Query 012460
Match_columns 463
No_of_seqs 170 out of 998
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 02:52:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012460.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012460hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00607 Gag_p24: gag gene pro 99.2 1.7E-12 3.6E-17 120.7 -0.4 60 304-384 146-206 (206)
2 PTZ00368 universal minicircle 98.4 1.3E-07 2.8E-12 82.6 2.7 41 422-462 103-147 (148)
3 COG5082 AIR1 Arginine methyltr 98.4 1.3E-07 2.8E-12 89.2 2.4 40 423-462 98-138 (190)
4 PTZ00368 universal minicircle 98.3 3.8E-07 8.3E-12 79.6 3.5 41 422-462 52-95 (148)
5 COG5082 AIR1 Arginine methyltr 98.2 8.9E-07 1.9E-11 83.6 3.3 39 422-460 60-113 (190)
6 KOG4400 E3 ubiquitin ligase in 98.2 1.2E-06 2.6E-11 83.1 3.5 39 423-462 144-182 (261)
7 PF00098 zf-CCHC: Zinc knuckle 97.7 1.7E-05 3.6E-10 49.8 1.5 16 424-439 2-17 (18)
8 PF00098 zf-CCHC: Zinc knuckle 97.7 1.8E-05 4E-10 49.6 1.2 17 446-462 2-18 (18)
9 KOG4400 E3 ubiquitin ligase in 97.6 2.9E-05 6.3E-10 73.8 2.0 39 424-462 120-161 (261)
10 KOG0119 Splicing factor 1/bran 96.2 0.0018 4E-08 69.0 1.5 40 422-461 261-302 (554)
11 PF13696 zf-CCHC_2: Zinc knuck 95.0 0.009 1.9E-07 43.0 0.8 17 446-462 10-26 (32)
12 smart00343 ZnF_C2HC zinc finge 94.0 0.022 4.7E-07 37.5 0.8 16 424-439 1-16 (26)
13 smart00343 ZnF_C2HC zinc finge 94.0 0.026 5.6E-07 37.2 1.1 17 446-462 1-17 (26)
14 PF13696 zf-CCHC_2: Zinc knuck 92.6 0.045 9.7E-07 39.5 0.6 21 421-441 7-27 (32)
15 PF13917 zf-CCHC_3: Zinc knuck 92.5 0.061 1.3E-06 40.6 1.2 19 422-440 4-22 (42)
16 PF13917 zf-CCHC_3: Zinc knuck 89.2 0.18 3.8E-06 38.1 1.0 17 445-461 5-21 (42)
17 KOG0109 RNA-binding protein LA 88.7 0.19 4E-06 51.7 1.1 31 318-351 77-107 (346)
18 PF14392 zf-CCHC_4: Zinc knuck 86.7 0.25 5.3E-06 37.2 0.5 17 423-439 32-48 (49)
19 KOG0109 RNA-binding protein LA 85.4 0.35 7.6E-06 49.7 1.0 23 421-443 159-181 (346)
20 PF14392 zf-CCHC_4: Zinc knuck 84.9 0.38 8.2E-06 36.2 0.7 17 446-462 33-49 (49)
21 COG5222 Uncharacterized conser 84.3 0.5 1.1E-05 49.0 1.5 21 421-441 175-195 (427)
22 PF15288 zf-CCHC_6: Zinc knuck 83.3 0.66 1.4E-05 35.1 1.4 12 424-435 3-14 (40)
23 PF15288 zf-CCHC_6: Zinc knuck 81.0 0.73 1.6E-05 34.9 0.9 17 446-462 3-21 (40)
24 COG5222 Uncharacterized conser 80.5 0.73 1.6E-05 47.8 1.0 18 445-462 177-194 (427)
25 PF14787 zf-CCHC_5: GAG-polypr 80.5 1.1 2.5E-05 33.3 1.7 20 423-442 3-22 (36)
26 KOG0314 Predicted E3 ubiquitin 70.9 4 8.7E-05 43.8 3.4 42 422-463 133-177 (448)
27 KOG0119 Splicing factor 1/bran 68.8 2.9 6.2E-05 45.7 1.9 32 410-441 270-304 (554)
28 PF14787 zf-CCHC_5: GAG-polypr 63.6 3 6.4E-05 31.2 0.6 17 446-462 4-20 (36)
29 KOG2044 5'-3' exonuclease HKE1 62.3 3.3 7.1E-05 47.4 0.8 22 441-462 257-278 (931)
30 KOG2673 Uncharacterized conser 60.7 4 8.7E-05 44.1 1.1 20 423-442 129-148 (485)
31 KOG0107 Alternative splicing f 54.0 9 0.0002 37.4 2.2 21 420-440 98-118 (195)
32 KOG3070 Predicted RNA-binding 53.3 9.6 0.00021 37.5 2.3 40 423-462 174-217 (235)
33 PF12353 eIF3g: Eukaryotic tra 44.3 11 0.00023 33.9 1.0 20 421-441 105-124 (128)
34 KOG2673 Uncharacterized conser 41.3 13 0.00027 40.5 1.1 17 446-462 130-146 (485)
35 KOG0341 DEAD-box protein abstr 38.9 18 0.00039 39.4 1.8 47 320-367 336-382 (610)
36 KOG2044 5'-3' exonuclease HKE1 25.8 30 0.00066 40.1 1.0 21 421-441 259-279 (931)
37 PRK04023 DNA polymerase II lar 24.3 58 0.0013 38.8 2.8 40 421-462 625-668 (1121)
38 COG1198 PriA Primosomal protei 24.2 54 0.0012 37.4 2.4 39 239-277 302-340 (730)
39 COG1644 RPB10 DNA-directed RNA 23.8 28 0.0006 28.9 0.1 13 422-434 4-17 (63)
