Query 047248
Match_columns 439
No_of_seqs 356 out of 1639
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:11:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047248hhsearch_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 4.2E-26 9.2E-31 229.5 16.8 252 44-370 78-332 (332)
2 KOG1677 CCCH-type Zn-finger pr 99.6 6.2E-16 1.3E-20 155.9 7.8 77 297-375 125-202 (332)
3 KOG2494 C3H1-type Zn-finger pr 99.4 1.2E-13 2.5E-18 137.9 4.5 213 98-380 38-259 (331)
4 KOG1040 Polyadenylation factor 99.4 9.4E-13 2E-17 133.2 7.9 85 49-168 74-158 (325)
5 KOG1492 C3H1-type Zn-finger pr 99.3 6E-13 1.3E-17 127.3 3.6 80 50-167 204-283 (377)
6 KOG1040 Polyadenylation factor 99.2 1.8E-11 3.9E-16 124.0 6.1 89 48-168 41-130 (325)
7 COG5084 YTH1 Cleavage and poly 98.7 9.1E-08 2E-12 95.5 11.6 89 50-169 72-160 (285)
8 KOG2494 C3H1-type Zn-finger pr 98.6 2.3E-08 4.9E-13 100.4 3.2 101 53-168 38-154 (331)
9 COG5063 CTH1 CCCH-type Zn-fing 98.6 4.5E-07 9.8E-12 90.4 11.3 225 96-379 114-343 (351)
10 PF00642 zf-CCCH: Zinc finger 98.5 5.7E-08 1.2E-12 64.1 1.5 27 302-328 1-27 (27)
11 COG5084 YTH1 Cleavage and poly 98.5 1.6E-07 3.6E-12 93.7 5.5 87 51-169 103-191 (285)
12 KOG1492 C3H1-type Zn-finger pr 98.4 1.2E-07 2.7E-12 91.2 3.3 80 52-167 233-312 (377)
13 PF00642 zf-CCCH: Zinc finger 98.3 1.9E-07 4E-12 61.7 0.8 26 50-75 1-26 (27)
14 KOG4791 Uncharacterized conser 98.3 6.3E-07 1.4E-11 93.7 4.4 83 53-170 4-87 (667)
15 COG5063 CTH1 CCCH-type Zn-fing 98.2 1.2E-06 2.7E-11 87.3 4.6 105 53-170 231-341 (351)
16 KOG1595 CCCH-type Zn-finger pr 98.1 2.4E-05 5.3E-10 83.3 10.8 92 62-174 207-298 (528)
17 smart00356 ZnF_C3H1 zinc finge 97.6 3.1E-05 6.7E-10 50.1 2.2 25 303-328 3-27 (27)
18 smart00356 ZnF_C3H1 zinc finge 97.5 5.9E-05 1.3E-09 48.7 2.4 25 51-76 3-27 (27)
19 KOG1595 CCCH-type Zn-finger pr 97.2 0.00027 5.8E-09 75.5 4.4 55 107-169 207-261 (528)
20 KOG2333 Uncharacterized conser 97.2 0.00012 2.7E-09 77.4 1.6 58 304-371 76-135 (614)
21 KOG1763 Uncharacterized conser 97.2 7.8E-05 1.7E-09 74.4 -0.2 75 46-124 86-193 (343)
22 KOG1763 Uncharacterized conser 96.9 0.00018 3.9E-09 71.9 -0.8 80 93-173 88-196 (343)
23 KOG2333 Uncharacterized conser 96.9 0.00046 1E-08 73.2 2.1 59 52-119 76-136 (614)
24 KOG2185 Predicted RNA-processi 96.6 0.001 2.2E-08 69.1 1.8 57 66-123 98-165 (486)
25 KOG3702 Nuclear polyadenylated 96.5 0.0032 6.9E-08 68.9 5.5 100 53-171 545-649 (681)
26 PF14608 zf-CCCH_2: Zinc finge 96.3 0.0023 4.9E-08 39.0 1.5 19 54-75 1-19 (19)
27 KOG4791 Uncharacterized conser 96.1 0.0045 9.7E-08 65.6 3.4 103 50-170 30-144 (667)
28 COG5252 Uncharacterized conser 96.0 0.0017 3.6E-08 63.4 0.0 78 45-123 78-177 (299)
29 COG5252 Uncharacterized conser 95.5 0.0039 8.5E-08 60.9 0.1 80 93-173 81-181 (299)
30 PF14608 zf-CCCH_2: Zinc finge 95.5 0.0095 2.1E-07 36.3 1.7 19 99-120 1-19 (19)
31 KOG2185 Predicted RNA-processi 95.1 0.0097 2.1E-07 62.1 1.7 33 45-78 133-165 (486)
32 COG5152 Uncharacterized conser 94.9 0.0095 2.1E-07 57.0 0.7 26 53-78 142-167 (259)
33 COG5152 Uncharacterized conser 94.5 0.012 2.7E-07 56.2 0.6 26 305-330 142-167 (259)
34 KOG3702 Nuclear polyadenylated 93.7 0.11 2.4E-06 57.3 5.9 75 63-168 587-666 (681)
35 KOG2202 U2 snRNP splicing fact 93.6 0.03 6.5E-07 55.4 1.2 27 347-374 149-175 (260)
36 KOG2202 U2 snRNP splicing fact 91.9 0.061 1.3E-06 53.3 0.9 31 140-171 149-179 (260)
37 KOG1813 Predicted E3 ubiquitin 91.1 0.071 1.5E-06 53.8 0.4 25 53-77 187-211 (313)
38 KOG1813 Predicted E3 ubiquitin 91.1 0.082 1.8E-06 53.4 0.8 27 305-331 187-213 (313)
39 KOG1039 Predicted E3 ubiquitin 88.6 0.16 3.5E-06 52.6 0.6 25 98-123 9-33 (344)
40 PF10650 zf-C3H1: Putative zin 86.9 0.42 9.2E-06 30.7 1.5 23 98-121 1-23 (23)
41 KOG1039 Predicted E3 ubiquitin 85.3 0.31 6.6E-06 50.6 0.5 25 53-78 9-33 (344)
42 PF10650 zf-C3H1: Putative zin 81.9 0.82 1.8E-05 29.4 1.2 21 145-166 2-22 (23)
43 KOG0153 Predicted RNA-binding 81.3 1.5 3.2E-05 45.5 3.5 31 46-77 155-185 (377)
44 KOG0153 Predicted RNA-binding 64.2 4.1 8.9E-05 42.3 1.9 29 93-122 157-185 (377)
45 PF10283 zf-CCHH: Zinc-finger 43.2 7.1 0.00015 25.9 -0.2 9 361-369 2-10 (26)
46 KOG2135 Proteins containing th 28.9 26 0.00056 38.1 1.0 37 43-79 203-239 (526)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.94 E-value=4.2e-26 Score=229.50 Aligned_cols=252 Identities=39% Similarity=0.756 Sum_probs=170.6
Q ss_pred CCCCCCCCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhh-hhccCCCCCCCCCccccccccccCCCC-CCCCCCCCCC
Q 047248 44 GSLPERPGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIAT-ARIKGDYPERVGQPECQYYLKTGTCKF-GATCKFHHPR 121 (439)
Q Consensus 44 ~~~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~-~~~~~e~Per~~~p~C~~f~ktG~Ck~-G~~CkF~H~~ 121 (439)
..|++++++.+|.+|++++.|.++..|+|+|+..+...... .......+++.++++|++|.++|.|+| |++|+|+|..
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~ 157 (332)
T KOG1677|consen 78 SPYPERSGEGDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVRRSRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGL 157 (332)
T ss_pred CcCCCCCCccccccccccCCCCCCCCCCccCcccccccCCccccccccCcccccCCcceeeecCccccccCchhhhcCCc
Confidence 46999999999999999999999999999999633221111 134567889999999999999999999 9999999999
Q ss_pred CCcCccccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCcCCcCCcccc
Q 047248 122 DKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPNNMMVSLRGSPVYPTVQSPTTPSQQSYAGGITN 201 (439)
Q Consensus 122 ~~~~~~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~~~~~~~s~~~p~~qs~~~~~~~~y~~~~~~ 201 (439)
.+.+... .++..+.+.+.++++|.+|+++|.|+||.+|+|.|+......+.... + .+.. .+.+++|+ ..
