Query 024209
Match_columns 271
No_of_seqs 250 out of 1791
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 02:53:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024209.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024209hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00368 universal minicircle 99.9 1.8E-27 4E-32 198.9 10.0 133 88-261 2-148 (148)
2 PTZ00368 universal minicircle 99.9 5.9E-26 1.3E-30 189.8 9.5 126 49-188 1-148 (148)
3 COG5082 AIR1 Arginine methyltr 99.8 3.1E-20 6.8E-25 159.5 6.3 101 131-263 60-175 (190)
4 COG5082 AIR1 Arginine methyltr 99.8 2.1E-19 4.6E-24 154.3 7.9 83 43-126 55-141 (190)
5 KOG4400 E3 ubiquitin ligase in 99.7 2.6E-17 5.7E-22 149.6 11.3 191 48-260 24-240 (261)
6 KOG4400 E3 ubiquitin ligase in 99.6 1.4E-14 3.1E-19 131.7 12.0 179 48-267 54-257 (261)
7 PF00098 zf-CCHC: Zinc knuckle 98.2 6.9E-07 1.5E-11 48.9 1.2 17 244-260 2-18 (18)
8 PF00098 zf-CCHC: Zinc knuckle 97.9 4.8E-06 1E-10 45.5 1.7 17 224-240 2-18 (18)
9 PF13696 zf-CCHC_2: Zinc knuck 96.2 0.0036 7.9E-08 39.1 2.2 19 242-260 8-26 (32)
10 PF13917 zf-CCHC_3: Zinc knuck 95.7 0.0055 1.2E-07 40.7 1.5 18 242-259 4-21 (42)
11 PF13696 zf-CCHC_2: Zinc knuck 95.7 0.0066 1.4E-07 38.0 1.5 20 169-188 8-27 (32)
12 smart00343 ZnF_C2HC zinc finge 93.9 0.031 6.8E-07 32.8 1.2 16 245-260 2-17 (26)
13 KOG0119 Splicing factor 1/bran 92.6 0.082 1.8E-06 52.1 2.6 41 223-263 262-306 (554)
14 PF13917 zf-CCHC_3: Zinc knuck 92.1 0.074 1.6E-06 35.3 1.1 19 222-240 4-22 (42)
15 smart00343 ZnF_C2HC zinc finge 91.6 0.087 1.9E-06 30.9 1.0 17 224-240 1-17 (26)
16 KOG0109 RNA-binding protein LA 90.7 0.13 2.8E-06 47.8 1.6 19 222-240 160-178 (346)
17 KOG0119 Splicing factor 1/bran 90.5 0.19 4.1E-06 49.6 2.6 39 151-189 262-305 (554)
18 PF14392 zf-CCHC_4: Zinc knuck 90.1 0.12 2.7E-06 35.1 0.7 25 41-65 24-48 (49)
19 KOG4368 Predicted RNA binding 88.5 0.3 6.4E-06 49.2 2.3 17 3-19 601-617 (757)
20 KOG0109 RNA-binding protein LA 85.7 0.4 8.8E-06 44.5 1.4 24 242-265 160-183 (346)
21 PF15288 zf-CCHC_6: Zinc knuck 85.2 0.69 1.5E-05 30.4 1.9 19 244-262 3-23 (40)
22 PF14392 zf-CCHC_4: Zinc knuck 83.9 0.4 8.8E-06 32.5 0.4 18 222-239 31-48 (49)
23 PF15288 zf-CCHC_6: Zinc knuck 82.6 0.7 1.5E-05 30.4 1.2 18 223-240 2-21 (40)
24 PF14787 zf-CCHC_5: GAG-polypr 80.7 1.1 2.3E-05 28.8 1.4 18 49-66 3-20 (36)
25 COG5222 Uncharacterized conser 79.5 1.4 3.1E-05 41.2 2.5 22 241-262 175-196 (427)
26 PF14787 zf-CCHC_5: GAG-polypr 75.1 1.8 4E-05 27.7 1.3 16 224-239 4-19 (36)
27 KOG0314 Predicted E3 ubiquitin 73.6 4.9 0.00011 39.6 4.5 23 241-263 157-179 (448)
28 COG5222 Uncharacterized conser 67.2 2.4 5.1E-05 39.7 0.8 19 48-66 176-194 (427)
29 KOG0314 Predicted E3 ubiquitin 61.6 9.9 0.00022 37.5 3.9 59 46-104 110-176 (448)
30 KOG0107 Alternative splicing f 51.1 31 0.00068 30.1 4.8 34 225-264 103-136 (195)
31 KOG2044 5'-3' exonuclease HKE1 45.6 9.1 0.0002 40.3 0.8 21 45-65 257-277 (931)
32 KOG0132 RNA polymerase II C-te 38.3 25 0.00054 37.1 2.6 26 3-28 343-368 (894)
33 KOG4246 Predicted DNA-binding 35.9 13 0.00028 39.4 0.2 17 23-39 344-360 (1194)
34 PF06495 Transformer: Fruit fl 29.7 37 0.0008 29.4 1.9 11 4-14 59-69 (182)
35 PF00937 Corona_nucleoca: Coro 29.0 19 0.00042 34.5 0.1 14 4-17 164-177 (355)
36 COG1198 PriA Primosomal protei 28.5 67 0.0015 33.9 4.0 55 41-114 428-484 (730)
37 KOG2548 SWAP mRNA splicing reg 27.2 29 0.00063 35.0 1.0 12 5-16 388-399 (653)
38 KOG3116 Predicted C3H1-type Zn 26.9 18 0.0004 30.6 -0.4 19 222-240 27-45 (177)
39 PF12353 eIF3g: Eukaryotic tra 24.0 40 0.00087 27.6 1.1 19 221-240 105-123 (128)
40 KOG2673 Uncharacterized conser 23.5 31 0.00067 34.2 0.4 22 245-266 131-152 (485)