40 KOG3794 CBF1-interacting corep 21.9 43 0.00092 36.2 1.1 18 445-462 125-144 (453)
41 KOG0107 Alternative splicing f 20.9 47 0.001 32.6 1.1 18 445-462 101-118 (195)
42 PF08499 PDEase_I_N: 3'5'-cycl 20.9 59 0.0013 26.6 1.5 30 297-326 4-33 (59)
43 KOG3116 Predicted C3H1-type Zn 20.9 30 0.00066 33.2 -0.2 22 422-443 27-48 (177)
44 PF07282 OrfB_Zn_ribbon: Putat 20.3 43 0.00093 25.9 0.6 30 422-455 28-57 (69)
45 COG0484 DnaJ DnaJ-class molecu 20.1 51 0.0011 34.9 1.2 38 421-458 158-197 (371)
No 1
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=99.21 E-value=1.7e-12 Score=120.73 Aligned_cols=60 Identities=18% Similarity=0.313 Sum_probs=52.2
Q ss_pred cccccchHHHHHHHHHHhhhhccCCCCcccccccccccccCCCCCCcc-ccccccccCCccccCcchhhhHHhhhhhhhh
Q 012460 304 GVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS-DMRLGRRVEDTVSVGPIVGERQQKKRRKKTR 382 (463)
Q Consensus 304 ~LraEqa~qdVknwMt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe-mMTaCqGVgGgv~~gPs~~Em~QKkkthKaR 382 (463)
.++.+++.+++++||+.+|++|||||||++| |++|++ ++||| ||++|||||+ |. ||++
T Consensus 146 a~~~~~~~~~~~~~~~~~L~~eNAN~~C~~~----~~~l~~--~~~lee~~~~C~~vg~-----~~----------~k~~ 204 (206)
T PF00607_consen 146 AIRREQGENEVKNILIRQLAYENANPDCRRI----IRPLGK--DAPLEEMIRACQGVGG-----PS----------HKAQ 204 (206)
T ss_dssp HHHCSSSTHHHHHHHHHHHHHHTS-HHHHHH----HHHH-T--TSTHHHHHHHTTTTSS-----TT----------SSSB
T ss_pred HHhhcccccchhhHHHHHhhhccchHHHHHH----HHccCC--CCCHHHHHHHhhccCC-----Hh----------hhhh
Confidence 3789999999999999999999999999999 999986 77788 9999999996 77 7777
Q ss_pred hh
Q 012460 383 VI 384 (463)
Q Consensus 383 VL 384 (463)
++
T Consensus 205 ~l 206 (206)
T PF00607_consen 205 AL 206 (206)
T ss_dssp BH
T ss_pred cC
Confidence 54
No 2
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.41 E-value=1.3e-07 Score=82.58 Aligned_cols=41 Identities=32% Similarity=0.803 Sum_probs=35.2
Q ss_pred cccccccCCCCcccccccCC----CCCCCceecCCCcccccCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQ----KQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaP----KK~KgCfkCGk~GH~AKDCPq 462 (463)
...||+||+.||++++||.+ .....||+||+.||++++||+
T Consensus 103 ~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 103 RRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred chhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCCC
Confidence 46899999999999999985 233579999999999999996
No 3
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.40 E-value=1.3e-07 Score=89.22 Aligned_cols=40 Identities=35% Similarity=0.867 Sum_probs=21.3
Q ss_pred ccccccCCCCcccccc-cCCCCCCCceecCCCcccccCCCC
Q 012460 423 ETCSNCGKENHTAATC-KMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 423 IKCFNCGKEGHiARNC-PaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
++||+||+-||++++| |.+.+.+.|+.|...+|++++||+
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~ 138 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPS 138 (190)
T ss_pred cccccccccCccccccCcccccCcceeccCCCccccccCcc
Confidence 4555555555555555 344444455555555555555554
No 4
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=98.32 E-value=3.8e-07 Score=79.64 Aligned_cols=41 Identities=29% Similarity=0.777 Sum_probs=30.5
Q ss_pred cccccccCCCCcccccccCCC---CCCCceecCCCcccccCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQK---QNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPK---K~KgCfkCGk~GH~AKDCPq 462 (463)
...||+||+.||++++||.+. ....||+||+.||++++||+
T Consensus 52 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~ 95 (148)
T PTZ00368 52 ERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPN 95 (148)
