Query 024873
Match_columns 261
No_of_seqs 294 out of 1925
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 08:04:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024873.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024873hhsearch_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 3.4E-27 7.3E-32 194.9 10.4 133 84-251 2-148 (148)
2 PTZ00368 universal minicircle 99.9 6.5E-27 1.4E-31 193.2 9.3 126 45-184 1-148 (148)
3 COG5082 AIR1 Arginine methyltr 99.8 1.9E-20 4.2E-25 158.2 8.4 84 39-123 55-142 (190)
4 COG5082 AIR1 Arginine methyltr 99.8 9.4E-20 2E-24 154.0 6.2 121 102-244 61-188 (190)
5 KOG4400 E3 ubiquitin ligase in 99.7 2E-17 4.4E-22 148.5 11.4 194 42-251 22-241 (261)
6 KOG4400 E3 ubiquitin ligase in 99.6 5.2E-15 1.1E-19 132.9 12.9 172 44-240 54-250 (261)
7 PF00098 zf-CCHC: Zinc knuckle 98.1 2E-06 4.3E-11 46.1 1.7 16 214-229 2-17 (18)
8 PF00098 zf-CCHC: Zinc knuckle 98.0 2.7E-06 5.8E-11 45.6 1.7 17 46-62 2-18 (18)
9 PF13696 zf-CCHC_2: Zinc knuck 96.1 0.0027 5.9E-08 38.9 1.0 21 164-184 7-27 (32)
10 PF13696 zf-CCHC_2: Zinc knuck 95.7 0.009 2E-07 36.6 2.2 18 213-230 9-26 (32)
11 PF13917 zf-CCHC_3: Zinc knuck 95.3 0.011 2.4E-07 38.5 1.7 18 232-249 4-21 (42)
12 PF13917 zf-CCHC_3: Zinc knuck 93.3 0.066 1.4E-06 34.9 2.1 19 165-183 4-22 (42)
13 smart00343 ZnF_C2HC zinc finge 93.3 0.051 1.1E-06 31.3 1.5 15 235-249 2-16 (26)
14 PF14392 zf-CCHC_4: Zinc knuck 93.2 0.03 6.5E-07 37.5 0.4 27 36-62 23-49 (49)
15 smart00343 ZnF_C2HC zinc finge 92.5 0.059 1.3E-06 31.0 0.9 17 46-62 1-17 (26)
16 KOG0119 Splicing factor 1/bran 92.2 0.1 2.2E-06 50.7 2.5 37 44-80 261-302 (554)
17 KOG0109 RNA-binding protein LA 92.1 0.072 1.6E-06 48.6 1.5 21 233-253 161-181 (346)
18 KOG0119 Splicing factor 1/bran 92.0 0.12 2.6E-06 50.2 2.9 38 147-184 262-304 (554)
19 PF15288 zf-CCHC_6: Zinc knuck 86.8 0.37 8E-06 31.0 1.3 18 45-62 2-21 (40)
20 PF15288 zf-CCHC_6: Zinc knuck 85.5 0.72 1.6E-05 29.7 2.1 21 233-253 2-24 (40)
21 PF14392 zf-CCHC_4: Zinc knuck 82.4 0.54 1.2E-05 31.4 0.6 16 167-182 33-48 (49)
22 KOG0109 RNA-binding protein LA 80.0 0.98 2.1E-05 41.4 1.5 26 38-63 154-179 (346)
23 COG5222 Uncharacterized conser 76.4 2.1 4.4E-05 39.5 2.5 22 232-253 176-197 (427)
24 PF14787 zf-CCHC_5: GAG-polypr 74.4 1.9 4.1E-05 27.1 1.2 18 45-62 3-20 (36)
25 KOG0314 Predicted E3 ubiquitin 72.9 5.6 0.00012 38.7 4.6 25 232-256 158-182 (448)
26 PF14787 zf-CCHC_5: GAG-polypr 69.4 3 6.4E-05 26.2 1.3 16 234-249 4-19 (36)
27 COG5222 Uncharacterized conser 64.2 4.3 9.4E-05 37.4 1.8 21 102-122 177-197 (427)
28 KOG0314 Predicted E3 ubiquitin 46.1 26 0.00057 34.1 4.0 17 214-230 160-176 (448)
29 COG1198 PriA Primosomal protei 40.8 26 0.00057 36.3 3.3 58 37-114 428-487 (730)
30 KOG2044 5'-3' exonuclease HKE1 30.8 21 0.00047 37.1 0.8 22 42-63 258-279 (931)
31 KOG3116 Predicted C3H1-type Zn 30.7 12 0.00026 31.1 -0.8 24 163-186 25-48 (177)