41 KOG4246 Predicted DNA-binding 23.3 33 0.00071 36.6 0.6 21 24-44 353-373 (1194)
42 PF12353 eIF3g: Eukaryotic tra 23.1 52 0.0011 26.9 1.6 22 241-263 105-126 (128)
43 KOG3973 Uncharacterized conser 22.1 85 0.0018 30.3 3.0 20 201-220 365-384 (465)
44 PF00684 DnaJ_CXXCXGXG: DnaJ c 21.0 45 0.00096 23.7 0.7 11 152-162 43-53 (66)
45 KOG2044 5'-3' exonuclease HKE1 20.6 42 0.00092 35.5 0.8 19 222-240 260-278 (931)
46 PRK14890 putative Zn-ribbon RN 20.4 99 0.0022 22.0 2.4 10 48-57 7-16 (59)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.94 E-value=1.8e-27 Score=198.92 Aligned_cols=133 Identities=34% Similarity=0.819 Sum_probs=92.8
Q ss_pred cCcCCCCCCCCCCCCCC--------CCccccCCCCCcCCCCCCCCcccCCCCcccccCCCCCCCCcCCCCCccccccCCC
Q 024209 88 RCWNCREPGHMASNCHN--------EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKT 159 (271)
Q Consensus 88 ~C~~Cg~~GH~~~~Cp~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~ 159 (271)
+||+|++.||++++||+ ...||+|++.||++++||..... .....|++|++.||++.+||+... .
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 46666666666666665 24677777777777777765321 123456666666666666654210 0
Q ss_pred CcccccCCCCCCCCccccCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCC
Q 024209 160 GHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCV 239 (271)
Q Consensus 160 GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp 239 (271)
.....|++|++.||++++||+.... + ....+||+|++.||+++|||
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 0235799999999999999985421 0 12478999999999999999
Q ss_pred CC------CcceEcCCCCCcCCCCCCCC
Q 024209 240 GP------LIICRNCGGRGHMAYECPSG 261 (271)
Q Consensus 240 ~~------~~~C~~Cg~~GH~~~~Cp~~ 261 (271)
++ .++||+|+++|||++|||+.
T Consensus 121 ~~~~~~~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 121 NAGKRPGGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CccccCCCCCccccCCCcCcccccCCCC
Confidence 84 58999999999999999974
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.93 E-value=5.9e-26 Score=189.83 Aligned_cols=126 Identities=43% Similarity=0.976 Sum_probs=77.7
Q ss_pred cccccCCCCCCCCCCCCCC--------cccccCCCCCCccCCCCCcccCcCCCCCCCCCCCCCCCCccccCCCCCcCCCC
Q 024209 49 NLCNNCKRPGHFARECPNV--------AVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARD 120 (271)
Q Consensus 49 ~~C~nCg~~GH~~~~Cp~~--------~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~ 120 (271)
++||||++.||++++||.. ..||+|+..||++.+||.... -.....|++|++.||++++
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~-------------~~~~~~C~~Cg~~GH~~~~ 67 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPG-------------GRGERSCYNCGKTGHLSRE 67 (148)
T ss_pred CcCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCC-------------CCCCcccCCCCCcCcCccc
Confidence 5899999999999999972 245555555555555554210 0001235555555555555
Q ss_pred CCCCcccCCCCcccccCCCCCCCCcCCCCCc-------cccccCCCCcccccCCC-------CCCCCccccCCcCCCCCC
Q 024209 121 CSTHVQSGGDLRLCNNCYKPGHIAADCTNDK-------ACKNCRKTGHIARDCQN-------EPVCNLCNIAGHVARQCP 186 (271)
Q Consensus 121 Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~~~-------~C~~Cg~~GH~~~~Cp~-------~~~C~~C~~~GH~a~~Cp 186 (271)
||...... ..+.|++|++.||++.+|++.. +||+|++.||++++||+ .++||+|++.|||++|||
T Consensus 68 Cp~~~~~~-~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp 146 (148)
T PTZ00368 68 CPEAPPGS-GPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCP 146 (148)
T ss_pred CCCcccCC-CCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCC
Confidence 55543211 2345666666666666665422 46666666666666665 368999999999999999
Q ss_pred CC
Q 024209 187 KG 188 (271)
Q Consensus 187 ~~ 188 (271)
+.