T Consensus 158 ~e~r~~~--~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~~~~~~~---~-~~~~--~~~~~~~~---~~ 226 (332)
T KOG1677|consen 158 EELRLPS--SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPEDRASNRHP---Y-PVSR--NPQPQSYG---LT 226 (332)
T ss_pred ccccccc--cchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCccccccccCC---c-cccc--cccccccc---hh
Confidence 8876322 34567788899999999999999999999999999998654322111 1 1111 22344454 34
Q ss_pred ccccccCCCC-CCCCCCCCCccccCCCcccCCCCCCCCCCCCCCCCchhhhccCCCCcccCCCCCCCCCCCCCCCccccc
Q 047248 202 WSRASFIPSP-RWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSVSSSENLQQTSGNSQIYGASRQTEPSNSGSQGTMSSF 280 (439)
Q Consensus 202 ~~~~~~~p~~-~~~~~~~y~p~~~~~g~~~~~~w~~y~~~~~~~~s~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~ 280 (439)
|.+..++... .++- .|.+...+++++|...-.+.. ..... ..
T Consensus 227 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~p~~~~~~~~-----------------~~~~~------~~------------ 269 (332)
T KOG1677|consen 227 ASRSSLLNQQSKLQQ--PFAPSGLSESVLPRSSQQNLL-----------------PQGLR------SS------------ 269 (332)
T ss_pred hcchhhccccccccc--cccccccccccCcCCcccccc-----------------ccccc------cc------------
Confidence 5555544432 1111 122222334444311000000 00000 00
Q ss_pred cCCCcccccccccccccCCCCCCCccchhhhhcCCCCCCCCcccCCCCCcCCCCCCcccCCCCCCCCCCCcCCccccccc
Q 047248 281 RSGSVPVGFYALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRERLLPVPDCVLSPIGLPLRPGEPLCIFYSRYG 360 (439)
Q Consensus 281 ~~~~~~~~~~~~q~~~~~perp~~~~C~~y~ktG~C~~G~~Ckf~Hp~~~~~~~~~~~l~~~g~p~r~~~~~C~~Y~~~G 360 (439)
....+.+.....+++.+++++.+++|++ |++| .+++ +|+|++...|..|+++|
T Consensus 270 -~~~~~~~~~~~~~~~~~~~~p~~~~~~~-~~~~-------------~~~l------------~~~~~~~~~~~~~~~~~ 322 (332)
T KOG1677|consen 270 -SSSHPSGSQENVNENGFRARPEQPECRS-MKSG-------------ENRL------------LPLRPGPGACTLFSRYG 322 (332)
T ss_pred -cccccccchhccccccCcCCCCCCccch-hccc-------------cccc------------cCCCCCccccccccccc
Confidence 0000111123346788999999999999 9999 2221 78999999999999999
Q ss_pred CCCCCCCCCC
Q 047248 361 ICKFGPSCKF 370 (439)
Q Consensus 361 ~Ck~G~~CkF 370 (439)
+|+||..|+|
T Consensus 323 ~~~~~~~~~~ 332 (332)
T KOG1677|consen 323 SCKFGPLCKF 332 (332)
T ss_pred ccCCCCcCCC
Confidence 9999999997
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.62 E-value=6.2e-16 Score=155.88 Aligned_cols=77 Identities=35% Similarity=0.711 Sum_probs=67.9
Q ss_pred cCCCCCCCccchhhhhcCCCCC-CCCcccCCCCCcCCCCCCcccCCCCCCCCCCCcCCcccccccCCCCCCCCCCCCCCC
Q 047248 297 VFPERPGQPECQFYMKTGDCKF-GAVCRFHHPRERLLPVPDCVLSPIGLPLRPGEPLCIFYSRYGICKFGPSCKFDHPMG 375 (439)
Q Consensus 297 ~~perp~~~~C~~y~ktG~C~~-G~~Ckf~Hp~~~~~~~~~~~l~~~g~p~r~~~~~C~~Y~~~G~Ck~G~~CkF~HP~~ 375 (439)
..|++.++++|++|+++|.|+| |++|||+|+++++.... .+...+++.++++++|.+|+++|.||||.+|+|+|+..
T Consensus 125 ~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~--~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 125 RKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS--SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEP 202 (332)
T ss_pred cCcccccCCcceeeecCccccccCchhhhcCCcccccccc--cchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCc
Confidence 3467889999999999999999 99999999999875321 23467899999999999999999999999999999975
No 3
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=99.41 E-value=1.2e-13 Score=137.90 Aligned_cols=213 Identities=20% Similarity=0.384 Sum_probs=128.7
Q ss_pred ccccccccccCCCCCCC-CCCCCCCCCcCccccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCCcc---cc
Q 047248 98 PECQYYLKTGTCKFGAT-CKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPNNM---MV 173 (439)
Q Consensus 98 p~C~~f~ktG~Ck~G~~-CkF~H~~~~~~~~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~---~~ 173 (439)
.+||.|+| |.|++|+. |||.|+.....+.. .+-..|.+|+ +|.|.+ ++|||.|+..+.+ .+
T Consensus 38 eVCReF~r-n~C~R~d~~CkfaHP~~~~~V~~------------g~v~aC~Ds~-kgrCsR-~nCkylHpp~hlkdql~i 102 (331)
T KOG2494|consen 38 EVCREFLR-NTCSRGDRECKFAHPPKNCQVSN------------GRVIACFDSQ-KGRCSR-ENCKYLHPPQHLKDQLKI 102 (331)
T ss_pred HHHHHHHh-ccccCCCccccccCCCCCCCccC------------CeEEEEeccc-cCccCc-ccceecCCChhhhhhhhh
Confidence 58999999 99999997 99999987554321 1234699998 999999 8999999988765 34
Q ss_pred cCCCCCCCCCCCCCCCCCcCCcCCccccccccccCCCCCCCCCCCCCcccc---CCCcccCCCCCCCCCCCC-CCCCchh
Q 047248 174 SLRGSPVYPTVQSPTTPSQQSYAGGITNWSRASFIPSPRWQGPSSYAPMLL---PQGMVSVPGWNTYSGQLG-SVSSSEN 249 (439)
Q Consensus 174 ~~~~s~~~p~~qs~~~~~~~~y~~~~~~~~~~~~~p~~~~~~~~~y~p~~~---~~g~~~~~~w~~y~~~~~-~~~s~~~ 249 (439)
.++...|+.....+....+++. +|..+.+ .|++. ..+-++.-.+|+|...+. .+..++
T Consensus 103 ngrn~l~lq~~~aA~~~q~~~~-------------~g~Pi~~----v~~f~~~~~~~g~~~~s~~~y~~~~Pg~~vp~~- 164 (331)
T KOG2494|consen 103 NGRNNLILQKTAAAMLAQQMQG-------------PGTPICS----VPMFATGPCLGGNTACSYWPYLPPVPGGLVPAD- 164 (331)
T ss_pred cccccHHHHHHHHhhhcccccC-------------CCccccc----cccccccccccCCCccccccccCCCCCCCCCCc-
Confidence 5555544444222222211111 1111111 01111 122234555666665331 222222
Q ss_pred hhccCCCCcccCCCCCCCCCCCCCCCccccccCCCcccccccccccccCCCCCCCccchhhhhcCCCCCCC-CcccCCCC
Q 047248 250 LQQTSGNSQIYGASRQTEPSNSGSQGTMSSFRSGSVPVGFYALQRESVFPERPGQPECQFYMKTGDCKFGA-VCRFHHPR 328 (439)
Q Consensus 250 ~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~perp~~~~C~~y~ktG~C~~G~-~Ckf~Hp~ 328 (439)
.+....+| .++.++|.....-.++.....++.+.|+- ..|.|..++ .|+|.|+.
T Consensus 165 ---~~p~~~~~--------------------~~g~p~v~~~~~~~~~k~~r~~~~e~~~~--~~gn~~r~e~d~~f~~~~ 219 (331)
T KOG2494|consen 165 ---GLPTTPVF--------------------VPGGPGVPGPGLVGGQKLLRSDRLEVCRE--QRGNCRRGEQDAQFAHPA 219 (331)
T ss_pred ---CCCCCccc--------------------cCCCCcccccccccccccccCCCCCCCcc--cccccccchhHHHHhhhh
Confidence 22222233 22222333333334466677788888988 569999999 69999999
Q ss_pred CcCCCCCCcccCCCCCCCCCCCcCCcccccccCCCCCCCCCCCCCCCCCCCC
Q 047248 329 ERLLPVPDCVLSPIGLPLRPGEPLCIFYSRYGICKFGPSCKFDHPMGIFTYN 380 (439)
Q Consensus 329 ~~~~~~~~~~l~~~g~p~r~~~~~C~~Y~~~G~Ck~G~~CkF~HP~~~~~~~ 380 (439)
+......+ .....+|..|. +|.|-- .+||+.|+..+..++
T Consensus 220 k~~~~~s~----------~~t~~~~~~~t-~~~~~~-en~~~~~~~~h~~~~ 259 (331)
T KOG2494|consen 220 KSIMIDSN----------DNTVEVCLRYT-KGRCET-ENCKYFHAPAHDQAS 259 (331)
T ss_pred hhhhcccC----------CCcchhccccc-cceech-hcccccCchHHHHHH
Confidence 76533221 33456899999 899975 799999997666443
No 4
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.37 E-value=9.4e-13 Score=133.19 Aligned_cols=85 Identities=29% Similarity=0.725 Sum_probs=64.4
Q ss_pred CCCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCccc
Q 047248 49 RPGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAG 128 (439)
Q Consensus 49 Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~ 128 (439)
..++.+|+||+| |.|+.||.|.|+|..+.. ++++|.||..+|.|..+.+|.|.|......
