Query psy16574
Match_columns 152
No_of_seqs 222 out of 1384
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 16:29:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16574.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16574hhsearch_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 1.6E-32 3.5E-37 200.8 10.0 134 7-149 1-148 (148)
2 PTZ00368 universal minicircle 99.9 8.5E-25 1.8E-29 159.9 8.4 107 5-116 26-147 (148)
3 COG5082 AIR1 Arginine methyltr 99.9 4.6E-24 1E-28 159.7 6.4 112 36-151 60-175 (190)
4 COG5082 AIR1 Arginine methyltr 99.9 7.9E-23 1.7E-27 153.0 7.1 117 4-143 58-189 (190)
5 KOG4400|consensus 99.7 1.8E-16 4E-21 125.6 8.5 137 4-151 22-185 (261)
6 KOG4400|consensus 99.6 1.1E-15 2.4E-20 121.2 8.1 105 5-119 71-185 (261)
7 PF00098 zf-CCHC: Zinc knuckle 98.4 1.8E-07 3.8E-12 44.7 1.4 17 132-148 2-18 (18)
8 PF00098 zf-CCHC: Zinc knuckle 98.3 2.4E-07 5.1E-12 44.2 1.4 16 8-23 2-17 (18)
9 PF13696 zf-CCHC_2: Zinc knuck 96.8 0.0005 1.1E-08 37.3 0.8 19 7-25 9-27 (32)
10 PF13696 zf-CCHC_2: Zinc knuck 96.7 0.00065 1.4E-08 36.9 0.9 20 130-149 8-27 (32)
11 PF13917 zf-CCHC_3: Zinc knuck 96.2 0.0025 5.4E-08 36.8 1.2 21 4-24 2-22 (42)
12 PF13917 zf-CCHC_3: Zinc knuck 95.8 0.005 1.1E-07 35.6 1.2 18 130-147 4-21 (42)
13 KOG0119|consensus 95.7 0.0072 1.6E-07 51.8 2.4 39 36-74 261-303 (554)
14 smart00343 ZnF_C2HC zinc finge 95.1 0.0097 2.1E-07 30.5 0.9 17 132-148 1-17 (26)
15 KOG0119|consensus 95.1 0.019 4.2E-07 49.2 3.0 47 3-55 258-304 (554)
16 smart00343 ZnF_C2HC zinc finge 94.8 0.013 2.8E-07 30.0 0.8 17 8-24 1-17 (26)
17 PF15288 zf-CCHC_6: Zinc knuck 92.0 0.094 2E-06 29.9 1.3 20 7-26 2-23 (40)
18 PF14392 zf-CCHC_4: Zinc knuck 91.2 0.073 1.6E-06 31.5 0.3 19 130-148 31-49 (49)
19 PF15288 zf-CCHC_6: Zinc knuck 91.0 0.16 3.5E-06 28.9 1.6 18 99-116 2-21 (40)
20 PF14392 zf-CCHC_4: Zinc knuck 90.9 0.08 1.7E-06 31.3 0.3 16 8-23 33-48 (49)
21 PF14787 zf-CCHC_5: GAG-polypr 89.2 0.34 7.3E-06 26.9 1.9 21 7-27 3-23 (36)
22 KOG0109|consensus 87.2 0.34 7.4E-06 39.3 1.5 22 7-28 161-182 (346)
23 KOG0109|consensus 86.8 0.35 7.7E-06 39.2 1.4 22 98-119 160-181 (346)
24 PF14787 zf-CCHC_5: GAG-polypr 84.7 0.55 1.2E-05 26.1 1.1 18 132-149 4-21 (36)
25 COG5222 Uncharacterized conser 84.5 0.57 1.2E-05 38.2 1.6 20 77-96 176-195 (427)
26 COG5222 Uncharacterized conser 84.2 0.41 8.8E-06 39.1 0.6 21 6-26 176-196 (427)
27 KOG0314|consensus 78.9 2.9 6.3E-05 35.9 3.9 58 38-95 114-176 (448)
28 KOG0314|consensus 78.5 2.8 6.1E-05 36.0 3.8 59 8-75 114-177 (448)
29 KOG3116|consensus 59.7 2.4 5.3E-05 31.1 -0.5 18 8-25 29-46 (177)
30 KOG3116|consensus 49.7 4.3 9.4E-05 29.8 -0.5 20 36-55 27-46 (177)
31 PF12353 eIF3g: Eukaryotic tra 38.2 16 0.00036 25.9 1.0 19 36-55 106-124 (128)