32 KOG3116 Predicted C3H1-type Zn 24.6 20 0.00044 29.8 -0.5 24 40-63 23-46 (177)
33 COG5179 TAF1 Transcription ini 23.5 22 0.00048 36.1 -0.6 13 45-57 938-950 (968)
34 PF12353 eIF3g: Eukaryotic tra 22.8 50 0.0011 26.5 1.5 19 211-230 105-123 (128)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.94 E-value=3.4e-27 Score=194.93 Aligned_cols=133 Identities=38% Similarity=0.883 Sum_probs=87.3
Q ss_pred hcccCCCCCCCCCCCCC--------CCccccCCCCCcCCCCCCCCCCCCCCCcccccccCCCCcccccCCCcccCCCCCC
Q 024873 84 LCWNCREPGHMAGNCPN--------EGICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKT 155 (261)
Q Consensus 84 ~C~~C~~~GH~~~~Cp~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~C~~Cg~~ 155 (261)
+||+|++.||++++||+ ...||+|++.||++++||..... .....|++|++.||++.+||+...
T Consensus 2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~Cg~~GH~~~~Cp~~~~------- 73 (148)
T PTZ00368 2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGG-RGERSCYNCGKTGHLSRECPEAPP------- 73 (148)
T ss_pred cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCC-CCCcccCCCCCcCcCcccCCCccc-------
Confidence 34444444444444443 24788888888888888765321 112345555555555555544210
Q ss_pred CcccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCCC----
Q 024873 156 GHLARDCPNDPICNLCNVSGHVARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGP---- 231 (261)
Q Consensus 156 GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~~---- 231 (261)
+ .....|++|++.||++++||+.+.. ....++||+|++.||++++||..
T Consensus 74 ~------~~~~~C~~Cg~~GH~~~~C~~~~~~---------------------~~~~~~C~~Cg~~gH~~~~C~~~~~~~ 126 (148)
T PTZ00368 74 G------SGPRSCYNCGQTGHISRECPNRAKG---------------------GAARRACYNCGGEGHISRDCPNAGKRP 126 (148)
T ss_pred C------CCCcccCcCCCCCcccccCCCcccc---------------------cccchhhcccCcCCcchhcCCCccccC
Confidence 0 0124799999999999999986421 01246899999999999999874
Q ss_pred --CceeeccCCCCcccCCCCCC
Q 024873 232 --LMVCHNCGGRGHLAYECPSG 251 (261)
Q Consensus 232 --~~~C~~Cg~~GH~~~~C~~~ 251 (261)
.+.||+|++.|||++|||+.
T Consensus 127 ~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 127 GGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CCCCccccCCCcCcccccCCCC
Confidence 57999999999999999973
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.94 E-value=6.5e-27 Score=193.22 Aligned_cols=126 Identities=42% Similarity=0.982 Sum_probs=78.1
Q ss_pred ccccccCcCCCCCCCCCCC--------cccCCCCCCCCccccccchhhcccCCCCCCCCCCCCCCCccccCCCCCcCCCC
Q 024873 45 NLCKNCKRPGHFARECPNV--------AICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARD 116 (261)
Q Consensus 45 ~~C~~Cg~~GH~a~~Cp~~--------~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~~~~Cp~~~~C~~Cg~~GH~~~~ 116 (261)
++||+|++.||++++||.. ..||+|++.||++.+||.... -.....||+|++.||++++
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 4799999999999999972 345555555555555554210 0001245555555555555
