Query 013033
Match_columns 451
No_of_seqs 366 out of 1872
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 23:44:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013033.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013033hhsearch_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 4.1E-23 9E-28 209.2 16.6 122 41-163 77-203 (332)
2 KOG1677 CCCH-type Zn-finger pr 99.7 7.1E-17 1.5E-21 163.8 8.2 79 279-359 125-204 (332)
3 KOG1040 Polyadenylation factor 99.4 4.7E-13 1E-17 135.5 7.0 85 47-162 74-158 (325)
4 KOG1492 C3H1-type Zn-finger pr 99.3 6.3E-13 1.4E-17 126.8 3.5 82 46-161 202-283 (377)
5 KOG2494 C3H1-type Zn-finger pr 99.3 5.4E-12 1.2E-16 126.1 6.8 214 93-359 38-256 (331)
6 KOG1040 Polyadenylation factor 99.1 4.8E-11 1E-15 121.1 6.6 88 47-162 42-130 (325)
7 COG5063 CTH1 CCCH-type Zn-fing 99.1 1.7E-10 3.8E-15 114.1 9.9 194 49-363 114-345 (351)
8 COG5063 CTH1 CCCH-type Zn-fing 99.1 1.4E-10 3.1E-15 114.7 7.8 179 91-358 114-300 (351)
9 KOG2494 C3H1-type Zn-finger pr 98.6 5.4E-08 1.2E-12 97.7 6.0 101 51-163 38-155 (331)
10 COG5084 YTH1 Cleavage and poly 98.6 4E-07 8.8E-12 90.9 11.7 88 49-163 73-160 (285)
11 PF00642 zf-CCCH: Zinc finger 98.5 2.7E-08 5.9E-13 65.4 1.0 27 284-310 1-27 (27)
12 COG5084 YTH1 Cleavage and poly 98.5 1.2E-07 2.6E-12 94.7 5.6 88 48-163 102-191 (285)
13 KOG1492 C3H1-type Zn-finger pr 98.5 6.8E-08 1.5E-12 92.6 2.5 83 49-163 232-314 (377)
14 PF00642 zf-CCCH: Zinc finger 98.4 5.3E-08 1.2E-12 64.0 -0.3 27 330-356 1-27 (27)
15 KOG1595 CCCH-type Zn-finger pr 98.2 2.4E-05 5.3E-10 83.3 13.2 58 287-359 237-294 (528)
16 KOG4791 Uncharacterized conser 98.1 2.1E-06 4.6E-11 89.8 4.6 83 51-163 4-86 (667)
17 KOG1595 CCCH-type Zn-finger pr 98.1 1.5E-05 3.3E-10 84.8 10.4 86 60-163 207-293 (528)
18 smart00356 ZnF_C3H1 zinc finge 97.8 1.5E-05 3.3E-10 51.5 2.4 26 330-356 2-27 (27)
19 KOG2333 Uncharacterized conser 97.7 1.4E-05 3.1E-10 84.2 2.8 61 285-355 75-137 (614)
20 smart00356 ZnF_C3H1 zinc finge 97.7 1.8E-05 3.9E-10 51.1 2.1 25 284-309 2-26 (27)
21 KOG4791 Uncharacterized conser 97.7 2.1E-05 4.6E-10 82.4 2.4 53 92-162 3-55 (667)
22 KOG1763 Uncharacterized conser 97.6 1.4E-05 2.9E-10 79.5 -0.2 76 42-118 84-192 (343)
23 KOG2333 Uncharacterized conser 97.4 4.9E-05 1.1E-09 80.3 1.2 63 92-163 76-140 (614)
24 KOG1763 Uncharacterized conser 97.1 0.00011 2.4E-09 73.2 0.2 74 283-357 89-191 (343)
25 COG5252 Uncharacterized conser 96.7 0.00042 9.2E-09 67.3 0.3 74 283-357 82-176 (299)
26 KOG2185 Predicted RNA-processi 96.3 0.0018 3.9E-08 67.2 2.1 32 86-118 134-165 (486)
27 KOG3702 Nuclear polyadenylated 96.1 0.012 2.6E-07 64.5 7.2 103 51-168 545-652 (681)
28 COG5252 Uncharacterized conser 96.1 0.0019 4.2E-08 62.8 0.9 75 43-118 78-177 (299)
29 KOG2185 Predicted RNA-processi 96.0 0.0043 9.4E-08 64.5 2.9 56 106-162 98-164 (486)
30 PF14608 zf-CCCH_2: Zinc finge 95.9 0.0051 1.1E-07 37.2 1.6 19 94-115 1-19 (19)
31 PF14608 zf-CCCH_2: Zinc finge 95.6 0.0072 1.6E-07 36.6 1.6 19 52-73 1-19 (19)
32 KOG3702 Nuclear polyadenylated 94.6 0.096 2.1E-06 57.7 7.7 23 92-118 544-566 (681)
33 COG5152 Uncharacterized conser 94.5 0.014 3E-07 55.7 0.8 26 51-76 142-167 (259)
34 COG5152 Uncharacterized conser 94.4 0.014 3E-07 55.7 0.7 27 333-359 142-168 (259)
35 KOG1039 Predicted E3 ubiquitin 90.6 0.092 2E-06 54.4 0.6 25 93-118 9-33 (344)
36 KOG2202 U2 snRNP splicing fact 89.3 0.11 2.4E-06 51.4 0.1 29 328-357 148-176 (260)
37 KOG1813 Predicted E3 ubiquitin 88.7 0.14 2.9E-06 51.8 0.2 25 51-75 187-211 (313)
38 KOG1813 Predicted E3 ubiquitin 88.7 0.13 2.8E-06 52.0 -0.0 26 334-359 188-213 (313)
39 KOG2202 U2 snRNP splicing fact 88.6 0.13 2.8E-06 51.0 -0.1 29 134-163 149-177 (260)
40 PF10650 zf-C3H1: Putative zin 87.6 0.31 6.7E-06 31.0 1.2 22 93-115 1-22 (23)
41 KOG1039 Predicted E3 ubiquitin 85.7 0.3 6.5E-06 50.7 0.6 25 138-163 9-33 (344)
42 PF10650 zf-C3H1: Putative zin 80.5 1.3 2.9E-05 28.2 1.8 22 138-160 1-22 (23)
43 KOG0153 Predicted RNA-binding 77.8 1.8 4E-05 44.8 2.9 29 46-75 157-185 (377)
44 KOG0153 Predicted RNA-binding 66.4 3.6 7.9E-05 42.7 2.0 29 88-117 157-185 (377)
45 PF10283 zf-CCHH: Zinc-finger 26.4 20 0.00044 23.5 -0.1 11 297-307 2-12 (26)
46 KOG3454 U1 snRNP-specific prot 23.7 5E+02 0.011 24.5 8.3 27 140-166 55-81 (165)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.90 E-value=4.1e-23 Score=209.24 Aligned_cols=122 Identities=44% Similarity=0.906 Sum_probs=104.1
Q ss_pred CCCCCCCCCCcCCccccccCCCCCCCCCCCCCch-hhhc-cc--cccccCCCCccccccccccccccCCC-CCCCCCCCC
Q 013033 41 ASPYPARPGEPDCLFYRRTGLCGYGSNCRFNHPA-YAAQ-GA--QYREELPERNGQPDCGYYLKTGTCKY-GSTCKYHHP 115 (451)
Q Consensus 41 ~~~~p~rpg~~~C~~f~rtG~C~~G~~C~F~H~~-~~~~-~~--~~~~~~Per~~~p~C~~FlktG~Ck~-G~~CrF~H~ 115 (451)
...|+++..+.+|.+|.+++.|.++..|+|+|+. .... .. ......+++.++++|++|.++|.|+| |++|+|+|.
