Query 026649
Match_columns 235
No_of_seqs 267 out of 1763
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 10:47:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026649hhsearch_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 1.9E-28 4.1E-33 198.6 10.2 133 52-225 2-148 (148)
2 PTZ00368 universal minicircle 99.9 3.1E-27 6.8E-32 191.5 9.4 128 13-152 1-148 (148)
3 COG5082 AIR1 Arginine methyltr 99.8 3.7E-21 8E-26 159.7 6.5 105 94-230 59-178 (190)
4 COG5082 AIR1 Arginine methyltr 99.8 6.3E-20 1.4E-24 152.3 6.7 85 5-90 53-141 (190)
5 KOG4400 E3 ubiquitin ligase in 99.8 5.6E-18 1.2E-22 149.2 12.4 194 11-226 23-242 (261)
6 KOG4400 E3 ubiquitin ligase in 99.6 1.7E-15 3.7E-20 133.4 9.7 106 95-228 72-186 (261)
7 PF00098 zf-CCHC: Zinc knuckle 98.2 5.7E-07 1.2E-11 47.4 1.5 16 208-223 2-17 (18)
8 PF00098 zf-CCHC: Zinc knuckle 98.1 2.2E-06 4.7E-11 45.1 1.8 17 188-204 2-18 (18)
9 PF13696 zf-CCHC_2: Zinc knuck 96.8 0.001 2.2E-08 40.1 2.1 19 206-224 8-26 (32)
10 PF13696 zf-CCHC_2: Zinc knuck 96.4 0.0016 3.4E-08 39.2 1.1 22 131-152 6-27 (32)
11 PF13917 zf-CCHC_3: Zinc knuck 96.4 0.002 4.4E-08 41.2 1.6 19 205-223 3-21 (42)
12 smart00343 ZnF_C2HC zinc finge 94.2 0.026 5.6E-07 32.0 1.3 17 208-224 1-17 (26)
13 PF14392 zf-CCHC_4: Zinc knuck 94.2 0.017 3.7E-07 38.0 0.5 25 5-29 24-48 (49)
14 PF13917 zf-CCHC_3: Zinc knuck 93.4 0.042 9E-07 35.2 1.2 19 186-204 4-22 (42)
15 KOG0109 RNA-binding protein LA 93.3 0.043 9.4E-07 49.1 1.6 17 187-203 161-177 (346)
16 smart00343 ZnF_C2HC zinc finge 92.8 0.052 1.1E-06 30.7 1.0 17 188-204 1-17 (26)
17 KOG0119 Splicing factor 1/bran 91.8 0.12 2.7E-06 49.2 2.7 37 116-152 263-304 (554)
18 KOG0119 Splicing factor 1/bran 90.6 0.19 4.2E-06 47.9 2.7 39 187-225 262-304 (554)
19 KOG0109 RNA-binding protein LA 88.0 0.26 5.6E-06 44.3 1.4 23 206-228 160-182 (346)
20 PF14787 zf-CCHC_5: GAG-polypr 86.6 0.48 1E-05 29.2 1.6 18 208-225 4-21 (36)
21 PF15288 zf-CCHC_6: Zinc knuck 86.5 0.37 8E-06 30.5 1.1 12 14-25 3-14 (40)
22 COG5222 Uncharacterized conser 86.2 0.53 1.2E-05 42.4 2.4 22 205-226 175-196 (427)
23 PF15288 zf-CCHC_6: Zinc knuck 83.6 0.67 1.5E-05 29.3 1.3 18 207-224 2-21 (40)
24 KOG0314 Predicted E3 ubiquitin 83.2 1.7 3.8E-05 41.3 4.5 42 187-228 134-180 (448)
25 PF14392 zf-CCHC_4: Zinc knuck 81.6 0.59 1.3E-05 30.6 0.5 17 187-203 32-48 (49)
26 PF14787 zf-CCHC_5: GAG-polypr 79.3 1.2 2.5E-05 27.5 1.2 17 13-29 3-19 (36)
27 COG5222 Uncharacterized conser 71.1 1.8 3.9E-05 39.1 0.8 21 134-154 177-197 (427)