Q ss_pred CCCCCCCCCCCcccccccCCCCcccccCCC-------cccCCCCCCCcccCCCCCC-------CCCCCCCcCCCCCCCCC
Q 024873 117 CTAPPLPPGDLRLCNNCYKQGHFAADCTND-------KACNNCRKTGHLARDCPND-------PICNLCNVSGHVARHCP 182 (261)
Q Consensus 117 Cp~~~~~~~~~~~C~~Cg~~GH~a~dCp~~-------~~C~~Cg~~GH~~~~Cp~~-------~~C~~C~~~GH~a~~Cp 182 (261)
||...... ..+.|++|++.||++.+|++. .+|++|++.||++++||+. +.||+|++.||+++|||
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 234455555555555555542 2566666666666666652 58999999999999999
Q ss_pred CC
Q 024873 183 KS 184 (261)
Q Consensus 183 ~~ 184 (261)
++
T Consensus 147 ~~ 148 (148)
T PTZ00368 147 DK 148 (148)
T ss_pred CC
Confidence 74
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.82 E-value=1.9e-20 Score=158.17 Aligned_cols=84 Identities=33% Similarity=0.852 Sum_probs=72.9
Q ss_pred CCCcCcccccccCcCCCCCCCCCCCcccCCCCCCCCccccccchhhcccCCCCCCCCCCC-CCC---CccccCCCCCcCC
Q 024873 39 RGYSQSNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTTKALCWNCREPGHMAGNC-PNE---GICHTCGKAGHRA 114 (261)
Q Consensus 39 ~~~~~~~~C~~Cg~~GH~a~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~~~~C-p~~---~~C~~Cg~~GH~~ 114 (261)
.......+||||++.||+++||| ..+|++|...||.+..||..++|++|++.||++++| |.. ..|+.|...+|++
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 44456889999999999999999 579999988999999999888999999999999999 543 5899999999999
Q ss_pred CCCCCCCCC
Q 024873 115 RDCTAPPLP 123 (261)
Q Consensus 115 ~~Cp~~~~~ 123 (261)
++||+.|+.
T Consensus 134 ~~Cp~~~k~ 142 (190)
T COG5082 134 EDCPSIWKH 142 (190)
T ss_pred ccCcccccc
Confidence 999998863
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=9.4e-20 Score=154.02 Aligned_cols=121 Identities=36% Similarity=0.783 Sum_probs=96.1
Q ss_pred CccccCCCCCcCCCCCCCCCCCCCCCcccccccCCCCcccccCCCcccCCCCCCCcccCCC-CC---CCCCCCCCcCCCC
Q 024873 102 GICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDC-PN---DPICNLCNVSGHV 177 (261)
Q Consensus 102 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dCp~~~~C~~Cg~~GH~~~~C-p~---~~~C~~C~~~GH~ 177 (261)
..||+||+.||+++|||. .+|++|...||.+..||..++|++||+.||++++| |. .+.|+.|...+|+
T Consensus 61 ~~C~nCg~~GH~~~DCP~--------~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~ 132 (190)
T COG5082 61 PVCFNCGQNGHLRRDCPH--------SICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHS 132 (190)
T ss_pred cccchhcccCcccccCCh--------hHhhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCccc
Confidence 689999999999999993 47999988999999999999999999999999999 53 4589999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCCC---CceeeccCCCCcc
Q 024873 178 ARHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGP---LMVCHNCGGRGHL 244 (261)
Q Consensus 178 a~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~~---~~~C~~Cg~~GH~ 244 (261)
+++||..|...-... ..+.+..+.||+|+..+||+.||+.+ ... |.+++.+|.
