Query 030604
Match_columns 174
No_of_seqs 191 out of 1599
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 16:15:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00368 universal minicircle 100.0 7.5E-30 1.6E-34 194.2 9.8 128 10-164 2-148 (148)
2 PTZ00368 universal minicircle 99.9 2E-25 4.4E-30 169.8 8.9 115 1-143 12-147 (148)
3 COG5082 AIR1 Arginine methyltr 99.9 5E-22 1.1E-26 155.0 7.7 123 8-158 60-189 (190)
4 COG5082 AIR1 Arginine methyltr 99.8 4.1E-21 8.8E-26 149.9 6.3 106 33-170 59-179 (190)
5 KOG4400 E3 ubiquitin ligase in 99.6 1.8E-15 3.9E-20 124.9 10.1 155 9-168 25-187 (261)
6 KOG4400 E3 ubiquitin ligase in 99.6 1.4E-14 3E-19 119.7 8.6 142 2-164 85-241 (261)
7 PF00098 zf-CCHC: Zinc knuckle 98.3 3.2E-07 6.8E-12 45.6 1.5 16 147-162 2-17 (18)
8 PF00098 zf-CCHC: Zinc knuckle 98.2 8.1E-07 1.8E-11 44.1 1.7 17 127-143 2-18 (18)
9 PF13696 zf-CCHC_2: Zinc knuck 97.0 0.00046 9.9E-09 39.1 2.0 17 126-142 9-25 (32)
10 PF13696 zf-CCHC_2: Zinc knuck 96.7 0.00075 1.6E-08 38.2 1.0 22 6-27 6-27 (32)
11 PF13917 zf-CCHC_3: Zinc knuck 96.5 0.0015 3.3E-08 39.3 1.8 18 145-162 4-21 (42)
12 smart00343 ZnF_C2HC zinc finge 94.7 0.019 4.2E-07 30.6 1.5 15 148-162 2-16 (26)
13 KOG0119 Splicing factor 1/bran 94.6 0.027 6E-07 50.3 2.8 42 9-52 262-303 (554)
14 smart00343 ZnF_C2HC zinc finge 93.8 0.031 6.6E-07 29.8 1.0 17 127-143 1-17 (26)
15 PF13917 zf-CCHC_3: Zinc knuck 93.6 0.044 9.5E-07 33.0 1.5 18 8-25 4-21 (42)
16 KOG0119 Splicing factor 1/bran 93.5 0.061 1.3E-06 48.2 2.9 39 126-164 262-304 (554)
17 PF15288 zf-CCHC_6: Zinc knuck 90.9 0.25 5.4E-06 29.4 2.4 19 147-165 3-23 (40)
18 KOG0109 RNA-binding protein LA 89.8 0.16 3.5E-06 42.8 1.3 16 127-142 162-177 (346)
19 PF14392 zf-CCHC_4: Zinc knuck 89.6 0.14 3.1E-06 31.5 0.7 16 10-25 33-48 (49)
20 COG5222 Uncharacterized conser 86.2 0.4 8.6E-06 40.7 1.5 21 144-164 175-195 (427)
21 PF14787 zf-CCHC_5: GAG-polypr 86.1 0.58 1.2E-05 27.1 1.7 18 147-164 4-21 (36)
22 PF14392 zf-CCHC_4: Zinc knuck 85.9 0.34 7.4E-06 29.8 0.7 18 34-51 31-48 (49)
23 PF15288 zf-CCHC_6: Zinc knuck 85.3 0.55 1.2E-05 27.9 1.4 19 9-27 2-22 (40)
24 KOG0109 RNA-binding protein LA 83.5 0.53 1.1E-05 39.8 1.1 25 137-166 157-181 (346)
25 PF14787 zf-CCHC_5: GAG-polypr 82.8 0.95 2.1E-05 26.2 1.6 21 9-29 3-23 (36)
26 KOG0314 Predicted E3 ubiquitin 81.6 2.1 4.6E-05 38.2 4.2 39 126-164 134-177 (448)
27 COG5222 Uncharacterized conser 72.4 2 4.2E-05 36.6 1.3 21 9-29 177-197 (427)
28 KOG0314 Predicted E3 ubiquitin 64.9 7.5 0.00016 34.8 3.4 60 35-94 113-180 (448)
29 KOG2673 Uncharacterized conser 42.7 9.3 0.0002 34.3 0.4 24 148-171 131-154 (485)
30 KOG2044 5'-3' exonuclease HKE1 33.8 18 0.00039 34.8 0.8 17 127-143 262-278 (931)
31 KOG3116 Predicted C3H1-type Zn 33.2 9.6 0.00021 29.2 -0.9 19 34-52 27-45 (177)
32 PF12353 eIF3g: Eukaryotic tra 33.0 29 0.00064 25.6 1.7 19 124-143 105-123 (128)
33 KOG2044 5'-3' exonuclease HKE1 32.3 21 0.00045 34.4 0.9 20 33-52 259-278 (931)
34 KOG0107 Alternative splicing f 31.9 36 0.00078 26.9 2.0 33 126-164 101-133 (195)
35 PF05741 zf-nanos: Nanos RNA b 27.5 36 0.00077 21.6 1.1 16 55-70 35-53 (55)
36 KOG3116 Predicted C3H1-type Zn 27.1 18 0.00039 27.8 -0.4 22 51-72 25-46 (177)
37 PF12353 eIF3g: Eukaryotic tra 23.0 54 0.0012 24.2 1.6 24 143-167 104-127 (128)
38 KOG2673 Uncharacterized conser 20.6 58 0.0013 29.4 1.5 20 10-29 130-149 (485)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.96 E-value=7.5e-30 Score=194.21 Aligned_cols=128 Identities=38% Similarity=0.972 Sum_probs=110.3
