999999999999764
No 8
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.64 E-value=3.3e-07 Score=92.53 Aligned_cols=87 Identities=24% Similarity=0.492 Sum_probs=68.4
Q ss_pred CCcCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCc
Q 011853 43 DEADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSN 122 (476)
Q Consensus 43 gt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~ 122 (476)
.+..|.+|+..+-+...-.|.+.|..... ....+|++|++ |.|+.+..|.|+|..+....
T Consensus 73 n~~~~~~~~~~~~~~~~~s~~~~~~~~~~----------------~s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~s--- 132 (285)
T COG5084 73 NTVACISRNFNSIRGSRLSTPNNHVNPVL----------------SSSVVCKFFLR-GLCKSGFSCEFLHEYDLRSS--- 132 (285)
T ss_pred cccccccccccCCccccccCCccccCccc----------------cCCcccchhcc-ccCcCCCccccccCCCcccc---
Confidence 45679999876666666689999886431 24468999999 99999999999998885421
Q ss_pred cccCCCCCCCCCCccccccccccccCCCCCCCccCCCCC
Q 011853 123 VSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQP 161 (476)
Q Consensus 123 ~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~ 161 (476)
-...|++|...|.|..|..|.+.|.++
T Consensus 133 ------------~~~~c~~Fs~~G~cs~g~~c~~~h~dp 159 (285)
T COG5084 133 ------------QGPPCRSFSLKGSCSSGPSCGYSHIDP 159 (285)
T ss_pred ------------cCCCcccccccceeccCCCCCccccCc
Confidence 124899996569999999999999983
No 9
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.59 E-value=5.4e-08 Score=97.89 Aligned_cols=103 Identities=20% Similarity=0.419 Sum_probs=80.4
Q ss_pred cCCcchhccCCCCC---CCCCCCC---CCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCC
Q 011853 45 ADCIHYVRTGFCAY---GSRCRFN---HPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAG 118 (476)
Q Consensus 45 ~~C~~f~rtG~C~~---Gd~CkF~---H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~ 118 (476)
.+|.-|.+.|.|++ |+.|.|+ |+.+++.... .-..++++.|..|.+-|.|.||.+|.|.|..++.-
T Consensus 231 ~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~--------k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~i 302 (351)
T COG5063 231 ELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKK--------KKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDI 302 (351)
T ss_pred HHhhccCcCCCCccccccccccccccccccccccccc--------cccccccCCccchhhcccCccccccccccCChhhc
Confidence 89999999999999 9999999 9988765321 11236789999999999999999999999887542
Q ss_pred CCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCC
Q 011853 119 SVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQP 161 (476)
Q Consensus 119 ~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~ 161 (476)
.. ... ...+| ....|+-++++|.|+.|.+|.|.|.+.
T Consensus 303 e~-~~~-~~~~y----~~~~crt~~~~g~~p~g~~~c~~~dkk 339 (351)
T COG5063 303 EM-YEE-ASLGY----LDGPCRTRAKGGAFPSGGAVCKSFDKK 339 (351)
T ss_pred cc-ccc-ccccc----cccccccccccCccCCCCchhhccccc
Confidence 11 000 11122 345899999999999999999999874
No 10
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.50 E-value=4.7e-07 Score=91.23 Aligned_cols=197 Identities=18% Similarity=0.355 Sum_probs=129.1
Q ss_pred CCcCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCc
Q 011853 43 DEADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSN 122 (476)
Q Consensus 43 gt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~ 122 (476)
+++.|.-=..-+.|++++.|.|+|........ ..+.+.+++-|..|..-|.|.++.+|-|.|-.-.......
T Consensus 114 kt~~l~ss~~~~~~~~p~~n~fahs~~issl~--------~~~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~~q~ 185 (351)
T COG5063 114 KTEMLRSSTEIPYCRYPDKNPFAHSKAISSLA--------QTHPKYKTESLEVFINPGYVPYSKRCCFISLPLTDINLQP 185 (351)
T ss_pred cchhhhccccccccccCCCCcCCCcccccccc--------ccCccccccceeEEecCCccccccccccccccccccCcch
Confidence 45666653334899999999999997764321 3455678899999999999999998999884432110000
Q ss_pred c-------ccCCCC-----------------------CCCCCC-ccccccccccccCCC---CCCCccC---CCCCCCCC
Q 011853 123 V-------SLNYYG-----------------------YPLRPG-EKECSYYMKTRQCKF---GATCKFH---HPQPAGVP 165 (476)
Q Consensus 123 ~-------~ln~~g-----------------------~P~rp~-~~~C~~f~ktG~C~~---G~~CrF~---Hp~~~~~~ 165 (476)
. ..+..+ .+++.. -.+|.-|...|.|++ |+.|.|+ |.......
T Consensus 186 l~~rkpks~~~~~s~t~~kes~a~P~~~~~~~~~e~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~ 265 (351)
T COG5063 186 LSQRKPKSGKNCTSYTLGKESDAHPHDELIYQKQEQNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKS 265 (351)
T ss_pred hhccCcccCcCccccccccccccCchhhhhhhhhhccchhhcCCHHHhhccCcCCCCccccccccccccccccccccccc
Confidence 0 000011 122211 257999999999999 9999999 77432100
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCCCCcccccCCccccCCCCCCCCcCCCC
Q 011853 166 APTPSPAPQVAAVPTPVPAPALYPPLQSPSVPSAQQYGVVVARPPLLHGSYVQGPYGPVLVSPSMFSLQGWSPYATSLNP 245 (476)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~~~~~r~~~~p~s~~~~~y~p~~~~~g~vp~~~w~~y~~~~~p 245 (476)
T Consensus 266 -------------------------------------------------------------------------------- 265 (351)
T COG5063 266 -------------------------------------------------------------------------------- 265 (351)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCccCCCcccccccccCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCCCCCCCCC
Q 011853 246 ISSPGTGTQSSVGSSSIYGITQLSASAPAYTGTYQSLPSSVGPSSSSQKEHPFPERPGQQECQYYMKTGDCKFGSSCRFH 325 (476)
Q Consensus 246 ~~s~~~~~~~~~~~~~~yg~~~~~~~~~~~~~~~~~~~s~~~P~~~~~k~~~~p~rp~~~~C~yy~k~G~Ck~G~~Ckf~ 325 (476)
..+-+.| ....|..+.+.|.|.+|..|.|.