T ss_pred CcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCC
Confidence 346888888888888887764 33468888888888888875
No 5
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=98.20 E-value=8.9e-07 Score=83.65 Aligned_cols=39 Identities=31% Similarity=0.803 Sum_probs=29.6
Q ss_pred cccccccCCCCcccccccC---------C------CCCCCceecCCCcccccCC
Q 012460 422 SETCSNCGKENHTAATCKM---------Q------KQNKPCFLCGSFKHRWKNC 460 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPa---------P------KK~KgCfkCGk~GH~AKDC 460 (463)
...|||||+.||++++||. . .+.+.||+||..||++++|
T Consensus 60 ~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDC 113 (190)
T ss_pred ccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCcccccc
Confidence 4577777777777777771 0 1236799999999999999
No 6
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.17 E-value=1.2e-06 Score=83.09 Aligned_cols=39 Identities=28% Similarity=0.853 Sum_probs=35.8
Q ss_pred ccccccCCCCcccccccCCCCCCCceecCCCcccccCCCC
Q 012460 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
+.||+||+.||++.+||.+ ....||.|+..||.+++||.
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~-~~~~c~~c~~~~h~~~~C~~ 182 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN-KGGTCFRCGKVGHGSRDCPS 182 (261)
T ss_pred CccCCCCcCCcchhhCCCC-CCCccccCCCcceecccCCc
Confidence 7899999999999999987 34679999999999999996
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=97.71 E-value=1.7e-05 Score=49.83 Aligned_cols=16 Identities=44% Similarity=1.039 Sum_probs=7.9
Q ss_pred cccccCCCCccccccc
Q 012460 424 TCSNCGKENHTAATCK 439 (463)
Q Consensus 424 KCFNCGKEGHiARNCP 439 (463)
.||+||+.||++++||
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 3455555555555444
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=97.66 E-value=1.8e-05 Score=49.63 Aligned_cols=17 Identities=35% Similarity=0.893 Sum_probs=16.1
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.||+||+.||++++||+
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 59999999999999996
No 9
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.59 E-value=2.9e-05 Score=73.76 Aligned_cols=39 Identities=26% Similarity=0.680 Sum_probs=26.2
Q ss_pred cccccCCCCccc-ccccCCCCC--CCceecCCCcccccCCCC
Q 012460 424 TCSNCGKENHTA-ATCKMQKQN--KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 424 KCFNCGKEGHiA-RNCPaPKK~--KgCfkCGk~GH~AKDCPq 462 (463)
.||+|+..||.. .+|...... ..||.||+.||+..+||+
T Consensus 120 ~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~ 161 (261)
T KOG4400|consen 120 SCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPE 161 (261)
T ss_pred eeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCC
Confidence 466666666666 333322222 349999999999999984
No 10
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.24 E-value=0.0018 Score=69.02 Aligned_cols=40 Identities=30% Similarity=0.758 Sum_probs=35.0
Q ss_pred cccccccCCCCcccccccCCC--CCCCceecCCCcccccCCC
Q 012460 422 SETCSNCGKENHTAATCKMQK--QNKPCFLCGSFKHRWKNCK 461 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPK--K~KgCfkCGk~GH~AKDCP 461 (463)
...|.+||..||...+|+... ....|+.||..||++++|+
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 468999999999999999872 2237999999999999997
No 11
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.04 E-value=0.009 Score=43.00 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=11.1
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.|+.|++.||+.++||+
T Consensus 10 ~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 10 VCHRCGQKGHWIQDCPT 26 (32)
T ss_pred EeecCCCCCccHhHCCC
Confidence 46666666666666664
No 12
>smart00343 ZnF_C2HC zinc finger.