Q ss_pred CCccCCCCCcCcCCCCCCccC-CCCcccccccCCCCCCCccccCc------ccccccccCCccccCCCCCc------ccc
Q 030604 10 ICHSCGKTGHRARDCSTHVQS-GGDLRLCNNCYKPGHIAADCTND------KACKNCRKTGHIARDCQNEP------VCN 76 (174)
Q Consensus 10 ~C~~Cg~~GH~~~~Cp~~~~~-~~~~~~C~~C~~~GH~~~~C~~~------~~C~~Cg~~GH~~~~Cp~~~------~C~ 76 (174)
+||+|++.||++++||..... ......||+|++.||++.+||.. ..|++|++.||++++||+.. .|+
T Consensus 2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~ 81 (148)
T PTZ00368 2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGPRSCY 81 (148)
T ss_pred cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCCcccC
Confidence 799999999999999984321 23467999999999999999984 36999999999999999753 799
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCCC------Ccceec
Q 030604 77 LCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP------LIICRN 150 (174)
Q Consensus 77 ~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~------~~~C~~ 150 (174)
+|++.||++++||+..... ...++||+|++.||+++|||+. .++||+
T Consensus 82 ~Cg~~GH~~~~C~~~~~~~---------------------------~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~ 134 (148)
T PTZ00368 82 NCGQTGHISRECPNRAKGG---------------------------AARRACYNCGGEGHISRDCPNAGKRPGGDKTCYN 134 (148)
T ss_pred cCCCCCcccccCCCccccc---------------------------ccchhhcccCcCCcchhcCCCccccCCCCCcccc
Confidence 9999999999999966421 1236899999999999999984 589999
Q ss_pred cCCCCcCCCCCCCC
Q 030604 151 CGGRGHMAYECPSG 164 (174)
Q Consensus 151 Cg~~GH~a~~C~~~ 164 (174)
|+++|||++|||+.
T Consensus 135 Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 135 CGQTGHLSRDCPDK 148 (148)
T ss_pred CCCcCcccccCCCC
Confidence 99999999999974
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.92 E-value=2e-25 Score=169.81 Aligned_cols=115 Identities=38% Similarity=0.893 Sum_probs=98.3
Q ss_pred CCCCCCC--------CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccCc------ccccccccCCccc
Q 030604 1 MASNCHN--------EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTND------KACKNCRKTGHIA 66 (174)
Q Consensus 1 ~~~~c~~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~~------~~C~~Cg~~GH~~ 66 (174)
||++||. ...||+|++.||++++||..... .....|++|++.||++.+||+. ..|++|++.||++
T Consensus 12 ~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~ 90 (148)
T PTZ00368 12 QSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGG-RGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHIS 90 (148)
T ss_pred CcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCC-CCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCccc
Confidence 6899997 46899999999999999986421 2356899999999999999884 3799999999999
Q ss_pred cCCCCCc-------cccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCC
Q 030604 67 RDCQNEP-------VCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSR 139 (174)
Q Consensus 67 ~~Cp~~~-------~C~~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~ 139 (174)
++||+.. +|++|++.||++++||+.+... ...++||+|+++|||++
T Consensus 91 ~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~---------------------------~~~~~C~~Cg~~gH~~~ 143 (148)
T PTZ00368 91 RECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRP---------------------------GGDKTCYNCGQTGHLSR 143 (148)
T ss_pred ccCCCcccccccchhhcccCcCCcchhcCCCccccC---------------------------CCCCccccCCCcCcccc
Confidence 9999744 7999999999999999975421 12368999999999999
Q ss_pred CCCC
Q 030604 140 DCVG 143 (174)
Q Consensus 140 dCp~ 143 (174)
|||.