28 KOG0107 Alternative splicing f 64.0 16 0.00034 30.8 5.0 34 189-228 103-136 (195)
29 KOG2044 5'-3' exonuclease HKE1 62.2 3 6.5E-05 42.3 0.5 21 9-29 257-277 (931)
30 PF01485 IBR: IBR domain; Int 53.4 12 0.00026 24.8 2.2 13 51-63 49-61 (64)
31 KOG0314 Predicted E3 ubiquitin 52.7 20 0.00044 34.2 4.3 18 187-204 159-176 (448)
32 KOG2673 Uncharacterized conser 46.4 7.7 0.00017 37.0 0.4 26 208-233 130-155 (485)
33 KOG0107 Alternative splicing f 45.5 19 0.00041 30.3 2.5 19 206-224 100-118 (195)
34 KOG3116 Predicted C3H1-type Zn 30.2 14 0.0003 30.1 -0.5 19 186-204 27-45 (177)
35 PF12353 eIF3g: Eukaryotic tra 24.4 46 0.001 26.2 1.5 19 185-204 105-123 (128)
36 PF12353 eIF3g: Eukaryotic tra 20.9 60 0.0013 25.6 1.5 22 205-227 105-126 (128)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.95 E-value=1.9e-28 Score=198.63 Aligned_cols=133 Identities=34% Similarity=0.819 Sum_probs=89.1
Q ss_pred cCCCCCCCCCCCCCCCC--------ccccccCCCCCcCCccCCCCcccCCCCcccccCCCCCCCCCCCCCcccccccccC
Q 026649 52 RCWNCREPGHMASNCHN--------EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKT 123 (235)
Q Consensus 52 ~C~~Cg~~GH~~~~Cp~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~ 123 (235)
+||+|++.||++++||+ ...||+|++.||++++||..... .....|++|++.||++++||+... .
T Consensus 2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~Cg~~GH~~~~Cp~~~~------~ 74 (148)
T PTZ00368 2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGG-RGERSCYNCGKTGHLSRECPEAPP------G 74 (148)
T ss_pred cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCC-CCCcccCCCCCcCcCcccCCCccc------C
Confidence 45555555555555554 23577777777777777654321 123445555555555555554210 0
Q ss_pred ccccCCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCccccccCCCCccCCCCC
Q 026649 124 GHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCV 203 (235)
Q Consensus 124 GH~~~~Cp~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~rdC~ 203 (235)
.....|++|++.||++++||+.... . ....+||+|++.||+++|||
T Consensus 75 -------~~~~~C~~Cg~~GH~~~~C~~~~~~-----~----------------------~~~~~C~~Cg~~gH~~~~C~ 120 (148)
T PTZ00368 75 -------SGPRSCYNCGQTGHISRECPNRAKG-----G----------------------AARRACYNCGGEGHISRDCP 120 (148)
T ss_pred -------CCCcccCcCCCCCcccccCCCcccc-----c----------------------ccchhhcccCcCCcchhcCC
Confidence 0234799999999999999985421 0 12368999999999999999
Q ss_pred CC------CcceecCCCCCcCCCCCCCC
Q 026649 204 GP------LIICRNCGGRGHMAYECPSG 225 (235)
Q Consensus 204 ~~------~~~C~~Cg~~GH~~~~Cp~~ 225 (235)
.. .+.||+|++.|||++|||+.