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~ 156 (332)
T KOG1677|consen 77 SSPYPERSGEGDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVRRSRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHG 156 (332)
T ss_pred cCcCCCCCCccccccccccCCCCCCCCCCccCcccccccCCccccccccCcccccCCcceeeecCccccccCchhhhcCC
Confidence 4569999998999999999999999999999996 3222 21 35577899999999999999999999 999999999
Q ss_pred CCCCCCCCceecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 116 KDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 116 ~~~~~~~~~~~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
........ .++..+.+.+.++++|.+|.++|.|+||.+|+|.|+...
T Consensus 157 ~~e~r~~~-~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~ 203 (332)
T KOG1677|consen 157 LEELRLPS-SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPE 203 (332)
T ss_pred cccccccc-cchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcc
Confidence 88654221 345677888999999999999999999999999999875
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.67 E-value=7.1e-17 Score=163.77 Aligned_cols=79 Identities=34% Similarity=0.777 Sum_probs=69.6
Q ss_pred CCCCCCCCccccchhccccccC-CCCCccCCcchhhhccccccCCCCCCCCCCCCcCCccccccccCCCCCCCccCCCCC
Q 013033 279 NLPERPDQPDCRYYMNTGTCKY-GADCKFHHPKERIAQSAASNIGPLGLPSRPGQAICSNYSMYGICKFGPTCRFDHPYA 357 (451)
Q Consensus 279 ~~p~r~~~~lC~~f~~tG~C~~-G~~Ckf~H~~~~l~~~~~~~l~p~~~p~r~~t~~C~~y~~~G~CkfG~~C~F~H~~~ 357 (451)
..++++++++|++|+++|.|+| |++|||+|+.++++... .+...+++.++||++|.+|.++|.|+||.+|+|+|+..
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 4567789999999999999999 99999999999998532 23456688999999999999999999999999999987
Q ss_pred CC
Q 013033 358 GY 359 (451)
Q Consensus 358 ~~ 359 (451)
..
T Consensus 203 ~~ 204 (332)
T KOG1677|consen 203 ED 204 (332)
T ss_pred cc
Confidence 44
No 3
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.39 E-value=4.7e-13 Score=135.54 Aligned_cols=85 Identities=31% Similarity=0.706 Sum_probs=69.3
Q ss_pred CCCCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCcee
Q 013033 47 RPGEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSF 126 (451)
Q Consensus 47 rpg~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~ 126 (451)
-.++++|+||++ |.|+.||.|.|+|..+.. +.+.|.||..+|.|..+++|.|.|.....
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~~~~-------------k~rec~ff~~~g~c~~~~~c~y~h~dpqt------- 132 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHEYDLT-------------KMRECKFFSLFGECTNGKDCPYLHGDPQT------- 132 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhhhhhc-------------ccccccccccccccccccCCcccCCChhh-------
Confidence 567889999997 999999999999987543 44679999889999988999999987421
Q ss_pred cccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 013033 127 NILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQP 162 (451)
Q Consensus 127 ~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~ 162 (451)
..++|..|.. |+|+.|..|++.|...
T Consensus 133 ---------~~k~c~~~~~-g~c~~g~~c~~~h~~~ 158 (325)
T KOG1040|consen 133 ---------AIKKCKWYKE-GFCRGGPSCKKRHERK 158 (325)
T ss_pred ---------hhhccchhhh-ccCCCcchhhhhhhcc
Confidence 2366998886 9999999999998853
No 4
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=99.33 E-value=6.3e-13 Score=126.79 Aligned_cols=82 Identities=29% Similarity=0.786 Sum_probs=69.4
Q ss_pred CCCCCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCce
Q 013033 46 ARPGEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVS 125 (451)
Q Consensus 46 ~rpg~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~ 125 (451)
..|..+.|+||..+|.|.+|..|+|.|...+. .+|..|+ +|.|...+.|..+|..+..
T Consensus 202 nspsavycryynangicgkgaacrfvheptrk---------------ticpkfl-ngrcnkaedcnlsheldpr------ 259 (377)
T KOG1492|consen 202 NSPSAVYCRYYNANGICGKGAACRFVHEPTRK---------------TICPKFL-NGRCNKAEDCNLSHELDPR------ 259 (377)
T ss_pred CCCceeEEEEecCCCcccCCceeeeecccccc---------------ccChHHh-cCccCchhcCCcccccCcc------
Confidence 34567889999999999999999999987643 4699999 5999999999999988742
Q ss_pred ecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCC
Q 013033 126 FNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQ 161 (451)
Q Consensus 126 ~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~ 161 (451)
..+.|+||+- |.|. ..+|||.|..
T Consensus 260 ----------ripacryfll-gkcn-npncryvhih 283 (377)
T KOG1492|consen 260 ----------RIPACRYFLL-GKCN-NPNCRYVHIH 283 (377)
T ss_pred ----------ccchhhhhhh-ccCC-CCCceEEEEe
Confidence 2356999995 9997 7999999984
No 5
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=99.27 E-value=5.4e-12 Score=126.05 Aligned_cols=214 Identities=23% Similarity=0.462 Sum_probs=131.1
Q ss_pred cccccccccccCCCCCC-CCCCCCCCCCCCCCceecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCcCC
Q 013033 93 PDCGYYLKTGTCKYGST-CKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPSSLGTALPL 171 (451)
Q Consensus 93 p~C~~FlktG~Ck~G~~-CrF~H~~~~~~~~~~~~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~~~g~~~p~ 171 (451)
.+||.|+| |.|++|++ |||.|+....... ..+...|.+|++ |.|. .++|||.|+..... .++.+
T Consensus 38 eVCReF~r-n~C~R~d~~CkfaHP~~~~~V~-----------~g~v~aC~Ds~k-grCs-R~nCkylHpp~hlk-dql~i 102 (331)
T KOG2494|consen 38 EVCREFLR-NTCSRGDRECKFAHPPKNCQVS-----------NGRVIACFDSQK-GRCS-RENCKYLHPPQHLK-DQLKI 102 (331)
T ss_pred HHHHHHHh-ccccCCCccccccCCCCCCCcc-----------CCeEEEEecccc-CccC-cccceecCCChhhh-hhhhh
Confidence 57999998 99999998 9999998753322 123357999997 9998 58899999988743 36666
Q ss_pred CCCCCCCCCCC-CcCCCCCCCCCCCCCcccccCCCCcCcCcCCCccccccc-cCCCCCccCCCCCCCCCCCCC-CCCCCC
Q 013033 172 TGNASLGSMGS-SVLPSSGLQYAGSLPTWSLQRAPYLSSRLQGTQSYMPLI-VSPSQGIVPAPGWNTYMGNIG-PLSPTS 248 (451)
Q Consensus 172 ~~~~~~~~~~~-~~~p~s~~~~~~~~~~~~~~r~~~i~~~~q~p~~y~p~~-~~p~~g~vp~~~w~~y~~~~~-p~~~~~ 248 (451)
++......... ..+....++. .+.+.-. +|++ +.|..+-++...+++|+..+. +..++.
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 66533110000 0011111110 0111111 1111 234456666666777777542 344555
Q ss_pred CCCCCcccccCCCCCCccccchhhhccccCCCCCCCCCccccchhccccccCCCC-CccCCcchhhhccccccCCCCCCC
Q 013033 249 IAGSNLIYSSRNQGDLGAGAQMHILSASSQNLPERPDQPDCRYYMNTGTCKYGAD-CKFHHPKERIAQSAASNIGPLGLP 327 (451)
Q Consensus 249 ~~~~~~~y~~~~~~~~~~~~~~~~~s~~~~~~p~r~~~~lC~~f~~tG~C~~G~~-Ckf~H~~~~l~~~~~~~l~p~~~p 327 (451)
++...++|..........+ ....+......+.++|+. ..|.|..++. |+|.|+.+.+......