T Consensus 144 dCp~ 147 (148)
T PTZ00368 144 DCPD 147 (148)
T ss_pred cCCC
Confidence 9995
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.86 E-value=5e-22 Score=154.97 Aligned_cols=123 Identities=33% Similarity=0.733 Sum_probs=100.6
Q ss_pred CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccCcccccccccCCccccCC-CC---CccccccccCCC
Q 030604 8 EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDC-QN---EPVCNLCNIAGH 83 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~GH~~~~C-p~---~~~C~~C~~~GH 83 (174)
+.+||+|++.||+++|||. ++|++|...||.+..||+.++|++||+.||++++| |. .+.|+.|...+|
T Consensus 60 ~~~C~nCg~~GH~~~DCP~--------~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H 131 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPH--------SICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRH 131 (190)
T ss_pred ccccchhcccCcccccCCh--------hHhhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCcc
Confidence 4789999999999999994 59999988999999999988999999999999999 54 358999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCCC---CcceeccCCCCcCC
Q 030604 84 VARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP---LIICRNCGGRGHMA 158 (174)
Q Consensus 84 ~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~~---~~~C~~Cg~~GH~a 158 (174)
++.+||..|+.+.... ..+.+..+.||+|+..+|+++||+.+ .+. |.++..+|+.
T Consensus 132 ~s~~Cp~~~k~y~~~~-------------------~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~~-~~~~~~~~~~ 189 (190)
T COG5082 132 SSEDCPSIWKHYVLNN-------------------GDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVP-YVCGKKGYVS 189 (190)
T ss_pred ccccCccccccccccc-------------------CCCcceeeeccccCCccccCCCCCCCcccccc-ccccccccCC
Confidence 9999999998654320 11224567899999999999999863 233 6777776653
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.83 E-value=4.1e-21 Score=149.89 Aligned_cols=106 Identities=33% Similarity=0.765 Sum_probs=95.0
Q ss_pred CcccccccCCCCCCCccccCcccccccccCCccccCCCCCccccccccCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC
Q 030604 33 DLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC-PKGDSLGERGGGGGGERGGGGGG 111 (174)
Q Consensus 33 ~~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~~~~C-p~~~~~~~~~g~~~~~~~~~~~~ 111 (174)
...+||+|++.||++.+|| ..+|++|...||.+..||...+|++|++.||++++| |.++.
T Consensus 59 ~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~------------------ 119 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQ------------------ 119 (190)
T ss_pred cccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCccccc------------------
Confidence 4679999999999999999 599999988999999999989999999999999999 56553
Q ss_pred CCCCCCCcccCccccccccCCCCCCCCCCCCC--------------CCcceeccCCCCcCCCCCCCCCCCCCC
Q 030604 112 DGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--------------PLIICRNCGGRGHMAYECPSGRIADRG 170 (174)
Q Consensus 112 ~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~--------------~~~~C~~Cg~~GH~a~~C~~~~~~~~~ 170 (174)
.+.|+.|+..+|++++||. ..+.||+|+..+||+.+|+.++.+...