T Consensus 121 ~~~~~~~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 121 NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CccccCCCCCccccCCCcCcccccCCCC
Confidence 84 58999999999999999973
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.94 E-value=3.1e-27 Score=191.48 Aligned_cols=128 Identities=42% Similarity=0.965 Sum_probs=82.1
Q ss_pred ccccccCCCCccCCCCCCCcccCCCCCCCCCCccccccccCCCCCCCCCCCCCCCCc------cccccCCCCCcCCccCC
Q 026649 13 NLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNE------GICHSCGKTGHRARDCS 86 (235)
Q Consensus 13 ~~C~~C~~~GH~~~~Cp~~~~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~~------~~C~~Cg~~GH~~~~Cp 86 (235)
++||+|++.||++++||... ..+.. ....||+|++.||++++||+. ..|++|++.||++++||
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~------~~~~~-----~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp 69 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSA------PAGAA-----KARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECP 69 (148)
T ss_pred CcCCCCCCCCcCcccCcCCC------CCCCC-----CCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCC
Confidence 47999999999999998731 00000 013444444444444444442 24666666666666666
Q ss_pred CCcccCCCCcccccCCCCCCCCCCCCCcc-------cccccccCccccCCCCCC-------CCCCccccCCCCCCCCCCC
Q 026649 87 THVQSGGDLRLCNNCYKPGHIAADCTNDK-------ACKNCRKTGHIARDCQNE-------PVCNLCNIAGHVARQCPKG 152 (235)
Q Consensus 87 ~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~-------~C~~Cg~~GH~~~~Cp~~-------~~C~~C~~~GH~~~~Cp~~ 152 (235)
+.... ...+.|++|++.||++++||+.. .||+|++.||++++||+. ++||+|++.|||++|||++
T Consensus 70 ~~~~~-~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 70 EAPPG-SGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CcccC-CCCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCCCC
Confidence 54322 13456777777777777776532 577777777777777763 5899999999999999873
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.83 E-value=3.7e-21 Score=159.66 Aligned_cols=105 Identities=33% Similarity=0.781 Sum_probs=83.8
Q ss_pred CCcccccCCCCCCCCCCCCCcccccccccCccccCCCCCCCCCCccccCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC
Q 026649 94 DLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC-PKGDSLGERGGGGGGERGGGGGG 172 (235)
Q Consensus 94 ~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~~~~C-p~~~~~~~~~~~~~~~~~~~~g~ 172 (235)
+.+.|++|++.||+++||| .++||+|...+|.+..||+..+|++|++.||++++| |..+
T Consensus 59 ~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~------------------- 118 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD------------------- 118 (190)
T ss_pred cccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccc-------------------
Confidence 4567888888888888888 478888866888888888888888888888888888 4543
Q ss_pred CCCCCCCCCCCccCccccccCCCCccCCCCCC--------------CCcceecCCCCCcCCCCCCCCCCCCC
Q 026649 173 DGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--------------PLIICRNCGGRGHMAYECPSGRIADR 230 (235)
Q Consensus 173 ~~~~~~~~~~~~~~~~C~~C~~~gH~~rdC~~--------------~~~~C~~Cg~~GH~~~~Cp~~~~~~~ 230 (235)
+.+.|+.|+...|.+++||. ..+.||+|+..+||++||+.++.+..
T Consensus 119 ------------~~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~ 178 (190)
T COG5082 119 ------------QQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRV 178 (190)
T ss_pred ------------cCcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCccccc
Confidence 34678888888888888886 25789999999999999987665543
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.80 E-value=6.3e-20 Score=152.33 Aligned_cols=85 Identities=33% Similarity=0.905 Sum_probs=70.3
Q ss_pred ccccCcCCccccccCCCCccCCCCCCCcccCCCCCCCCCCccccccccCCCCCCCCCCCCCC-CCc---cccccCCCCCc
Q 026649 5 VLSFMSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNC-HNE---GICHSCGKTGH 80 (235)
Q Consensus 5 ~~~~~~~~~~C~~C~~~GH~~~~Cp~~~~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~~~~C-p~~---~~C~~Cg~~GH 80 (235)
+..+.....+|+||++.||++++|| ..+|++|...||.+..||..++|++|++.||++++| |.. ..|+.|....|
T Consensus 53 ~~~~~~~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H 131 (190)
T COG5082 53 VSAIREENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRH 131 (190)
T ss_pred cccccccccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCcc
Confidence 3344455779999999999999999 569999977899999999888899999999999999 543 36888888888
Q ss_pred CCccCCCCcc
Q 026649 81 RARDCSTHVQ 90 (235)
Q Consensus 81 ~~~~Cp~~~~ 90 (235)
++++||++|+
T Consensus 132 ~s~~Cp~~~k 141 (190)
T COG5082 132 SSEDCPSIWK 141 (190)
T ss_pred ccccCccccc
Confidence 8888888886
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=5.6e-18 Score=149.20 Aligned_cols=194 Identities=29% Similarity=0.617 Sum_probs=149.8
Q ss_pred CCccccccCCCCccCCCCCCCc-----------ccCCCCCCCCCCccccccccCCCCCCCCCCCCCCCC-ccccccCCCC
Q 026649 11 QGNLCNNCKRPGHFARECPNVA-----------VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN-EGICHSCGKT 78 (235)
Q Consensus 11 ~~~~C~~C~~~GH~~~~Cp~~~-----------~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~ 78 (235)
....++++.+.+|.+..++... .+..+...+|+...++. ..|+.|++.+|..++|+. ...|++|++.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~c~~~g~~~~~~~~~~~~~~~c~~C~~~ 101 (261)
T KOG4400|consen 23 SSPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPE-VSCYICGEKGHLGRRCTRIAAACFNCGEG 101 (261)
T ss_pred cchhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCC-ceeeecCCCCchhhcCcccchhhhhCCCC
Confidence 4568999999999999998652 34445566677666766 699999999999999996 6789999999
Q ss_pred CcCCccCCCCcccCCCCcccccCCCCCCCC-CCCC-----CcccccccccCccccCCCCC--CCCCCccccCCCCCCCCC
Q 026649 79 GHRARDCSTHVQSGGDLRLCNNCYKPGHIA-ADCT-----NDKACKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCP 150 (235)
Q Consensus 79 GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~~-~~Cp-----~~~~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~~~~Cp 150 (235)
||++++||.++........||.|++.+|.. .++. ..+.||+|++.||++.+||+ ..+||.|+..+|++++||
T Consensus 102 gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~ 181 (261)
T KOG4400|consen 102 GHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCP 181 (261)
T ss_pred ccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCC
Confidence 999999999987443466899999999999 4332 22459999999999999994 789999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCccccccCCCCccCCCCCC------CCcceecCCCCCcCCCCCCC
Q 026649 151 KGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG------PLIICRNCGGRGHMAYECPS 224 (235)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~rdC~~------~~~~C~~Cg~~GH~~~~Cp~ 224 (235)
.+......... .. ...-.++ +...+|+.++++. ....+|++...+|.+.+|-+
T Consensus 182 ~~~~~~~~~~~--------------~~------~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (261)
T KOG4400|consen 182 SKQKSKSKQGG--------------QR------KGFGACY-DYPQGHKQRACGGSGPDDNFNDSCYNKLSSGKLDQDCKQ 240 (261)
T ss_pred ccccccccCcc--------------cc------cccccCc-cccccccccccCCCCcccccccccccccccccccchhhh
Confidence 98754211110 00 0112233 6678999999876 46788888888888877765
Q ss_pred CC
Q 026649 225 GR 226 (235)
Q Consensus 225 ~~ 226 (235)
..
T Consensus 241 ~~ 242 (261)
T KOG4400|consen 241 SS 242 (261)
T ss_pred hc
Confidence 43
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.62 E-value=1.7e-15 Score=133.44 Aligned_cols=106 Identities=37% Similarity=0.773 Sum_probs=63.0
Q ss_pred CcccccCCCCCCCCCCCCC-cccccccccCccccCCCCCC-------CCCCccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 026649 95 LRLCNNCYKPGHIAADCTN-DKACKNCRKTGHIARDCQNE-------PVCNLCNIAGHVARQCPKGDSLGERGGGGGGER 166 (235)
Q Consensus 95 ~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~GH~~~~Cp~~-------~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~ 166 (235)
...|++|++.+|++.+|+. ...|++|++.||++++||.. ..||.|+..||.. |+......
T Consensus 72 ~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~--~~~~~~~~---------- 139 (261)
T KOG4400|consen 72 EVSCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRG--CPDADPVD---------- 139 (261)
T ss_pred CceeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcccccceeeccCCCcccc--Cccccccc----------
Confidence 3456666666666666653 34566666666666666532 2466777777776 33222100
Q ss_pred CCCCCCCCCCCCCCCCCccCccccccCCCCccCCCCCCC-CcceecCCCCCcCCCCCCCCCCC
Q 026649 167 GGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRIA 228 (235)
Q Consensus 167 ~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~rdC~~~-~~~C~~Cg~~GH~~~~Cp~~~~~ 228 (235)
..+. +.||+|+++|||++|||.+ ...||.|++.+|++++||+....