T Consensus 147 ~~ 148 (148)
T PTZ00368 147 DK 148 (148)
T ss_pred CC
Confidence 73
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.81 E-value=3.1e-20 Score=159.46 Aligned_cols=101 Identities=35% Similarity=0.807 Sum_probs=54.0
Q ss_pred CcccccCCCCCCCCcCCCCCccccccCCCCcccccCCCCCCCCccccCCcCCCCC-CCCCCCCCCCCCCCCCCCCCCCCC
Q 024209 131 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC-PKGDSLGERGGGGGGERGGGGGGD 209 (271)
Q Consensus 131 ~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~C-p~~~~~~~~~~~~~~~~~~~~g~~ 209 (271)
.+.|++|++.||++.||| ..+|++|...+|.+..||..++|++|++.||++++| |..+
T Consensus 60 ~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~-------------------- 118 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD-------------------- 118 (190)
T ss_pred ccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccc--------------------
Confidence 345555555555555555 345555544555555555555555555555555555 3322
Q ss_pred CCCCCCCCCcccCccccccCCCCCcCCCCCC--------------CCcceEcCCCCCcCCCCCCCCCc
Q 024209 210 GGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--------------PLIICRNCGGRGHMAYECPSGRI 263 (271)
Q Consensus 210 ~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~--------------~~~~C~~Cg~~GH~~~~Cp~~~~ 263 (271)
..+.|+.|...+|.+++||. ..+.||+|+..+||+.||+.++.
T Consensus 119 -----------~~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~ 175 (190)
T COG5082 119 -----------QQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS 175 (190)
T ss_pred -----------cCcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCcc
Confidence 12445555555555555554 24556666666666666665443
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.79 E-value=2.1e-19 Score=154.32 Aligned_cols=83 Identities=33% Similarity=0.897 Sum_probs=74.6
Q ss_pred ccCCCCcccccCCCCCCCCCCCCCCcccccCCCCCCccCCCCCcccCcCCCCCCCCCCCC-CCC---CccccCCCCCcCC
Q 024209 43 RSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNC-HNE---GICHSCGKTGHRA 118 (271)
Q Consensus 43 ~~~~~~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~C-p~~---~~C~~Cg~~GH~~ 118 (271)
.......+||||++.||+++||| ..+|++|...||.+..||..++|++|++.||++++| |.. ..|+.|....|++
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s 133 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSS 133 (190)
T ss_pred cccccccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCcccc
Confidence 33445789999999999999999 679999988999999999988999999999999999 553 4799999999999
Q ss_pred CCCCCCcc
Q 024209 119 RDCSTHVQ 126 (271)
Q Consensus 119 ~~Cp~~~~ 126 (271)
.+||.+|+
T Consensus 134 ~~Cp~~~k 141 (190)
T COG5082 134 EDCPSIWK 141 (190)
T ss_pred ccCccccc
Confidence 99999997
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.72 E-value=2.6e-17 Score=149.56 Aligned_cols=191 Identities=30% Similarity=0.625 Sum_probs=144.8
Q ss_pred CcccccCCCCCCCCCCCCCCc-----------ccccCCCCCCccCCCCCcccCcCCCCCCCCCCCCCC-CCccccCCCCC
Q 024209 48 GNLCNNCKRPGHFARECPNVA-----------VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN-EGICHSCGKTG 115 (271)
Q Consensus 48 ~~~C~nCg~~GH~~~~Cp~~~-----------~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~G 115 (271)
...++.+.+.+|.+..|+... .+..+...+|....++. ..|+.|++.||+..+|+. ...|++|++.|
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~c~~~g~~~~~~~~~~~~~~~c~~C~~~g 102 (261)
T KOG4400|consen 24 SPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPE-VSCYICGEKGHLGRRCTRIAAACFNCGEGG 102 (261)
T ss_pred chhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCC-ceeeecCCCCchhhcCcccchhhhhCCCCc
Confidence 578899999999999998642 34445566777777776 799999999999999996 67899999999
Q ss_pred cCCCCCCCCcccCCCCcccccCCCCCCCC-cCCC-----CCccccccCCCCcccccCCC--CCCCCccccCCcCCCCCCC
Q 024209 116 HRARDCSTHVQSGGDLRLCNNCYKPGHIA-ADCT-----NDKACKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCPK 187 (271)
Q Consensus 116 H~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a-~dC~-----~~~~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~a~~Cp~ 187 (271)
|++++||.++........|+.|++.||.. .++. ....||+|++.||++.+||. ...||.|++.+|++++||.
T Consensus 103 H~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~ 182 (261)
T KOG4400|consen 103 HIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPS 182 (261)
T ss_pred cchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCc
Confidence 99999999987433455789999999999 3332 22459999999999999994 7899999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCC------CCcceEcCCCCCcCCCCCCC
Q 024209 188 GDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG------PLIICRNCGGRGHMAYECPS 260 (271)
Q Consensus 188 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~------~~~~C~~Cg~~GH~~~~Cp~ 260 (271)
........... . ..--.++ +...+|+.++++. ....+|++...+|.+.+|-+
T Consensus 183 ~~~~~~~~~~~------------------~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (261)
T KOG4400|consen 183 KQKSKSKQGGQ------------------R--KGFGACY-DYPQGHKQRACGGSGPDDNFNDSCYNKLSSGKLDQDCKQ 240 (261)
T ss_pred cccccccCccc------------------c--cccccCc-cccccccccccCCCCcccccccccccccccccccchhhh
Confidence 87532111100 0 0111233 5678888888875 35667777766666665543
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.58 E-value=1.4e-14 Score=131.68 Aligned_cols=179 Identities=33% Similarity=0.694 Sum_probs=131.8
Q ss_pred CcccccCCCCCCCCCCCCCCcccccCCCCCCccCCCCC-cccCcCCCCCCCCCCCCCCCC-------ccccCCCCCcCC-
Q 024209 48 GNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTT-QARCWNCREPGHMASNCHNEG-------ICHSCGKTGHRA- 118 (271)
Q Consensus 48 ~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~GH~~~~Cp~~~-------~C~~Cg~~GH~~- 118 (271)
...+..+...+|+...++.. .|+.|++.+|....|+. ...|++|++.||++++|++.. .||.|+..+|..