T Consensus 120 -------------~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~~ 179 (190)
T COG5082 120 -------------QKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVP 179 (190)
T ss_pred -------------CcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCcccccc
Confidence 3579999999999999998 268999999999999999988765443
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.63 E-value=1.8e-15 Score=124.92 Aligned_cols=155 Identities=28% Similarity=0.547 Sum_probs=107.1
Q ss_pred CCCccCCCCCcCcCCCCCCccCC----CCcccccccCCCCCCCccccCcccccccccCCccccCCCC-CccccccccCCC
Q 030604 9 GICHSCGKTGHRARDCSTHVQSG----GDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN-EPVCNLCNIAGH 83 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~~~----~~~~~C~~C~~~GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~-~~~C~~C~~~GH 83 (174)
..++.++..+|.+..++...... .....+..+...+|+...++. ..|+.|++.||+..+|+. ...|++|++.||
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH 103 (261)
T KOG4400|consen 25 PNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPE-VSCYICGEKGHLGRRCTRIAAACFNCGEGGH 103 (261)
T ss_pred hhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCC-ceeeecCCCCchhhcCcccchhhhhCCCCcc
Confidence 46888999999999998765431 123344456666677777776 778888888888888874 567888888888
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCC-CcccCccccccccCCCCCCCCCCCCCC-CcceeccCCCCcCCCC
Q 030604 84 VARQCPKGDSLGERGGGGGGERGG-GGGGDGGGGG-GRYVGYHDVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYE 160 (174)
Q Consensus 84 ~~~~Cp~~~~~~~~~g~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~C~~Cg~~GH~~~dCp~~-~~~C~~Cg~~GH~a~~ 160 (174)
++++|+..+..... . .....++ -+|.. .... .....+. +.||+|+++|||++|||.+ ...||.|++.+|++++
T Consensus 104 ~~~~c~~~~~~~~~-~-~~~~~c~~~gh~~-~~~~~~~~~~~~-~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~ 179 (261)
T KOG4400|consen 104 IERDCPEAGKEGSS-E-TSCYSCGKTGHRG-CPDADPVDGPKP-AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRD 179 (261)
T ss_pred chhhCCcccCcccc-c-ceeeccCCCcccc-CcccccccCCCC-CccCCCCcCCcchhhCCCCCCCccccCCCcceeccc
Confidence 88888887765420 0 0001122 12222 0000 1122234 7899999999999999986 8999999999999999
Q ss_pred CCCCCCCC
Q 030604 161 CPSGRIAD 168 (174)
Q Consensus 161 C~~~~~~~ 168 (174)
||......
T Consensus 180 C~~~~~~~ 187 (261)
T KOG4400|consen 180 CPSKQKSK 187 (261)
T ss_pred CCcccccc
Confidence 99886553
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.55 E-value=1.4e-14 Score=119.68 Aligned_cols=142 Identities=30% Similarity=0.622 Sum_probs=97.3
Q ss_pred CCCCCC-CCCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCC-cccc-----CcccccccccCCccccCCCC--C
Q 030604 2 ASNCHN-EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIA-ADCT-----NDKACKNCRKTGHIARDCQN--E 72 (174)
Q Consensus 2 ~~~c~~-~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~-~~C~-----~~~~C~~Cg~~GH~~~~Cp~--~ 72 (174)
++.|+. ...|++|++.||++++||.+.........|+.|+..||.. .++. ..+.||+|++.||++.+||. .
T Consensus 85 ~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~ 164 (261)
T KOG4400|consen 85 GRRCTRIAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPENKG 164 (261)
T ss_pred hhcCcccchhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCCCC
Confidence 456665 6789999999999999998865322245789999999998 3322 12359999999999999994 6
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccccCCCCCCCCCCCCC------CCc
Q 030604 73 PVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG------PLI 146 (174)
Q Consensus 73 ~~C~~C~~~GH~~~~Cp~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~dCp~------~~~ 146 (174)
..|++|++.+|++.+||............. .....++ +...+|+.++++. ...
T Consensus 165 ~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~--------------------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 223 (261)
T KOG4400|consen 165 GTCFRCGKVGHGSRDCPSKQKSKSKQGGQR--------------------KGFGACY-DYPQGHKQRACGGSGPDDNFND 223 (261)
T ss_pred CccccCCCcceecccCCccccccccCcccc--------------------cccccCc-cccccccccccCCCCccccccc
Confidence 789999999999999998887533222100 0011233 5566777777765 245
Q ss_pred ceeccCCCCcCCCCCCCC
Q 030604 147 ICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 147 ~C~~Cg~~GH~a~~C~~~ 164 (174)
.+|++...+|.+.+|-..