Probab=94.05 E-value=0.022 Score=37.53 Aligned_cols=16 Identities=56% Similarity=1.184 Sum_probs=11.6
Q ss_pred cccccCCCCccccccc
Q 012460 424 TCSNCGKENHTAATCK 439 (463)
Q Consensus 424 KCFNCGKEGHiARNCP 439 (463)
.||+||+.||++++||
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4777777777777776
No 13
>smart00343 ZnF_C2HC zinc finger.
Probab=94.02 E-value=0.026 Score=37.17 Aligned_cols=17 Identities=29% Similarity=0.852 Sum_probs=15.4
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.||+||..||++++||+
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 39999999999999983
No 14
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=92.63 E-value=0.045 Score=39.50 Aligned_cols=21 Identities=24% Similarity=0.669 Sum_probs=18.7
Q ss_pred CcccccccCCCCcccccccCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP 441 (463)
..-.|+.|++.||+.++||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 356899999999999999984
No 15
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.46 E-value=0.061 Score=40.57 Aligned_cols=19 Identities=26% Similarity=0.718 Sum_probs=16.8
Q ss_pred cccccccCCCCcccccccC
Q 012460 422 SETCSNCGKENHTAATCKM 440 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPa 440 (463)
...|.+|++.||+..+|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5689999999999999994
No 16
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=89.22 E-value=0.18 Score=38.14 Aligned_cols=17 Identities=29% Similarity=0.564 Sum_probs=16.0
Q ss_pred CCceecCCCcccccCCC
Q 012460 445 KPCFLCGSFKHRWKNCK 461 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCP 461 (463)
..|.+|++.||+..+||
T Consensus 5 ~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECP 21 (42)
T ss_pred CcCcccCCCCcchhhCC
Confidence 56999999999999999
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=88.71 E-value=0.19 Score=51.67 Aligned_cols=31 Identities=10% Similarity=-0.003 Sum_probs=24.3
Q ss_pred HHHhhhhccCCCCcccccccccccccCCCCCCcc
Q 012460 318 VQTTATITGANDGVKSVEMNNLYSLRLEDDKPLS 351 (463)
Q Consensus 318 Mt~TllVQNANpDcKSi~~~~LkaLgpe~~~tLe 351 (463)
.++++-|=|--|.|-+.| |+++...+++..|
T Consensus 77 ~stkl~vgNis~tctn~E---lRa~fe~ygpvie 107 (346)
T KOG0109|consen 77 ASTKLHVGNISPTCTNQE---LRAKFEKYGPVIE 107 (346)
T ss_pred CccccccCCCCccccCHH---HhhhhcccCCcee
Confidence 467788888888888884 8888877777765
No 18
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=86.69 E-value=0.25 Score=37.15 Aligned_cols=17 Identities=29% Similarity=0.866 Sum_probs=11.4
Q ss_pred ccccccCCCCccccccc
Q 012460 423 ETCSNCGKENHTAATCK 439 (463)
Q Consensus 423 IKCFNCGKEGHiARNCP 439 (463)
..||+||..||...+||
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 45777777777666665
No 19
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=85.41 E-value=0.35 Score=49.74 Aligned_cols=23 Identities=30% Similarity=0.810 Sum_probs=20.0
Q ss_pred CcccccccCCCCcccccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaPKK 443 (463)
....||.||++||++.+||.++.
T Consensus 159 Dq~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 159 DQSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred CHHHheeccccccccccCCccCC
Confidence 35689999999999999998853
No 20
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=84.88 E-value=0.38 Score=36.15 Aligned_cols=17 Identities=41% Similarity=0.935 Sum_probs=15.7
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.|+.||..||..++||.
T Consensus 33 ~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 33 FCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhcCCCCcCcCHhHcCC
Confidence 59999999999999984
No 21
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.30 E-value=0.5 Score=49.00 Aligned_cols=21 Identities=24% Similarity=0.650 Sum_probs=18.0
Q ss_pred CcccccccCCCCcccccccCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP 441 (463)
..-.||.||+.||+..+||..