T Consensus 54 ~~~~~~~~~~~~~~~~~~~~-~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~ 132 (261)
T KOG4400|consen 54 GPGCVSTSPNGPLKSECPEV-SCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGC 132 (261)
T ss_pred CCcccccccCcccCCCCCCc-eeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcccccceeeccCCCccccC
Confidence 34556678888888888875 89999999999999985 578999999999999999852 578999999999
Q ss_pred CCCCCCcccCCCCcccccCCCCCCCCcCCCC--CccccccCCCCcccccCCCCC--------------CCCccccCCcCC
Q 024209 119 RDCSTHVQSGGDLRLCNNCYKPGHIAADCTN--DKACKNCRKTGHIARDCQNEP--------------VCNLCNIAGHVA 182 (271)
Q Consensus 119 ~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~--~~~C~~Cg~~GH~~~~Cp~~~--------------~C~~C~~~GH~a 182 (271)
.++..... +.. +.||+|++.||+..+||+ ...|+.|+..+|++++||... .++ +...+|+.
T Consensus 133 ~~~~~~~~-~~~-~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 209 (261)
T KOG4400|consen 133 PDADPVDG-PKP-AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSKSKQGGQRKGFGACY-DYPQGHKQ 209 (261)
T ss_pred cccccccC-CCC-CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccccccCcccccccccCc-cccccccc
Confidence 33322211 112 679999999999999994 578999999999999999521 233 34566777
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCCCCcceEcCCCCCcCCCCCCCCC
Q 024209 183 RQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGR 262 (271)
Q Consensus 183 ~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~~~~~C~~Cg~~GH~~~~Cp~~~ 262 (271)
++++...... .....+|++...+|.+.+| .+.++++++|...+
T Consensus 210 ~~~~~~~~~~---------------------------~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~ 252 (261)
T KOG4400|consen 210 RACGGSGPDD---------------------------NFNDSCYNKLSSGKLDQDC----------KQSSMKSNSCGTKR 252 (261)
T ss_pred cccCCCCccc---------------------------ccccccccccccccccchh----------hhhccccccccchh
Confidence 6665544311 1247789999888888777 45556666666555
Q ss_pred cCCCC
Q 024209 263 IADRG 267 (271)
Q Consensus 263 ~~~~~ 267 (271)
+....
T Consensus 253 ~~~~~ 257 (261)
T KOG4400|consen 253 LFYNT 257 (261)
T ss_pred hcccc
Confidence 55544
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=98.18 E-value=6.9e-07 Score=48.87 Aligned_cols=17 Identities=53% Similarity=1.253 Sum_probs=10.0
Q ss_pred ceEcCCCCCcCCCCCCC
Q 024209 244 ICRNCGGRGHMAYECPS 260 (271)
Q Consensus 244 ~C~~Cg~~GH~~~~Cp~ 260 (271)
.||+|++.||+++|||+
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 45666666666666653
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=97.95 E-value=4.8e-06 Score=45.50 Aligned_cols=17 Identities=41% Similarity=1.028 Sum_probs=16.0
Q ss_pred cccccCCCCCcCCCCCC
Q 024209 224 ICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 224 ~C~~C~~~gH~~~dCp~ 240 (271)
+||+|+++||+++|||+
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=96.23 E-value=0.0036 Score=39.10 Aligned_cols=19 Identities=37% Similarity=1.097 Sum_probs=12.1
Q ss_pred CcceEcCCCCCcCCCCCCC
Q 024209 242 LIICRNCGGRGHMAYECPS 260 (271)
Q Consensus 242 ~~~C~~Cg~~GH~~~~Cp~ 260 (271)
.-+|+.|++.|||..|||+
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 4556666666666666665
No 10
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.74 E-value=0.0055 Score=40.71 Aligned_cols=18 Identities=50% Similarity=1.383 Sum_probs=13.5
Q ss_pred CcceEcCCCCCcCCCCCC
Q 024209 242 LIICRNCGGRGHMAYECP 259 (271)
Q Consensus 242 ~~~C~~Cg~~GH~~~~Cp 259 (271)
.+.|.+|++.|||..|||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 466777777777777777
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.65 E-value=0.0066 Score=37.95 Aligned_cols=20 Identities=35% Similarity=0.846 Sum_probs=14.4
Q ss_pred CCCCCccccCCcCCCCCCCC
Q 024209 169 EPVCNLCNIAGHVARQCPKG 188 (271)
Q Consensus 169 ~~~C~~C~~~GH~a~~Cp~~ 188 (271)
.-+|+.|+++||+..|||++
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 45677777777777777773
No 12
>smart00343 ZnF_C2HC zinc finger.