T Consensus 224 ~~~~~~~~~~~~~~~~~~ 241 (261)
T KOG4400|consen 224 SCYNKLSSGKLDQDCKQS 241 (261)
T ss_pred ccccccccccccchhhhh
Confidence 666666666666665543
No 7
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. 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: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.30 E-value=3.2e-07 Score=45.62 Aligned_cols=16 Identities=56% Similarity=1.329 Sum_probs=8.2
Q ss_pred ceeccCCCCcCCCCCC
Q 030604 147 ICRNCGGRGHMAYECP 162 (174)
Q Consensus 147 ~C~~Cg~~GH~a~~C~ 162 (174)
.||+|++.||++++||
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 3555555555555554
No 8
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. 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: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.20 E-value=8.1e-07 Score=44.14 Aligned_cols=17 Identities=41% Similarity=1.028 Sum_probs=16.0
Q ss_pred ccccCCCCCCCCCCCCC
Q 030604 127 ICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 127 ~C~~Cg~~GH~~~dCp~ 143 (174)
+||+|+++||+++|||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999984
No 9
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.04 E-value=0.00046 Score=39.11 Aligned_cols=17 Identities=41% Similarity=1.034 Sum_probs=8.8
Q ss_pred cccccCCCCCCCCCCCC
Q 030604 126 VICRSCNQMGHMSRDCV 142 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp 142 (174)
.+|+.|++.||+.+|||
T Consensus 9 Y~C~~C~~~GH~i~dCP 25 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCP 25 (32)
T ss_pred CEeecCCCCCccHhHCC
Confidence 34555555555555555
No 10
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.68 E-value=0.00075 Score=38.22 Aligned_cols=22 Identities=41% Similarity=0.989 Sum_probs=16.1
Q ss_pred CCCCCCccCCCCCcCcCCCCCC
Q 030604 6 HNEGICHSCGKTGHRARDCSTH 27 (174)
Q Consensus 6 ~~~~~C~~Cg~~GH~~~~Cp~~ 27 (174)
|..-+|+.|++.||+.+|||..
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCCEeecCCCCCccHhHCCCC
Confidence 4456788888888888888773
No 11
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.54 E-value=0.0015 Score=39.32 Aligned_cols=18 Identities=50% Similarity=1.383 Sum_probs=13.4
Q ss_pred CcceeccCCCCcCCCCCC
Q 030604 145 LIICRNCGGRGHMAYECP 162 (174)
Q Consensus 145 ~~~C~~Cg~~GH~a~~C~ 162 (174)
.+.|.+|++.|||..+|+
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 456777777777777777
No 12
>smart00343 ZnF_C2HC zinc finger.
Probab=94.75 E-value=0.019 Score=30.56 Aligned_cols=15 Identities=60% Similarity=1.517 Sum_probs=9.5
Q ss_pred eeccCCCCcCCCCCC
Q 030604 148 CRNCGGRGHMAYECP 162 (174)
Q Consensus 148 C~~Cg~~GH~a~~C~ 162 (174)
|++|++.||++++||
T Consensus 2 C~~CG~~GH~~~~C~ 16 (26)
T smart00343 2 CYNCGKEGHIARDCP 16 (26)
T ss_pred CccCCCCCcchhhCC
Confidence 566666666666665
No 13
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=94.57 E-value=0.027 Score=50.29 Aligned_cols=42 Identities=36% Similarity=0.877 Sum_probs=23.8
Q ss_pred CCCccCCCCCcCcCCCCCCccCCCCcccccccCCCCCCCccccC
Q 030604 9 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~C~~~GH~~~~C~~ 52 (174)
..|.+|+..||..-+||.... ....+|++|+..||++.+|+.
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~--~~~n~c~~cg~~gH~~~dc~~ 303 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIP--NTTNVCKICGPLGHISIDCKV 303 (554)
T ss_pred ccccccCCCccccccCCcccc--cccccccccCCcccccccCCC
Confidence 456666666666666666521 112266666666666666654
No 14
>smart00343 ZnF_C2HC zinc finger.
Probab=93.77 E-value=0.031 Score=29.77 Aligned_cols=17 Identities=41% Similarity=1.060 Sum_probs=15.4
Q ss_pred ccccCCCCCCCCCCCCC
Q 030604 127 ICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 127 ~C~~Cg~~GH~~~dCp~ 143 (174)
.|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999984
No 15
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=93.57 E-value=0.044 Score=32.99 Aligned_cols=18 Identities=33% Similarity=0.955 Sum_probs=12.3
Q ss_pred CCCCccCCCCCcCcCCCC
Q 030604 8 EGICHSCGKTGHRARDCS 25 (174)
Q Consensus 8 ~~~C~~Cg~~GH~~~~Cp 25 (174)
...|.+|++.||++.+||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 356777777777777776
No 16
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=93.54 E-value=0.061 Score=48.16 Aligned_cols=39 Identities=36% Similarity=0.928 Sum_probs=35.4
Q ss_pred cccccCCCCCCCCCCCCCC----CcceeccCCCCcCCCCCCCC
Q 030604 126 VICRSCNQMGHMSRDCVGP----LIICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~~----~~~C~~Cg~~GH~a~~C~~~ 164 (174)
..|.+|+..||-.-|||.. ..+|..|+..|||++||+..