T Consensus 165 ~~p~~~~~~~g~p~v~~~~------~~~~~k~~r~~~~e~~~~--~~gn~~r~e~d~~f~~~~k~~~~~s~~-------- 228 (331)
T KOG2494|consen 165 GLPTTPVFVPGGPGVPGPG------LVGGQKLLRSDRLEVCRE--QRGNCRRGEQDAQFAHPAKSIMIDSND-------- 228 (331)
T ss_pred CCCCCccccCCCCcccccc------cccccccccCCCCCCCcc--cccccccchhHHHHhhhhhhhhcccCC--------
Confidence 5666666654433111111 012345556677889998 4688999884 9999998887665431
Q ss_pred CCCCCcCCccccccccCCCCCCCccCCCCCCC
Q 013033 328 SRPGQAICSNYSMYGICKFGPTCRFDHPYAGY 359 (451)
Q Consensus 328 ~r~~t~~C~~y~~~G~CkfG~~C~F~H~~~~~ 359 (451)
.-..+|.-|.+ |.|- -++|++.|+....
T Consensus 229 --~t~~~~~~~t~-~~~~-~en~~~~~~~~h~ 256 (331)
T KOG2494|consen 229 --NTVEVCLRYTK-GRCE-TENCKYFHAPAHD 256 (331)
T ss_pred --Ccchhcccccc-ceec-hhcccccCchHHH
Confidence 12458888887 9997 7789999997643
No 6
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.15 E-value=4.8e-11 Score=121.07 Aligned_cols=88 Identities=27% Similarity=0.687 Sum_probs=69.3
Q ss_pred CCCCcCCcccccc-CCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCce
Q 013033 47 RPGEPDCLFYRRT-GLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVS 125 (451)
Q Consensus 47 rpg~~~C~~f~rt-G~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~ 125 (451)
|-+...|.++.+. -.|.+|..|.+.|.... +..+..+|+||++ |.|+.|+.|-|+|..+..
T Consensus 42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~vcK~~l~-glC~kgD~C~Flhe~~~~------ 103 (325)
T KOG1040|consen 42 ESGRATCEFNESREKPCERGPICPKSHNDVS-----------DSRGKVVCKHWLR-GLCKKGDQCEFLHEYDLT------ 103 (325)
T ss_pred ccccchhcccccCCCCccCCCCCccccCCcc-----------ccCCceeehhhhh-hhhhccCcCcchhhhhhc------
Confidence 3345678887732 35889999999998742 1125678999997 999999999999987432
Q ss_pred ecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 013033 126 FNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQP 162 (451)
Q Consensus 126 ~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~ 162 (451)
+.++|.||..+|.|..|..|.|.|.++
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 235699999999999999999999965
No 7
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.14 E-value=1.7e-10 Score=114.08 Aligned_cols=194 Identities=15% Similarity=0.255 Sum_probs=132.2
Q ss_pred CCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCC------
Q 013033 49 GEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAG------ 122 (451)
Q Consensus 49 g~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~------ 122 (451)
+++.|+.-...+.|++++.|.|+|...+..- ...+.+.++.-|..|+.-|.|.++.+|-|.|-.-.....
T Consensus 114 kt~~l~ss~~~~~~~~p~~n~fahs~~issl----~~~~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~~q~l~~r 189 (351)
T COG5063 114 KTEMLRSSTEIPYCRYPDKNPFAHSKAISSL----AQTHPKYKTESLEVFINPGYVPYSKRCCFISLPLTDINLQPLSQR 189 (351)
T ss_pred cchhhhccccccccccCCCCcCCCccccccc----cccCccccccceeEEecCCccccccccccccccccccCcchhhcc
Confidence 3456665433489999999999999764321 223445566779999988999999999998854322110
Q ss_pred -C-ce---------ecccCCC--------------CCC-CCCCCCCCCCCCcCCC---CCCCCCC---CCCCCCCCCCcC
Q 013033 123 -P-VS---------FNILGLP--------------MRQ-DEKSCPYYMRTGSCKF---GVACKFH---HPQPSSLGTALP 170 (451)
Q Consensus 123 -~-~~---------~~~~g~P--------------~r~-~~~~C~~y~k~G~C~~---G~~CrF~---H~~~~~~g~~~p 170 (451)
+ .. .+....| ++. ...+|.-|-..|.|++ |+.|.|+ |......
T Consensus 190 kpks~~~~~s~t~~kes~a~P~~~~~~~~~e~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~----- 264 (351)
T COG5063 190 KPKSGKNCTSYTLGKESDAHPHDELIYQKQEQNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELK----- 264 (351)
T ss_pred CcccCcCccccccccccccCchhhhhhhhhhccchhhcCCHHHhhccCcCCCCcccccccccccccccccccccc-----
Confidence 0 00 1111111 110 1256888888899999 8889888 6621100
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCCCcccccCCCCcCcCcCCCccccccccCCCCCccCCCCCCCCCCCCCCCCCCCCC
Q 013033 171 LTGNASLGSMGSSVLPSSGLQYAGSLPTWSLQRAPYLSSRLQGTQSYMPLIVSPSQGIVPAPGWNTYMGNIGPLSPTSIA 250 (451)
Q Consensus 171 ~~~~~~~~~~~~~~~p~s~~~~~~~~~~~~~~r~~~i~~~~q~p~~y~p~~~~p~~g~vp~~~w~~y~~~~~p~~~~~~~ 250 (451)
T Consensus 265 -------------------------------------------------------------------------------- 264 (351)
T COG5063 265 -------------------------------------------------------------------------------- 264 (351)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCcccccCCCCCCccccchhhhccccCCCCCCCCCccccchhccccccCCCCCccCCcchhhhccccccCCCCCCCCCC
Q 013033 251 GSNLIYSSRNQGDLGAGAQMHILSASSQNLPERPDQPDCRYYMNTGTCKYGADCKFHHPKERIAQSAASNIGPLGLPSRP 330 (451)
Q Consensus 251 ~~~~~y~~~~~~~~~~~~~~~~~s~~~~~~p~r~~~~lC~~f~~tG~C~~G~~Ckf~H~~~~l~~~~~~~l~p~~~p~r~ 330 (451)
...-..-++|+.|..|.+.|+|+||.+|.|.||.+++...... --+.|
T Consensus 265 --------------------------~k~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~~~~------~~~~y 312 (351)
T COG5063 265 --------------------------SKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEMYEE------ASLGY 312 (351)
T ss_pred --------------------------ccccccccccCCccchhhcccCccccccccccCChhhcccccc------ccccc
Confidence 0000111488999999999999999999999999987654321 12356
Q ss_pred CCcCCccccccccCCCCCCCccCCCCCCCCCcc
Q 013033 331 GQAICSNYSMYGICKFGPTCRFDHPYAGYPINY 363 (451)
Q Consensus 331 ~t~~C~~y~~~G~CkfG~~C~F~H~~~~~~~~~ 363 (451)
...+|+.++++|.|++|-+|.|.|....+...+
T Consensus 313 ~~~~crt~~~~g~~p~g~~~c~~~dkkn~~~s~ 345 (351)
T COG5063 313 LDGPCRTRAKGGAFPSGGAVCKSFDKKNLDFSV 345 (351)
T ss_pred cccccccccccCccCCCCchhhccccchhhhhh
Confidence 677999999999999999999999988765433
No 8
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=99.11 E-value=1.4e-10 Score=114.73 Aligned_cols=179 Identities=18% Similarity=0.337 Sum_probs=111.6
Q ss_pred cccccccccccccCCCCCCCCCCCCCCCCCCCCceecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCcC
Q 013033 91 GQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPSSLGTALP 170 (451)
Q Consensus 91 ~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~~~g~~~p 170 (451)
+++.|+.-..-+.|++++.|.|+|......-.. .+.+.+++-|..|...|.|+++.+|-|.|....... -.+
T Consensus 114 kt~~l~ss~~~~~~~~p~~n~fahs~~issl~~-------~~~K~kt~slev~in~~~vp~s~~~~~~slP~t~~~-~q~ 185 (351)
T COG5063 114 KTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQ-------THPKYKTESLEVFINPGYVPYSKRCCFISLPLTDIN-LQP 185 (351)
T ss_pred cchhhhccccccccccCCCCcCCCccccccccc-------cCccccccceeEEecCCccccccccccccccccccC-cch
Confidence 445666543338899999999999987543221 234566778999998999999999999988554210 111
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCCCcccccCCCCcCcCcCCCccccccccCCCCCccCCCCCCCCCCCCCCCCCCCCC
Q 013033 171 LTGNASLGSMGSSVLPSSGLQYAGSLPTWSLQRAPYLSSRLQGTQSYMPLIVSPSQGIVPAPGWNTYMGNIGPLSPTSIA 250 (451)
Q Consensus 171 ~~~~~~~~~~~~~~~p~s~~~~~~~~~~~~~~r~~~i~~~~q~p~~y~p~~~~p~~g~vp~~~w~~y~~~~~p~~~~~~~ 250 (451)
+.+. -+ .....-.+..+.|.....|.+ ..+ |
T Consensus 186 l~~r----------kp----ks~~~~~s~t~~kes~a~P~~----------~~~------------~------------- 216 (351)
T COG5063 186 LSQR----------KP----KSGKNCTSYTLGKESDAHPHD----------ELI------------Y------------- 216 (351)
T ss_pred hhcc----------Cc----ccCcCccccccccccccCchh----------hhh------------h-------------
Confidence 1100 00 000000111111111111100 000 0
Q ss_pred CCCcccccCCCCCCccccchhhhccccCCCCCCCCC--ccccchhccccccC---CCCCccC---CcchhhhccccccCC
Q 013033 251 GSNLIYSSRNQGDLGAGAQMHILSASSQNLPERPDQ--PDCRYYMNTGTCKY---GADCKFH---HPKERIAQSAASNIG 322 (451)
Q Consensus 251 ~~~~~y~~~~~~~~~~~~~~~~~s~~~~~~p~r~~~--~lC~~f~~tG~C~~---G~~Ckf~---H~~~~l~~~~~~~l~ 322 (451)
+. .++.- .-+++ .+|.-|-+.|.|+| |++|+|+ ||..++....