Probab=93.87 E-value=0.031 Score=32.82 Aligned_cols=16 Identities=56% Similarity=1.425 Sum_probs=11.3
Q ss_pred eEcCCCCCcCCCCCCC
Q 024209 245 CRNCGGRGHMAYECPS 260 (271)
Q Consensus 245 C~~Cg~~GH~~~~Cp~ 260 (271)
|++|++.||++.+||+
T Consensus 2 C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 2 CYNCGKEGHIARDCPK 17 (26)
T ss_pred CccCCCCCcchhhCCc
Confidence 6777777777777763
No 13
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.64 E-value=0.082 Score=52.07 Aligned_cols=41 Identities=34% Similarity=0.865 Sum_probs=36.1
Q ss_pred ccccccCCCCCcCCCCCCC----CcceEcCCCCCcCCCCCCCCCc
Q 024209 223 VICRSCNQMGHMSRDCVGP----LIICRNCGGRGHMAYECPSGRI 263 (271)
Q Consensus 223 ~~C~~C~~~gH~~~dCp~~----~~~C~~Cg~~GH~~~~Cp~~~~ 263 (271)
..|.+|+..||..-|||.. ..+|..|+..|||+.||+...+
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~q 306 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVNDQ 306 (554)
T ss_pred ccccccCCCccccccCCcccccccccccccCCcccccccCCCccc
Confidence 5799999999999999972 3499999999999999998733
No 14
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.06 E-value=0.074 Score=35.33 Aligned_cols=19 Identities=37% Similarity=0.896 Sum_probs=17.3
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
...|.+|++.|||..+||+
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4789999999999999993
No 15
>smart00343 ZnF_C2HC zinc finger.
Probab=91.64 E-value=0.087 Score=30.90 Aligned_cols=17 Identities=41% Similarity=1.060 Sum_probs=15.5
Q ss_pred cccccCCCCCcCCCCCC
Q 024209 224 ICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 224 ~C~~C~~~gH~~~dCp~ 240 (271)
.|++|++.||++++||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999984
No 16
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=90.71 E-value=0.13 Score=47.76 Aligned_cols=19 Identities=32% Similarity=0.735 Sum_probs=11.8
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
...||.|+++|||+.+||.
T Consensus 160 q~~cyrcGkeghwskEcP~ 178 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPV 178 (346)
T ss_pred HHHheeccccccccccCCc
Confidence 3556666666666666663
No 17
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=90.49 E-value=0.19 Score=49.60 Aligned_cols=39 Identities=41% Similarity=0.997 Sum_probs=27.2
Q ss_pred ccccccCCCCcccccCCCC-----CCCCccccCCcCCCCCCCCC
Q 024209 151 KACKNCRKTGHIARDCQNE-----PVCNLCNIAGHVARQCPKGD 189 (271)
Q Consensus 151 ~~C~~Cg~~GH~~~~Cp~~-----~~C~~C~~~GH~a~~Cp~~~ 189 (271)
..|.+|+..||...+||.. .+|..|+..||++.||+...
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~ 305 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVND 305 (554)
T ss_pred ccccccCCCccccccCCcccccccccccccCCcccccccCCCcc
Confidence 3566666666666666642 27888888888888887763
No 18
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=90.05 E-value=0.12 Score=35.10 Aligned_cols=25 Identities=32% Similarity=0.679 Sum_probs=20.6
Q ss_pred ccccCCCCcccccCCCCCCCCCCCC
Q 024209 41 TRRSFSQGNLCNNCKRPGHFARECP 65 (271)
Q Consensus 41 ~~~~~~~~~~C~nCg~~GH~~~~Cp 65 (271)
...++..+..|++|+..||...+||
T Consensus 24 ~v~YE~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 24 KVKYERLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred EEEECCcChhhcCCCCcCcCHhHcC
Confidence 3455666889999999999999997
No 19
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=88.45 E-value=0.3 Score=49.15 Aligned_cols=17 Identities=82% Similarity=0.837 Sum_probs=8.1
Q ss_pred CccccccccccCCCCCC
Q 024209 3 SRSRSISRSRSRSRSRS 19 (271)
Q Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (271)
+|+|++|++|||||++.
T Consensus 601 ~RdrsrskSRSRSpS~~ 617 (757)
T KOG4368|consen 601 SRSRSRSKSRSRSPSRS 617 (757)
T ss_pred ccccccccccCCCcccc
Confidence 44444444444444443
No 20
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=85.66 E-value=0.4 Score=44.55 Aligned_cols=24 Identities=38% Similarity=0.780 Sum_probs=20.6
Q ss_pred CcceEcCCCCCcCCCCCCCCCcCC
Q 024209 242 LIICRNCGGRGHMAYECPSGRIAD 265 (271)
Q Consensus 242 ~~~C~~Cg~~GH~~~~Cp~~~~~~ 265 (271)
.-.||.||.+|||+.|||..+..+
T Consensus 160 q~~cyrcGkeghwskEcP~~~~~r 183 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRTGR 183 (346)
T ss_pred HHHheeccccccccccCCccCCCc
Confidence 468999999999999999876543
No 21
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=85.23 E-value=0.69 Score=30.40 Aligned_cols=19 Identities=47% Similarity=1.006 Sum_probs=8.9
Q ss_pred ceEcCCCCCcCC--CCCCCCC
Q 024209 244 ICRNCGGRGHMA--YECPSGR 262 (271)
Q Consensus 244 ~C~~Cg~~GH~~--~~Cp~~~ 262 (271)
.|.+||..||+. +.||...