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence 6899999999999999973 33899999999999999977
No 17
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=90.87 E-value=0.25 Score=29.37 Aligned_cols=19 Identities=47% Similarity=1.006 Sum_probs=9.2
Q ss_pred ceeccCCCCcCC--CCCCCCC
Q 030604 147 ICRNCGGRGHMA--YECPSGR 165 (174)
Q Consensus 147 ~C~~Cg~~GH~a--~~C~~~~ 165 (174)
.|.+||..||++ +.||...
T Consensus 3 kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred cccccccccccccCccCCCCC
Confidence 455555555544 3455443
No 18
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=89.78 E-value=0.16 Score=42.83 Aligned_cols=16 Identities=38% Similarity=0.943 Sum_probs=8.6
Q ss_pred ccccCCCCCCCCCCCC
Q 030604 127 ICRSCNQMGHMSRDCV 142 (174)
Q Consensus 127 ~C~~Cg~~GH~~~dCp 142 (174)
.||.|+++|||+.+||
T Consensus 162 ~cyrcGkeghwskEcP 177 (346)
T KOG0109|consen 162 GCYRCGKEGHWSKECP 177 (346)
T ss_pred HheeccccccccccCC
Confidence 4555555555555555
No 19
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=89.64 E-value=0.14 Score=31.51 Aligned_cols=16 Identities=38% Similarity=1.286 Sum_probs=9.0
Q ss_pred CCccCCCCCcCcCCCC
Q 030604 10 ICHSCGKTGHRARDCS 25 (174)
Q Consensus 10 ~C~~Cg~~GH~~~~Cp 25 (174)
.|+.|+..||...+||
T Consensus 33 ~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECP 48 (49)
T ss_pred hhcCCCCcCcCHhHcC
Confidence 4555555555555554
No 20
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.22 E-value=0.4 Score=40.72 Aligned_cols=21 Identities=38% Similarity=1.053 Sum_probs=14.2
Q ss_pred CCcceeccCCCCcCCCCCCCC
Q 030604 144 PLIICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 144 ~~~~C~~Cg~~GH~a~~C~~~ 164 (174)
+...||+||++|||..+||-.
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CceeEEecCCCCchhhcCCCC
Confidence 356677777777777777743
No 21
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=86.11 E-value=0.58 Score=27.11 Aligned_cols=18 Identities=44% Similarity=0.839 Sum_probs=7.3
Q ss_pred ceeccCCCCcCCCCCCCC
Q 030604 147 ICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 147 ~C~~Cg~~GH~a~~C~~~ 164 (174)
.|.+|++-.|+|+||-..
T Consensus 4 ~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRSK 21 (36)
T ss_dssp C-TTTSSSCS-TTT---T
T ss_pred cCcccCCCcchhhhhhhh
Confidence 455555555555555443
No 22
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=85.89 E-value=0.34 Score=29.77 Aligned_cols=18 Identities=33% Similarity=0.851 Sum_probs=12.4
Q ss_pred cccccccCCCCCCCcccc
Q 030604 34 LRLCNNCYKPGHIAADCT 51 (174)
Q Consensus 34 ~~~C~~C~~~GH~~~~C~ 51 (174)
...|+.|+..||...+||
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 456777777777777765
No 23
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=85.34 E-value=0.55 Score=27.91 Aligned_cols=19 Identities=32% Similarity=0.787 Sum_probs=10.7
Q ss_pred CCCccCCCCCcCc--CCCCCC
Q 030604 9 GICHSCGKTGHRA--RDCSTH 27 (174)
Q Consensus 9 ~~C~~Cg~~GH~~--~~Cp~~ 27 (174)
+.|.+||..||++ +.||..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 3466666666665 445543
No 24
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=83.47 E-value=0.53 Score=39.82 Aligned_cols=25 Identities=40% Similarity=0.880 Sum_probs=21.2
Q ss_pred CCCCCCCCCcceeccCCCCcCCCCCCCCCC
Q 030604 137 MSRDCVGPLIICRNCGGRGHMAYECPSGRI 166 (174)
Q Consensus 137 ~~~dCp~~~~~C~~Cg~~GH~a~~C~~~~~ 166 (174)
+.+.+- ||.||+.|||+.|||..+.