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~~~~----------------k~rec~ff~~~g~c~~~~~c~y~h~dpqt~--- 133 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHEYDLT----------------KMRECKFFSLFGECTNGKDCPYLHGDPQTA--- 133 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhhhhhc----------------ccccccccccccccccccCCcccCCChhhh---
Confidence 456678888887 888888888888877332 356788888888888888888888864322
Q ss_pred cccccccCCCCcccccccccccccccCCCCCCCCCCCCCC
Q 047248 129 RVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQP 168 (439)
Q Consensus 129 ~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~ 168 (439)
.++|..|. .|+|..|+.|++.|...
T Consensus 134 --------------~k~c~~~~-~g~c~~g~~c~~~h~~~ 158 (325)
T KOG1040|consen 134 --------------IKKCKWYK-EGFCRGGPSCKKRHERK 158 (325)
T ss_pred --------------hhccchhh-hccCCCcchhhhhhhcc
Confidence 35688777 88888888888888655
No 5
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=99.33 E-value=6e-13 Score=127.33 Aligned_cols=80 Identities=38% Similarity=0.901 Sum_probs=70.2
Q ss_pred CCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCcccc
Q 047248 50 PGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGR 129 (439)
Q Consensus 50 pg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~ 129 (439)
|....|+||...|.|..|..|+|.|.+.++ .+|.-|+. |.|...+.|...|..+..++
T Consensus 204 psavycryynangicgkgaacrfvheptrk------------------ticpkfln-grcnkaedcnlsheldprri--- 261 (377)
T KOG1492|consen 204 PSAVYCRYYNANGICGKGAACRFVHEPTRK------------------TICPKFLN-GRCNKAEDCNLSHELDPRRI--- 261 (377)
T ss_pred CceeEEEEecCCCcccCCceeeeecccccc------------------ccChHHhc-CccCchhcCCcccccCcccc---
Confidence 556789999999999999999999998764 48999998 99999999999999877653
Q ss_pred ccccccCCCCcccccccccccccccCCCCCCCCCCCCC
Q 047248 130 VSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQ 167 (439)
Q Consensus 130 v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~ 167 (439)
+.|+||+ .|.|.+ .+|+|.|..
T Consensus 262 --------------pacryfl-lgkcnn-pncryvhih 283 (377)
T KOG1492|consen 262 --------------PACRYFL-LGKCNN-PNCRYVHIH 283 (377)
T ss_pred --------------chhhhhh-hccCCC-CCceEEEEe
Confidence 4699999 999998 999998843
No 6
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.19 E-value=1.8e-11 Score=123.96 Aligned_cols=89 Identities=28% Similarity=0.691 Sum_probs=70.9
Q ss_pred CCCCCcCccchhh-cCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCc
Q 047248 48 ERPGEPDCSYYIR-TGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGI 126 (439)
Q Consensus 48 ~Rpg~~~C~yy~r-tG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~ 126 (439)
++.+...|.++.+ .-.|.+|..|.+.|...+ +..+..+|+||++ |.|+.|+.|-|+|..+..
T Consensus 41 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~vcK~~l~-glC~kgD~C~Flhe~~~~-- 103 (325)
T KOG1040|consen 41 DESGRATCEFNESREKPCERGPICPKSHNDVS--------------DSRGKVVCKHWLR-GLCKKGDQCEFLHEYDLT-- 103 (325)
T ss_pred cccccchhcccccCCCCccCCCCCccccCCcc--------------ccCCceeehhhhh-hhhhccCcCcchhhhhhc--
Confidence 4445678988862 157999999999997642 0114679999999 999999999999987332
Q ss_pred cccccccccCCCCcccccccccccccccCCCCCCCCCCCCCC
Q 047248 127 AGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQP 168 (439)
Q Consensus 127 ~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~ 168 (439)
..++|.||...|.|.+|..|.|.|.++
T Consensus 104 ---------------k~rec~ff~~~g~c~~~~~c~y~h~dp 130 (325)
T KOG1040|consen 104 ---------------KMRECKFFSLFGECTNGKDCPYLHGDP 130 (325)
T ss_pred ---------------ccccccccccccccccccCCcccCCCh
Confidence 235899999999999999999999876
No 7
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.72 E-value=9.1e-08 Score=95.46 Aligned_cols=89 Identities=22% Similarity=0.456 Sum_probs=70.2
Q ss_pred CCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCcccc
Q 047248 50 PGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGR 129 (439)
Q Consensus 50 pg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~ 129 (439)
..+..|.+|+..+.+...-.|++.|..... + ...+|++|+. |.|+.+..|.|+|..+....
T Consensus 72 gn~~~~~~~~~~~~~~~~~s~~~~~~~~~~-----------~----s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~s--- 132 (285)
T COG5084 72 GNTVACISRNFNSIRGSRLSTPNNHVNPVL-----------S----SSVVCKFFLR-GLCKSGFSCEFLHEYDLRSS--- 132 (285)
T ss_pred CcccccccccccCCccccccCCccccCccc-----------c----CCcccchhcc-ccCcCCCccccccCCCcccc---
Confidence 345679999876777666789999975321 1 2357999999 99999999999999876542
Q ss_pred ccccccCCCCcccccccccccccccCCCCCCCCCCCCCCC
Q 047248 130 VSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPN 169 (439)
Q Consensus 130 v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~ 169 (439)
-...|++|...|.|..|..|.+.|.++.
T Consensus 133 ------------~~~~c~~Fs~~G~cs~g~~c~~~h~dp~ 160 (285)
T COG5084 133 ------------QGPPCRSFSLKGSCSSGPSCGYSHIDPD 160 (285)
T ss_pred ------------cCCCcccccccceeccCCCCCccccCcc
Confidence 1347999988999999999999998853
No 8
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.60 E-value=2.3e-08 Score=100.44 Aligned_cols=101 Identities=29% Similarity=0.599 Sum_probs=67.0
Q ss_pred cCccchhhcCCCCCCCC-CCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCc----c
Q 047248 53 PDCSYYIRTGLCRFGAT-CRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGI----A 127 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~-CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~----~ 127 (439)
++||-|+| |.|++||. |||.|+.....+. ++ .-..|..|+| |.|. .++|||+|+....+. .
T Consensus 38 eVCReF~r-n~C~R~d~~CkfaHP~~~~~V~-----~g------~v~aC~Ds~k-grCs-R~nCkylHpp~hlkdql~in 103 (331)
T KOG2494|consen 38 EVCREFLR-NTCSRGDRECKFAHPPKNCQVS-----NG------RVIACFDSQK-GRCS-RENCKYLHPPQHLKDQLKIN 103 (331)
T ss_pred HHHHHHHh-ccccCCCccccccCCCCCCCcc-----CC------eEEEEecccc-CccC-cccceecCCChhhhhhhhhc
Confidence 68999999 99999999 9999998643211 11 1246999999 9999 678999998776542 1
Q ss_pred cccc--ccc------cCCCCcccccccc--cccccccCCCCC-CCCCCCCCC
Q 047248 128 GRVS--LNV------LGYPLRPNEIECA--YYLRTGQCKFGS-TCKFHHPQP 168 (439)
Q Consensus 128 ~~v~--~n~------~G~P~r~~~~~C~--~y~~~G~C~~G~-~CkF~Hp~~ 168 (439)
.... +.. ......++.++|. .|. ++.|..|. +|+|.|...