T Consensus 140 ---------------~~~~-~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~ 186 (261)
T KOG4400|consen 140 ---------------GPKP-AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKS 186 (261)
T ss_pred ---------------CCCC-CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccc
Confidence 0022 6677777777777777765 67777777777777777765443
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=98.23 E-value=5.7e-07 Score=47.40 Aligned_cols=16 Identities=56% Similarity=1.329 Sum_probs=8.9
Q ss_pred ceecCCCCCcCCCCCC
Q 026649 208 ICRNCGGRGHMAYECP 223 (235)
Q Consensus 208 ~C~~Cg~~GH~~~~Cp 223 (235)
.||+|++.||+++|||
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 4555555555555555
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=98.07 E-value=2.2e-06 Score=45.15 Aligned_cols=17 Identities=41% Similarity=1.028 Sum_probs=15.9
Q ss_pred cccccCCCCccCCCCCC
Q 026649 188 ICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 188 ~C~~C~~~gH~~rdC~~ 204 (235)
+||+|+++||+++|||+
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=96.79 E-value=0.001 Score=40.05 Aligned_cols=19 Identities=37% Similarity=1.097 Sum_probs=10.6
Q ss_pred CcceecCCCCCcCCCCCCC
Q 026649 206 LIICRNCGGRGHMAYECPS 224 (235)
Q Consensus 206 ~~~C~~Cg~~GH~~~~Cp~ 224 (235)
.-+|+.|++.|||..|||+
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 3455555555555555555
No 10
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.36 E-value=0.0016 Score=39.20 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=16.4
Q ss_pred CCCCCCCccccCCCCCCCCCCC
Q 026649 131 QNEPVCNLCNIAGHVARQCPKG 152 (235)
Q Consensus 131 p~~~~C~~C~~~GH~~~~Cp~~ 152 (235)
|..-+|++|+++||+.++||++
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCCEeecCCCCCccHhHCCCC
Confidence 3445788888888888888874
No 11
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.35 E-value=0.002 Score=41.25 Aligned_cols=19 Identities=47% Similarity=1.316 Sum_probs=15.0
Q ss_pred CCcceecCCCCCcCCCCCC
Q 026649 205 PLIICRNCGGRGHMAYECP 223 (235)
Q Consensus 205 ~~~~C~~Cg~~GH~~~~Cp 223 (235)
..+.|.+|++.|||..|||
T Consensus 3 ~~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCCcCcccCCCCcchhhCC
Confidence 3567888888888888888
No 12
>smart00343 ZnF_C2HC zinc finger.
Probab=94.22 E-value=0.026 Score=31.98 Aligned_cols=17 Identities=53% Similarity=1.300 Sum_probs=11.6
Q ss_pred ceecCCCCCcCCCCCCC
Q 026649 208 ICRNCGGRGHMAYECPS 224 (235)
Q Consensus 208 ~C~~Cg~~GH~~~~Cp~ 224 (235)
.|++|++.||++++||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 36677777777777763
No 13
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=94.15 E-value=0.017 Score=37.97 Aligned_cols=25 Identities=32% Similarity=0.789 Sum_probs=21.2
Q ss_pred ccccCcCCccccccCCCCccCCCCC
Q 026649 5 VLSFMSQGNLCNNCKRPGHFARECP 29 (235)
Q Consensus 5 ~~~~~~~~~~C~~C~~~GH~~~~Cp 29 (235)
.+.|...+.+|++|+..||..++||
T Consensus 24 ~v~YE~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 24 KVKYERLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred EEEECCcChhhcCCCCcCcCHhHcC
Confidence 3567778899999999999999997
No 14
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=93.40 E-value=0.042 Score=35.19 Aligned_cols=19 Identities=37% Similarity=0.896 Sum_probs=17.3
Q ss_pred CccccccCCCCccCCCCCC
Q 026649 186 DVICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 186 ~~~C~~C~~~gH~~rdC~~ 204 (235)
...|.+|++.|||..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4789999999999999993
No 15
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=93.28 E-value=0.043 Score=49.10 Aligned_cols=17 Identities=35% Similarity=0.868 Sum_probs=9.6
Q ss_pred ccccccCCCCccCCCCC
Q 026649 187 VICRSCNQMGHMSRDCV 203 (235)
Q Consensus 187 ~~C~~C~~~gH~~rdC~ 203 (235)
..||+|+++|||+++||
T Consensus 161 ~~cyrcGkeghwskEcP 177 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECP 177 (346)
T ss_pred HHheeccccccccccCC
Confidence 44555555555555555
No 16
>smart00343 ZnF_C2HC zinc finger.