T Consensus 133 s~~Cp~~~k~y~~~~-------------~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~~-~~~~~~~~~ 188 (190)
T COG5082 133 SEDCPSIWKHYVLNN-------------GDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVP-YVCGKKGYV 188 (190)
T ss_pred cccCccccccccccc-------------CCCcceeeeccccCCccccCCCCCCCcccccc-ccccccccC
Confidence 999999997432111 11223456788888888888888753 122 666666654
No 5
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.73 E-value=2e-17 Score=148.52 Aligned_cols=194 Identities=29% Similarity=0.605 Sum_probs=145.0
Q ss_pred cCcccccccCcCCCCCCCCCCC-----------cccCCCCCCCCccccccchhhcccCCCCCCCCCCCCC-CCccccCCC
Q 024873 42 SQSNLCKNCKRPGHFARECPNV-----------AICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPN-EGICHTCGK 109 (261)
Q Consensus 42 ~~~~~C~~Cg~~GH~a~~Cp~~-----------~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~~~~Cp~-~~~C~~Cg~ 109 (261)
.....+++++..+|.+..|+.. ..+..+...+|....++. .+|+.|++.||++.+|+. ..+||+|++
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~c~~~g~~~~~~~~~~~~~~~c~~C~~ 100 (261)
T KOG4400|consen 22 DSSPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPE-VSCYICGEKGHLGRRCTRIAAACFNCGE 100 (261)
T ss_pred ccchhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCC-ceeeecCCCCchhhcCcccchhhhhCCC
Confidence 3467889999999999999864 234445556666666775 589999999999999996 689999999
Q ss_pred CCcCCCCCCCCCCCCCCCcccccccCCCCcc-ccc-----CCCcccCCCCCCCcccCCCCC--CCCCCCCCcCCCCCCCC
Q 024873 110 AGHRARDCTAPPLPPGDLRLCNNCYKQGHFA-ADC-----TNDKACNNCRKTGHLARDCPN--DPICNLCNVSGHVARHC 181 (261)
Q Consensus 110 ~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a-~dC-----p~~~~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~a~~C 181 (261)
.||++++||.++........||.|+..||.. .++ +....||+|++.||++.+||+ ...||.|++.||++++|
T Consensus 101 ~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C 180 (261)
T KOG4400|consen 101 GGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDC 180 (261)
T ss_pred CccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccC
Confidence 9999999999987533345789999999999 333 222459999999999999995 67999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCC------CCceeeccCCCCcccCCCCCC
Q 024873 182 PKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMG------PLMVCHNCGGRGHLAYECPSG 251 (261)
Q Consensus 182 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~------~~~~C~~Cg~~GH~~~~C~~~ 251 (261)
|........... .. ...-.++ +...+|+.++++. ....+|++...+|...+|.+.
T Consensus 181 ~~~~~~~~~~~~------------~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (261)
T KOG4400|consen 181 PSKQKSKSKQGG------------QR--KGFGACY-DYPQGHKQRACGGSGPDDNFNDSCYNKLSSGKLDQDCKQS 241 (261)
T ss_pred CccccccccCcc------------cc--cccccCc-cccccccccccCCCCcccccccccccccccccccchhhhh
Confidence 998653111000 00 0011233 5677788888765 246777777777777776543
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=99.62 E-value=5.2e-15 Score=132.91 Aligned_cols=172 Identities=36% Similarity=0.776 Sum_probs=127.3
Q ss_pred cccccccCcCCCCCCCCCCCcccCCCCCCCCccccccc-hhhcccCCCCCCCCCCCCCC-------CccccCCCCCcCCC
Q 024873 44 SNLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTT-KALCWNCREPGHMAGNCPNE-------GICHTCGKAGHRAR 115 (261)
Q Consensus 44 ~~~C~~Cg~~GH~a~~Cp~~~~C~~Cg~~GH~~~~Cp~-~~~C~~C~~~GH~~~~Cp~~-------~~C~~Cg~~GH~~~ 115 (261)
...+..+...+|+-..++.. .|+.|++.+|...+|+. ..+|++|++.||++++|+.. ..||.|+..||..
T Consensus 54 ~~~~~~~~~~~~~~~~~~~~-~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~- 131 (261)
T KOG4400|consen 54 GPGCVSTSPNGPLKSECPEV-SCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRG- 131 (261)
T ss_pred CCcccccccCcccCCCCCCc-eeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcccccceeeccCCCcccc-
Confidence 44556678888888888886 89999999999999985 57899999999999999965 2578999999999
Q ss_pred CCCCCCCCCCC-CcccccccCCCCcccccCC--CcccCCCCCCCcccCCCCCCC--------------CCCCCCcCCCCC
Q 024873 116 DCTAPPLPPGD-LRLCNNCYKQGHFAADCTN--DKACNNCRKTGHLARDCPNDP--------------ICNLCNVSGHVA 178 (261)
Q Consensus 116 ~Cp~~~~~~~~-~~~C~~Cg~~GH~a~dCp~--~~~C~~Cg~~GH~~~~Cp~~~--------------~C~~C~~~GH~a 178 (261)
|+........ .+.||+|++.||+..+||. ...|+.|++.+|++++||... .++ +...+|+.