T Consensus 104 grn~l~lq~~~aA~~~q~~~~~g~Pi~~v~~f~-~~~~~~g~~~~s~~~y~~ 154 (331)
T KOG2494|consen 104 GRNNLILQKTAAAMLAQQMQGPGTPICSVPMFA-TGPCLGGNTACSYWPYLP 154 (331)
T ss_pred ccccHHHHHHHHhhhcccccCCCcccccccccc-ccccccCCCccccccccC
Confidence 1110 000 0112224566777 555 67777654 477777665
No 9
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.57 E-value=4.5e-07 Score=90.41 Aligned_cols=225 Identities=14% Similarity=0.143 Sum_probs=121.1
Q ss_pred CCccccccccccCCCCCCCCCCCCCCCCcCccccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCCcccccC
Q 047248 96 GQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPNNMMVSL 175 (439)
Q Consensus 96 ~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~~~~~ 175 (439)
++++|+.-.--+.|+++..|.|+|+......+. .+.+.++.-|..+...|.|+++.+|-|.|-.......
T Consensus 114 kt~~l~ss~~~~~~~~p~~n~fahs~~issl~~--------~~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~~-- 183 (351)
T COG5063 114 KTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQ--------THPKYKTESLEVFINPGYVPYSKRCCFISLPLTDINL-- 183 (351)
T ss_pred cchhhhccccccccccCCCCcCCCccccccccc--------cCccccccceeEEecCCccccccccccccccccccCc--
Confidence 456777643348999999999999977654221 2334456678889989999999999999877654311
Q ss_pred CCCCCCCCCCCCCCCC--cCCcCCccccccccccCCCCCCCCCCCCCccccCCCcccCCCCCCCCCCCCCCCCchhhhcc
Q 047248 176 RGSPVYPTVQSPTTPS--QQSYAGGITNWSRASFIPSPRWQGPSSYAPMLLPQGMVSVPGWNTYSGQLGSVSSSENLQQT 253 (439)
Q Consensus 176 ~~s~~~p~~qs~~~~~--~~~y~~~~~~~~~~~~~p~~~~~~~~~y~p~~~~~g~~~~~~w~~y~~~~~~~~s~~~~~~~ 253 (439)
.+..|--.-.+ ...|..+..+...+...--...|. ..-.-|.++ +-...+-+
T Consensus 184 -----q~l~~rkpks~~~~~s~t~~kes~a~P~~~~~~~~~e----------------~n~~L~kt~-----~~lc~~ft 237 (351)
T COG5063 184 -----QPLSQRKPKSGKNCTSYTLGKESDAHPHDELIYQKQE----------------QNKPLYKTN-----PELCESFT 237 (351)
T ss_pred -----chhhccCcccCcCccccccccccccCchhhhhhhhhh----------------ccchhhcCC-----HHHhhccC
Confidence 01100000000 111222222111111000000000 000001110 00000001
Q ss_pred CCCCccc---CCCCCCCCCCCCCCCccccccCCCcccccccccccccCCCCCCCccchhhhhcCCCCCCCCcccCCCCCc
Q 047248 254 SGNSQIY---GASRQTEPSNSGSQGTMSSFRSGSVPVGFYALQRESVFPERPGQPECQFYMKTGDCKFGAVCRFHHPRER 330 (439)
Q Consensus 254 ~~~~~~y---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~perp~~~~C~~y~ktG~C~~G~~Ckf~Hp~~~ 330 (439)
.--+.-| |..+|..-.+ +|+ --+. .+.--....++.|..|.+.|+|.||.+|.|.|+.+.
T Consensus 238 ~kg~~p~~~sG~~~q~a~~~---HGl--------N~l~------~k~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~ 300 (351)
T COG5063 238 RKGTCPYWISGVKCQFACRG---HGL--------NELK------SKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDS 300 (351)
T ss_pred cCCCCccccccccccccccc---ccc--------cccc------ccccccccccCCccchhhcccCccccccccccCChh
Confidence 1111223 4444432211 221 1111 111123456788999999999999999999999987
Q ss_pred CCCCCCcccCCCCCCCCCCCcCCcccccccCCCCCCCCCCCCCCCCCCC
Q 047248 331 LLPVPDCVLSPIGLPLRPGEPLCIFYSRYGICKFGPSCKFDHPMGIFTY 379 (439)
Q Consensus 331 ~~~~~~~~l~~~g~p~r~~~~~C~~Y~~~G~Ck~G~~CkF~HP~~~~~~ 379 (439)
.+....- .-+.+....|.-++++|.|++|-+|.|.|....+..
T Consensus 301 ~ie~~~~------~~~~y~~~~crt~~~~g~~p~g~~~c~~~dkkn~~~ 343 (351)
T COG5063 301 DIEMYEE------ASLGYLDGPCRTRAKGGAFPSGGAVCKSFDKKNLDF 343 (351)
T ss_pred hcccccc------ccccccccccccccccCccCCCCchhhccccchhhh
Confidence 7654320 112334568999999999999999999988765543
No 10
>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=98.47 E-value=5.7e-08 Score=64.11 Aligned_cols=27 Identities=44% Similarity=1.027 Sum_probs=21.8
Q ss_pred CCCccchhhhhcCCCCCCCCcccCCCC
Q 047248 302 PGQPECQFYMKTGDCKFGAVCRFHHPR 328 (439)
Q Consensus 302 p~~~~C~~y~ktG~C~~G~~Ckf~Hp~ 328 (439)
+++++|++|+++|.|+||++|+|+|++
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 468899999999999999999999974
No 11
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.47 E-value=1.6e-07 Score=93.66 Aligned_cols=87 Identities=29% Similarity=0.720 Sum_probs=71.3
Q ss_pred CCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCccccc
Q 047248 51 GEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRV 130 (439)
Q Consensus 51 g~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v 130 (439)
...+|++|.+ |.|+.|..|.|+|..+... .-++.|++|...|.|..|..|.|.|......
T Consensus 103 s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~--------------s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~~----- 162 (285)
T COG5084 103 SSVVCKFFLR-GLCKSGFSCEFLHEYDLRS--------------SQGPPCRSFSLKGSCSSGPSCGYSHIDPDSF----- 162 (285)
T ss_pred CCcccchhcc-ccCcCCCccccccCCCccc--------------ccCCCcccccccceeccCCCCCccccCcccc-----
Confidence 3478999998 9999999999999988641 1257899996669999999999999974332
Q ss_pred cccccCCCCcccccccccccc--cccCCCCCCCCCCCCCCC
Q 047248 131 SLNVLGYPLRPNEIECAYYLR--TGQCKFGSTCKFHHPQPN 169 (439)
Q Consensus 131 ~~n~~G~P~r~~~~~C~~y~~--~G~C~~G~~CkF~Hp~~~ 169 (439)
...|.+|.. +++|++|..|+|.|....
T Consensus 163 ------------~~~~~~~~~~~~~f~p~g~~c~~~H~~~~ 191 (285)
T COG5084 163 ------------AGNCDQYSGATYGFCPLGASCKFSHTLKR 191 (285)
T ss_pred ------------cccccccCcccccccCCCCcccccccccc
Confidence 235777764 799999999999998864
No 12
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=98.43 E-value=1.2e-07 Score=91.20 Aligned_cols=80 Identities=25% Similarity=0.714 Sum_probs=62.3
Q ss_pred CcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCcccccc
Q 047248 52 EPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVS 131 (439)
Q Consensus 52 ~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~ 131 (439)
+.+|..|++ |+|...+.|...|..+.. ..+.|+||+- |.|. ..+|+|.|..-...
T Consensus 233 kticpkfln-grcnkaedcnlsheldpr----------------ripacryfll-gkcn-npncryvhihysen------ 287 (377)
T KOG1492|consen 233 KTICPKFLN-GRCNKAEDCNLSHELDPR----------------RIPACRYFLL-GKCN-NPNCRYVHIHYSEN------ 287 (377)
T ss_pred cccChHHhc-CccCchhcCCcccccCcc----------------ccchhhhhhh-ccCC-CCCceEEEEeecCC------
Confidence 479999997 999999999999998753 2478999997 9998 78999999865443
Q ss_pred ccccCCCCcccccccccccccccCCCCCCCCCCCCC
Q 047248 132 LNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQ 167 (439)
Q Consensus 132 ~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~ 167 (439)
.++|-.|.+.|+|..|..|+-.|..