T Consensus 266 ----------------------------------------------k~k~~~f----rTePcinwe~sGyc~yg~Rc~F~ 295 (351)
T COG5063 266 ----------------------------------------------KKKKQNF----RTEPCINWEKSGYCPYGLRCCFK 295 (351)
T ss_pred ----------------------------------------------ccccccc----ccCCccchhhcccCccccccccc
Confidence 0000111 13679999999999999999999
Q ss_pred CCCCccCCCCCcccCCCCCCCCCCCccCccccccCCCCCCCCCCCCCCCCCCCCCCCC
Q 011853 326 HPRELIVPKMDVTLSPFGLPLRPGAAPCTHYVQRGVCKFGPACKFDHPMGMLSYSPSA 383 (476)
Q Consensus 326 Hp~~~~~~~~~~~l~~~g~p~Rpg~~~C~~y~~~G~Ck~G~~Crf~Hp~~~~~~~~sa 383 (476)
|--+... .......+|+- ..+|.-+++.|.|..|-.|.|.|.+-.+..+..+
T Consensus 296 hgd~~~i--e~~~~~~~~y~----~~~crt~~~~g~~p~g~~~c~~~dkkn~~~s~~~ 347 (351)
T COG5063 296 HGDDSDI--EMYEEASLGYL----DGPCRTRAKGGAFPSGGAVCKSFDKKNLDFSVKA 347 (351)
T ss_pred cCChhhc--ccccccccccc----ccccccccccCccCCCCchhhccccchhhhhhhh
Confidence 9433211 11111112322 3469999999999999999999988877776654
No 11
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.48 E-value=1e-07 Score=100.48 Aligned_cols=86 Identities=23% Similarity=0.583 Sum_probs=66.1
Q ss_pred cCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCccc
Q 011853 45 ADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVS 124 (476)
Q Consensus 45 ~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~ 124 (476)
.+|.||+ ...|++++.|.|.|-.+.+. ...+|.+|+..-.|+. .|+|.|..-..-
T Consensus 4 ~dcyff~-ys~cKk~d~c~~rh~E~al~----------------n~t~C~~w~~~~~C~k--~C~YRHSe~~~k------ 58 (667)
T KOG4791|consen 4 EDCYFFF-YSTCKKGDSCPFRHCEAALG----------------NETVCTLWQEGRCCRK--VCRYRHSEIDKK------ 58 (667)
T ss_pred ccchhhh-hhhhhccCcCcchhhHHHhc----------------CcchhhhhhhcCcccc--cccchhhHHhhh------
Confidence 6899998 59999999999999866532 3458999999555665 699999765321
Q ss_pred cCCCCCCCCCCcccccccccccc-CCCCCCCccCCCCCCCCCC
Q 011853 125 LNYYGYPLRPGEKECSYYMKTRQ-CKFGATCKFHHPQPAGVPA 166 (476)
Q Consensus 125 ln~~g~P~rp~~~~C~~f~ktG~-C~~G~~CrF~Hp~~~~~~~ 166 (476)
..+.+|.+|.+ +. |. .++|-|.|..+...++
T Consensus 59 ---------r~e~~CYwe~~-p~gC~-k~~CgfRH~~pPLkg~ 90 (667)
T KOG4791|consen 59 ---------RSEIPCYWENQ-PTGCQ-KLNCGFRHNRPPLKGV 90 (667)
T ss_pred ---------cCcccceeecC-CCccC-CCccccccCCCchhhh
Confidence 13468999998 77 98 6999999977655543
No 12
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.46 E-value=1.9e-07 Score=94.26 Aligned_cols=87 Identities=32% Similarity=0.693 Sum_probs=71.8
Q ss_pred CCcCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCc
Q 011853 43 DEADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSN 122 (476)
Q Consensus 43 gt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~ 122 (476)
...+|++|++ |.|+.|..|.|+|..+... .....|++|...|.|..|..|.|.|.....