T Consensus 217 --------------------~~---~e~n~-~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~----- 267 (351)
T COG5063 217 --------------------QK---QEQNK-PLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKK----- 267 (351)
T ss_pred --------------------hh---hhccc-hhhcCCHHHhhccCcCCCCccccccccccccccccccccccccc-----
Confidence 00 01111 11355 89999999999999 9999999 9977665432
Q ss_pred CCCCCCCCCCcCCccccccccCCCCCCCccCCCCCC
Q 013033 323 PLGLPSRPGQAICSNYSMYGICKFGPTCRFDHPYAG 358 (451)
Q Consensus 323 p~~~p~r~~t~~C~~y~~~G~CkfG~~C~F~H~~~~ 358 (451)
.-..++|++|.+|..-|+|+||.||.|.|..+.
T Consensus 268 ---k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~ 300 (351)
T COG5063 268 ---KKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDS 300 (351)
T ss_pred ---cccccccCCccchhhcccCccccccccccCChh
Confidence 335789999999999999999999999999763
No 9
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.60 E-value=5.4e-08 Score=97.74 Aligned_cols=101 Identities=26% Similarity=0.496 Sum_probs=69.5
Q ss_pred cCCccccccCCCCCCCC-CCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCC-----c
Q 013033 51 PDCLFYRRTGLCGYGSN-CRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGP-----V 124 (451)
Q Consensus 51 ~~C~~f~rtG~C~~G~~-C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~-----~ 124 (451)
++|+.|+| |.|++|++ |||+|+...... +.-+...|..|+| |.|. .++|||+|+....+..- .
T Consensus 38 eVCReF~r-n~C~R~d~~CkfaHP~~~~~V--------~~g~v~aC~Ds~k-grCs-R~nCkylHpp~hlkdql~ingrn 106 (331)
T KOG2494|consen 38 EVCREFLR-NTCSRGDRECKFAHPPKNCQV--------SNGRVIACFDSQK-GRCS-RENCKYLHPPQHLKDQLKINGRN 106 (331)
T ss_pred HHHHHHHh-ccccCCCccccccCCCCCCCc--------cCCeEEEEecccc-CccC-cccceecCCChhhhhhhhhcccc
Confidence 67999999 99999999 999999763211 1113356999996 9998 58899999887543211 0
Q ss_pred --eec------ccCCCCCCCCCCCC--CCCCCCcCCCC-CCCCCCCCCCC
Q 013033 125 --SFN------ILGLPMRQDEKSCP--YYMRTGSCKFG-VACKFHHPQPS 163 (451)
Q Consensus 125 --~~~------~~g~P~r~~~~~C~--~y~k~G~C~~G-~~CrF~H~~~~ 163 (451)
.+. ..+.+...+.++|. .|. ++-|.-| ..|+|.|..+.
T Consensus 107 ~l~lq~~~aA~~~q~~~~~g~Pi~~v~~f~-~~~~~~g~~~~s~~~y~~~ 155 (331)
T KOG2494|consen 107 NLILQKTAAAMLAQQMQGPGTPICSVPMFA-TGPCLGGNTACSYWPYLPP 155 (331)
T ss_pred cHHHHHHHHhhhcccccCCCcccccccccc-ccccccCCCccccccccCC
Confidence 000 01112224677888 666 5888877 46999999774
No 10
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.59 E-value=4e-07 Score=90.94 Aligned_cols=88 Identities=24% Similarity=0.533 Sum_probs=68.7
Q ss_pred CCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCceecc
Q 013033 49 GEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNI 128 (451)
Q Consensus 49 g~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~ 128 (451)
.+..|.+|+..+.+...-+|.+.|..... ..-.+|++|++ |.|+-+..|.|+|..+....
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 45669999976667777789999976421 12357999996 99999999999999875331
Q ss_pred cCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 129 LGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 129 ~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
....|++|...|.|..|..|.+.|.++.
T Consensus 133 -------~~~~c~~Fs~~G~cs~g~~c~~~h~dp~ 160 (285)
T COG5084 133 -------QGPPCRSFSLKGSCSSGPSCGYSHIDPD 160 (285)
T ss_pred -------cCCCcccccccceeccCCCCCccccCcc
Confidence 1345999966799999999999999753
No 11
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.52 E-value=2.7e-08 Score=65.37 Aligned_cols=27 Identities=41% Similarity=1.038 Sum_probs=22.1
Q ss_pred CCCccccchhccccccCCCCCccCCcc
Q 013033 284 PDQPDCRYYMNTGTCKYGADCKFHHPK 310 (451)
Q Consensus 284 ~~~~lC~~f~~tG~C~~G~~Ckf~H~~ 310 (451)
+++++|++|+++|.|+||++|+|+|++
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 478999999999999999999999974
No 12
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.51 E-value=1.2e-07 Score=94.69 Aligned_cols=88 Identities=31% Similarity=0.680 Sum_probs=71.5
Q ss_pred CCCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCceec
Q 013033 48 PGEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFN 127 (451)
Q Consensus 48 pg~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~ 127 (451)
...++|++|++ |.|+.|..|.|+|..+.+.. ..+.|++|...|.|..|..|.|.|.....
T Consensus 102 ~s~V~c~~~~~-g~c~s~~~c~~lh~~d~~~s-----------~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~-------- 161 (285)
T COG5084 102 SSSVVCKFFLR-GLCKSGFSCEFLHEYDLRSS-----------QGPPCRSFSLKGSCSSGPSCGYSHIDPDS-------- 161 (285)
T ss_pred cCCcccchhcc-ccCcCCCccccccCCCcccc-----------cCCCcccccccceeccCCCCCccccCccc--------
Confidence 44689999998 99999999999999886421 24679999556999999999999987432
Q ss_pred ccCCCCCCCCCCCCCCCC--CCcCCCCCCCCCCCCCCC
Q 013033 128 ILGLPMRQDEKSCPYYMR--TGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 128 ~~g~P~r~~~~~C~~y~k--~G~C~~G~~CrF~H~~~~ 163 (451)
....|.+|.. +++|+.|..|+|.|....