T Consensus 132 -~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 209 (261)
T KOG4400|consen 132 -CPDADPVDGPKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSKSKQGGQRKGFGACY-DYPQGHKQ 209 (261)
T ss_pred -CcccccccCCCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccccccCcccccccccCc-cccccccc
Confidence 3332211111 1679999999999999993 589999999999999999631 222 33566666
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCcCCCcccccCCCCCceeeccCC
Q 024873 179 RHCPKSGGLGDRYSGGSGARGSGGSGARGGGYRDIVCRNCQQLGHMSRDCMGPLMVCHNCGG 240 (261)
Q Consensus 179 ~~Cp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~GH~~~dC~~~~~~C~~Cg~ 240 (261)
++++..+.. ......+|++...+|.+.+|-...+.+..|+.
T Consensus 210 ~~~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 (261)
T KOG4400|consen 210 RACGGSGPD---------------------DNFNDSCYNKLSSGKLDQDCKQSSMKSNSCGT 250 (261)
T ss_pred cccCCCCcc---------------------cccccccccccccccccchhhhhccccccccc
Confidence 666554321 12356789999999988887765555555544
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=98.08 E-value=2e-06 Score=46.07 Aligned_cols=16 Identities=50% Similarity=1.144 Sum_probs=9.9
Q ss_pred ccccCcCCCcccccCC
Q 024873 214 VCRNCQQLGHMSRDCM 229 (261)
Q Consensus 214 ~C~~C~~~GH~~~dC~ 229 (261)
+||+|+++||+++|||
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 4666666666666665
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=98.03 E-value=2.7e-06 Score=45.55 Aligned_cols=17 Identities=59% Similarity=1.402 Sum_probs=12.6
Q ss_pred cccccCcCCCCCCCCCC
Q 024873 46 LCKNCKRPGHFARECPN 62 (261)
Q Consensus 46 ~C~~Cg~~GH~a~~Cp~ 62 (261)
+||+|++.||++++||+
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 57777777777777764
No 9
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.07 E-value=0.0027 Score=38.86 Aligned_cols=21 Identities=29% Similarity=0.816 Sum_probs=16.2
Q ss_pred CCCCCCCCCcCCCCCCCCCCC
Q 024873 164 NDPICNLCNVSGHVARHCPKS 184 (261)
Q Consensus 164 ~~~~C~~C~~~GH~a~~Cp~~ 184 (261)
..-+|++|++.||+.++||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 344788888888888888874
No 10
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.69 E-value=0.009 Score=36.57 Aligned_cols=18 Identities=44% Similarity=0.929 Sum_probs=9.6
Q ss_pred cccccCcCCCcccccCCC
Q 024873 213 IVCRNCQQLGHMSRDCMG 230 (261)
Q Consensus 213 ~~C~~C~~~GH~~~dC~~ 230 (261)
.+|+.|++.|||.+|||.
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 455555555555555553
No 11
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.30 E-value=0.011 Score=38.54 Aligned_cols=18 Identities=50% Similarity=1.363 Sum_probs=13.4
Q ss_pred CceeeccCCCCcccCCCC
Q 024873 232 LMVCHNCGGRGHLAYECP 249 (261)
Q Consensus 232 ~~~C~~Cg~~GH~~~~C~ 249 (261)
...|.+|++.||+..|||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 456777777777777777
No 12
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=93.35 E-value=0.066 Score=34.88 Aligned_cols=19 Identities=32% Similarity=0.793 Sum_probs=15.3
Q ss_pred CCCCCCCCcCCCCCCCCCC
Q 024873 165 DPICNLCNVSGHVARHCPK 183 (261)
Q Consensus 165 ~~~C~~C~~~GH~a~~Cp~ 183 (261)
...|.+|++.||+..+||+
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3578888888888888884
No 13
>smart00343 ZnF_C2HC zinc finger.
Probab=93.34 E-value=0.051 Score=31.31 Aligned_cols=15 Identities=60% Similarity=1.515 Sum_probs=9.2
Q ss_pred eeccCCCCcccCCCC
Q 024873 235 CHNCGGRGHLAYECP 249 (261)
Q Consensus 235 C~~Cg~~GH~~~~C~ 249 (261)
|++|++.||++++||
T Consensus 2 C~~CG~~GH~~~~C~ 16 (26)
T smart00343 2 CYNCGKEGHIARDCP 16 (26)
T ss_pred CccCCCCCcchhhCC
Confidence 556666666666665
No 14
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=93.20 E-value=0.03 Score=37.51 Aligned_cols=27 Identities=30% Similarity=0.609 Sum_probs=23.1
Q ss_pred CCCCCCcCcccccccCcCCCCCCCCCC
Q 024873 36 GSRRGYSQSNLCKNCKRPGHFARECPN 62 (261)
Q Consensus 36 ~~~~~~~~~~~C~~Cg~~GH~a~~Cp~ 62 (261)
-.-.|+..+.+|++|+..||...+||.