T Consensus 103 s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~---------------s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~----- 161 (285)
T COG5084 103 SSVVCKFFLR-GLCKSGFSCEFLHEYDLRS---------------SQGPPCRSFSLKGSCSSGPSCGYSHIDPDS----- 161 (285)
T ss_pred CCcccchhcc-ccCcCCCccccccCCCccc---------------ccCCCcccccccceeccCCCCCccccCccc-----
Confidence 4578999997 9999999999999988642 135689999655999999999999986432
Q ss_pred cccCCCCCCCCCCccccccccc--cccCCCCCCCccCCCCCC
Q 011853 123 VSLNYYGYPLRPGEKECSYYMK--TRQCKFGATCKFHHPQPA 162 (476)
Q Consensus 123 ~~ln~~g~P~rp~~~~C~~f~k--tG~C~~G~~CrF~Hp~~~ 162 (476)
....|.+|.+ +++|.+|..|+|.|..-+
T Consensus 162 ------------~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~ 191 (285)
T COG5084 162 ------------FAGNCDQYSGATYGFCPLGASCKFSHTLKR 191 (285)
T ss_pred ------------ccccccccCcccccccCCCCcccccccccc
Confidence 1247888874 699999999999999864
No 13
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.35 E-value=3e-07 Score=93.57 Aligned_cols=102 Identities=28% Similarity=0.529 Sum_probs=67.6
Q ss_pred CcCCcchhccCCCCCCCC-CCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCc
Q 011853 44 EADCIHYVRTGFCAYGSR-CRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSN 122 (476)
Q Consensus 44 t~~C~~f~rtG~C~~Gd~-CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~ 122 (476)
-++|+.|+| |.|.+||+ |||+|+.....+ . .-+-.-|.+|++ |.|.+.. |||+|+.....+.--
T Consensus 37 ~eVCReF~r-n~C~R~d~~CkfaHP~~~~~V------~------~g~v~aC~Ds~k-grCsR~n-CkylHpp~hlkdql~ 101 (331)
T KOG2494|consen 37 LEVCREFLR-NTCSRGDRECKFAHPPKNCQV------S------NGRVIACFDSQK-GRCSREN-CKYLHPPQHLKDQLK 101 (331)
T ss_pred HHHHHHHHh-ccccCCCccccccCCCCCCCc------c------CCeEEEEecccc-CccCccc-ceecCCChhhhhhhh
Confidence 389999999 99999999 999999775322 1 123456999999 9998755 999998874321100
Q ss_pred --cccC----------CCCCCCCCCccccc--cccccccCCCCC-CCccCCCCC
Q 011853 123 --VSLN----------YYGYPLRPGEKECS--YYMKTRQCKFGA-TCKFHHPQP 161 (476)
Q Consensus 123 --~~ln----------~~g~P~rp~~~~C~--~f~ktG~C~~G~-~CrF~Hp~~ 161 (476)
.+++ ..+-..-++.++|. .|. ++.|.-|. .|+|.|...
T Consensus 102 ingrn~l~lq~~~aA~~~q~~~~~g~Pi~~v~~f~-~~~~~~g~~~~s~~~y~~ 154 (331)
T KOG2494|consen 102 INGRNNLILQKTAAAMLAQQMQGPGTPICSVPMFA-TGPCLGGNTACSYWPYLP 154 (331)
T ss_pred hcccccHHHHHHHHhhhcccccCCCcccccccccc-ccccccCCCccccccccC
Confidence 0000 00111124667888 554 47787664 688888765
No 14
>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=98.32 E-value=1.5e-07 Score=62.86 Aligned_cols=26 Identities=38% Similarity=0.950 Sum_probs=21.7
Q ss_pred CCCcCCcchhccCCCCCCCCCCCCCC
Q 011853 42 PDEADCIHYVRTGFCAYGSRCRFNHP 67 (476)
Q Consensus 42 pgt~~C~~f~rtG~C~~Gd~CkF~H~ 67 (476)
+++++|++|+++|.|++|++|+|+|+
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 57899999999999999999999997
No 15
>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=98.24 E-value=2.2e-07 Score=62.03 Aligned_cols=27 Identities=37% Similarity=1.091 Sum_probs=21.6
Q ss_pred CCCcCcccccccCCCCCCCCCCCCCCC
Q 011853 88 VGQPVCQYYMRTGTCKYGASCKYHHPR 114 (476)
Q Consensus 88 ~ktp~C~~flrtG~Ck~G~~CkF~H~~ 114 (476)
+++++|++|+++|.|++|++|+|+|+.
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 367899999999999999999999973
No 16
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=98.06 E-value=1.3e-06 Score=92.96 Aligned_cols=59 Identities=25% Similarity=0.675 Sum_probs=52.5
Q ss_pred cccccccccC--CCCCCCCCCCCCCCCCccCCCCCcccCCCCCCCCCCCccCccccccCCCCCCCCCCCCC
Q 011853 304 QQECQYYMKT--GDCKFGSSCRFHHPRELIVPKMDVTLSPFGLPLRPGAAPCTHYVQRGVCKFGPACKFDH 372 (476)
Q Consensus 304 ~~~C~yy~k~--G~Ck~G~~Ckf~Hp~~~~~~~~~~~l~~~g~p~Rpg~~~C~~y~~~G~Ck~G~~Crf~H 372 (476)
..+|.-.+.. ..|.||++|||.|+++++...+..+| .+.|++|...|+|.||-+|||.-
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Di----------g~~Cp~f~s~G~Cp~G~~CRFl~ 136 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDI----------GPSCPVFESLGFCPYGFKCRFLG 136 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHHhccCccc----------CCccceeeccccCCccceeehhh
Confidence 5789999965 36999999999999999998888877 46899999999999999999963
No 17
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.81 E-value=4.1e-05 Score=82.50 Aligned_cols=91 Identities=22% Similarity=0.452 Sum_probs=68.7
Q ss_pred CCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCC
Q 011853 54 GFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSLNYYGYPLR 133 (476)
Q Consensus 54 G~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~ln~~g~P~r 133 (476)
+.|.-+-.|.|.|+-+..+..+.. .|. +.-.+|.-|-+ |.|++||.|.|.|..-+. +=.|.+
T Consensus 207 ~~shDwteCPf~HpgEkARRRDPR-----kyh--Ys~tpCPefrk-G~C~rGD~CEyaHgvfEc----------wLHPa~ 268 (528)
T KOG1595|consen 207 PRSHDWTECPFAHPGEKARRRDPR-----KYH--YSSTPCPEFRK-GSCERGDSCEYAHGVFEC----------WLHPAR 268 (528)
T ss_pred ccCCCcccCCccCCCcccccCCcc-----ccc--ccCccCccccc-CCCCCCCccccccceehh----------hcCHHH
Confidence 467778899999977665422111 122 45678999999 999999999999987754 123667
Q ss_pred CCccccccccccccCCCCCCCccCCCCCCCCCC
Q 011853 134 PGEKECSYYMKTRQCKFGATCKFHHPQPAGVPA 166 (476)
Q Consensus 134 p~~~~C~~f~ktG~C~~G~~CrF~Hp~~~~~~~ 166 (476)
.++..|+.- |.|++ .-|-|+|........