T Consensus 288 -----------apicfefakygfcelgtscknqhil 312 (377)
T KOG1492|consen 288 -----------APICFEFAKYGFCELGTSCKNQHIL 312 (377)
T ss_pred -----------Cceeeeehhcceeccccccccceee
Confidence 2356666666666666666666654
No 13
>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=98.30 E-value=1.9e-07 Score=61.65 Aligned_cols=26 Identities=42% Similarity=1.011 Sum_probs=21.1
Q ss_pred CCCcCccchhhcCCCCCCCCCCCCCC
Q 047248 50 PGEPDCSYYIRTGLCRFGATCRFNHP 75 (439)
Q Consensus 50 pg~~~C~yy~rtG~C~~Gd~CkF~H~ 75 (439)
+++++|++|+++|.|++|++|+|+|+
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 36789999999999999999999997
No 14
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.28 E-value=6.3e-07 Score=93.71 Aligned_cols=83 Identities=23% Similarity=0.604 Sum_probs=63.9
Q ss_pred cCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCccccccc
Q 047248 53 PDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSL 132 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~ 132 (439)
++|.||.- -.|++++.|.|.|.-.-. -....|++|+..-.|+. .|+|.|..-...
T Consensus 4 ~dcyff~y-s~cKk~d~c~~rh~E~al---------------~n~t~C~~w~~~~~C~k--~C~YRHSe~~~k------- 58 (667)
T KOG4791|consen 4 EDCYFFFY-STCKKGDSCPFRHCEAAL---------------GNETVCTLWQEGRCCRK--VCRYRHSEIDKK------- 58 (667)
T ss_pred ccchhhhh-hhhhccCcCcchhhHHHh---------------cCcchhhhhhhcCcccc--cccchhhHHhhh-------
Confidence 58999985 899999999999975432 13468999999767774 999999854332
Q ss_pred cccCCCCccccccccccccccc-CCCCCCCCCCCCCCCc
Q 047248 133 NVLGYPLRPNEIECAYYLRTGQ-CKFGSTCKFHHPQPNN 170 (439)
Q Consensus 133 n~~G~P~r~~~~~C~~y~~~G~-C~~G~~CkF~Hp~~~~ 170 (439)
.++..|.++. .+. |.+ ++|-|.|..+.+
T Consensus 59 --------r~e~~CYwe~-~p~gC~k-~~CgfRH~~pPL 87 (667)
T KOG4791|consen 59 --------RSEIPCYWEN-QPTGCQK-LNCGFRHNRPPL 87 (667)
T ss_pred --------cCcccceeec-CCCccCC-CccccccCCCch
Confidence 1356798888 566 998 999999976544
No 15
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.21 E-value=1.2e-06 Score=87.34 Aligned_cols=105 Identities=25% Similarity=0.469 Sum_probs=78.9
Q ss_pred cCccchhhcCCCCC---CCCCCCC---CCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCc
Q 047248 53 PDCSYYIRTGLCRF---GATCRFN---HPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGI 126 (439)
Q Consensus 53 ~~C~yy~rtG~C~~---Gd~CkF~---H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~ 126 (439)
.+|.-|.+.|.|.+ |+.|.|+ |..+.... ...+..| +++.|..|.+.|.|.||.+|.|.|..+....
T Consensus 231 ~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~---k~k~~~f----rTePcinwe~sGyc~yg~Rc~F~hgd~~~ie 303 (351)
T COG5063 231 ELCESFTRKGTCPYWISGVKCQFACRGHGLNELKS---KKKKQNF----RTEPCINWEKSGYCPYGLRCCFKHGDDSDIE 303 (351)
T ss_pred HHhhccCcCCCCccccccccccccccccccccccc---ccccccc----ccCCccchhhcccCccccccccccCChhhcc
Confidence 68999999999999 9999999 99776321 1112233 4578999999999999999999998776532
Q ss_pred cccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCCc
Q 047248 127 AGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPNN 170 (439)
Q Consensus 127 ~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~ 170 (439)
.. +.. ..|| ..-.|+-+++.|.|+.|.+|.|.|.+...
T Consensus 304 ~~-~~~-~~~y----~~~~crt~~~~g~~p~g~~~c~~~dkkn~ 341 (351)
T COG5063 304 MY-EEA-SLGY----LDGPCRTRAKGGAFPSGGAVCKSFDKKNL 341 (351)
T ss_pred cc-ccc-cccc----cccccccccccCccCCCCchhhccccchh
Confidence 11 100 1122 23469999999999999999999987653
No 16
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.06 E-value=2.4e-05 Score=83.32 Aligned_cols=92 Identities=24% Similarity=0.424 Sum_probs=67.4
Q ss_pred CCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCccccccccccCCCCcc
Q 047248 62 GLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRP 141 (439)
Q Consensus 62 G~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~n~~G~P~r~ 141 (439)
+.|.-+..|.|.|+-++... +....|.- .-..|..|.| |.|+.|++|.|.|..-+.- | -|.+.
T Consensus 207 ~~shDwteCPf~HpgEkARR----RDPRkyhY--s~tpCPefrk-G~C~rGD~CEyaHgvfEcw------L----HPa~Y 269 (528)
T KOG1595|consen 207 PRSHDWTECPFAHPGEKARR----RDPRKYHY--SSTPCPEFRK-GSCERGDSCEYAHGVFECW------L----HPARY 269 (528)
T ss_pred ccCCCcccCCccCCCccccc----CCcccccc--cCccCccccc-CCCCCCCccccccceehhh------c----CHHHh
Confidence 46777889999997664321 11122222 2457999998 9999999999999976642 1 25566
Q ss_pred cccccccccccccCCCCCCCCCCCCCCCccccc
Q 047248 142 NEIECAYYLRTGQCKFGSTCKFHHPQPNNMMVS 174 (439)
Q Consensus 142 ~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~~~~ 174 (439)
++..|++- |.|++ .-|-|+|....+-.+.
T Consensus 270 RT~~CkDg---~~C~R-rvCfFAH~~eqLR~l~ 298 (528)
T KOG1595|consen 270 RTRKCKDG---GYCPR-RVCFFAHSPEQLRPLP 298 (528)
T ss_pred ccccccCC---CCCcc-ceEeeecChHHhcccC
Confidence 88899985 89999 9999999988765443
No 17
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.64 E-value=3.1e-05 Score=50.06 Aligned_cols=25 Identities=40% Similarity=1.060 Sum_probs=21.9
Q ss_pred CCccchhhhhcCCCCCCCCcccCCCC
Q 047248 303 GQPECQFYMKTGDCKFGAVCRFHHPR 328 (439)
Q Consensus 303 ~~~~C~~y~ktG~C~~G~~Ckf~Hp~ 328 (439)
++.+|++| ++|.|++|++|+|.|..
T Consensus 3 k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 3 KTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 45689999 77999999999999963
No 18
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.54 E-value=5.9e-05 Score=48.75 Aligned_cols=25 Identities=32% Similarity=1.055 Sum_probs=21.5
Q ss_pred CCcCccchhhcCCCCCCCCCCCCCCC
Q 047248 51 GEPDCSYYIRTGLCRFGATCRFNHPP 76 (439)
Q Consensus 51 g~~~C~yy~rtG~C~~Gd~CkF~H~~ 76 (439)
++.+|++| ++|.|.+|++|+|.|+.
T Consensus 3 k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 3 KTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 45689999 56999999999999973
No 19
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.25 E-value=0.00027 Score=75.54 Aligned_cols=55 Identities=22% Similarity=0.463 Sum_probs=39.8
Q ss_pred cCCCCCCCCCCCCCCCCcCccccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCC
Q 047248 107 GTCKFGATCKFHHPRDKAGIAGRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPN 169 (439)
Q Consensus 107 G~Ck~G~~CkF~H~~~~~~~~~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~ 169 (439)
+.|.-+.+|.|.|+-++.+--....+.. .-..|+.|. +|.|+.|+.|.|.|...+
T Consensus 207 ~~shDwteCPf~HpgEkARRRDPRkyhY-------s~tpCPefr-kG~C~rGD~CEyaHgvfE 261 (528)
T KOG1595|consen 207 PRSHDWTECPFAHPGEKARRRDPRKYHY-------SSTPCPEFR-KGSCERGDSCEYAHGVFE 261 (528)
T ss_pred ccCCCcccCCccCCCcccccCCcccccc-------cCccCcccc-cCCCCCCCccccccceeh
Confidence 4677778999999766654222222222 234799998 699999999999997764
No 20
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=97.22 E-value=0.00012 Score=77.43 Aligned_cols=58 Identities=33% Similarity=0.782 Sum_probs=46.9
Q ss_pred Cccchhhhhc--CCCCCCCCcccCCCCCcCCCCCCcccCCCCCCCCCCCcCCcccccccCCCCCCCCCCC
Q 047248 304 QPECQFYMKT--GDCKFGAVCRFHHPRERLLPVPDCVLSPIGLPLRPGEPLCIFYSRYGICKFGPSCKFD 371 (439)
Q Consensus 304 ~~~C~~y~kt--G~C~~G~~Ckf~Hp~~~~~~~~~~~l~~~g~p~r~~~~~C~~Y~~~G~Ck~G~~CkF~ 371 (439)
..+|.-...+ -.|+||++|||.|+.+....+.. -.+| ..|.+|...|+|+||-+|+|.