T Consensus 23 ~~v~YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 23 VKVKYERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred EEEEECCcChhhcCCCCcCcCHhHcCC
Confidence 445677889999999999999999974
No 15
>smart00343 ZnF_C2HC zinc finger.
Probab=92.51 E-value=0.059 Score=31.04 Aligned_cols=17 Identities=53% Similarity=1.312 Sum_probs=11.5
Q ss_pred cccccCcCCCCCCCCCC
Q 024873 46 LCKNCKRPGHFARECPN 62 (261)
Q Consensus 46 ~C~~Cg~~GH~a~~Cp~ 62 (261)
.|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 36777777777777763
No 16
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.15 E-value=0.1 Score=50.67 Aligned_cols=37 Identities=38% Similarity=1.004 Sum_probs=24.5
Q ss_pred cccccccCcCCCCCCCCCCC-----cccCCCCCCCCcccccc
Q 024873 44 SNLCKNCKRPGHFARECPNV-----AICHNCGLPGHIASECT 80 (261)
Q Consensus 44 ~~~C~~Cg~~GH~a~~Cp~~-----~~C~~Cg~~GH~~~~Cp 80 (261)
+.+|.+|+..||...+||.. .+|..|+..||++.+|+
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~ 302 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCK 302 (554)
T ss_pred cccccccCCCccccccCCcccccccccccccCCcccccccCC
Confidence 56888888888888888864 14444554455444444
No 17
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=92.14 E-value=0.072 Score=48.58 Aligned_cols=21 Identities=43% Similarity=0.912 Sum_probs=15.2
Q ss_pred ceeeccCCCCcccCCCCCCCC
Q 024873 233 MVCHNCGGRGHLAYECPSGRF 253 (261)
Q Consensus 233 ~~C~~Cg~~GH~~~~C~~~~~ 253 (261)
-+||.||++|||++|||..+.
T Consensus 161 ~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHheeccccccccccCCccCC
Confidence 477788888888888876544
No 18
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.02 E-value=0.12 Score=50.16 Aligned_cols=38 Identities=39% Similarity=1.020 Sum_probs=31.8
Q ss_pred cccCCCCCCCcccCCCCCC-----CCCCCCCcCCCCCCCCCCC
Q 024873 147 KACNNCRKTGHLARDCPND-----PICNLCNVSGHVARHCPKS 184 (261)
Q Consensus 147 ~~C~~Cg~~GH~~~~Cp~~-----~~C~~C~~~GH~a~~Cp~~ 184 (261)
..|.+|+..||...+||.+ .+|++|+..||++.||+..
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 5788888888888888864 2799999999999999877
No 19
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=86.81 E-value=0.37 Score=31.01 Aligned_cols=18 Identities=44% Similarity=0.995 Sum_probs=10.7
Q ss_pred ccccccCcCCCCC--CCCCC
Q 024873 45 NLCKNCKRPGHFA--RECPN 62 (261)
Q Consensus 45 ~~C~~Cg~~GH~a--~~Cp~ 62 (261)
+.|.+||+.||++ +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 3566666666665 45554
No 20
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=85.53 E-value=0.72 Score=29.69 Aligned_cols=21 Identities=38% Similarity=0.942 Sum_probs=11.0
Q ss_pred ceeeccCCCCccc--CCCCCCCC
Q 024873 233 MVCHNCGGRGHLA--YECPSGRF 253 (261)
Q Consensus 233 ~~C~~Cg~~GH~~--~~C~~~~~ 253 (261)
+.|.+||.-||+. +.||...+
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~ 24 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCW 24 (40)
T ss_pred ccccccccccccccCccCCCCCC
Confidence 3455555555554 45555443
No 21
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=82.44 E-value=0.54 Score=31.36 Aligned_cols=16 Identities=38% Similarity=1.022 Sum_probs=9.1
Q ss_pred CCCCCCcCCCCCCCCC
Q 024873 167 ICNLCNVSGHVARHCP 182 (261)
Q Consensus 167 ~C~~C~~~GH~a~~Cp 182 (261)
.|+.|+..||...+||
T Consensus 33 ~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECP 48 (49)
T ss_pred hhcCCCCcCcCHhHcC
Confidence 4555555555555555
No 22
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=79.97 E-value=0.98 Score=41.39 Aligned_cols=26 Identities=31% Similarity=0.805 Sum_probs=22.3
Q ss_pred CCCCcCcccccccCcCCCCCCCCCCC
Q 024873 38 RRGYSQSNLCKNCKRPGHFARECPNV 63 (261)
Q Consensus 38 ~~~~~~~~~C~~Cg~~GH~a~~Cp~~ 63 (261)
.++..+...|+.||++||++.+||..