T Consensus 162 --------~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~ 191 (285)
T COG5084 162 --------FAGNCDQYSGATYGFCPLGASCKFSHTLKR 191 (285)
T ss_pred --------ccccccccCcccccccCCCCcccccccccc
Confidence 2345887774 699999999999999753
No 13
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=98.47 E-value=6.8e-08 Score=92.65 Aligned_cols=83 Identities=25% Similarity=0.652 Sum_probs=69.2
Q ss_pred CCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCceecc
Q 013033 49 GEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNI 128 (451)
Q Consensus 49 g~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~ 128 (451)
.+..|..|+ +|.|.+.+.|...|..+.+ +.+.|+||+ .|.|. ..+|||.|..-..
T Consensus 232 rkticpkfl-ngrcnkaedcnlsheldpr-------------ripacryfl-lgkcn-npncryvhihyse--------- 286 (377)
T KOG1492|consen 232 RKTICPKFL-NGRCNKAEDCNLSHELDPR-------------RIPACRYFL-LGKCN-NPNCRYVHIHYSE--------- 286 (377)
T ss_pred ccccChHHh-cCccCchhcCCcccccCcc-------------ccchhhhhh-hccCC-CCCceEEEEeecC---------
Confidence 367899999 5999999999999998753 347899999 59997 7999999975421
Q ss_pred cCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 129 LGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 129 ~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
..++|.-|.+.|+|..|..|+-.|...-
T Consensus 287 -------napicfefakygfcelgtscknqhilqc 314 (377)
T KOG1492|consen 287 -------NAPICFEFAKYGFCELGTSCKNQHILQC 314 (377)
T ss_pred -------CCceeeeehhcceeccccccccceeeee
Confidence 2357999999999999999999998653
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=98.38 E-value=5.3e-08 Score=63.99 Aligned_cols=27 Identities=33% Similarity=0.753 Sum_probs=22.0
Q ss_pred CCCcCCccccccccCCCCCCCccCCCC
Q 013033 330 PGQAICSNYSMYGICKFGPTCRFDHPY 356 (451)
Q Consensus 330 ~~t~~C~~y~~~G~CkfG~~C~F~H~~ 356 (451)
||+.+|++|+++|.|+||++|+|.|+.
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 578899999999999999999999973
No 15
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.15 E-value=2.4e-05 Score=83.32 Aligned_cols=58 Identities=24% Similarity=0.556 Sum_probs=47.8
Q ss_pred ccccchhccccccCCCCCccCCcchhhhccccccCCCCCCCCCCCCcCCccccccccCCCCCCCccCCCCCCC
Q 013033 287 PDCRYYMNTGTCKYGADCKFHHPKERIAQSAASNIGPLGLPSRPGQAICSNYSMYGICKFGPTCRFDHPYAGY 359 (451)
Q Consensus 287 ~lC~~f~~tG~C~~G~~Ckf~H~~~~l~~~~~~~l~p~~~p~r~~t~~C~~y~~~G~CkfG~~C~F~H~~~~~ 359 (451)
..|-.|.+ |.|+.||.|.|+|+.-|-- |+ |.+|||..|+.- |+|+- .-|.|.|-...+
T Consensus 237 tpCPefrk-G~C~rGD~CEyaHgvfEcw------LH----Pa~YRT~~CkDg---~~C~R-rvCfFAH~~eqL 294 (528)
T KOG1595|consen 237 TPCPEFRK-GSCERGDSCEYAHGVFECW------LH----PARYRTRKCKDG---GYCPR-RVCFFAHSPEQL 294 (528)
T ss_pred ccCccccc-CCCCCCCccccccceehhh------cC----HHHhccccccCC---CCCcc-ceEeeecChHHh
Confidence 44999988 9999999999999776633 33 469999999765 89996 779999998755
No 16
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.13 E-value=2.1e-06 Score=89.76 Aligned_cols=83 Identities=25% Similarity=0.668 Sum_probs=63.4
Q ss_pred cCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCceecccC
Q 013033 51 PDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILG 130 (451)
Q Consensus 51 ~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~~g 130 (451)
++|.||+. -.|++++.|.|.|...... ...+|++|+..-.|+ +.|+|.|..-...
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-STCKKGDSCPFRHCEAALG------------NETVCTLWQEGRCCR--KVCRYRHSEIDKK---------- 58 (667)
T ss_pred ccchhhhh-hhhhccCcCcchhhHHHhc------------CcchhhhhhhcCccc--ccccchhhHHhhh----------
Confidence 57999984 8999999999999876431 234799999744576 4999999765322
Q ss_pred CCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 131 LPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 131 ~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
..+.+|.++++...|. .++|-|.|..|.
T Consensus 59 ----r~e~~CYwe~~p~gC~-k~~CgfRH~~pP 86 (667)
T KOG4791|consen 59 ----RSEIPCYWENQPTGCQ-KLNCGFRHNRPP 86 (667)
T ss_pred ----cCcccceeecCCCccC-CCccccccCCCc
Confidence 1356799999844498 699999997654
No 17
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.10 E-value=1.5e-05 Score=84.84 Aligned_cols=86 Identities=24% Similarity=0.457 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCchhhh-ccccccccCCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCceecccCCCCCCCCC
Q 013033 60 GLCGYGSNCRFNHPAYAA-QGAQYREELPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEK 138 (451)
Q Consensus 60 G~C~~G~~C~F~H~~~~~-~~~~~~~~~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~~g~P~r~~~~ 138 (451)
+.|.-+..|.|.|+.... .-.-.+-.| .-..|.-|.| |.|+.||.|.|.|..-+..-. |.++++.
T Consensus 207 ~~shDwteCPf~HpgEkARRRDPRkyhY----s~tpCPefrk-G~C~rGD~CEyaHgvfEcwLH---------Pa~YRT~ 272 (528)
T KOG1595|consen 207 PRSHDWTECPFAHPGEKARRRDPRKYHY----SSTPCPEFRK-GSCERGDSCEYAHGVFECWLH---------PARYRTR 272 (528)
T ss_pred ccCCCcccCCccCCCcccccCCcccccc----cCccCccccc-CCCCCCCccccccceehhhcC---------HHHhccc
Confidence 578888999999975422 110011122 3357999996 999999999999997654322 5578888
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 139 SCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 139 ~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
.|++- |.|+. .-|-|+|....
T Consensus 273 ~CkDg---~~C~R-rvCfFAH~~eq 293 (528)
T KOG1595|consen 273 KCKDG---GYCPR-RVCFFAHSPEQ 293 (528)
T ss_pred cccCC---CCCcc-ceEeeecChHH
Confidence 99984 88997 99999999765
No 18
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.79 E-value=1.5e-05 Score=51.46 Aligned_cols=26 Identities=31% Similarity=0.911 Sum_probs=22.9
Q ss_pred CCCcCCccccccccCCCCCCCccCCCC
Q 013033 330 PGQAICSNYSMYGICKFGPTCRFDHPY 356 (451)
Q Consensus 330 ~~t~~C~~y~~~G~CkfG~~C~F~H~~ 356 (451)
+++.+|++| ++|.|++|++|+|.|..