32 KOG2044|consensus 36.2 16 0.00034 33.8 0.7 22 4-25 258-279 (931)
33 KOG2044|consensus 33.0 21 0.00044 33.1 1.0 15 80-94 263-277 (931)
34 PF05741 zf-nanos: Nanos RNA b 32.4 15 0.00033 22.3 0.0 7 78-84 34-40 (55)
35 PF12353 eIF3g: Eukaryotic tra 31.1 24 0.00053 25.0 0.9 19 98-117 106-124 (128)
36 KOG2673|consensus 30.9 26 0.00057 30.3 1.2 21 131-151 129-149 (485)
37 KOG0107|consensus 27.8 31 0.00068 26.2 1.0 19 130-148 100-118 (195)
38 smart00647 IBR In Between Ring 22.0 1E+02 0.0022 18.1 2.4 9 80-88 51-59 (64)
No 1
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.98 E-value=1.6e-32 Score=200.83 Aligned_cols=134 Identities=39% Similarity=0.987 Sum_probs=114.8
Q ss_pred cccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC-----CCcccccCCCCcccccCCCC----CC
Q psy16574 7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE-----SVTCYNCSGQGHVAKDCTVK----SS 77 (152)
Q Consensus 7 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~-----~~~C~~Cg~~GH~~~~Cp~~----~~ 77 (152)
++||+|++.||++++||.... .+..+.+.||+|++.||++++||.. ...||+|++.||++.+||.. ..
T Consensus 1 ~~C~~C~~~GH~~~~c~~~~~---~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~ 77 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNSAP---AGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGP 77 (148)
T ss_pred CcCCCCCCCCcCcccCcCCCC---CCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCC
Confidence 479999999999999998642 1234468999999999999999986 24799999999999999984 24
Q ss_pred cccccCCCCCCCCCCCCCCC-----CcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCC
Q psy16574 78 IICYNCNSSGHFARNCPNDS-----SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLV 149 (152)
Q Consensus 78 ~~C~~Cg~~GH~~~~Cp~~~-----~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~ 149 (152)
..|++|++.||++++||+.+ ...||+|++.||++++||+.|... ...++||+|++.|||++|||++
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~------~~~~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRP------GGDKTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccC------CCCCccccCCCcCcccccCCCC
Confidence 58999999999999999965 358999999999999999986422 2357999999999999999974
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=99.91 E-value=8.5e-25 Score=159.95 Aligned_cols=107 Identities=38% Similarity=1.057 Sum_probs=93.5
Q ss_pred CccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC-----CCcccccCCCCcccccCCCCC---
Q psy16574 5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE-----SVTCYNCSGQGHVAKDCTVKS--- 76 (152)
Q Consensus 5 ~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~-----~~~C~~Cg~~GH~~~~Cp~~~--- 76 (152)
....||+|+++||++++||..... .....|++|++.||++++||.. ...||+|++.||++++||+..