Probab=92.82 E-value=0.052 Score=30.73 Aligned_cols=17 Identities=41% Similarity=1.060 Sum_probs=15.4
Q ss_pred cccccCCCCccCCCCCC
Q 026649 188 ICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 188 ~C~~C~~~gH~~rdC~~ 204 (235)
+|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999983
No 17
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=91.84 E-value=0.12 Score=49.19 Aligned_cols=37 Identities=41% Similarity=0.985 Sum_probs=20.7
Q ss_pred cccccccCccccCCCCCC-----CCCCccccCCCCCCCCCCC
Q 026649 116 ACKNCRKTGHIARDCQNE-----PVCNLCNIAGHVARQCPKG 152 (235)
Q Consensus 116 ~C~~Cg~~GH~~~~Cp~~-----~~C~~C~~~GH~~~~Cp~~ 152 (235)
.|.+|+..+|-..+||.. .+|.+|+..||+++||+.+
T Consensus 263 ~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 263 ACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCCccccccCCcccccccccccccCCcccccccCCCc
Confidence 344444444444444432 2677777777777777665
No 18
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=90.62 E-value=0.19 Score=47.91 Aligned_cols=39 Identities=36% Similarity=0.928 Sum_probs=35.3
Q ss_pred ccccccCCCCccCCCCCCC----CcceecCCCCCcCCCCCCCC
Q 026649 187 VICRSCNQMGHMSRDCVGP----LIICRNCGGRGHMAYECPSG 225 (235)
Q Consensus 187 ~~C~~C~~~gH~~rdC~~~----~~~C~~Cg~~GH~~~~Cp~~ 225 (235)
..|.+|+..||-.-|||.. ..+|..|+..|||+.||+..
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 6799999999999999972 34999999999999999976
No 19
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=88.04 E-value=0.26 Score=44.27 Aligned_cols=23 Identities=39% Similarity=0.819 Sum_probs=19.7
Q ss_pred CcceecCCCCCcCCCCCCCCCCC
Q 026649 206 LIICRNCGGRGHMAYECPSGRIA 228 (235)
Q Consensus 206 ~~~C~~Cg~~GH~~~~Cp~~~~~ 228 (235)
.-.||+||++|||++|||..+..
T Consensus 160 q~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred HHHheeccccccccccCCccCCC
Confidence 46899999999999999986543
No 20
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=86.64 E-value=0.48 Score=29.19 Aligned_cols=18 Identities=44% Similarity=0.839 Sum_probs=7.0
Q ss_pred ceecCCCCCcCCCCCCCC
Q 026649 208 ICRNCGGRGHMAYECPSG 225 (235)
Q Consensus 208 ~C~~Cg~~GH~~~~Cp~~ 225 (235)
.|.+|++-.|||.||-+.
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 21
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=86.52 E-value=0.37 Score=30.47 Aligned_cols=12 Identities=42% Similarity=0.933 Sum_probs=6.9
Q ss_pred cccccCCCCccC
Q 026649 14 LCNNCKRPGHFA 25 (235)
Q Consensus 14 ~C~~C~~~GH~~ 25 (235)
.|.+|+.+||++
T Consensus 3 kC~~CG~~GH~~ 14 (40)
T PF15288_consen 3 KCKNCGAFGHMR 14 (40)
T ss_pred cccccccccccc
Confidence 455566666655
No 22
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.17 E-value=0.53 Score=42.44 Aligned_cols=22 Identities=36% Similarity=1.028 Sum_probs=17.0
Q ss_pred CCcceecCCCCCcCCCCCCCCC
Q 026649 205 PLIICRNCGGRGHMAYECPSGR 226 (235)
Q Consensus 205 ~~~~C~~Cg~~GH~~~~Cp~~~ 226 (235)
++-.||+||++|||...||...