T Consensus 154 apgmgDq~~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 154 APGMGDQSGCYRCGKEGHWSKECPVD 179 (346)
T ss_pred CCCCCCHHHheeccccccccccCCcc
Confidence 45667788999999999999999974
No 23
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=76.45 E-value=2.1 Score=39.46 Aligned_cols=22 Identities=36% Similarity=0.856 Sum_probs=13.7
Q ss_pred CceeeccCCCCcccCCCCCCCC
Q 024873 232 LMVCHNCGGRGHLAYECPSGRF 253 (261)
Q Consensus 232 ~~~C~~Cg~~GH~~~~C~~~~~ 253 (261)
.-.||+||+.|||..+||..+.
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCC
Confidence 4566666666666666665443
No 24
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=74.44 E-value=1.9 Score=27.06 Aligned_cols=18 Identities=39% Similarity=0.903 Sum_probs=9.3
Q ss_pred ccccccCcCCCCCCCCCC
Q 024873 45 NLCKNCKRPGHFARECPN 62 (261)
Q Consensus 45 ~~C~~Cg~~GH~a~~Cp~ 62 (261)
..|++|++-.|+|.+|-.
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 467777777777777754
No 25
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.89 E-value=5.6 Score=38.67 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=14.4
Q ss_pred CceeeccCCCCcccCCCCCCCCCCC
Q 024873 232 LMVCHNCGGRGHLAYECPSGRFLDR 256 (261)
Q Consensus 232 ~~~C~~Cg~~GH~~~~C~~~~~~~~ 256 (261)
...|++|+..||+.+.||.......
T Consensus 158 sy~c~rc~~~g~wikacptv~~~~~ 182 (448)
T KOG0314|consen 158 SYKCVKCPTPGPWIKACPTVSGSYS 182 (448)
T ss_pred CcceecCCCCCccceeccccCCccc
Confidence 4566666666666666665544433
No 26
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=69.40 E-value=3 Score=26.19 Aligned_cols=16 Identities=44% Similarity=0.902 Sum_probs=7.0
Q ss_pred eeeccCCCCcccCCCC
Q 024873 234 VCHNCGGRGHLAYECP 249 (261)
Q Consensus 234 ~C~~Cg~~GH~~~~C~ 249 (261)
.|.+|++-.|+|.||-
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 4555555556665554
No 27
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.21 E-value=4.3 Score=37.39 Aligned_cols=21 Identities=29% Similarity=0.768 Sum_probs=16.7
Q ss_pred CccccCCCCCcCCCCCCCCCC
Q 024873 102 GICHTCGKAGHRARDCTAPPL 122 (261)
Q Consensus 102 ~~C~~Cg~~GH~~~~Cp~~~~ 122 (261)
..||+||+.||+..+||....
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred eeEEecCCCCchhhcCCCCCC
Confidence 478888888888888887543
No 28
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.11 E-value=26 Score=34.13 Aligned_cols=17 Identities=24% Similarity=0.602 Sum_probs=8.5
Q ss_pred ccccCcCCCcccccCCC
Q 024873 214 VCRNCQQLGHMSRDCMG 230 (261)
Q Consensus 214 ~C~~C~~~GH~~~dC~~ 230 (261)
.|++|.+.||+...||.