T Consensus 26 ~~~~C~~Cg~~GH~~~~Cp~~~~~-----~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~ 100 (148)
T PTZ00368 26 KARPCYKCGEPGHLSRECPSAPGG-----RGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGG 100 (148)
T ss_pred CCccCccCCCCCcCcccCcCCCCC-----CCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCccccc
Confidence 456899999999999999987421 1346899999999999999986 347999999999999999842
Q ss_pred --CcccccCCCCCCCCCCCCCCC-----CcCCcccCCCCcCCCCCCC
Q psy16574 77 --SIICYNCNSSGHFARNCPNDS-----SKRCYACHQAGHMAKECPG 116 (152)
Q Consensus 77 --~~~C~~Cg~~GH~~~~Cp~~~-----~~~C~~C~~~GH~~~~Cp~ 116 (152)
...|++|++.||++++||+.+ .+.||+|++.|||++|||+
T Consensus 101 ~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 101 AARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred ccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCCC
Confidence 458999999999999999963 5799999999999999997
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.90 E-value=4.6e-24 Score=159.65 Aligned_cols=112 Identities=35% Similarity=0.891 Sum_probs=96.9
Q ss_pred CccceecCCCCcCcccCCCCCCcccccCCCCcccccCCCCCCcccccCCCCCCCCCCC-CCCC-CcCCcccCCCCcCCCC
Q psy16574 36 GIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC-PNDS-SKRCYACHQAGHMAKE 113 (152)
Q Consensus 36 ~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~C-p~~~-~~~C~~C~~~GH~~~~ 113 (152)
..+||+||+.||++++||. .+||+|...||.+..||. .+.|++||+.||++++| |.++ .+.|+.|...+|++++
T Consensus 60 ~~~C~nCg~~GH~~~DCP~--~iC~~C~~~~H~s~~C~~--~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~ 135 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPH--SICYNCSWDGHRSNHCPK--PKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSED 135 (190)
T ss_pred ccccchhcccCcccccCCh--hHhhhcCCCCcccccCCc--ccccccccccCccccccCcccccCcceeccCCCcccccc
Confidence 5789999999999999994 599999889999999999 48999999999999999 6766 5689999999999999
Q ss_pred CCCCCCCCCCC--ccccccccccccccccccCCCCCCCcC
Q psy16574 114 CPGQTAGKSPE--PVVDMSLTCYVCGHQGHLSYDCKLVQK 151 (152)
Q Consensus 114 Cp~~~~~~~~~--~~~~~~~~C~~Cg~~GH~~~~C~~~~~ 151 (152)
||+.|+.+... ......++||+|+..+||+.||++...
T Consensus 136 Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~ 175 (190)
T COG5082 136 CPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS 175 (190)
T ss_pred CcccccccccccCCCcceeeeccccCCccccCCCCCCCcc
Confidence 99999765322 233446799999999999999997654
No 4
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=99.88 E-value=7.9e-23 Score=153.03 Aligned_cols=117 Identities=37% Similarity=0.939 Sum_probs=102.3
Q ss_pred CCccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCCCCcccccCCCCcccccC-CCC-CCcccc
Q psy16574 4 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDC-TVK-SSIICY 81 (152)
Q Consensus 4 ~~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~GH~~~~C-p~~-~~~~C~ 81 (152)
+.+.+||+|++.||+++||| . .+|++|...||.+..||.. .+|++||+.||++++| |.+ ....|+
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP-~-----------~iC~~C~~~~H~s~~C~~~-~~C~~Cg~~GH~~~dC~P~~~~~~~C~ 124 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCP-H-----------SICYNCSWDGHRSNHCPKP-KKCYNCGETGHLSRDCNPSKDQQKSCF 124 (190)
T ss_pred ccccccchhcccCcccccCC-h-----------hHhhhcCCCCcccccCCcc-cccccccccCccccccCcccccCccee
Confidence 56789999999999999999 3 4899998899999999998 8999999999999999 565 456999
Q ss_pred cCCCCCCCCCCCCCCC-------------CcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccC
Q psy16574 82 NCNSSGHFARNCPNDS-------------SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLS 143 (152)
Q Consensus 82 ~Cg~~GH~~~~Cp~~~-------------~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~ 143 (152)
.|...+|++++||..| .+.||+|+..+|++.||+..|+... . |.++..+|+.
T Consensus 125 ~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~---------~-~~~~~~~~~~ 189 (190)
T COG5082 125 DCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRV---------P-YVCGKKGYVS 189 (190)
T ss_pred ccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCccccc---------c-ccccccccCC
Confidence 9999999999999988 4789999999999999999985432 1 6677776653
No 5
>KOG4400|consensus
Probab=99.67 E-value=1.8e-16 Score=125.65 Aligned_cols=137 Identities=33% Similarity=0.804 Sum_probs=103.3
Q ss_pred CCccccccccccCccCCCCCCCCCCC---C---CC------------CCCCccceecCCCCcCcccCCCCCCcccccCCC
Q psy16574 4 TSTIQCYNCFDFGHYQYSCPQKSSAD---A---RG------------DKVGIVCYKCNNYGHFARECATESVTCYNCSGQ 65 (152)
Q Consensus 4 ~~~~~C~~C~~~GH~~~~Cp~~~~~~---~---~~------------~~~~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~ 65 (152)
++...++++++.+|.+..++...... . .+ ......|+.|++.||.+.+|+.....|++|++.