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~---~Dig-------~~Cp~f~s~G~Cp~G~~CRFl 135 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKA---PDIG-------PSCPVFESLGFCPYGFKCRFL 135 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHHhccC---cccC-------CccceeeccccCCccceeehh
Confidence 4679998887 57999999999999987644422 1222 589999999999999999995
No 21
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.20 E-value=7.8e-05 Score=74.43 Aligned_cols=75 Identities=23% Similarity=0.578 Sum_probs=51.3
Q ss_pred CCCCCCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCC-----------------------CCCCccccc
Q 047248 46 LPERPGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPE-----------------------RVGQPECQY 102 (439)
Q Consensus 46 ~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Pe-----------------------r~~~p~C~~ 102 (439)
--+.|...+|.||.. |.|..|+.|+|+|+........ ....|+. .....+|+|
T Consensus 86 ~gvDPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~e---K~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKf 161 (343)
T KOG1763|consen 86 KGVDPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKKE---KIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKF 161 (343)
T ss_pred cCCCchHHHHHHHhc-cCCCCCCcccccchHHHhhhcc---chhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHH
Confidence 345577789999986 9999999999999976432111 1112221 113358999
Q ss_pred ccc------cc---CCCCCC-CCCCCCCCCCc
Q 047248 103 YLK------TG---TCKFGA-TCKFHHPRDKA 124 (439)
Q Consensus 103 f~k------tG---~Ck~G~-~CkF~H~~~~~ 124 (439)
|+- .| .|.+|. .|.|.|-....
T Consensus 162 FLeAvE~~kYGWfW~CPnGg~~C~YrHaLP~G 193 (343)
T KOG1763|consen 162 FLEAVENGKYGWFWECPNGGDKCIYRHALPEG 193 (343)
T ss_pred HHHHHhcCCccceeECCCCCCeeeeeecCCcc
Confidence 985 12 699887 89999986543
No 22
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=96.89 E-value=0.00018 Score=71.91 Aligned_cols=80 Identities=26% Similarity=0.647 Sum_probs=52.8
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCCCCcCccccccc-------------------cccCCCCcccccccccccc--
Q 047248 93 ERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSL-------------------NVLGYPLRPNEIECAYYLR-- 151 (439)
Q Consensus 93 er~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~-------------------n~~G~P~r~~~~~C~~y~~-- 151 (439)
..++..+|.||.. |.|..|+.|+|+|+....+...-..+ ...|-|.-....+|.||+.
T Consensus 88 vDPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeAv 166 (343)
T KOG1763|consen 88 VDPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEAV 166 (343)
T ss_pred CCchHHHHHHHhc-cCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHHH
Confidence 3446779999998 99999999999998665432211111 1112121223458999872
Q ss_pred ----cc---cCCCCC-CCCCCCCCCCcccc
Q 047248 152 ----TG---QCKFGS-TCKFHHPQPNNMMV 173 (439)
Q Consensus 152 ----~G---~C~~G~-~CkF~Hp~~~~~~~ 173 (439)
.| .|++|. .|.|.|-.+..+.+
T Consensus 167 E~~kYGWfW~CPnGg~~C~YrHaLP~GyVL 196 (343)
T KOG1763|consen 167 ENGKYGWFWECPNGGDKCIYRHALPEGYVL 196 (343)
T ss_pred hcCCccceeECCCCCCeeeeeecCCcchhh
Confidence 22 299976 79999999887643
No 23
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=96.89 E-value=0.00046 Score=73.25 Aligned_cols=59 Identities=31% Similarity=0.667 Sum_probs=46.4
Q ss_pred CcCccchhhc--CCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCC
Q 047248 52 EPDCSYYIRT--GLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHH 119 (439)
Q Consensus 52 ~~~C~yy~rt--G~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H 119 (439)
..+|.-...+ ..|.||++|+|.|+++.-.+.... . -.+.|.+|...|.|.||-.|+|+-
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~--------D-ig~~Cp~f~s~G~Cp~G~~CRFl~ 136 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAP--------D-IGPSCPVFESLGFCPYGFKCRFLG 136 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHHhccCc--------c-cCCccceeeccccCCccceeehhh
Confidence 4689999886 589999999999998764332111 1 136799999999999999999974
No 24
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.56 E-value=0.001 Score=69.15 Aligned_cols=57 Identities=33% Similarity=0.695 Sum_probs=40.9
Q ss_pred CCCCCCCCCCCchhhh-----h------hhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCC
Q 047248 66 FGATCRFNHPPNRKLA-----I------ATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDK 123 (439)
Q Consensus 66 ~Gd~CkF~H~~~~~~~-----~------~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~ 123 (439)
-|++|.+-|.-.+..- + ...+..-.+|..-.+.+|.||+. |.|+|+++|+|+|...-
T Consensus 98 ~GsKcsaph~ss~gl~yHna~I~g~E~sarvRVlfl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V 165 (486)
T KOG2185|consen 98 DGSKCSAPHTSSRGLYYHNARIIGFEGSARVRVLFLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLDV 165 (486)
T ss_pred cCCcccccccCCccceecceeEEeeccccceEEEeecCcchhhccchHhhc-cccccCcccccccCccc
Confidence 5888888887665411 0 01122234677778899999998 99999999999998653
No 25
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=96.54 E-value=0.0032 Score=68.88 Aligned_cols=100 Identities=26% Similarity=0.580 Sum_probs=60.4
Q ss_pred cCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCC-----CCCCCCCCCCcCcc
Q 047248 53 PDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGA-----TCKFHHPRDKAGIA 127 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~-----~CkF~H~~~~~~~~ 127 (439)
.+|+||.. |. +..|.|.|+....+. .-+|...-...|.+-.. .|+||. .|.|.|......+.
T Consensus 545 ~~Cky~~~---Ct-~a~Ce~~HPtaa~~~-------~s~p~k~fa~~~~ks~p--~Ck~~~kCtasDC~~sH~~~~~pvq 611 (681)
T KOG3702|consen 545 TRCKYGPA---CT-SAECEFAHPTAAENA-------KSLPNKKFASKCLKSHP--GCKFGKKCTASDCNYSHAGRRIPVQ 611 (681)
T ss_pred ccccCCCc---CC-chhhhhcCCcchhhh-------hccccccccccceeccc--ccccccccccccCcccccCCCCCCc
Confidence 58999976 98 899999999765321 11222222334555543 566554 67899987654111
Q ss_pred ccccccccCCCCcccccccccccccccCCCCCCCCCCCCCCCcc
Q 047248 128 GRVSLNVLGYPLRPNEIECAYYLRTGQCKFGSTCKFHHPQPNNM 171 (439)
Q Consensus 128 ~~v~~n~~G~P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~ 171 (439)
...+- .-++......+|+|+ +.|++ ..|+|.||+....
T Consensus 612 -~t~ip-~~~~~~ti~~~CrY~---pnCrn-m~C~F~HPk~cRf 649 (681)
T KOG3702|consen 612 -PTRIP-PPFPGGTIRGLCRYR---PNCRN-MQCKFYHPKTCRF 649 (681)
T ss_pred -cccCC-CCCCCCCccccceec---cCcCC-ccccccCCccccc
Confidence 00000 000112235579986 58998 8999999998754
No 26
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.30 E-value=0.0023 Score=39.03 Aligned_cols=19 Identities=37% Similarity=0.996 Sum_probs=17.0
Q ss_pred CccchhhcCCCCCCCCCCCCCC
Q 047248 54 DCSYYIRTGLCRFGATCRFNHP 75 (439)
Q Consensus 54 ~C~yy~rtG~C~~Gd~CkF~H~ 75 (439)
+|+||.. |++|++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 5999965 999999999996
No 27
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.09 E-value=0.0045 Score=65.62 Aligned_cols=103 Identities=17% Similarity=0.232 Sum_probs=66.9
Q ss_pred CCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCc-c-
Q 047248 50 PGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGI-A- 127 (439)
Q Consensus 50 pg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~-~- 127 (439)
....+|++|+..-.|+. .|+|.|..-... .....|.|+.+.-.|. ..+|-|.|....+.- .