T Consensus 3 kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred cccccccccccccCccCCCCC
Confidence 444555555544 3355443
No 22
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=83.85 E-value=0.4 Score=32.52 Aligned_cols=18 Identities=28% Similarity=0.909 Sum_probs=10.7
Q ss_pred CccccccCCCCCcCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCV 239 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp 239 (271)
+..|++|+..||...+||
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 345666666666666665
No 23
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=82.63 E-value=0.7 Score=30.37 Aligned_cols=18 Identities=39% Similarity=1.017 Sum_probs=15.7
Q ss_pred ccccccCCCCCcC--CCCCC
Q 024209 223 VICRSCNQMGHMS--RDCVG 240 (271)
Q Consensus 223 ~~C~~C~~~gH~~--~dCp~ 240 (271)
++|.+||..||++ +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 6899999999998 56984
No 24
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=80.71 E-value=1.1 Score=28.80 Aligned_cols=18 Identities=39% Similarity=0.898 Sum_probs=9.3
Q ss_pred cccccCCCCCCCCCCCCC
Q 024209 49 NLCNNCKRPGHFARECPN 66 (271)
Q Consensus 49 ~~C~nCg~~GH~~~~Cp~ 66 (271)
..|+.|++..||+.+|-.
T Consensus 3 ~~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRS 20 (36)
T ss_dssp -C-TTTSSSCS-TTT---
T ss_pred ccCcccCCCcchhhhhhh
Confidence 467777777777777743
No 25
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.53 E-value=1.4 Score=41.17 Aligned_cols=22 Identities=36% Similarity=1.028 Sum_probs=14.3
Q ss_pred CCcceEcCCCCCcCCCCCCCCC
Q 024209 241 PLIICRNCGGRGHMAYECPSGR 262 (271)
Q Consensus 241 ~~~~C~~Cg~~GH~~~~Cp~~~ 262 (271)
+.-.||+||+.|||...||...
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred CceeEEecCCCCchhhcCCCCC
Confidence 4566777777777777776543
No 26
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=75.14 E-value=1.8 Score=27.70 Aligned_cols=16 Identities=25% Similarity=0.750 Sum_probs=6.4
Q ss_pred cccccCCCCCcCCCCC
Q 024209 224 ICRSCNQMGHMSRDCV 239 (271)
Q Consensus 224 ~C~~C~~~gH~~~dCp 239 (271)
.|.+|++-.|||+||-
T Consensus 4 ~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 4 LCPRCGKGFHWASECR 19 (36)
T ss_dssp C-TTTSSSCS-TTT--
T ss_pred cCcccCCCcchhhhhh
Confidence 3555555555555553
No 27
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.57 E-value=4.9 Score=39.63 Aligned_cols=23 Identities=26% Similarity=0.509 Sum_probs=13.0
Q ss_pred CCcceEcCCCCCcCCCCCCCCCc
Q 024209 241 PLIICRNCGGRGHMAYECPSGRI 263 (271)
Q Consensus 241 ~~~~C~~Cg~~GH~~~~Cp~~~~ 263 (271)
+...||+|...|||...||....
T Consensus 157 psy~c~rc~~~g~wikacptv~~ 179 (448)
T KOG0314|consen 157 PSYKCVKCPTPGPWIKACPTVSG 179 (448)
T ss_pred CCcceecCCCCCccceeccccCC
Confidence 44556666666666666655443
No 28
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.19 E-value=2.4 Score=39.74 Aligned_cols=19 Identities=37% Similarity=1.158 Sum_probs=17.3
Q ss_pred CcccccCCCCCCCCCCCCC
Q 024209 48 GNLCNNCKRPGHFARECPN 66 (271)
Q Consensus 48 ~~~C~nCg~~GH~~~~Cp~ 66 (271)
.-+||.||+.|||..+||.
T Consensus 176 gY~CyRCGqkgHwIqnCpT 194 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPT 194 (427)
T ss_pred ceeEEecCCCCchhhcCCC
Confidence 3589999999999999986
No 29
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.61 E-value=9.9 Score=37.53 Aligned_cols=59 Identities=25% Similarity=0.540 Sum_probs=42.1
Q ss_pred CCCcccccCCCCCCCCCCCCC--CcccccCCCCCCccCCCCC------cccCcCCCCCCCCCCCCCC
Q 024209 46 SQGNLCNNCKRPGHFARECPN--VAVCNNCGLPGHIASECTT------QARCWNCREPGHMASNCHN 104 (271)
Q Consensus 46 ~~~~~C~nCg~~GH~~~~Cp~--~~~C~~Cg~~GH~~~~Cp~------~~~C~~Cg~~GH~~~~Cp~ 104 (271)
....+++.+++.||..+.+.. ..+|..|-..+|+-..+.. ...|++|..+||+...||.