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 567799999 66999999999999973
No 19
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=97.75 E-value=1.4e-05 Score=84.19 Aligned_cols=61 Identities=30% Similarity=0.750 Sum_probs=53.3
Q ss_pred CCccccchhcc--ccccCCCCCccCCcchhhhccccccCCCCCCCCCCCCcCCccccccccCCCCCCCccCCC
Q 013033 285 DQPDCRYYMNT--GTCKYGADCKFHHPKERIAQSAASNIGPLGLPSRPGQAICSNYSMYGICKFGPTCRFDHP 355 (451)
Q Consensus 285 ~~~lC~~f~~t--G~C~~G~~Ckf~H~~~~l~~~~~~~l~p~~~p~r~~t~~C~~y~~~G~CkfG~~C~F~H~ 355 (451)
...||.-.... -.|.||++|||.|+.+........+|.+ -|.+|...|.|.||-+|||.-.
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Dig~----------~Cp~f~s~G~Cp~G~~CRFl~a 137 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDIGP----------SCPVFESLGFCPYGFKCRFLGA 137 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCcccCC----------ccceeeccccCCccceeehhhc
Confidence 46789999886 5799999999999999988777666665 8999999999999999999744
No 20
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.74 E-value=1.8e-05 Score=51.12 Aligned_cols=25 Identities=40% Similarity=1.089 Sum_probs=22.4
Q ss_pred CCCccccchhccccccCCCCCccCCc
Q 013033 284 PDQPDCRYYMNTGTCKYGADCKFHHP 309 (451)
Q Consensus 284 ~~~~lC~~f~~tG~C~~G~~Ckf~H~ 309 (451)
.++.+|++| ++|.|++|++|+|.|.
T Consensus 2 ~k~~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 2 YKTELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence 467899999 6699999999999995
No 21
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.66 E-value=2.1e-05 Score=82.43 Aligned_cols=53 Identities=26% Similarity=0.783 Sum_probs=41.8
Q ss_pred ccccccccccccCCCCCCCCCCCCCCCCCCCCceecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 013033 92 QPDCGYYLKTGTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQP 162 (451)
Q Consensus 92 ~p~C~~FlktG~Ck~G~~CrF~H~~~~~~~~~~~~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~ 162 (451)
.+.|.||+ ...||+++.|.|.|...... ....|.+|+..--|+ +.|+|.|.+-
T Consensus 3 ~~dcyff~-ys~cKk~d~c~~rh~E~al~---------------n~t~C~~w~~~~~C~--k~C~YRHSe~ 55 (667)
T KOG4791|consen 3 GEDCYFFF-YSTCKKGDSCPFRHCEAALG---------------NETVCTLWQEGRCCR--KVCRYRHSEI 55 (667)
T ss_pred cccchhhh-hhhhhccCcCcchhhHHHhc---------------CcchhhhhhhcCccc--ccccchhhHH
Confidence 35799999 59999999999999876433 235699999854455 5999999864
No 22
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.59 E-value=1.4e-05 Score=79.55 Aligned_cols=76 Identities=25% Similarity=0.647 Sum_probs=52.3
Q ss_pred CCCCCCCCCcCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCc-----------------------cccccccc
Q 013033 42 SPYPARPGEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERN-----------------------GQPDCGYY 98 (451)
Q Consensus 42 ~~~p~rpg~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~-----------------------~~p~C~~F 98 (451)
..--+-|+..+|.||.. |.|..|+.|+|+|+............|+... ...+|+||
T Consensus 84 v~~gvDPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfF 162 (343)
T KOG1763|consen 84 VPKGVDPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFF 162 (343)
T ss_pred cccCCCchHHHHHHHhc-cCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHH
Confidence 33456778899999995 9999999999999987532221111222111 12389999
Q ss_pred cc------cc---cCCCCC-CCCCCCCCCC
Q 013033 99 LK------TG---TCKYGS-TCKYHHPKDR 118 (451)
Q Consensus 99 lk------tG---~Ck~G~-~CrF~H~~~~ 118 (451)
+. .| .|.+|. .|-|.|....
T Consensus 163 LeAvE~~kYGWfW~CPnGg~~C~YrHaLP~ 192 (343)
T KOG1763|consen 163 LEAVENGKYGWFWECPNGGDKCIYRHALPE 192 (343)
T ss_pred HHHHhcCCccceeECCCCCCeeeeeecCCc
Confidence 84 22 599875 8999998764
No 23
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=97.42 E-value=4.9e-05 Score=80.30 Aligned_cols=63 Identities=22% Similarity=0.581 Sum_probs=49.0
Q ss_pred cccccccccc--ccCCCCCCCCCCCCCCCCCCCCceecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 92 QPDCGYYLKT--GTCKYGSTCKYHHPKDRNGAGPVSFNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 92 ~p~C~~Flkt--G~Ck~G~~CrF~H~~~~~~~~~~~~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
..+|.-.... ..|.||++|||.|+.....+... ......|++|...|+|++|-.|||+-....
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~---------~Dig~~Cp~f~s~G~Cp~G~~CRFl~aHld 140 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKA---------PDIGPSCPVFESLGFCPYGFKCRFLGAHLD 140 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHHhccC---------cccCCccceeeccccCCccceeehhhcccC
Confidence 4589999875 37999999999999986544321 122367999999999999999999755444
No 24
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.14 E-value=0.00011 Score=73.18 Aligned_cols=74 Identities=26% Similarity=0.614 Sum_probs=52.8
Q ss_pred CCCCccccchhccccccCCCCCccCCcchhhhccccccCCCCCCCC------------------CC-CCcCCcccc----
Q 013033 283 RPDQPDCRYYMNTGTCKYGADCKFHHPKERIAQSAASNIGPLGLPS------------------RP-GQAICSNYS---- 339 (451)
Q Consensus 283 r~~~~lC~~f~~tG~C~~G~~Ckf~H~~~~l~~~~~~~l~p~~~p~------------------r~-~t~~C~~y~---- 339 (451)
-|+..+|-+|.. |.|..|+.|+|+|+....+...-..|-+..... ++ ...+|+||.
T Consensus 89 DPKSvvCafFk~-g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeAvE 167 (343)
T KOG1763|consen 89 DPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEAVE 167 (343)
T ss_pred CchHHHHHHHhc-cCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHHHh
Confidence 378899999988 999999999999988876655432222211111 11 234999997
Q ss_pred --ccc---cCCCCC-CCccCCCCC
Q 013033 340 --MYG---ICKFGP-TCRFDHPYA 357 (451)
Q Consensus 340 --~~G---~CkfG~-~C~F~H~~~ 357 (451)
+|| .|++|- .|.|.|-+.
T Consensus 168 ~~kYGWfW~CPnGg~~C~YrHaLP 191 (343)
T KOG1763|consen 168 NGKYGWFWECPNGGDKCIYRHALP 191 (343)
T ss_pred cCCccceeECCCCCCeeeeeecCC
Confidence 455 499876 699999865
No 25
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.72 E-value=0.00042 Score=67.25 Aligned_cols=74 Identities=31% Similarity=0.683 Sum_probs=53.0
Q ss_pred CCCCccccchhccccccCCCCCccCCcchhhhccccccC----------CCCC-CCCCCCCcCCcccc------ccc---
Q 013033 283 RPDQPDCRYYMNTGTCKYGADCKFHHPKERIAQSAASNI----------GPLG-LPSRPGQAICSNYS------MYG--- 342 (451)
Q Consensus 283 r~~~~lC~~f~~tG~C~~G~~Ckf~H~~~~l~~~~~~~l----------~p~~-~p~r~~t~~C~~y~------~~G--- 342 (451)
-+++.+|-.|.. +.|..|+.|+|+|+.++.+...-.+| -|++ .|.--...+|+||. +||
T Consensus 82 dpK~~vcalF~~-~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W 160 (299)
T COG5252 82 DPKTVVCALFLN-KTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGW 160 (299)
T ss_pred CchhHHHHHhcc-CccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCcccee
Confidence 478899999988 99999999999999888776543211 1222 22222345999997 334
Q ss_pred cCCCC-CCCccCCCCC
Q 013033 343 ICKFG-PTCRFDHPYA 357 (451)
Q Consensus 343 ~CkfG-~~C~F~H~~~ 357 (451)
.|++| .+|-|.|-+.