T Consensus 157 mgDq~~-----cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 157 MGDQSG-----CYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred CCCHHH-----heeccccccccccCCccCC
Confidence 456777 9999999999999997654
No 25
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=82.84 E-value=0.95 Score=26.22 Aligned_cols=21 Identities=38% Similarity=0.923 Sum_probs=12.2
Q ss_pred CCCccCCCCCcCcCCCCCCcc
Q 030604 9 GICHSCGKTGHRARDCSTHVQ 29 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~ 29 (174)
..|++|++..|++.+|....+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 468889999999999887654
No 26
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.60 E-value=2.1 Score=38.21 Aligned_cols=39 Identities=31% Similarity=0.773 Sum_probs=24.8
Q ss_pred cccccCCCCCCCCCCCCC-----CCcceeccCCCCcCCCCCCCC
Q 030604 126 VICRSCNQMGHMSRDCVG-----PLIICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~-----~~~~C~~Cg~~GH~a~~C~~~ 164 (174)
.++..+..++|+..-+.. +...|++|...|||...||..
T Consensus 134 ~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 134 YVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred ceeeecccCccccccccccCCCCCCcceecCCCCCccceecccc
Confidence 456666666666655533 456777777777777777644
No 27
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.41 E-value=2 Score=36.65 Aligned_cols=21 Identities=33% Similarity=0.901 Sum_probs=13.2
Q ss_pred CCCccCCCCCcCcCCCCCCcc
Q 030604 9 GICHSCGKTGHRARDCSTHVQ 29 (174)
Q Consensus 9 ~~C~~Cg~~GH~~~~Cp~~~~ 29 (174)
-+||+||+.||+..+||...+
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eeEEecCCCCchhhcCCCCCC
Confidence 356666666666666665543
No 28
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.88 E-value=7.5 Score=34.82 Aligned_cols=60 Identities=20% Similarity=0.432 Sum_probs=36.1
Q ss_pred ccccccCCCCCCCccccC--cccccccccCCccccCCCC------CccccccccCCCCCCCCCCCCCC
Q 030604 35 RLCNNCYKPGHIAADCTN--DKACKNCRKTGHIARDCQN------EPVCNLCNIAGHVARQCPKGDSL 94 (174)
Q Consensus 35 ~~C~~C~~~GH~~~~C~~--~~~C~~Cg~~GH~~~~Cp~------~~~C~~C~~~GH~~~~Cp~~~~~ 94 (174)
..++.++..||....+.. ..++..+...+|....+.. ...|++|...||+...||.....
T Consensus 113 q~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~~~ 180 (448)
T KOG0314|consen 113 QMNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVSGS 180 (448)
T ss_pred hhccccccCCcccccCCCcccceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccCCc
Confidence 355666666666655533 2356666666666555543 23677777777777777766543
No 29
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=42.72 E-value=9.3 Score=34.27 Aligned_cols=24 Identities=38% Similarity=0.643 Sum_probs=17.0
Q ss_pred eeccCCCCcCCCCCCCCCCCCCCC
Q 030604 148 CRNCGGRGHMAYECPSGRIADRGY 171 (174)
Q Consensus 148 C~~Cg~~GH~a~~C~~~~~~~~~~ 171 (174)
||||+..-|-.+|||.+...++|-
T Consensus 131 CFNC~g~~hsLrdC~rp~d~s~I~ 154 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFDFSRIQ 154 (485)
T ss_pred ccccCCCCCccccCCCccccHHHH
Confidence 777777777777777776665553
No 30
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=33.81 E-value=18 Score=34.79 Aligned_cols=17 Identities=47% Similarity=1.040 Sum_probs=8.9
Q ss_pred ccccCCCCCCCCCCCCC
Q 030604 127 ICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 127 ~C~~Cg~~GH~~~dCp~ 143 (174)
.|+.|++.||.+.||..