T Consensus 269 YRT~~CkDg---~~C~R-rvCfFAH~~eqLR~l 297 (528)
T KOG1595|consen 269 YRTRKCKDG---GYCPR-RVCFFAHSPEQLRPL 297 (528)
T ss_pred hccccccCC---CCCcc-ceEeeecChHHhccc
Confidence 788999985 88998 999999987765443
No 18
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.81 E-value=9.5e-06 Score=86.02 Aligned_cols=53 Identities=28% Similarity=0.785 Sum_probs=42.3
Q ss_pred CcCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCC
Q 011853 90 QPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQP 161 (476)
Q Consensus 90 tp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~ 161 (476)
.+.|.||+. -.||+++.|.|.|...... ....|.+|+..-.|+ +.|+|.|-+.
T Consensus 3 ~~dcyff~y-s~cKk~d~c~~rh~E~al~----------------n~t~C~~w~~~~~C~--k~C~YRHSe~ 55 (667)
T KOG4791|consen 3 GEDCYFFFY-STCKKGDSCPFRHCEAALG----------------NETVCTLWQEGRCCR--KVCRYRHSEI 55 (667)
T ss_pred cccchhhhh-hhhhccCcCcchhhHHHhc----------------CcchhhhhhhcCccc--ccccchhhHH
Confidence 468999998 8999999999999776442 235899999844455 4999999874
No 19
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.68 E-value=2.9e-05 Score=50.78 Aligned_cols=26 Identities=35% Similarity=1.085 Sum_probs=22.3
Q ss_pred CCCcCcccccccCCCCCCCCCCCCCCC
Q 011853 88 VGQPVCQYYMRTGTCKYGASCKYHHPR 114 (476)
Q Consensus 88 ~ktp~C~~flrtG~Ck~G~~CkF~H~~ 114 (476)
.++.+|++| .+|.|++|++|+|+|+.
T Consensus 2 ~k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 467799999 55999999999999963
No 20
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.67 E-value=3.2e-05 Score=50.59 Aligned_cols=26 Identities=38% Similarity=1.096 Sum_probs=22.8
Q ss_pred CCCcCCcchhccCCCCCCCCCCCCCCC
Q 011853 42 PDEADCIHYVRTGFCAYGSRCRFNHPR 68 (476)
Q Consensus 42 pgt~~C~~f~rtG~C~~Gd~CkF~H~~ 68 (476)
.++.+|++| ++|.|.+|++|+|+|..
T Consensus 2 ~k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 467899999 57999999999999973
No 21
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.43 E-value=3.4e-05 Score=77.76 Aligned_cols=76 Identities=25% Similarity=0.624 Sum_probs=50.5
Q ss_pred CCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCcccc-------------------CCCCCCCCCCccccccccc----
Q 011853 88 VGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSL-------------------NYYGYPLRPGEKECSYYMK---- 144 (476)
Q Consensus 88 ~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~l-------------------n~~g~P~rp~~~~C~~f~k---- 144 (476)
++..+|.||.. |.|..|+.|+|+|+........-.++ ...+-|--....+|.||+.
T Consensus 90 PKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeAvE~ 168 (343)
T KOG1763|consen 90 PKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEAVEN 168 (343)
T ss_pred chHHHHHHHhc-cCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHHHhc
Confidence 57889999999 99999999999998774321111110 0011111112358999973
Q ss_pred --ccc---CCCCC-CCccCCCCCCCC
Q 011853 145 --TRQ---CKFGA-TCKFHHPQPAGV 164 (476)
Q Consensus 145 --tG~---C~~G~-~CrF~Hp~~~~~ 164 (476)
+|+ |++|. .|.|.|-.+...
T Consensus 169 ~kYGWfW~CPnGg~~C~YrHaLP~Gy 194 (343)
T KOG1763|consen 169 GKYGWFWECPNGGDKCIYRHALPEGY 194 (343)
T ss_pred CCccceeECCCCCCeeeeeecCCcch
Confidence 232 99996 999999987654
No 22
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.36 E-value=3.1e-05 Score=78.07 Aligned_cols=79 Identities=22% Similarity=0.516 Sum_probs=54.0
Q ss_pred CCCCCCCCcCCcchhccCCCCCCCCCCCCCCCCCCCcc------ccccCC--C-----------CCCCCCCCCcCccccc
Q 011853 37 SYPERPDEADCIHYVRTGFCAYGSRCRFNHPRDRGSVM------GAARAG--G-----------GEFPERVGQPVCQYYM 97 (476)
Q Consensus 37 ~yp~Rpgt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~------~~~r~~--~-----------~~~Per~ktp~C~~fl 97 (476)
..-+.|+..+|.||. .|.|..|+.|+|.|+....+-. ...|.. . ...|......+|+||+
T Consensus 85 ~~gvDPKSvvCafFk-~g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFL 163 (343)
T KOG1763|consen 85 PKGVDPKSVVCAFFK-QGTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFL 163 (343)
T ss_pred ccCCCchHHHHHHHh-ccCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHH
Confidence 345788999999998 4999999999999998664421 111111 0 0122223445899998
Q ss_pred cc---------CCCCCC-CCCCCCCCCCC
Q 011853 98 RT---------GTCKYG-ASCKYHHPRQG 116 (476)
Q Consensus 98 rt---------G~Ck~G-~~CkF~H~~~~ 116 (476)
-. -.|.+| +.|-|.|-...