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~ 101 (261)
T KOG4400|consen 22 DSSPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPEVSCYICGEKGHLGRRCTRIAAACFNCGEG 101 (261)
T ss_pred ccchhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCCceeeecCCCCchhhcCcccchhhhhCCCC
Confidence 45567888899999998888764321 0 00 123677999999999999998755789999999
Q ss_pred CcccccCCCCC-----CcccccCCCCCCCC-CCCCCCC---CcCCcccCCCCcCCCCCCCCCCCCCCCcccccccccccc
Q psy16574 66 GHVAKDCTVKS-----SIICYNCNSSGHFA-RNCPNDS---SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVC 136 (152)
Q Consensus 66 GH~~~~Cp~~~-----~~~C~~Cg~~GH~~-~~Cp~~~---~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~C 136 (152)
||++++||... ...|+.|+..+|.. .++.... .+.||+|++.||+..+||+. ....||.|
T Consensus 102 gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~-----------~~~~c~~c 170 (261)
T KOG4400|consen 102 GHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN-----------KGGTCFRC 170 (261)
T ss_pred ccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC-----------CCCccccC
Confidence 99999998862 23588999999988 3333222 25699999999999999876 13689999
Q ss_pred ccccccCCCCCCCcC
Q psy16574 137 GHQGHLSYDCKLVQK 151 (152)
Q Consensus 137 g~~GH~~~~C~~~~~ 151 (152)
++.||.+.|||..+.
T Consensus 171 ~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 171 GKVGHGSRDCPSKQK 185 (261)
T ss_pred CCcceecccCCcccc
Confidence 999999999998764
No 6
>KOG4400|consensus
Probab=99.62 E-value=1.1e-15 Score=121.20 Aligned_cols=105 Identities=30% Similarity=0.896 Sum_probs=84.2
Q ss_pred CccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC--C----CcccccCCCCccc-ccCCCC-C
Q psy16574 5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE--S----VTCYNCSGQGHVA-KDCTVK-S 76 (152)
Q Consensus 5 ~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~--~----~~C~~Cg~~GH~~-~~Cp~~-~ 76 (152)
..+.|+.|++.||.+++|+.. ...|++|++.||++++||.. . ..||.|+..||.. .++... .
T Consensus 71 ~~~~c~~~g~~~~~~~~~~~~----------~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~ 140 (261)
T KOG4400|consen 71 PEVSCYICGEKGHLGRRCTRI----------AAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDG 140 (261)
T ss_pred CCceeeecCCCCchhhcCccc----------chhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccC
Confidence 456799999999999999873 35899999999999999988 2 2578999999998 333221 1
Q ss_pred --CcccccCCCCCCCCCCCCCCCCcCCcccCCCCcCCCCCCCCCC
Q psy16574 77 --SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119 (152)
Q Consensus 77 --~~~C~~Cg~~GH~~~~Cp~~~~~~C~~C~~~GH~~~~Cp~~~~ 119 (152)
...||+|++.||+..+||+.....|+.|++.+|++.+||..+.
T Consensus 141 ~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 141 PKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQK 185 (261)
T ss_pred CCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCcccc
Confidence 1569999999999999995434789999999999999999874
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=98.37 E-value=1.8e-07 Score=44.67 Aligned_cols=17 Identities=41% Similarity=1.194 Sum_probs=11.9
Q ss_pred cccccccccccCCCCCC
Q psy16574 132 TCYVCGHQGHLSYDCKL 148 (152)
Q Consensus 132 ~C~~Cg~~GH~~~~C~~ 148 (152)
.||+|++.||+++|||+
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 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=98.34 E-value=2.4e-07 Score=44.22 Aligned_cols=16 Identities=44% Similarity=1.177 Sum_probs=10.0
Q ss_pred ccccccccCccCCCCC
Q psy16574 8 QCYNCFDFGHYQYSCP 23 (152)
Q Consensus 8 ~C~~C~~~GH~~~~Cp 23 (152)
+||+|++.||++++||
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 9
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.78 E-value=0.0005 Score=37.34 Aligned_cols=19 Identities=32% Similarity=0.786 Sum_probs=11.6
Q ss_pred cccccccccCccCCCCCCC
Q psy16574 7 IQCYNCFDFGHYQYSCPQK 25 (152)
Q Consensus 7 ~~C~~C~~~GH~~~~Cp~~ 25 (152)
-+|+.|++.||+.++||..