T Consensus 160 ~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 160 KCVKCPTPGPWIKACPT 176 (448)
T ss_pred ceecCCCCCccceeccc
Confidence 45555555555555543
No 29
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.81 E-value=26 Score=36.31 Aligned_cols=58 Identities=34% Similarity=0.738 Sum_probs=32.4
Q ss_pred CCCCCcCcccccccCcCCCCCCCCCCCcccCCCCC--CCCccccccchhhcccCCCCCCCCCCCCCCCccccCCCCCcCC
Q 024873 37 SRRGYSQSNLCKNCKRPGHFARECPNVAICHNCGL--PGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRA 114 (261)
Q Consensus 37 ~~~~~~~~~~C~~Cg~~GH~a~~Cp~~~~C~~Cg~--~GH~~~~Cp~~~~C~~C~~~GH~~~~Cp~~~~C~~Cg~~GH~~ 114 (261)
+|+++.....|..| ||++ .|-+|.. .=|... +...|..|+....+.. .|..||+. |+.
T Consensus 428 nRRGys~~l~C~~C---g~v~-------~Cp~Cd~~lt~H~~~---~~L~CH~Cg~~~~~p~------~Cp~Cgs~-~L~ 487 (730)
T COG1198 428 NRRGYAPLLLCRDC---GYIA-------ECPNCDSPLTLHKAT---GQLRCHYCGYQEPIPQ------SCPECGSE-HLR 487 (730)
T ss_pred ccCCccceeecccC---CCcc-------cCCCCCcceEEecCC---CeeEeCCCCCCCCCCC------CCCCCCCC-eeE
Confidence 47888889999999 4543 4444543 223332 2345666655544433 34456666 543
No 30
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=30.77 E-value=21 Score=37.09 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=16.5
Q ss_pred cCcccccccCcCCCCCCCCCCC
Q 024873 42 SQSNLCKNCKRPGHFARECPNV 63 (261)
Q Consensus 42 ~~~~~C~~Cg~~GH~a~~Cp~~ 63 (261)
.+...|+.||++||.+.+|.-.
T Consensus 258 ~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 258 NKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCcccchhhcccCCcHhhcCCc
Confidence 4566788888888888888653
No 31
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=30.67 E-value=12 Score=31.08 Aligned_cols=24 Identities=21% Similarity=0.484 Sum_probs=18.3
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCC
Q 024873 163 PNDPICNLCNVSGHVARHCPKSGG 186 (261)
Q Consensus 163 p~~~~C~~C~~~GH~a~~Cp~~~~ 186 (261)
++.+.|.+|-+.|||..+|.+...
T Consensus 25 ~~~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 25 GSSARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred ccchhHHHHHhhccceeeecCcee
Confidence 345678888888888888887754
No 32
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=24.64 E-value=20 Score=29.75 Aligned_cols=24 Identities=33% Similarity=0.782 Sum_probs=19.3
Q ss_pred CCcCcccccccCcCCCCCCCCCCC
Q 024873 40 GYSQSNLCKNCKRPGHFARECPNV 63 (261)
Q Consensus 40 ~~~~~~~C~~Cg~~GH~a~~Cp~~ 63 (261)
.+...+.|..|.+.||+..+|.+.
T Consensus 23 a~~~~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 23 AVGSSARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred hcccchhHHHHHhhccceeeecCc
Confidence 445677899999999999999764
No 33
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=23.47 E-value=22 Score=36.13 Aligned_cols=13 Identities=38% Similarity=0.951 Sum_probs=6.7
Q ss_pred ccccccCcCCCCC
Q 024873 45 NLCKNCKRPGHFA 57 (261)
Q Consensus 45 ~~C~~Cg~~GH~a 57 (261)
.+|-||||.||+.
T Consensus 938 r~C~nCGQvGHmk 950 (968)
T COG5179 938 RTCGNCGQVGHMK 950 (968)
T ss_pred eeccccccccccc
Confidence 3555555555553
No 34
>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=22.80 E-value=50 Score=26.53 Aligned_cols=19 Identities=26% Similarity=0.627 Sum_probs=12.0
Q ss_pred cccccccCcCCCcccccCCC
Q 024873 211 RDIVCRNCQQLGHMSRDCMG 230 (261)
Q Consensus 211 ~~~~C~~C~~~GH~~~dC~~ 230 (261)
..+.|+.|+ -.||...||-
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 5577777763
Done!