T Consensus 164 eAvE~~kYGWfW~CPnGg~~C~YrHaLP~ 192 (343)
T KOG1763|consen 164 EAVENGKYGWFWECPNGGDKCIYRHALPE 192 (343)
T ss_pred HHHhcCCccceeECCCCCCeeeeeecCCc
Confidence 52 259998 59999997664
No 23
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=97.00 E-value=0.00022 Score=76.40 Aligned_cols=63 Identities=17% Similarity=0.518 Sum_probs=47.8
Q ss_pred CCcCccccccc--CCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccC--CCCC
Q 011853 89 GQPVCQYYMRT--GTCKYGASCKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFH--HPQP 161 (476)
Q Consensus 89 ktp~C~~flrt--G~Ck~G~~CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~--Hp~~ 161 (476)
...+|.-..++ -.|.||++|+|.|+.+..-.....+ -.+.|.+|...|+|++|-.|||. |...
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~D----------ig~~Cp~f~s~G~Cp~G~~CRFl~aHld~ 141 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPD----------IGPSCPVFESLGFCPYGFKCRFLGAHLDI 141 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCcc----------cCCccceeeccccCCccceeehhhcccCc
Confidence 46799999995 4799999999999987532111111 12589999999999999999995 5443
No 24
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=96.89 E-value=0.00043 Score=74.84 Aligned_cols=59 Identities=22% Similarity=0.479 Sum_probs=50.3
Q ss_pred cCCcchhccCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCCCCC
Q 011853 45 ADCIHYVRTGFCAYGSRCRFNHPRDRGSVMGAARAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQGAG 118 (476)
Q Consensus 45 ~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~~~~r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~ 118 (476)
..|.-|.+ |.|..||.|.|+|++-+-- -+|+++++..|+.= |.|++ .-|-|+|..+..+
T Consensus 237 tpCPefrk-G~C~rGD~CEyaHgvfEcw----------LHPa~YRT~~CkDg---~~C~R-rvCfFAH~~eqLR 295 (528)
T KOG1595|consen 237 TPCPEFRK-GSCERGDSCEYAHGVFECW----------LHPARYRTRKCKDG---GYCPR-RVCFFAHSPEQLR 295 (528)
T ss_pred ccCccccc-CCCCCCCccccccceehhh----------cCHHHhccccccCC---CCCcc-ceEeeecChHHhc
Confidence 56888865 9999999999999987632 68999999999986 78999 6799999888653
No 25
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.66 E-value=0.00026 Score=69.68 Aligned_cols=79 Identities=24% Similarity=0.575 Sum_probs=54.8
Q ss_pred CCCCCCCCcCCcchhccCCCCCCCCCCCCCCCCCCCcc------ccccCCCCCC-----CCCCCCcCccccccc---C--
Q 011853 37 SYPERPDEADCIHYVRTGFCAYGSRCRFNHPRDRGSVM------GAARAGGGEF-----PERVGQPVCQYYMRT---G-- 100 (476)
Q Consensus 37 ~yp~Rpgt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~~~------~~~r~~~~~~-----Per~ktp~C~~flrt---G-- 100 (476)
..-+.|++.+|..|+. +.|..|+.|+|+|..++.+.. ..+|...... |--..-.+|+||+-. |
T Consensus 78 ragvdpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkY 156 (299)
T COG5252 78 RAGVDPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKY 156 (299)
T ss_pred ccccCchhHHHHHhcc-CccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCc
Confidence 3457789999999995 999999999999997765421 1122222222 222344689999842 2
Q ss_pred ----CCCCC-CCCCCCCCCCC
Q 011853 101 ----TCKYG-ASCKYHHPRQG 116 (476)
Q Consensus 101 ----~Ck~G-~~CkF~H~~~~ 116 (476)
.|.+| .+|-|.|....
T Consensus 157 gw~W~CPng~~~C~y~H~Lp~ 177 (299)
T COG5252 157 GWGWTCPNGNMRCSYIHKLPD 177 (299)
T ss_pred cceeeCCCCCceeeeeeccCc
Confidence 59888 78999997664
No 26
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.18 E-value=0.0027 Score=66.86 Aligned_cols=56 Identities=29% Similarity=0.734 Sum_probs=39.0
Q ss_pred CCCCCCCCCCCCCCC------ccc---cc--cCCCCCCCCCCCCcCcccccccCCCCCCCCCCCCCCCC
Q 011853 58 YGSRCRFNHPRDRGS------VMG---AA--RAGGGEFPERVGQPVCQYYMRTGTCKYGASCKYHHPRQ 115 (476)
Q Consensus 58 ~Gd~CkF~H~~~~~~------~~~---~~--r~~~~~~Per~ktp~C~~flrtG~Ck~G~~CkF~H~~~ 115 (476)
-|.+|.|-|...... +.+ .. |.- -.+|+-..+.+|.||+. |.|+|+.+|||.|...