T Consensus 262 ~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 262 RCFLCGQTGHEAKDCEG 278 (931)
T ss_pred cchhhcccCCcHhhcCC
Confidence 45555555555555543
No 31
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=33.24 E-value=9.6 Score=29.23 Aligned_cols=19 Identities=32% Similarity=0.854 Sum_probs=14.1
Q ss_pred cccccccCCCCCCCccccC
Q 030604 34 LRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 34 ~~~C~~C~~~GH~~~~C~~ 52 (174)
.+.|.+|.+.||+...|.+
T Consensus 27 ~~rCQKClq~GHWtYECk~ 45 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKN 45 (177)
T ss_pred chhHHHHHhhccceeeecC
Confidence 4677777777777777766
No 32
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=33.04 E-value=29 Score=25.65 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=10.4
Q ss_pred cccccccCCCCCCCCCCCCC
Q 030604 124 HDVICRSCNQMGHMSRDCVG 143 (174)
Q Consensus 124 ~~~~C~~Cg~~GH~~~dCp~ 143 (174)
..++|..|+ -.||...||.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPY 123 (128)
T ss_pred ceEEeCCCC-CCcccccCCc
Confidence 335566664 4466666653
No 33
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=32.28 E-value=21 Score=34.36 Aligned_cols=20 Identities=40% Similarity=0.727 Sum_probs=14.4
Q ss_pred CcccccccCCCCCCCccccC
Q 030604 33 DLRLCNNCYKPGHIAADCTN 52 (174)
Q Consensus 33 ~~~~C~~C~~~GH~~~~C~~ 52 (174)
+.+.||.|++.||.+.+|..
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEG 278 (931)
T ss_pred CcccchhhcccCCcHhhcCC
Confidence 45567777777777777765
No 34
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=31.86 E-value=36 Score=26.94 Aligned_cols=33 Identities=24% Similarity=0.497 Sum_probs=21.2
Q ss_pred cccccCCCCCCCCCCCCCCCcceeccCCCCcCCCCCCCC
Q 030604 126 VICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSG 164 (174)
Q Consensus 126 ~~C~~Cg~~GH~~~dCp~~~~~C~~Cg~~GH~a~~C~~~ 164 (174)
..||.|++.||+.+.|-+ +|.+ .++..+.+-.+
T Consensus 101 ~~~~r~G~rg~~~r~~~~----sy~r--~~r~~~rrrs~ 133 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD----SYSR--RSRSPRRRRSP 133 (195)
T ss_pred cccccCCCcccccccccc----cccc--cCCCcccccCC
Confidence 348888888888888864 3333 45555555444
No 35
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=27.45 E-value=36 Score=21.59 Aligned_cols=16 Identities=38% Similarity=0.899 Sum_probs=4.0
Q ss_pred cccccccCC---ccccCCC
Q 030604 55 ACKNCRKTG---HIARDCQ 70 (174)
Q Consensus 55 ~C~~Cg~~G---H~~~~Cp 70 (174)
+|..||..| |+.+.||
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP 53 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCP 53 (55)
T ss_dssp --TTT---GGG---GGG-T
T ss_pred cCCCCcCcCccccccccCc
Confidence 455555543 4555555
No 36
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=27.09 E-value=18 Score=27.80 Aligned_cols=22 Identities=27% Similarity=0.830 Sum_probs=14.8
Q ss_pred cCcccccccccCCccccCCCCC
Q 030604 51 TNDKACKNCRKTGHIARDCQNE 72 (174)
Q Consensus 51 ~~~~~C~~Cg~~GH~~~~Cp~~ 72 (174)
++.+.|..|.+.||....|.+.
T Consensus 25 ~~~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 25 GSSARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred ccchhHHHHHhhccceeeecCc
Confidence 3445677777777777777653
No 37
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=23.01 E-value=54 Score=24.21 Aligned_cols=24 Identities=25% Similarity=0.556 Sum_probs=19.8
Q ss_pred CCCcceeccCCCCcCCCCCCCCCCC
Q 030604 143 GPLIICRNCGGRGHMAYECPSGRIA 167 (174)
Q Consensus 143 ~~~~~C~~Cg~~GH~a~~C~~~~~~ 167 (174)
...+.|..|+ -.||...||....+
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd~~ 127 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKDTL 127 (128)
T ss_pred CceEEeCCCC-CCcccccCCccccc
Confidence 3579999997 78999999987543
No 38
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=20.63 E-value=58 Score=29.37 Aligned_cols=20 Identities=40% Similarity=0.886 Sum_probs=17.8
Q ss_pred CCccCCCCCcCcCCCCCCcc
Q 030604 10 ICHSCGKTGHRARDCSTHVQ 29 (174)
Q Consensus 10 ~C~~Cg~~GH~~~~Cp~~~~ 29 (174)
.||||+..-|..++||.+..
T Consensus 130 ~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred cccccCCCCCccccCCCccc
Confidence 38999999999999998864
Done!