T Consensus 30 ~n~t~C~~w~~~~~C~k--~C~YRHSe~~~k--------------r~e~~CYwe~~p~gC~-k~~CgfRH~~pPLkg~l~ 92 (667)
T KOG4791|consen 30 GNETVCTLWQEGRCCRK--VCRYRHSEIDKK--------------RSEIPCYWENQPTGCQ-KLNCGFRHNRPPLKGVLP 92 (667)
T ss_pred cCcchhhhhhhcCcccc--cccchhhHHhhh--------------cCcccceeecCCCccC-CCccccccCCCchhhhcc
Confidence 44578999998666665 899999743211 1345799999933499 789999996533321 1
Q ss_pred -----ccccccccCC---C--CcccccccccccccccCCCCCCCCCCCCCCCc
Q 047248 128 -----GRVSLNVLGY---P--LRPNEIECAYYLRTGQCKFGSTCKFHHPQPNN 170 (439)
Q Consensus 128 -----~~v~~n~~G~---P--~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~ 170 (439)
+.++...... + ..-....|-+++ .+.|..++.|-|.|+.+..
T Consensus 93 ~~p~~pe~ev~~~~~SAq~~sV~~~p~P~l~~~-K~~e~~~D~~s~Lh~P~A~ 144 (667)
T KOG4791|consen 93 TVPESPEEEVKASQLSAQQNSVQSNPSPQLRSV-KKVESSEDVPSPLHPPVAI 144 (667)
T ss_pred CCCCCcccccccccccCCCcccccCCchHHHHh-hhhhhhccccccCCCCccc
Confidence 1111100000 0 111245799998 8999999999999998654
No 28
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.03 E-value=0.0017 Score=63.38 Aligned_cols=78 Identities=21% Similarity=0.517 Sum_probs=52.4
Q ss_pred CCCCCCCCcCccchhhcCCCCCCCCCCCCCCCchhhhhhhh------h-cc--CCCCCCC---CCcccccccc---cc--
Q 047248 45 SLPERPGEPDCSYYIRTGLCRFGATCRFNHPPNRKLAIATA------R-IK--GDYPERV---GQPECQYYLK---TG-- 107 (439)
Q Consensus 45 ~~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~~~~~~~------~-~~--~e~Per~---~~p~C~~f~k---tG-- 107 (439)
.--+.|...+|..|+. +.|..|+.|+|+|..+........ + .. ....+|+ ...+|+||+- +|
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 4445678899999986 999999999999997643211110 1 01 1122333 3458999975 23
Q ss_pred ----CCCCCC-CCCCCCCCCC
Q 047248 108 ----TCKFGA-TCKFHHPRDK 123 (439)
Q Consensus 108 ----~Ck~G~-~CkF~H~~~~ 123 (439)
.|.+|. .|-|.|....
T Consensus 157 gw~W~CPng~~~C~y~H~Lp~ 177 (299)
T COG5252 157 GWGWTCPNGNMRCSYIHKLPD 177 (299)
T ss_pred cceeeCCCCCceeeeeeccCc
Confidence 699886 9999998665
No 29
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=95.48 E-value=0.0039 Score=60.88 Aligned_cols=80 Identities=28% Similarity=0.657 Sum_probs=53.4
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCCCCcCcccccccc------ccCCCC--cc---cccccccccc---cc-----
Q 047248 93 ERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLN------VLGYPL--RP---NEIECAYYLR---TG----- 153 (439)
Q Consensus 93 er~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~n------~~G~P~--r~---~~~~C~~y~~---~G----- 153 (439)
..++..+|..|+. +.|..|+.|+|+|.....+...-..+. ....|+ +| ...+|.||.. +|
T Consensus 81 vdpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~ 159 (299)
T COG5252 81 VDPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWG 159 (299)
T ss_pred cCchhHHHHHhcc-CccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccce
Confidence 3456789999998 999999999999997655432211111 111222 22 3568999862 23
Q ss_pred -cCCCC-CCCCCCCCCCCcccc
Q 047248 154 -QCKFG-STCKFHHPQPNNMMV 173 (439)
Q Consensus 154 -~C~~G-~~CkF~Hp~~~~~~~ 173 (439)
.|++| .+|.|.|-.+..+.+
T Consensus 160 W~CPng~~~C~y~H~Lp~GyVL 181 (299)
T COG5252 160 WTCPNGNMRCSYIHKLPDGYVL 181 (299)
T ss_pred eeCCCCCceeeeeeccCcccee
Confidence 29997 479999999886644
No 30
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.45 E-value=0.0095 Score=36.28 Aligned_cols=19 Identities=37% Similarity=1.023 Sum_probs=16.4
Q ss_pred cccccccccCCCCCCCCCCCCC
Q 047248 99 ECQYYLKTGTCKFGATCKFHHP 120 (439)
Q Consensus 99 ~C~~f~ktG~Ck~G~~CkF~H~ 120 (439)
.|+||. .|+++++|.|.|+
T Consensus 1 ~Ck~~~---~C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGP---NCTNGDNCPFSHP 19 (19)
T ss_pred CCcCcC---CCCCCCcCccCCc
Confidence 489886 4999999999996
No 31
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=95.14 E-value=0.0097 Score=62.10 Aligned_cols=33 Identities=33% Similarity=0.882 Sum_probs=28.6
Q ss_pred CCCCCCCCcCccchhhcCCCCCCCCCCCCCCCch
Q 047248 45 SLPERPGEPDCSYYIRTGLCRFGATCRFNHPPNR 78 (439)
Q Consensus 45 ~~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~ 78 (439)
.+|....-..|+||+. |.|+||++|+|.|...-
T Consensus 133 l~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V 165 (486)
T KOG2185|consen 133 LTPTHESMKPCKFFLE-GRCRFGENCRFSHGLDV 165 (486)
T ss_pred ecCcchhhccchHhhc-cccccCcccccccCccc
Confidence 5677777789999996 99999999999998753
No 32
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.85 E-value=0.0095 Score=57.00 Aligned_cols=26 Identities=35% Similarity=0.859 Sum_probs=24.1
Q ss_pred cCccchhhcCCCCCCCCCCCCCCCch
Q 047248 53 PDCSYYIRTGLCRFGATCRFNHPPNR 78 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~CkF~H~~~~ 78 (439)
.+|+-|..||.|.|||+|+|+|..+.
T Consensus 142 dVCKdyk~TGYCGYGDsCKflH~R~D 167 (259)
T COG5152 142 DVCKDYKETGYCGYGDSCKFLHDRSD 167 (259)
T ss_pred ccccchhhcccccCCchhhhhhhhhh
Confidence 58999999999999999999999764
No 33
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.54 E-value=0.012 Score=56.25 Aligned_cols=26 Identities=38% Similarity=0.894 Sum_probs=23.9
Q ss_pred ccchhhhhcCCCCCCCCcccCCCCCc
Q 047248 305 PECQFYMKTGDCKFGAVCRFHHPRER 330 (439)
Q Consensus 305 ~~C~~y~ktG~C~~G~~Ckf~Hp~~~ 330 (439)
.+|..|..||+|-|||+|||.|..+.
T Consensus 142 dVCKdyk~TGYCGYGDsCKflH~R~D 167 (259)
T COG5152 142 DVCKDYKETGYCGYGDSCKFLHDRSD 167 (259)
T ss_pred ccccchhhcccccCCchhhhhhhhhh
Confidence 46999999999999999999999873
No 34
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=93.71 E-value=0.11 Score=57.27 Aligned_cols=75 Identities=31% Similarity=0.787 Sum_probs=46.8
Q ss_pred CCCCCC-----CCCCCCCCchhhhhhhhhccCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCccccccccccCC
Q 047248 63 LCRFGA-----TCRFNHPPNRKLAIATARIKGDYPERVGQPECQYYLKTGTCKFGATCKFHHPRDKAGIAGRVSLNVLGY 137 (439)
Q Consensus 63 ~C~~Gd-----~CkF~H~~~~~~~~~~~~~~~e~Per~~~p~C~~f~ktG~Ck~G~~CkF~H~~~~~~~~~~v~~n~~G~ 137 (439)
.|++|. .|.|.|......+. .......++--..+.+|+|+ +.|+ .-.|+|.|++
T Consensus 587 ~Ck~~~kCtasDC~~sH~~~~~pvq-~t~ip~~~~~~ti~~~CrY~---pnCr-nm~C~F~HPk---------------- 645 (681)
T KOG3702|consen 587 GCKFGKKCTASDCNYSHAGRRIPVQ-PTRIPPPFPGGTIRGLCRYR---PNCR-NMQCKFYHPK---------------- 645 (681)
T ss_pred ccccccccccccCcccccCCCCCCc-cccCCCCCCCCCccccceec---cCcC-CccccccCCc----------------
Confidence 455553 35577765553211 11222233323345679988 6788 6789999995
Q ss_pred CCcccccccccccccccCCCCCCCCCCCCCC
Q 047248 138 PLRPNEIECAYYLRTGQCKFGSTCKFHHPQP 168 (439)
Q Consensus 138 P~r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~ 168 (439)
.|+|- -.|.+-..|-|.|+.+
T Consensus 646 -------~cRf~---~~c~~~~sc~fYh~r~ 666 (681)
T KOG3702|consen 646 -------TCRFN---TNCPNNPSCTFYHERP 666 (681)
T ss_pred -------ccccc---ccCCCCcccccccCCc
Confidence 36653 4788668899999876
No 35
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=93.57 E-value=0.03 Score=55.43 Aligned_cols=27 Identities=30% Similarity=0.556 Sum_probs=24.4
Q ss_pred CCCCcCCcccccccCCCCCCCCCCCCCC
Q 047248 347 RPGEPLCIFYSRYGICKFGPSCKFDHPM 374 (439)
Q Consensus 347 r~~~~~C~~Y~~~G~Ck~G~~CkF~HP~ 374 (439)
++++..|..|+++ .|.+|-.|.|.|..