T Consensus 98 ~GsKcsaph~ss~gl~yHna~I~g~E~sarvRVl-fl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 98 DGSKCSAPHTSSRGLYYHNARIIGFEGSARVRVL-FLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLD 164 (486)
T ss_pred cCCcccccccCCccceecceeEEeeccccceEEE-eecCcchhhccchHhhc-cccccCcccccccCcc
Confidence 477888887765531 011 10 110 15666667889999999 9999999999999766
No 27
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.05 E-value=0.0036 Score=65.91 Aligned_cols=32 Identities=28% Similarity=0.868 Sum_probs=27.4
Q ss_pred CCCCCCccccccccccccCCCCCCCccCCCCCC
Q 011853 130 YPLRPGEKECSYYMKTRQCKFGATCKFHHPQPA 162 (476)
Q Consensus 130 ~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~~ 162 (476)
+|.....++|.||+. |.|+|+.+|||.|...-
T Consensus 134 ~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V 165 (486)
T KOG2185|consen 134 TPTHESMKPCKFFLE-GRCRFGENCRFSHGLDV 165 (486)
T ss_pred cCcchhhccchHhhc-cccccCcccccccCccc
Confidence 455556789999998 99999999999998753
No 28
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.04 E-value=0.0014 Score=64.74 Aligned_cols=75 Identities=27% Similarity=0.687 Sum_probs=50.6
Q ss_pred CCCcCcccccccCCCCCCCCCCCCCCCCCCCCCCcccc------CCCCCC--CCC---Cccccccccc---cc------c
Q 011853 88 VGQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSL------NYYGYP--LRP---GEKECSYYMK---TR------Q 147 (476)
Q Consensus 88 ~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~l------n~~g~P--~rp---~~~~C~~f~k---tG------~ 147 (476)
+++.+|..|+. +.|..|+.|+|+|.........-..| ---..| .|| -..+|.||+. +| .
T Consensus 83 pK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~ 161 (299)
T COG5252 83 PKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWT 161 (299)
T ss_pred chhHHHHHhcc-CccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceee
Confidence 57889999999 99999999999999765432111111 001112 222 2478999863 23 2
Q ss_pred CCCC-CCCccCCCCCCC
Q 011853 148 CKFG-ATCKFHHPQPAG 163 (476)
Q Consensus 148 C~~G-~~CrF~Hp~~~~ 163 (476)
|++| .+|.|.|-.+.+
T Consensus 162 CPng~~~C~y~H~Lp~G 178 (299)
T COG5252 162 CPNGNMRCSYIHKLPDG 178 (299)
T ss_pred CCCCCceeeeeeccCcc
Confidence 9999 599999988764
No 29
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=95.84 E-value=0.014 Score=64.65 Aligned_cols=101 Identities=22% Similarity=0.563 Sum_probs=57.2
Q ss_pred cCCcchhccCCCCCCCCCCCCCCCCCCC--ccccccCCCCCCCCC--CCCcCcccccccCCCCCCCCCCCCCCCCCCCC-
Q 011853 45 ADCIHYVRTGFCAYGSRCRFNHPRDRGS--VMGAARAGGGEFPER--VGQPVCQYYMRTGTCKYGASCKYHHPRQGAGS- 119 (476)
Q Consensus 45 ~~C~~f~rtG~C~~Gd~CkF~H~~~~~~--~~~~~r~~~~~~Per--~ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~- 119 (476)
.+|+||. .|. +..|.|.|+..... +.+.+ .++++ .-.+-|+|=.+ |..-+ |.|.|.......
T Consensus 545 ~~Cky~~---~Ct-~a~Ce~~HPtaa~~~~s~p~k-----~fa~~~~ks~p~Ck~~~k---CtasD-C~~sH~~~~~pvq 611 (681)
T KOG3702|consen 545 TRCKYGP---ACT-SAECEFAHPTAAENAKSLPNK-----KFASKCLKSHPGCKFGKK---CTASD-CNYSHAGRRIPVQ 611 (681)
T ss_pred ccccCCC---cCC-chhhhhcCCcchhhhhccccc-----cccccceecccccccccc---ccccc-CcccccCCCCCCc
Confidence 6799998 488 88999999976621 11111 11111 11234554333 65444 889997765310
Q ss_pred CCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCCCCCC
Q 011853 120 VSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQPAGVP 165 (476)
Q Consensus 120 ~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~~~~~ 165 (476)
...+.- -++.-....+|+|+ |.|+ ...|+|.|++.-..+
T Consensus 612 ~t~ip~---~~~~~ti~~~CrY~---pnCr-nm~C~F~HPk~cRf~ 650 (681)
T KOG3702|consen 612 PTRIPP---PFPGGTIRGLCRYR---PNCR-NMQCKFYHPKTCRFN 650 (681)
T ss_pred cccCCC---CCCCCCccccceec---cCcC-CccccccCCcccccc
Confidence 001100 01111234689997 6698 589999999875443
No 30
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.84 E-value=0.0053 Score=37.88 Aligned_cols=19 Identities=32% Similarity=0.999 Sum_probs=16.8
Q ss_pred CcccccccCCCCCCCCCCCCCC
Q 011853 92 VCQYYMRTGTCKYGASCKYHHP 113 (476)
Q Consensus 92 ~C~~flrtG~Ck~G~~CkF~H~ 113 (476)
.|+||.. |+++++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 4998876 999999999996
No 31
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.78 E-value=0.0057 Score=37.75 Aligned_cols=19 Identities=37% Similarity=1.002 Sum_probs=16.8
Q ss_pred ccccccccccCCCCCCCccCCC
Q 011853 138 ECSYYMKTRQCKFGATCKFHHP 159 (476)
Q Consensus 138 ~C~~f~ktG~C~~G~~CrF~Hp 159 (476)
+|+||.. |+++++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 4898865 999999999996
No 32
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.11 E-value=0.007 Score=58.52 Aligned_cols=30 Identities=37% Similarity=0.863 Sum_probs=26.5
Q ss_pred CCcCCcchhccCCCCCCCCCCCCCCCCCCC
Q 011853 43 DEADCIHYVRTGFCAYGSRCRFNHPRDRGS 72 (476)
Q Consensus 43 gt~~C~~f~rtG~C~~Gd~CkF~H~~~~~~ 72 (476)
...+|+.|..||.|.|||.|+|+|..++..