T Consensus 161 ~CPng~~~C~y~H~Lp 176 (299)
T COG5252 161 TCPNGNMRCSYIHKLP 176 (299)
T ss_pred eCCCCCceeeeeeccC
Confidence 49988 5699999865
No 26
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.35 E-value=0.0018 Score=67.22 Aligned_cols=32 Identities=28% Similarity=0.923 Sum_probs=26.7
Q ss_pred CCCCccccccccccccccCCCCCCCCCCCCCCC
Q 013033 86 LPERNGQPDCGYYLKTGTCKYGSTCKYHHPKDR 118 (451)
Q Consensus 86 ~Per~~~p~C~~FlktG~Ck~G~~CrF~H~~~~ 118 (451)
+|.-..+..|.||+. |.|+|+++|||+|....
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 455556678999995 99999999999998764
No 27
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=96.15 E-value=0.012 Score=64.49 Aligned_cols=103 Identities=28% Similarity=0.618 Sum_probs=57.2
Q ss_pred cCCccccccCCCCCCCCCCCCCchhhhccccccccCCCCccccccccccccccCCCC-----CCCCCCCCCCCCCCCCce
Q 013033 51 PDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQYREELPERNGQPDCGYYLKTGTCKYG-----STCKYHHPKDRNGAGPVS 125 (451)
Q Consensus 51 ~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~~~~~~Per~~~p~C~~FlktG~Ck~G-----~~CrF~H~~~~~~~~~~~ 125 (451)
.+|+||.. |. +..|.|.|+...... ..+|+..-...|.+-. -.|+|| ..|.|.|........+-.
T Consensus 545 ~~Cky~~~---Ct-~a~Ce~~HPtaa~~~----~s~p~k~fa~~~~ks~--p~Ck~~~kCtasDC~~sH~~~~~pvq~t~ 614 (681)
T KOG3702|consen 545 TRCKYGPA---CT-SAECEFAHPTAAENA----KSLPNKKFASKCLKSH--PGCKFGKKCTASDCNYSHAGRRIPVQPTR 614 (681)
T ss_pred ccccCCCc---CC-chhhhhcCCcchhhh----hccccccccccceecc--cccccccccccccCcccccCCCCCCcccc
Confidence 56999986 99 889999999764211 1112111112233332 234444 568899987654211100
Q ss_pred ecccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCC
Q 013033 126 FNILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQPSSLGTA 168 (451)
Q Consensus 126 ~~~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~~~g~~ 168 (451)
+... .+.-....+|+|+-. |+ ...|+|.|++.-.+++.
T Consensus 615 ip~~-~~~~ti~~~CrY~pn---Cr-nm~C~F~HPk~cRf~~~ 652 (681)
T KOG3702|consen 615 IPPP-FPGGTIRGLCRYRPN---CR-NMQCKFYHPKTCRFNTN 652 (681)
T ss_pred CCCC-CCCCCccccceeccC---cC-CccccccCCcccccccc
Confidence 0000 011123467988654 88 58999999987655433
No 28
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.12 E-value=0.0019 Score=62.78 Aligned_cols=75 Identities=25% Similarity=0.571 Sum_probs=51.2
Q ss_pred CCCCCCCCcCCccccccCCCCCCCCCCCCCchhhhcccc----------cccc--CCCCcc---ccccccccc---cc--
Q 013033 43 PYPARPGEPDCLFYRRTGLCGYGSNCRFNHPAYAAQGAQ----------YREE--LPERNG---QPDCGYYLK---TG-- 102 (451)
Q Consensus 43 ~~p~rpg~~~C~~f~rtG~C~~G~~C~F~H~~~~~~~~~----------~~~~--~Per~~---~p~C~~Flk---tG-- 102 (451)
.--+-|++.+|..|. .+.|..|+.|+|+|+.+...... ..+. +-+|+. -.+|+||+. +|
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 RAGVDPKTVVCALFL-NKTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKY 156 (299)
T ss_pred ccccCchhHHHHHhc-cCccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCc
Confidence 445667889999999 59999999999999976432111 0111 112332 248999974 12
Q ss_pred ----cCCCC-CCCCCCCCCCC
Q 013033 103 ----TCKYG-STCKYHHPKDR 118 (451)
Q Consensus 103 ----~Ck~G-~~CrF~H~~~~ 118 (451)
.|.+| .+|-|.|....
T Consensus 157 gw~W~CPng~~~C~y~H~Lp~ 177 (299)
T COG5252 157 GWGWTCPNGNMRCSYIHKLPD 177 (299)
T ss_pred cceeeCCCCCceeeeeeccCc
Confidence 58887 58999998764
No 29
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=96.01 E-value=0.0043 Score=64.50 Aligned_cols=56 Identities=29% Similarity=0.729 Sum_probs=36.4
Q ss_pred CCCCCCCCCCCCCCC---CCCc-eec-------ccCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCC
Q 013033 106 YGSTCKYHHPKDRNG---AGPV-SFN-------ILGLPMRQDEKSCPYYMRTGSCKFGVACKFHHPQP 162 (451)
Q Consensus 106 ~G~~CrF~H~~~~~~---~~~~-~~~-------~~g~P~r~~~~~C~~y~k~G~C~~G~~CrF~H~~~ 162 (451)
-|++|.+-|...... .+.+ .+. ..-+|.....++|.||+. |.|+||.+|||.|...
T Consensus 98 ~GsKcsaph~ss~gl~yHna~I~g~E~sarvRVlfl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 98 DGSKCSAPHTSSRGLYYHNARIIGFEGSARVRVLFLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLD 164 (486)
T ss_pred cCCcccccccCCccceecceeEEeeccccceEEEeecCcchhhccchHhhc-cccccCcccccccCcc
Confidence 377888887765431 1110 000 011244445688999997 9999999999999864
No 30
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.86 E-value=0.0051 Score=37.24 Aligned_cols=19 Identities=32% Similarity=0.990 Sum_probs=16.7
Q ss_pred ccccccccccCCCCCCCCCCCC
Q 013033 94 DCGYYLKTGTCKYGSTCKYHHP 115 (451)
Q Consensus 94 ~C~~FlktG~Ck~G~~CrF~H~ 115 (451)
.|+||.. |+++++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 3998875 999999999996
No 31
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=95.64 E-value=0.0072 Score=36.56 Aligned_cols=19 Identities=47% Similarity=1.106 Sum_probs=16.8
Q ss_pred CCccccccCCCCCCCCCCCCCc
Q 013033 52 DCLFYRRTGLCGYGSNCRFNHP 73 (451)
Q Consensus 52 ~C~~f~rtG~C~~G~~C~F~H~ 73 (451)
.|+||.. |++|++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 4998874 999999999996
No 32
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=94.64 E-value=0.096 Score=57.70 Aligned_cols=23 Identities=26% Similarity=0.761 Sum_probs=19.8
Q ss_pred ccccccccccccCCCCCCCCCCCCCCC
Q 013033 92 QPDCGYYLKTGTCKYGSTCKYHHPKDR 118 (451)
Q Consensus 92 ~p~C~~FlktG~Ck~G~~CrF~H~~~~ 118 (451)
..+|.|+.. |. +..|.|.|+...
T Consensus 544 l~~Cky~~~---Ct-~a~Ce~~HPtaa 566 (681)
T KOG3702|consen 544 LTRCKYGPA---CT-SAECEFAHPTAA 566 (681)
T ss_pred eccccCCCc---CC-chhhhhcCCcch
Confidence 458999997 98 899999999765
No 33
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.46 E-value=0.014 Score=55.67 Aligned_cols=26 Identities=42% Similarity=0.972 Sum_probs=23.9
Q ss_pred cCCccccccCCCCCCCCCCCCCchhh
Q 013033 51 PDCLFYRRTGLCGYGSNCRFNHPAYA 76 (451)
Q Consensus 51 ~~C~~f~rtG~C~~G~~C~F~H~~~~ 76 (451)
.+|+.|..||.|.||+.|+|+|....