T Consensus 149 ~~rea~C~~~e~~-~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 149 DFREAICGQFERT-ECSRGGACNFMHVK 175 (260)
T ss_pred chhhhhhcccccc-cCCCCCcCcchhhh
Confidence 6788899999955 99999999999997
No 36
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=91.94 E-value=0.061 Score=53.27 Aligned_cols=31 Identities=23% Similarity=0.477 Sum_probs=26.1
Q ss_pred cccccccccccccccCCCCCCCCCCCCCCCcc
Q 047248 140 RPNEIECAYYLRTGQCKFGSTCKFHHPQPNNM 171 (439)
Q Consensus 140 r~~~~~C~~y~~~G~C~~G~~CkF~Hp~~~~~ 171 (439)
++.+..|..|. .+.|.+|..|.|.|......
T Consensus 149 ~~rea~C~~~e-~~~C~rG~~CnFmH~k~~sr 179 (260)
T KOG2202|consen 149 DFREAICGQFE-RTECSRGGACNFMHVKRLSR 179 (260)
T ss_pred chhhhhhcccc-cccCCCCCcCcchhhhhhhH
Confidence 45678899999 55999999999999986544
No 37
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.12 E-value=0.071 Score=53.83 Aligned_cols=25 Identities=36% Similarity=0.885 Sum_probs=23.5
Q ss_pred cCccchhhcCCCCCCCCCCCCCCCc
Q 047248 53 PDCSYYIRTGLCRFGATCRFNHPPN 77 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~CkF~H~~~ 77 (439)
.+|+-|..||.|.|||+|+|+|...
T Consensus 187 DicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 187 DICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred hhhhhhHhhCcccccchhhhhhhhh
Confidence 4899999999999999999999876
No 38
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.12 E-value=0.082 Score=53.41 Aligned_cols=27 Identities=37% Similarity=0.851 Sum_probs=24.2
Q ss_pred ccchhhhhcCCCCCCCCcccCCCCCcC
Q 047248 305 PECQFYMKTGDCKFGAVCRFHHPRERL 331 (439)
Q Consensus 305 ~~C~~y~ktG~C~~G~~Ckf~Hp~~~~ 331 (439)
-+|.-|..||+|-||++|+|.|.....
T Consensus 187 DicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 187 DICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred hhhhhhHhhCcccccchhhhhhhhhhc
Confidence 459999999999999999999988743
No 39
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.56 E-value=0.16 Score=52.59 Aligned_cols=25 Identities=44% Similarity=1.084 Sum_probs=23.3
Q ss_pred ccccccccccCCCCCCCCCCCCCCCC
Q 047248 98 PECQYYLKTGTCKFGATCKFHHPRDK 123 (439)
Q Consensus 98 p~C~~f~ktG~Ck~G~~CkF~H~~~~ 123 (439)
.+|+||++ |.|+||+.|+|.|.+..
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 68999999 99999999999999873
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=86.88 E-value=0.42 Score=30.68 Aligned_cols=23 Identities=43% Similarity=1.032 Sum_probs=19.4
Q ss_pred ccccccccccCCCCCCCCCCCCCC
Q 047248 98 PECQYYLKTGTCKFGATCKFHHPR 121 (439)
Q Consensus 98 p~C~~f~ktG~Ck~G~~CkF~H~~ 121 (439)
++|.|-++.|.|. .+.|.|.|-+
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 4799999966998 7899999953
No 41
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.25 E-value=0.31 Score=50.62 Aligned_cols=25 Identities=40% Similarity=1.014 Sum_probs=23.1
Q ss_pred cCccchhhcCCCCCCCCCCCCCCCch
Q 047248 53 PDCSYYIRTGLCRFGATCRFNHPPNR 78 (439)
Q Consensus 53 ~~C~yy~rtG~C~~Gd~CkF~H~~~~ 78 (439)
.+|+||.+ |.|+||+.|+|.|....
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 79999998 99999999999998763
No 42
>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=81.92 E-value=0.82 Score=29.39 Aligned_cols=21 Identities=38% Similarity=0.844 Sum_probs=18.1
Q ss_pred ccccccccccCCCCCCCCCCCC
Q 047248 145 ECAYYLRTGQCKFGSTCKFHHP 166 (439)
Q Consensus 145 ~C~~y~~~G~C~~G~~CkF~Hp 166 (439)
+|.|-++.|.|.. +.|.|.|-
T Consensus 2 lC~yEl~Gg~Cnd-~~C~~QHf 22 (23)
T PF10650_consen 2 LCPYELTGGVCND-PDCEFQHF 22 (23)
T ss_pred CCccccCCCeeCC-CCCCcccc
Confidence 6999996669987 89999995
No 43
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=81.32 E-value=1.5 Score=45.52 Aligned_cols=31 Identities=29% Similarity=0.741 Sum_probs=25.9
Q ss_pred CCCCCCCcCccchhhcCCCCCCCCCCCCCCCc
Q 047248 46 LPERPGEPDCSYYIRTGLCRFGATCRFNHPPN 77 (439)
Q Consensus 46 ~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~ 77 (439)
|-.|..-.+|.||.+ |.|++|+.|.|+|...
T Consensus 155 ~ykrn~p~Icsf~v~-geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 155 YYKRNRPHICSFFVK-GECKRGAECPYRHEKP 185 (377)
T ss_pred cccCCCCccccceee-ccccccccccccccCC
Confidence 434555579999998 8999999999999876
No 44
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=64.21 E-value=4.1 Score=42.34 Aligned_cols=29 Identities=34% Similarity=0.880 Sum_probs=24.8
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCCCC
Q 047248 93 ERVGQPECQYYLKTGTCKFGATCKFHHPRD 122 (439)
Q Consensus 93 er~~~p~C~~f~ktG~Ck~G~~CkF~H~~~ 122 (439)
+|..-.+|-||.+ |.||+|++|.|.|.+.
T Consensus 157 krn~p~Icsf~v~-geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 157 KRNRPHICSFFVK-GECKRGAECPYRHEKP 185 (377)
T ss_pred cCCCCccccceee-ccccccccccccccCC
Confidence 4444568999999 8999999999999877
No 45
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=43.17 E-value=7.1 Score=25.87 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=5.8
Q ss_pred CCCCCCCCC
Q 047248 361 ICKFGPSCK 369 (439)
Q Consensus 361 ~Ck~G~~Ck 369 (439)
.|+||.+|.
T Consensus 2 ~C~YG~~CY 10 (26)
T PF10283_consen 2 PCKYGAKCY 10 (26)
T ss_dssp E-TTGGG-S
T ss_pred CCCcchhhh
Confidence 499999995
No 46
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=28.87 E-value=26 Score=38.07 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=31.9
Q ss_pred CCCCCCCCCCcCccchhhcCCCCCCCCCCCCCCCchh
Q 047248 43 SGSLPERPGEPDCSYYIRTGLCRFGATCRFNHPPNRK 79 (439)
Q Consensus 43 ~~~~p~Rpg~~~C~yy~rtG~C~~Gd~CkF~H~~~~~ 79 (439)
-+.+..|..+..|++|-++|.|.+|+.|++.|..+..
T Consensus 203 tgp~ks~~s~~r~k~fee~g~~~r~el~p~~hg~~~v 239 (526)
T KOG2135|consen 203 TGPEKSRNSENRRKFFEEFGVLERGELCPTHHGCVPV 239 (526)
T ss_pred cCcccccccHHhhhhhHhhceeeecccccccccccee
Confidence 3466777778899999999999999999999987653
Done!