T Consensus 140 qpdVCKdyk~TGYCGYGDsCKflH~R~D~K 169 (259)
T COG5152 140 QPDVCKDYKETGYCGYGDSCKFLHDRSDFK 169 (259)
T ss_pred CcccccchhhcccccCCchhhhhhhhhhhh
Confidence 447899999999999999999999988643
No 33
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.09 E-value=0.019 Score=55.64 Aligned_cols=27 Identities=48% Similarity=0.993 Sum_probs=24.7
Q ss_pred CCcCcccccccCCCCCCCCCCCCCCCC
Q 011853 89 GQPVCQYYMRTGTCKYGASCKYHHPRQ 115 (476)
Q Consensus 89 ktp~C~~flrtG~Ck~G~~CkF~H~~~ 115 (476)
...+|+.|..||.|-||+.|+|+|.+.
T Consensus 140 qpdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 140 QPDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred CcccccchhhcccccCCchhhhhhhhh
Confidence 345899999999999999999999987
No 34
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=91.19 E-value=0.54 Score=52.67 Aligned_cols=44 Identities=30% Similarity=0.868 Sum_probs=33.0
Q ss_pred CCcCcccccccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccccccccCCCCCCCccCCCCCC
Q 011853 89 GQPVCQYYMRTGTCKYGASCKYHHPRQGAGSVSNVSLNYYGYPLRPGEKECSYYMKTRQCKFGATCKFHHPQPA 162 (476)
Q Consensus 89 ktp~C~~flrtG~Ck~G~~CkF~H~~~~~~~~~~~~ln~~g~P~rp~~~~C~~f~ktG~C~~G~~CrF~Hp~~~ 162 (476)
-+.+|+|+ +.|++= .|+|.|+.. |+|- -+|.+...|-|.|+.+.
T Consensus 624 i~~~CrY~---pnCrnm-~C~F~HPk~-----------------------cRf~---~~c~~~~sc~fYh~r~n 667 (681)
T KOG3702|consen 624 IRGLCRYR---PNCRNM-QCKFYHPKT-----------------------CRFN---TNCPNNPSCTFYHERPN 667 (681)
T ss_pred ccccceec---cCcCCc-cccccCCcc-----------------------cccc---ccCCCCcccccccCCcc
Confidence 45689997 559764 499999755 6664 34888889999999763
No 35
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.10 E-value=0.068 Score=54.56 Aligned_cols=29 Identities=38% Similarity=0.895 Sum_probs=25.9
Q ss_pred CCcCCcchhccCCCCCCCCCCCCCCCCCC
Q 011853 43 DEADCIHYVRTGFCAYGSRCRFNHPRDRG 71 (476)
Q Consensus 43 gt~~C~~f~rtG~C~~Gd~CkF~H~~~~~ 71 (476)
-..+|+-|..||.|.||+.|+|+|.....
T Consensus 185 qpDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 185 QPDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred CchhhhhhHhhCcccccchhhhhhhhhhc
Confidence 34789999999999999999999998754
No 36
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.86 E-value=0.15 Score=53.40 Aligned_cols=24 Identities=38% Similarity=1.146 Sum_probs=23.0
Q ss_pred cCcccccccCCCCCCCCCCCCCCCC
Q 011853 91 PVCQYYMRTGTCKYGASCKYHHPRQ 115 (476)
Q Consensus 91 p~C~~flrtG~Ck~G~~CkF~H~~~ 115 (476)
.+|+||++ |.|++|+.|+|.|.+.
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCc
Confidence 68999999 9999999999999887
No 37
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=88.33 E-value=0.17 Score=50.80 Aligned_cols=29 Identities=21% Similarity=0.660 Sum_probs=24.8
Q ss_pred CCCCcCcccccccCCCCCCCCCCCCCCCCC
Q 011853 87 RVGQPVCQYYMRTGTCKYGASCKYHHPRQG 116 (476)
Q Consensus 87 r~ktp~C~~flrtG~Ck~G~~CkF~H~~~~ 116 (476)
+++...|..|.+ +.|.+|..|.|+|.+..
T Consensus 149 ~~rea~C~~~e~-~~C~rG~~CnFmH~k~~ 177 (260)
T KOG2202|consen 149 DFREAICGQFER-TECSRGGACNFMHVKRL 177 (260)
T ss_pred chhhhhhccccc-ccCCCCCcCcchhhhhh
Confidence 356678999999 69999999999998753
No 38
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.23 E-value=0.15 Score=52.16 Aligned_cols=26 Identities=46% Similarity=1.040 Sum_probs=24.1
Q ss_pred CcCcccccccCCCCCCCCCCCCCCCC
Q 011853 90 QPVCQYYMRTGTCKYGASCKYHHPRQ 115 (476)
Q Consensus 90 tp~C~~flrtG~Ck~G~~CkF~H~~~ 115 (476)
..+|+.|--||.|.||+.|+|+|.+.
T Consensus 186 pDicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 186 PDICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred chhhhhhHhhCcccccchhhhhhhhh
Confidence 44899999999999999999999887
No 39
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.40 E-value=0.21 Score=52.32 Aligned_cols=25 Identities=44% Similarity=1.083 Sum_probs=23.5
Q ss_pred cccccccccccCCCCCCCccCCCCCC
Q 011853 137 KECSYYMKTRQCKFGATCKFHHPQPA 162 (476)
Q Consensus 137 ~~C~~f~ktG~C~~G~~CrF~Hp~~~ 162 (476)
.+|+||++ |.|++|+.|||.|..+.