T Consensus 9 Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CEeecCCCCCccHhHCCCC
Confidence 3566666666666666653
No 10
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=96.71 E-value=0.00065 Score=36.91 Aligned_cols=20 Identities=35% Similarity=0.816 Sum_probs=17.1
Q ss_pred cccccccccccccCCCCCCC
Q psy16574 130 SLTCYVCGHQGHLSYDCKLV 149 (152)
Q Consensus 130 ~~~C~~Cg~~GH~~~~C~~~ 149 (152)
.-.|+.|++.||+..|||+.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCEeecCCCCCccHhHCCCC
Confidence 45899999999999999984
No 11
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.19 E-value=0.0025 Score=36.85 Aligned_cols=21 Identities=33% Similarity=1.031 Sum_probs=13.9
Q ss_pred CCccccccccccCccCCCCCC
Q psy16574 4 TSTIQCYNCFDFGHYQYSCPQ 24 (152)
Q Consensus 4 ~~~~~C~~C~~~GH~~~~Cp~ 24 (152)
++...|.+|++.||++.+||.
T Consensus 2 ~~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 2 NARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCCcCcccCCCCcchhhCCC
Confidence 445667777777777777773
No 12
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=95.76 E-value=0.005 Score=35.57 Aligned_cols=18 Identities=39% Similarity=1.204 Sum_probs=12.6
Q ss_pred cccccccccccccCCCCC
Q psy16574 130 SLTCYVCGHQGHLSYDCK 147 (152)
Q Consensus 130 ~~~C~~Cg~~GH~~~~C~ 147 (152)
...|.+|++.||+..+|+
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 356777777777777777
No 13
>KOG0119|consensus
Probab=95.69 E-value=0.0072 Score=51.76 Aligned_cols=39 Identities=31% Similarity=0.766 Sum_probs=26.3
Q ss_pred CccceecCCCCcCcccCCCC----CCcccccCCCCcccccCCC
Q psy16574 36 GIVCYKCNNYGHFARECATE----SVTCYNCSGQGHVAKDCTV 74 (152)
Q Consensus 36 ~~~C~~Cg~~GH~~~~Cp~~----~~~C~~Cg~~GH~~~~Cp~ 74 (152)
..+|.+|+..||...+||.+ ..+|+.|+..||++.+|+.
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~ 303 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKV 303 (554)
T ss_pred cccccccCCCccccccCCcccccccccccccCCcccccccCCC
Confidence 35777777777777777766 2366666666666666655
No 14
>smart00343 ZnF_C2HC zinc finger.
Probab=95.13 E-value=0.0097 Score=30.49 Aligned_cols=17 Identities=47% Similarity=1.288 Sum_probs=12.6
Q ss_pred cccccccccccCCCCCC
Q psy16574 132 TCYVCGHQGHLSYDCKL 148 (152)
Q Consensus 132 ~C~~Cg~~GH~~~~C~~ 148 (152)
.|++|++.||++.+|++
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 37778888888888773
No 15
>KOG0119|consensus
Probab=95.07 E-value=0.019 Score=49.25 Aligned_cols=47 Identities=32% Similarity=0.726 Sum_probs=38.8
Q ss_pred CCCccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574 3 STSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE 55 (152)
Q Consensus 3 ~~~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~ 55 (152)
...+.+|.+|+..||-.-+||..... ...+|++|+..||++.+|+..
T Consensus 258 ~~d~~~c~~cg~~~H~q~~cp~r~~~------~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 258 DDDNRACRNCGSTGHKQYDCPGRIPN------TTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccccccCCCccccccCCccccc------ccccccccCCcccccccCCCc
Confidence 34457999999999999999997321 123899999999999999976
No 16
>smart00343 ZnF_C2HC zinc finger.