T Consensus 142 dVCKdyk~TGYCGYGDsCKflH~R~D 167 (259)
T COG5152 142 DVCKDYKETGYCGYGDSCKFLHDRSD 167 (259)
T ss_pred ccccchhhcccccCCchhhhhhhhhh
Confidence 57999999999999999999999763
No 34
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.42 E-value=0.014 Score=55.71 Aligned_cols=27 Identities=30% Similarity=0.942 Sum_probs=24.4
Q ss_pred cCCccccccccCCCCCCCccCCCCCCC
Q 013033 333 AICSNYSMYGICKFGPTCRFDHPYAGY 359 (451)
Q Consensus 333 ~~C~~y~~~G~CkfG~~C~F~H~~~~~ 359 (451)
-+|+.|.++|+|-||+.|+|.|....+
T Consensus 142 dVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 142 DVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred ccccchhhcccccCCchhhhhhhhhhh
Confidence 499999999999999999999997643
No 35
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.61 E-value=0.092 Score=54.44 Aligned_cols=25 Identities=40% Similarity=0.984 Sum_probs=23.1
Q ss_pred cccccccccccCCCCCCCCCCCCCCC
Q 013033 93 PDCGYYLKTGTCKYGSTCKYHHPKDR 118 (451)
Q Consensus 93 p~C~~FlktG~Ck~G~~CrF~H~~~~ 118 (451)
.+|+||++ |.|+||+.|||.|++..
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 68999997 99999999999999883
No 36
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=89.32 E-value=0.11 Score=51.37 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=24.8
Q ss_pred CCCCCcCCccccccccCCCCCCCccCCCCC
Q 013033 328 SRPGQAICSNYSMYGICKFGPTCRFDHPYA 357 (451)
Q Consensus 328 ~r~~t~~C~~y~~~G~CkfG~~C~F~H~~~ 357 (451)
.+++...|..|+. +.|.+|..|.|.|...
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 4556679999998 6999999999999963
No 37
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.72 E-value=0.14 Score=51.78 Aligned_cols=25 Identities=44% Similarity=1.003 Sum_probs=23.1
Q ss_pred cCCccccccCCCCCCCCCCCCCchh
Q 013033 51 PDCLFYRRTGLCGYGSNCRFNHPAY 75 (451)
Q Consensus 51 ~~C~~f~rtG~C~~G~~C~F~H~~~ 75 (451)
.+|+.|-.||.|.||+.|+|+|...
T Consensus 187 DicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 187 DICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred hhhhhhHhhCcccccchhhhhhhhh
Confidence 4599999999999999999999865
No 38
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.72 E-value=0.13 Score=51.97 Aligned_cols=26 Identities=38% Similarity=1.028 Sum_probs=23.8
Q ss_pred CCccccccccCCCCCCCccCCCCCCC
Q 013033 334 ICSNYSMYGICKFGPTCRFDHPYAGY 359 (451)
Q Consensus 334 ~C~~y~~~G~CkfG~~C~F~H~~~~~ 359 (451)
+|+.|..||+|-||+.|+|.|...-+
T Consensus 188 icKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 188 ICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred hhhhhHhhCcccccchhhhhhhhhhc
Confidence 89999999999999999999997633
No 39
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=88.56 E-value=0.13 Score=50.98 Aligned_cols=29 Identities=31% Similarity=0.553 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 134 RQDEKSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 134 r~~~~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
+..+..|..|.+ +.|.+|..|-|.|....
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 445688999997 69999999999999853
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=87.62 E-value=0.31 Score=31.03 Aligned_cols=22 Identities=36% Similarity=0.942 Sum_probs=18.4
Q ss_pred cccccccccccCCCCCCCCCCCC
Q 013033 93 PDCGYYLKTGTCKYGSTCKYHHP 115 (451)
Q Consensus 93 p~C~~FlktG~Ck~G~~CrF~H~ 115 (451)
++|.|-++.|.|. .+.|.|.|-
T Consensus 1 ~lC~yEl~Gg~Cn-d~~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCN-DPDCEFQHF 22 (23)
T ss_pred CCCccccCCCeeC-CCCCCcccc
Confidence 4799999755997 789999995
No 41
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.66 E-value=0.3 Score=50.71 Aligned_cols=25 Identities=44% Similarity=1.160 Sum_probs=23.3
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCC
Q 013033 138 KSCPYYMRTGSCKFGVACKFHHPQPS 163 (451)
Q Consensus 138 ~~C~~y~k~G~C~~G~~CrF~H~~~~ 163 (451)
.+|+||++ |.|+||+.|||.|..+.
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 68999997 99999999999999984
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=80.50 E-value=1.3 Score=28.21 Aligned_cols=22 Identities=36% Similarity=0.939 Sum_probs=18.6
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCC
Q 013033 138 KSCPYYMRTGSCKFGVACKFHHP 160 (451)
Q Consensus 138 ~~C~~y~k~G~C~~G~~CrF~H~ 160 (451)
++|.|-+.+|.|. -..|.|.|.
T Consensus 1 ~lC~yEl~Gg~Cn-d~~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCN-DPDCEFQHF 22 (23)
T ss_pred CCCccccCCCeeC-CCCCCcccc
Confidence 3699999866997 589999996
No 43
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=77.84 E-value=1.8 Score=44.77 Aligned_cols=29 Identities=28% Similarity=0.669 Sum_probs=24.5
Q ss_pred CCCCCcCCccccccCCCCCCCCCCCCCchh
Q 013033 46 ARPGEPDCLFYRRTGLCGYGSNCRFNHPAY 75 (451)
Q Consensus 46 ~rpg~~~C~~f~rtG~C~~G~~C~F~H~~~ 75 (451)
.|-.-.+|.||.+ |.|++|+.|.|+|+..
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 4444568999997 9999999999999865
No 44
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=66.43 E-value=3.6 Score=42.66 Aligned_cols=29 Identities=41% Similarity=0.976 Sum_probs=24.5
Q ss_pred CCccccccccccccccCCCCCCCCCCCCCC
Q 013033 88 ERNGQPDCGYYLKTGTCKYGSTCKYHHPKD 117 (451)
Q Consensus 88 er~~~p~C~~FlktG~Ck~G~~CrF~H~~~ 117 (451)
.|..-.+|.||.+ |.|++|++|.|.|.+.
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 3444468999997 8999999999999987
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=26.38 E-value=20 Score=23.53 Aligned_cols=11 Identities=55% Similarity=1.177 Sum_probs=6.0
Q ss_pred cccCCCCCccC
Q 013033 297 TCKYGADCKFH 307 (451)
Q Consensus 297 ~C~~G~~Ckf~ 307 (451)
.|+||.+|--.
T Consensus 2 ~C~YG~~CYRk 12 (26)
T PF10283_consen 2 PCKYGAKCYRK 12 (26)
T ss_dssp E-TTGGG-S--
T ss_pred CCCcchhhhcC
Confidence 49999999643
No 46
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=23.67 E-value=5e+02 Score=24.49 Aligned_cols=27 Identities=11% Similarity=0.091 Sum_probs=19.3
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCCCCCC
Q 013033 140 CPYYMRTGSCKFGVACKFHHPQPSSLG 166 (451)
Q Consensus 140 C~~y~k~G~C~~G~~CrF~H~~~~~~g 166 (451)
=.+..+.|.|..+.+|+|.|......+
T Consensus 55 ~~~~~~~g~~~~~~~~~~~~~~~~~~~ 81 (165)
T KOG3454|consen 55 LRFIGKKGQKVPFSNARFSAPPEPVKA 81 (165)
T ss_pred HhhhcccccCCccccccccCCcccccc
Confidence 344555578999999999998754333
Done!