T Consensus 110 p~~q~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 110 PLIQMNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPT 176 (448)
T ss_pred chhhhccccccCCcccccCCCcccceeeecccCccccccccccCCCCCCcceecCCCCCccceeccc
Confidence 335678888888888888843 3577788888887776654 2467777777777777775
No 30
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=51.13 E-value=31 Score=30.08 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=24.3
Q ss_pred ccccCCCCCcCCCCCCCCcceEcCCCCCcCCCCCCCCCcC
Q 024209 225 CRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIA 264 (271)
Q Consensus 225 C~~C~~~gH~~~dCp~~~~~C~~Cg~~GH~~~~Cp~~~~~ 264 (271)
||.|++.||+.+.|-+ +|.+ .++....+-.+.-+
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 9999999999999864 4444 46666666555544
No 31
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=45.58 E-value=9.1 Score=40.29 Aligned_cols=21 Identities=29% Similarity=0.635 Sum_probs=10.9
Q ss_pred CCCCcccccCCCCCCCCCCCC
Q 024209 45 FSQGNLCNNCKRPGHFARECP 65 (271)
Q Consensus 45 ~~~~~~C~nCg~~GH~~~~Cp 65 (271)
+.++..||.|+++||.+.+|.
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~ 277 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCE 277 (931)
T ss_pred CCCcccchhhcccCCcHhhcC
Confidence 344445555555555555554
No 32
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=38.25 E-value=25 Score=37.06 Aligned_cols=26 Identities=54% Similarity=0.507 Sum_probs=11.1
Q ss_pred CccccccccccCCCCCCcchhhhhcc
Q 024209 3 SRSRSISRSRSRSRSRSPRDRRFRSR 28 (271)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 28 (271)
+|+++.+++.|+++.++..+++.+++
T Consensus 343 ~r~r~~~~s~s~~~~~r~~RsrS~sr 368 (894)
T KOG0132|consen 343 SRSRSAPASASRSRRGRLSRSRSRSR 368 (894)
T ss_pred CCcCCCCcccccccccccccccCCCc
Confidence 34444444444444444444444443
No 33
>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]
Probab=35.90 E-value=13 Score=39.42 Aligned_cols=17 Identities=41% Similarity=0.417 Sum_probs=6.8
Q ss_pred hhhhcccccCCCCCcch
Q 024209 23 RRFRSRHSSYCDPPLRR 39 (271)
Q Consensus 23 ~~~~~~~~~~~~~~~~r 39 (271)
++.+++|.-+.+.|++|
T Consensus 344 sr~rs~rRErer~prRr 360 (1194)
T KOG4246|consen 344 SRQRSRRRERERIPRRR 360 (1194)
T ss_pred ccccccchhhhcchHhh
Confidence 33333333344444433
No 34
>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus
Probab=29.67 E-value=37 Score=29.40 Aligned_cols=11 Identities=91% Similarity=0.972 Sum_probs=4.4
Q ss_pred ccccccccccC
Q 024209 4 RSRSISRSRSR 14 (271)
Q Consensus 4 ~~~~~~~~~~~ 14 (271)
|++|+|++++|
T Consensus 59 RSRSRSrSr~R 69 (182)
T PF06495_consen 59 RSRSRSRSRSR 69 (182)
T ss_pred ccccccccccc
Confidence 33444444433
No 35
>PF00937 Corona_nucleoca: Coronavirus nucleocapsid protein; InterPro: IPR001218 The entry represents the Coronavirus nucleocapsid protein. Sequence comparison of the N genes of five strains of the coronavirus Murine hepatitis virus suggests a three domain structure for the nucleocapsid protein []. There seems to be a specific interaction between the coronavirus Mouse hepatitis virus A59 nucleocapsid protein and packaging signal [].; GO: 0019013 viral nucleocapsid; PDB: 2GE7_A 2GEC_A 2GE8_B 2BXX_B 2BTL_A 2CA1_B 3HD4_A 2C86_A 2CJR_F 2OG3_A ....
Probab=28.97 E-value=19 Score=34.48 Aligned_cols=14 Identities=79% Similarity=0.778 Sum_probs=0.0
Q ss_pred ccccccccccCCCC
Q 024209 4 RSRSISRSRSRSRS 17 (271)
Q Consensus 4 ~~~~~~~~~~~~~~ 17 (271)
+||+.||+.|||.+
T Consensus 164 ~Sr~~SRs~SRs~S 177 (355)
T PF00937_consen 164 RSRSNSRSSSRSQS 177 (355)
T ss_dssp --------------
T ss_pred CCCCCccccccccc
Confidence 44444444444444
No 36
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.50 E-value=67 Score=33.86 Aligned_cols=55 Identities=35% Similarity=0.738 Sum_probs=33.3
Q ss_pred ccccCCCCcccccCCCCCCCCCCCCCCcccccCCCC--CCccCCCCCcccCcCCCCCCCCCCCCCCCCccccCCCC
Q 024209 41 TRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLP--GHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKT 114 (271)
Q Consensus 41 ~~~~~~~~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~--GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~ 114 (271)
+|++++..+.|..||-. ..|-+|... =|... ....|..|+....+...||+ ||+.