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCch
Confidence 59999999 99999999999999984
No 40
>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=83.18 E-value=0.76 Score=29.93 Aligned_cols=23 Identities=35% Similarity=1.015 Sum_probs=18.3
Q ss_pred cCcccccccCCCCCCCCCCCCCCC
Q 011853 91 PVCQYYMRTGTCKYGASCKYHHPR 114 (476)
Q Consensus 91 p~C~~flrtG~Ck~G~~CkF~H~~ 114 (476)
++|.|-++.|.|.. +.|.|.|-+
T Consensus 1 ~lC~yEl~Gg~Cnd-~~C~~QHfr 23 (23)
T PF10650_consen 1 PLCPYELTGGVCND-PDCEFQHFR 23 (23)
T ss_pred CCCccccCCCeeCC-CCCCccccC
Confidence 47999999669964 559999953
No 41
>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=81.15 E-value=0.99 Score=29.41 Aligned_cols=23 Identities=26% Similarity=0.728 Sum_probs=18.9
Q ss_pred cccccccccccCCCCCCCccCCCC
Q 011853 137 KECSYYMKTRQCKFGATCKFHHPQ 160 (476)
Q Consensus 137 ~~C~~f~ktG~C~~G~~CrF~Hp~ 160 (476)
++|.|-+..|.|. .+.|.|.|-+
T Consensus 1 ~lC~yEl~Gg~Cn-d~~C~~QHfr 23 (23)
T PF10650_consen 1 PLCPYELTGGVCN-DPDCEFQHFR 23 (23)
T ss_pred CCCccccCCCeeC-CCCCCccccC
Confidence 3799999856996 7899999953
No 42
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=69.23 E-value=1.9 Score=43.44 Aligned_cols=29 Identities=31% Similarity=0.566 Sum_probs=25.4
Q ss_pred CCCCCcCCcchhccCCCCCCCCCCCCCCCC
Q 011853 40 ERPDEADCIHYVRTGFCAYGSRCRFNHPRD 69 (476)
Q Consensus 40 ~Rpgt~~C~~f~rtG~C~~Gd~CkF~H~~~ 69 (476)
-++++.+|..|.+ +.|.+|..|.|.|...
T Consensus 148 T~~rea~C~~~e~-~~C~rG~~CnFmH~k~ 176 (260)
T KOG2202|consen 148 TDFREAICGQFER-TECSRGGACNFMHVKR 176 (260)
T ss_pred Cchhhhhhccccc-ccCCCCCcCcchhhhh
Confidence 4568899999998 6999999999999874
No 43
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=69.06 E-value=2.8 Score=44.07 Aligned_cols=30 Identities=33% Similarity=0.944 Sum_probs=26.3
Q ss_pred CCCCCcCcccccccCCCCCCCCCCCCCCCCC
Q 011853 86 ERVGQPVCQYYMRTGTCKYGASCKYHHPRQG 116 (476)
Q Consensus 86 er~ktp~C~~flrtG~Ck~G~~CkF~H~~~~ 116 (476)
.|....+|-||.+ |.||+|+.|.|.|.+..
T Consensus 157 krn~p~Icsf~v~-geckRG~ec~yrhEkp~ 186 (377)
T KOG0153|consen 157 KRNRPHICSFFVK-GECKRGAECPYRHEKPP 186 (377)
T ss_pred cCCCCccccceee-ccccccccccccccCCC
Confidence 4566779999999 89999999999998873
No 44
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=65.25 E-value=3.9 Score=43.02 Aligned_cols=28 Identities=36% Similarity=0.925 Sum_probs=24.6
Q ss_pred CccccccccccccCCCCCCCccCCCCCCC
Q 011853 135 GEKECSYYMKTRQCKFGATCKFHHPQPAG 163 (476)
Q Consensus 135 ~~~~C~~f~ktG~C~~G~~CrF~Hp~~~~ 163 (476)
.-.+|.||.+ |.|++|+.|.|.|.++.+
T Consensus 160 ~p~Icsf~v~-geckRG~ec~yrhEkp~d 187 (377)
T KOG0153|consen 160 RPHICSFFVK-GECKRGAECPYRHEKPPD 187 (377)
T ss_pred CCccccceee-ccccccccccccccCCCC
Confidence 3468999999 999999999999999843
No 45
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=24.16 E-value=31 Score=37.91 Aligned_cols=38 Identities=16% Similarity=0.117 Sum_probs=32.3
Q ss_pred CCCCCCCCCCCcCCcchhccCCCCCCCCCCCCCCCCCC
Q 011853 34 GAESYPERPDEADCIHYVRTGFCAYGSRCRFNHPRDRG 71 (476)
Q Consensus 34 ~~~~yp~Rpgt~~C~~f~rtG~C~~Gd~CkF~H~~~~~ 71 (476)
.-..+.-|.....|++|.++|.|.+|+.|++.|..+.+
T Consensus 202 rtgp~ks~~s~~r~k~fee~g~~~r~el~p~~hg~~~v 239 (526)
T KOG2135|consen 202 RTGPEKSRNSENRRKFFEEFGVLERGELCPTHHGCVPV 239 (526)
T ss_pred ccCcccccccHHhhhhhHhhceeeecccccccccccee
Confidence 33456667788899999999999999999999998764
No 46
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=20.74 E-value=56 Score=35.98 Aligned_cols=35 Identities=20% Similarity=0.316 Sum_probs=29.0
Q ss_pred CCCCCCcccccccccCCCCCCCCCCCCCCCCCccC
Q 011853 298 FPERPGQQECQYYMKTGDCKFGSSCRFHHPRELIV 332 (476)
Q Consensus 298 ~p~rp~~~~C~yy~k~G~Ck~G~~Ckf~Hp~~~~~ 332 (476)
++.|-....|.+|.++|.|+.|+.|+++|-.+.+.
T Consensus 206 ~ks~~s~~r~k~fee~g~~~r~el~p~~hg~~~vv 240 (526)
T KOG2135|consen 206 EKSRNSENRRKFFEEFGVLERGELCPTHHGCVPVV 240 (526)
T ss_pred ccccccHHhhhhhHhhceeeeccccccccccceeE
Confidence 44455678999999999999999999999776553
Done!