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred CceeEEecCCCCchhhcCCCCC
Confidence 4677888888888888888643
No 23
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=83.60 E-value=0.67 Score=29.30 Aligned_cols=18 Identities=50% Similarity=1.233 Sum_probs=9.6
Q ss_pred cceecCCCCCcCC--CCCCC
Q 026649 207 IICRNCGGRGHMA--YECPS 224 (235)
Q Consensus 207 ~~C~~Cg~~GH~~--~~Cp~ 224 (235)
+.|.+||..||+. +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 3455555555554 45554
No 24
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.25 E-value=1.7 Score=41.28 Aligned_cols=42 Identities=29% Similarity=0.690 Sum_probs=25.6
Q ss_pred ccccccCCCCccCCCCCC-----CCcceecCCCCCcCCCCCCCCCCC
Q 026649 187 VICRSCNQMGHMSRDCVG-----PLIICRNCGGRGHMAYECPSGRIA 228 (235)
Q Consensus 187 ~~C~~C~~~gH~~rdC~~-----~~~~C~~Cg~~GH~~~~Cp~~~~~ 228 (235)
.++-.|..++||-.-+.. +...||+|...|||...||.+...
T Consensus 134 ~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~~~ 180 (448)
T KOG0314|consen 134 YVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVSGS 180 (448)
T ss_pred ceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccCCc
Confidence 345555555555544432 567777777777777777765443
No 25
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=81.63 E-value=0.59 Score=30.58 Aligned_cols=17 Identities=29% Similarity=0.976 Sum_probs=10.1
Q ss_pred ccccccCCCCccCCCCC
Q 026649 187 VICRSCNQMGHMSRDCV 203 (235)
Q Consensus 187 ~~C~~C~~~gH~~rdC~ 203 (235)
..|++|+..||..++||
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 44666666666666664
No 26
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=79.25 E-value=1.2 Score=27.50 Aligned_cols=17 Identities=41% Similarity=0.933 Sum_probs=7.7
Q ss_pred ccccccCCCCccCCCCC
Q 026649 13 NLCNNCKRPGHFARECP 29 (235)
Q Consensus 13 ~~C~~C~~~GH~~~~Cp 29 (235)
..|++|++--|++++|-
T Consensus 3 ~~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECR 19 (36)
T ss_dssp -C-TTTSSSCS-TTT--
T ss_pred ccCcccCCCcchhhhhh
Confidence 45666666666666664
No 27
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=71.07 E-value=1.8 Score=39.14 Aligned_cols=21 Identities=33% Similarity=0.797 Sum_probs=16.4
Q ss_pred CCCCccccCCCCCCCCCCCCC
Q 026649 134 PVCNLCNIAGHVARQCPKGDS 154 (235)
Q Consensus 134 ~~C~~C~~~GH~~~~Cp~~~~ 154 (235)
-+||+||++||+..+||.+..
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eeEEecCCCCchhhcCCCCCC
Confidence 468888888888888887653
No 28
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=63.98 E-value=16 Score=30.75 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=24.6
Q ss_pred ccccCCCCccCCCCCCCCcceecCCCCCcCCCCCCCCCCC
Q 026649 189 CRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIA 228 (235)
Q Consensus 189 C~~C~~~gH~~rdC~~~~~~C~~Cg~~GH~~~~Cp~~~~~ 228 (235)
||.|++.||+.+.|.+ +|.+ .++..+.+-++...
T Consensus 103 ~~r~G~rg~~~r~~~~----sy~r--~~r~~~rrrs~~rs 136 (195)
T KOG0107|consen 103 CYRCGERGHIGRNCKD----SYSR--RSRSPRRRRSPSRS 136 (195)
T ss_pred cccCCCcccccccccc----cccc--cCCCcccccCCCCC
Confidence 9999999999998853 5544 46666666655544
No 29
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=62.19 E-value=3 Score=42.26 Aligned_cols=21 Identities=29% Similarity=0.657 Sum_probs=12.0
Q ss_pred CcCCccccccCCCCccCCCCC
Q 026649 9 MSQGNLCNNCKRPGHFARECP 29 (235)
Q Consensus 9 ~~~~~~C~~C~~~GH~~~~Cp 29 (235)
++++..|+.|+++||.+.+|.