Probab=94.80 E-value=0.013 Score=29.98 Aligned_cols=17 Identities=47% Similarity=1.145 Sum_probs=11.5
Q ss_pred ccccccccCccCCCCCC
Q psy16574 8 QCYNCFDFGHYQYSCPQ 24 (152)
Q Consensus 8 ~C~~C~~~GH~~~~Cp~ 24 (152)
.|++|++.||++++||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 36677777777777763
No 17
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=91.99 E-value=0.094 Score=29.89 Aligned_cols=20 Identities=40% Similarity=0.974 Sum_probs=14.3
Q ss_pred cccccccccCccC--CCCCCCC
Q psy16574 7 IQCYNCFDFGHYQ--YSCPQKS 26 (152)
Q Consensus 7 ~~C~~C~~~GH~~--~~Cp~~~ 26 (152)
+.|.+||+.||++ +.||...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 4677888888877 4577764
No 18
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=91.16 E-value=0.073 Score=31.52 Aligned_cols=19 Identities=32% Similarity=0.838 Sum_probs=15.6
Q ss_pred cccccccccccccCCCCCC
Q psy16574 130 SLTCYVCGHQGHLSYDCKL 148 (152)
Q Consensus 130 ~~~C~~Cg~~GH~~~~C~~ 148 (152)
..+|++|+..||...+||+
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4578889999998888874
No 19
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=90.99 E-value=0.16 Score=28.93 Aligned_cols=18 Identities=44% Similarity=0.984 Sum_probs=10.2
Q ss_pred cCCcccCCCCcCC--CCCCC
Q psy16574 99 KRCYACHQAGHMA--KECPG 116 (152)
Q Consensus 99 ~~C~~C~~~GH~~--~~Cp~ 116 (152)
+.|.+||..||+. +.||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 4566666666654 34553
No 20
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=90.88 E-value=0.08 Score=31.34 Aligned_cols=16 Identities=38% Similarity=1.061 Sum_probs=9.9
Q ss_pred ccccccccCccCCCCC
Q psy16574 8 QCYNCFDFGHYQYSCP 23 (152)
Q Consensus 8 ~C~~C~~~GH~~~~Cp 23 (152)
.|++|+..||..++||
T Consensus 33 ~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECP 48 (49)
T ss_pred hhcCCCCcCcCHhHcC
Confidence 4666666666666665
No 21
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=89.22 E-value=0.34 Score=26.90 Aligned_cols=21 Identities=24% Similarity=0.369 Sum_probs=13.0
Q ss_pred cccccccccCccCCCCCCCCC
Q psy16574 7 IQCYNCFDFGHYQYSCPQKSS 27 (152)
Q Consensus 7 ~~C~~C~~~GH~~~~Cp~~~~ 27 (152)
..|++|++..|++++|.....
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 469999999999999988754
No 22
>KOG0109|consensus
Probab=87.21 E-value=0.34 Score=39.33 Aligned_cols=22 Identities=32% Similarity=0.827 Sum_probs=19.1
Q ss_pred cccccccccCccCCCCCCCCCC
Q psy16574 7 IQCYNCFDFGHYQYSCPQKSSA 28 (152)
Q Consensus 7 ~~C~~C~~~GH~~~~Cp~~~~~ 28 (152)
..|+.||++|||+.+||.....
T Consensus 161 ~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 161 SGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred HHheeccccccccccCCccCCC
Confidence 3699999999999999998643
No 23
>KOG0109|consensus
Probab=86.76 E-value=0.35 Score=39.24 Aligned_cols=22 Identities=41% Similarity=1.002 Sum_probs=18.3
Q ss_pred CcCCcccCCCCcCCCCCCCCCC
Q psy16574 98 SKRCYACHQAGHMAKECPGQTA 119 (152)
Q Consensus 98 ~~~C~~C~~~GH~~~~Cp~~~~ 119 (152)
...||.|+++||++++||..+.
T Consensus 160 q~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHHheeccccccccccCCccCC
Confidence 4579999999999999998873
No 24
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=84.68 E-value=0.55 Score=26.06 Aligned_cols=18 Identities=28% Similarity=0.652 Sum_probs=8.7
Q ss_pred cccccccccccCCCCCCC
Q psy16574 132 TCYVCGHQGHLSYDCKLV 149 (152)
Q Consensus 132 ~C~~Cg~~GH~~~~C~~~ 149 (152)
.|++|++-.|.++||..+
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 566677777777776554
No 25
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.51 E-value=0.57 Score=38.24 Aligned_cols=20 Identities=40% Similarity=1.283 Sum_probs=11.7
Q ss_pred CcccccCCCCCCCCCCCCCC
Q psy16574 77 SIICYNCNSSGHFARNCPND 96 (152)
Q Consensus 77 ~~~C~~Cg~~GH~~~~Cp~~ 96 (152)
...||+||+.||+..+||..