T Consensus 428 nRRGys~~l~C~~Cg~v----------~~Cp~Cd~~lt~H~~~---~~L~CH~Cg~~~~~p~~Cp~------Cgs~ 484 (730)
T COG1198 428 NRRGYAPLLLCRDCGYI----------AECPNCDSPLTLHKAT---GQLRCHYCGYQEPIPQSCPE------CGSE 484 (730)
T ss_pred ccCCccceeecccCCCc----------ccCCCCCcceEEecCC---CeeEeCCCCCCCCCCCCCCC------CCCC
Confidence 56888888999999633 345555432 24433 23577777766555554443 6665
No 37
>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]
Probab=27.21 E-value=29 Score=35.03 Aligned_cols=12 Identities=83% Similarity=0.833 Sum_probs=4.9
Q ss_pred cccccccccCCC
Q 024209 5 SRSISRSRSRSR 16 (271)
Q Consensus 5 ~~~~~~~~~~~~ 16 (271)
++|.||++|||+
T Consensus 388 srssSrsssRSr 399 (653)
T KOG2548|consen 388 SRSSSRSSSRSR 399 (653)
T ss_pred cccccccccccc
Confidence 344444444333
No 38
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=26.90 E-value=18 Score=30.59 Aligned_cols=19 Identities=32% Similarity=0.807 Sum_probs=15.3
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
.+.|-+|.+.|||..+|.+
T Consensus 27 ~~rCQKClq~GHWtYECk~ 45 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKN 45 (177)
T ss_pred chhHHHHHhhccceeeecC
Confidence 4678888888888888875
No 39
>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=24.00 E-value=40 Score=27.56 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=16.4
Q ss_pred cCccccccCCCCCcCCCCCC
Q 024209 221 HDVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 221 ~~~~C~~C~~~gH~~~dCp~ 240 (271)
..++|..|+ -.||...||-
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 468999996 7799999994
No 40
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=23.51 E-value=31 Score=34.19 Aligned_cols=22 Identities=41% Similarity=0.795 Sum_probs=16.1
Q ss_pred eEcCCCCCcCCCCCCCCCcCCC
Q 024209 245 CRNCGGRGHMAYECPSGRIADR 266 (271)
Q Consensus 245 C~~Cg~~GH~~~~Cp~~~~~~~ 266 (271)
||||+..-|--+|||.+...-+
T Consensus 131 CFNC~g~~hsLrdC~rp~d~s~ 152 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFDFSR 152 (485)
T ss_pred ccccCCCCCccccCCCccccHH
Confidence 7888888887888887765543
No 41
>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]
Probab=23.35 E-value=33 Score=36.56 Aligned_cols=21 Identities=29% Similarity=0.265 Sum_probs=9.9
Q ss_pred hhhcccccCCCCCcchhcccc
Q 024209 24 RFRSRHSSYCDPPLRRETRRS 44 (271)
Q Consensus 24 ~~~~~~~~~~~~~~~r~~~~~ 44 (271)
++++-|.+.|.-|+-+..++.
T Consensus 353 rer~prRr~R~~pRy~~r~~k 373 (1194)
T KOG4246|consen 353 RERIPRRRERQGPRYRERKRK 373 (1194)
T ss_pred hhcchHhhhhccchHHHhhhc
Confidence 333335555555555544443
No 42
>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=23.08 E-value=52 Score=26.88 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=18.7
Q ss_pred CCcceEcCCCCCcCCCCCCCCCc
Q 024209 241 PLIICRNCGGRGHMAYECPSGRI 263 (271)
Q Consensus 241 ~~~~C~~Cg~~GH~~~~Cp~~~~ 263 (271)
..+.|..|+ -.||...||....
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 569999996 7799999998654
No 43
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=22.14 E-value=85 Score=30.29 Aligned_cols=20 Identities=60% Similarity=1.151 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCCCCCCCCcc
Q 024209 201 ERGGGGGGDGGGGGGRYVGY 220 (271)
Q Consensus 201 ~~~~~~g~~~~~~~~~~~~~ 220 (271)
.+++++|+.||++.++++++
T Consensus 365 ~~gGrGgGRGggG~GGGggy 384 (465)
T KOG3973|consen 365 NWGGRGGGRGGGGRGGGGGY 384 (465)
T ss_pred CCCCCCCCCCCCCCCCCCCC
Confidence 44555555554333333333
No 44
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=20.95 E-value=45 Score=23.71 Aligned_cols=11 Identities=45% Similarity=1.072 Sum_probs=5.5
Q ss_pred cccccCCCCcc
Q 024209 152 ACKNCRKTGHI 162 (271)
Q Consensus 152 ~C~~Cg~~GH~ 162 (271)
.|..|...|.+
T Consensus 43 ~C~~C~G~G~~ 53 (66)
T PF00684_consen 43 TCPKCGGTGKI 53 (66)
T ss_dssp E-TTTSSSSEE
T ss_pred ECCCCcceeeE
Confidence 45555555554
No 45
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=20.59 E-value=42 Score=35.55 Aligned_cols=19 Identities=42% Similarity=0.884 Sum_probs=13.1
Q ss_pred CccccccCCCCCcCCCCCC
Q 024209 222 DVICRSCNQMGHMSRDCVG 240 (271)
Q Consensus 222 ~~~C~~C~~~gH~~~dCp~ 240 (271)
+..|+.||++||.+.||..
T Consensus 260 ~~~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEG 278 (931)
T ss_pred cccchhhcccCCcHhhcCC
Confidence 4557777777777777764
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.42 E-value=99 Score=22.03 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=5.4
Q ss_pred CcccccCCCC
Q 024209 48 GNLCNNCKRP 57 (271)
Q Consensus 48 ~~~C~nCg~~ 57 (271)
+.+|..|+..
T Consensus 7 ~~~CtSCg~~ 16 (59)
T PRK14890 7 PPKCTSCGIE 16 (59)
T ss_pred CccccCCCCc
Confidence 3456666544
Done!