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~ 277 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCE 277 (931)
T ss_pred CCCcccchhhcccCCcHhhcC
Confidence 555555555555555555554
No 30
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=53.39 E-value=12 Score=24.76 Aligned_cols=13 Identities=38% Similarity=0.894 Sum_probs=8.5
Q ss_pred ccCCCCCCCCCCC
Q 026649 51 ARCWNCREPGHMA 63 (235)
Q Consensus 51 ~~C~~Cg~~GH~~ 63 (235)
.+|+.|+++-|..
T Consensus 49 ~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 49 EFCFKCGEPWHEG 61 (64)
T ss_dssp EECSSSTSESCTT
T ss_pred cCccccCcccCCC
Confidence 5677777766653
No 31
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.69 E-value=20 Score=34.21 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=11.5
Q ss_pred ccccccCCCCccCCCCCC
Q 026649 187 VICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 187 ~~C~~C~~~gH~~rdC~~ 204 (235)
.+|++|.+.|||...||.
T Consensus 159 y~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 159 YKCVKCPTPGPWIKACPT 176 (448)
T ss_pred cceecCCCCCccceeccc
Confidence 556666666666666664
No 32
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=46.37 E-value=7.7 Score=37.00 Aligned_cols=26 Identities=38% Similarity=0.621 Sum_probs=22.1
Q ss_pred ceecCCCCCcCCCCCCCCCCCCCCCC
Q 026649 208 ICRNCGGRGHMAYECPSGRIADRGYR 233 (235)
Q Consensus 208 ~C~~Cg~~GH~~~~Cp~~~~~~~~~~ 233 (235)
.|+||+..-|-.+|||.+..+.||.|
T Consensus 130 ~CFNC~g~~hsLrdC~rp~d~s~I~r 155 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPRPFDFSRIQR 155 (485)
T ss_pred cccccCCCCCccccCCCccccHHHHH
Confidence 38999999999999999988887754
No 33
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=45.50 E-value=19 Score=30.32 Aligned_cols=19 Identities=37% Similarity=0.919 Sum_probs=16.9
Q ss_pred CcceecCCCCCcCCCCCCC
Q 026649 206 LIICRNCGGRGHMAYECPS 224 (235)
Q Consensus 206 ~~~C~~Cg~~GH~~~~Cp~ 224 (235)
...||+||+.|||.+.|.+
T Consensus 100 ~~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 100 RGFCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccccCCCcccccccccc
Confidence 3459999999999999988
No 34
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=30.16 E-value=14 Score=30.14 Aligned_cols=19 Identities=32% Similarity=0.807 Sum_probs=14.8
Q ss_pred CccccccCCCCccCCCCCC
Q 026649 186 DVICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 186 ~~~C~~C~~~gH~~rdC~~ 204 (235)
.+.|-+|-+.|||..+|.+
T Consensus 27 ~~rCQKClq~GHWtYECk~ 45 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKN 45 (177)
T ss_pred chhHHHHHhhccceeeecC
Confidence 4678888888888888865
No 35
>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=24.37 E-value=46 Score=26.25 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=12.2
Q ss_pred cCccccccCCCCccCCCCCC
Q 026649 185 HDVICRSCNQMGHMSRDCVG 204 (235)
Q Consensus 185 ~~~~C~~C~~~gH~~rdC~~ 204 (235)
..++|+.|+ -.||...||-
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 446677774 5677777763
No 36
>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=20.89 E-value=60 Score=25.59 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=18.2
Q ss_pred CCcceecCCCCCcCCCCCCCCCC
Q 026649 205 PLIICRNCGGRGHMAYECPSGRI 227 (235)
Q Consensus 205 ~~~~C~~Cg~~GH~~~~Cp~~~~ 227 (235)
..+.|..|+ -.||...||....
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyKd~ 126 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYKDT 126 (128)
T ss_pred ceEEeCCCC-CCcccccCCcccc
Confidence 469999996 6899999997543
Done!