T Consensus 176 gY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred ceeEEecCCCCchhhcCCCC
Confidence 45566666666666666543
No 26
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.16 E-value=0.41 Score=39.06 Aligned_cols=21 Identities=33% Similarity=0.861 Sum_probs=18.4
Q ss_pred ccccccccccCccCCCCCCCC
Q psy16574 6 TIQCYNCFDFGHYQYSCPQKS 26 (152)
Q Consensus 6 ~~~C~~C~~~GH~~~~Cp~~~ 26 (152)
+-+||.||+.|||..+||...
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred ceeEEecCCCCchhhcCCCCC
Confidence 347999999999999999864
No 27
>KOG0314|consensus
Probab=78.86 E-value=2.9 Score=35.91 Aligned_cols=58 Identities=22% Similarity=0.592 Sum_probs=28.1
Q ss_pred cceecCCCCcCcccCCCC-CCcccccCCCCcccccCCCC----CCcccccCCCCCCCCCCCCC
Q psy16574 38 VCYKCNNYGHFARECATE-SVTCYNCSGQGHVAKDCTVK----SSIICYNCNSSGHFARNCPN 95 (152)
Q Consensus 38 ~C~~Cg~~GH~~~~Cp~~-~~~C~~Cg~~GH~~~~Cp~~----~~~~C~~Cg~~GH~~~~Cp~ 95 (152)
.++.++..||..+.+... ..++-++...+|+...+... ....|++|...||+.+.||.
T Consensus 114 ~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacpt 176 (448)
T KOG0314|consen 114 MNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPT 176 (448)
T ss_pred hccccccCCcccccCCCcccceeeecccCccccccccccCCCCCCcceecCCCCCccceeccc
Confidence 455555555555555433 34455555555555554432 23344444444444444444
No 28
>KOG0314|consensus
Probab=78.52 E-value=2.8 Score=36.00 Aligned_cols=59 Identities=29% Similarity=0.510 Sum_probs=46.6
Q ss_pred ccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC-----CCcccccCCCCcccccCCCC
Q psy16574 8 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE-----SVTCYNCSGQGHVAKDCTVK 75 (152)
Q Consensus 8 ~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~-----~~~C~~Cg~~GH~~~~Cp~~ 75 (152)
+++.+++.|+.++.+.... ..++..+-..+|+..-+... ...|++|...||+...||..
T Consensus 114 ~~~~~~~~~~~~~~~t~~~---------~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 114 MNGRMGGRGFGMRRQTPPP---------GYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred hccccccCCcccccCCCcc---------cceeeecccCccccccccccCCCCCCcceecCCCCCccceecccc
Confidence 5777888888888885543 36888888888888877765 66789999999999999874
No 29
>KOG3116|consensus
Probab=59.71 E-value=2.4 Score=31.13 Aligned_cols=18 Identities=39% Similarity=1.178 Sum_probs=8.8
Q ss_pred ccccccccCccCCCCCCC
Q psy16574 8 QCYNCFDFGHYQYSCPQK 25 (152)
Q Consensus 8 ~C~~C~~~GH~~~~Cp~~ 25 (152)
.|.+|.|.|||..+|.+.
T Consensus 29 rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 29 RCQKCLQAGHWTYECKNK 46 (177)
T ss_pred hHHHHHhhccceeeecCc
Confidence 445555555555555443
No 30
>KOG3116|consensus
Probab=49.74 E-value=4.3 Score=29.84 Aligned_cols=20 Identities=35% Similarity=0.816 Sum_probs=16.7
Q ss_pred CccceecCCCCcCcccCCCC
Q psy16574 36 GIVCYKCNNYGHFARECATE 55 (152)
Q Consensus 36 ~~~C~~Cg~~GH~~~~Cp~~ 55 (152)
.+.|.+|.+.|||..+|.+.
T Consensus 27 ~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred chhHHHHHhhccceeeecCc
Confidence 46788888888888888876
No 31
>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=38.22 E-value=16 Score=25.93 Aligned_cols=19 Identities=21% Similarity=0.677 Sum_probs=16.0
Q ss_pred CccceecCCCCcCcccCCCC
Q psy16574 36 GIVCYKCNNYGHFARECATE 55 (152)
Q Consensus 36 ~~~C~~Cg~~GH~~~~Cp~~ 55 (152)
.+.|..|+ -.|+...||..
T Consensus 106 ~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 106 KVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred eEEeCCCC-CCcccccCCcc
Confidence 68899996 67999999975
No 32
>KOG2044|consensus
Probab=36.21 E-value=16 Score=33.84 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=13.9
Q ss_pred CCccccccccccCccCCCCCCC
Q psy16574 4 TSTIQCYNCFDFGHYQYSCPQK 25 (152)
Q Consensus 4 ~~~~~C~~C~~~GH~~~~Cp~~ 25 (152)
+....|+.||+.||.+.+|...
T Consensus 258 ~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 258 NKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCcccchhhcccCCcHhhcCCc
Confidence 3445567777777777776554
No 33
>KOG2044|consensus
Probab=33.03 E-value=21 Score=33.12 Aligned_cols=15 Identities=40% Similarity=1.203 Sum_probs=6.4
Q ss_pred cccCCCCCCCCCCCC
Q psy16574 80 CYNCNSSGHFARNCP 94 (152)
Q Consensus 80 C~~Cg~~GH~~~~Cp 94 (152)
|+.||+.||.+.+|.
T Consensus 263 C~~cgq~gh~~~dc~ 277 (931)
T KOG2044|consen 263 CFLCGQTGHEAKDCE 277 (931)
T ss_pred chhhcccCCcHhhcC
Confidence 444444444444443
No 34
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=32.37 E-value=15 Score=22.32 Aligned_cols=7 Identities=29% Similarity=0.947 Sum_probs=1.2
Q ss_pred cccccCC
Q psy16574 78 IICYNCN 84 (152)
Q Consensus 78 ~~C~~Cg 84 (152)
..|..||
T Consensus 34 y~Cp~Cg 40 (55)
T PF05741_consen 34 YVCPICG 40 (55)
T ss_dssp ---TTT-
T ss_pred CcCCCCc
Confidence 3343443
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=31.11 E-value=24 Score=25.04 Aligned_cols=19 Identities=26% Similarity=0.810 Sum_probs=14.1
Q ss_pred CcCCcccCCCCcCCCCCCCC
Q psy16574 98 SKRCYACHQAGHMAKECPGQ 117 (152)
Q Consensus 98 ~~~C~~C~~~GH~~~~Cp~~ 117 (152)
.+.|.+|+ ..||...||..
T Consensus 106 ~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 106 KVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred eEEeCCCC-CCcccccCCcc
Confidence 46788885 66888888864
No 36
>KOG2673|consensus
Probab=30.87 E-value=26 Score=30.27 Aligned_cols=21 Identities=29% Similarity=0.558 Sum_probs=17.1
Q ss_pred ccccccccccccCCCCCCCcC
Q psy16574 131 LTCYVCGHQGHLSYDCKLVQK 151 (152)
Q Consensus 131 ~~C~~Cg~~GH~~~~C~~~~~ 151 (152)
..||||+..-|-.+|||.+..
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccccCCCCCccccCCCccc
Confidence 458999999999999988653
No 37
>KOG0107|consensus
Probab=27.79 E-value=31 Score=26.21 Aligned_cols=19 Identities=42% Similarity=1.006 Sum_probs=14.9
Q ss_pred cccccccccccccCCCCCC
Q psy16574 130 SLTCYVCGHQGHLSYDCKL 148 (152)
Q Consensus 130 ~~~C~~Cg~~GH~~~~C~~ 148 (152)
...|++||+.||+.+.|..
T Consensus 100 ~~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 100 RGFCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccccCCCcccccccccc
Confidence 4568888888888888765
No 38
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.96 E-value=1e+02 Score=18.05 Aligned_cols=9 Identities=33% Similarity=1.132 Sum_probs=3.3
Q ss_pred cccCCCCCC
Q psy16574 80 CYNCNSSGH 88 (152)
Q Consensus 80 C~~Cg~~GH 88 (152)
|++|+...|
T Consensus 51 C~~C~~~~H 59 (64)
T smart00647 51 CFRCKVPWH 59 (64)
T ss_pred CCCCCCcCC
Confidence 333333333
Done!