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CceeEEecCCCCchhhcCCCC
Confidence 456799999999999999975
No 22
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=83.31 E-value=0.66 Score=35.08 Aligned_cols=12 Identities=42% Similarity=0.958 Sum_probs=6.7
Q ss_pred cccccCCCCccc
Q 012460 424 TCSNCGKENHTA 435 (463)
Q Consensus 424 KCFNCGKEGHiA 435 (463)
+|.+||..||++
T Consensus 3 kC~~CG~~GH~~ 14 (40)
T PF15288_consen 3 KCKNCGAFGHMR 14 (40)
T ss_pred cccccccccccc
Confidence 455555555554
No 23
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=81.03 E-value=0.73 Score=34.87 Aligned_cols=17 Identities=41% Similarity=0.897 Sum_probs=14.5
Q ss_pred CceecCCCcccc--cCCCC
Q 012460 446 PCFLCGSFKHRW--KNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~A--KDCPq 462 (463)
.|..||..||+. +.||.
T Consensus 3 kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred cccccccccccccCccCCC
Confidence 499999999998 56884
No 24
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.52 E-value=0.73 Score=47.83 Aligned_cols=18 Identities=33% Similarity=0.800 Sum_probs=16.3
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
-.||+||+.||+...||-
T Consensus 177 Y~CyRCGqkgHwIqnCpT 194 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPT 194 (427)
T ss_pred eeEEecCCCCchhhcCCC
Confidence 469999999999999983
No 25
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=80.47 E-value=1.1 Score=33.34 Aligned_cols=20 Identities=35% Similarity=0.797 Sum_probs=12.1
Q ss_pred ccccccCCCCcccccccCCC
Q 012460 423 ETCSNCGKENHTAATCKMQK 442 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPK 442 (463)
..|++|++..|++.+|.+..
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 47999999999999998764
No 26
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.90 E-value=4 Score=43.76 Aligned_cols=42 Identities=21% Similarity=0.489 Sum_probs=31.2
Q ss_pred cccccccCCCCcccccccCC---CCCCCceecCCCcccccCCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQ---KQNKPCFLCGSFKHRWKNCKQV 463 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaP---KK~KgCfkCGk~GH~AKDCPqV 463 (463)
...|..|-..+|+...|..- .-.-.|++|+..||..+.||.+
T Consensus 133 ~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 133 GYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred cceeeecccCccccccccccCCCCCCcceecCCCCCccceecccc
Confidence 46677777777777766542 1124599999999999999975
No 27
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=68.77 E-value=2.9 Score=45.66 Aligned_cols=32 Identities=28% Similarity=0.702 Sum_probs=25.3
Q ss_pred CCCCCCCCCCC---CcccccccCCCCcccccccCC
Q 012460 410 RKPRYFDPPGW---NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 410 RGpRyFdgPkk---g~IKCFNCGKEGHiARNCPaP 441 (463)
.+++.|+|+.. -...|+.||..||++.+|+..
T Consensus 270 ~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 270 TGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred CccccccCCcccccccccccccCCcccccccCCCc
Confidence 36677888743 123899999999999999987
No 28
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=63.61 E-value=3 Score=31.18 Aligned_cols=17 Identities=29% Similarity=0.571 Sum_probs=11.5
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.|++||+..|.+.+|..
T Consensus 4 ~CprC~kg~Hwa~~C~s 20 (36)
T PF14787_consen 4 LCPRCGKGFHWASECRS 20 (36)
T ss_dssp C-TTTSSSCS-TTT---
T ss_pred cCcccCCCcchhhhhhh
Confidence 59999999999999964
No 29
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=62.26 E-value=3.3 Score=47.42 Aligned_cols=22 Identities=36% Similarity=0.914 Sum_probs=18.2
Q ss_pred CCCCCCceecCCCcccccCCCC
Q 012460 441 QKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 441 PKK~KgCfkCGk~GH~AKDCPq 462 (463)
|.+.+.|+.||++||.+++|.-
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~g 278 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCEG 278 (931)
T ss_pred CCCcccchhhcccCCcHhhcCC
Confidence 4455679999999999999963
No 30
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=60.69 E-value=4 Score=44.10 Aligned_cols=20 Identities=30% Similarity=0.712 Sum_probs=18.1
Q ss_pred ccccccCCCCcccccccCCC
Q 012460 423 ETCSNCGKENHTAATCKMQK 442 (463)
Q Consensus 423 IKCFNCGKEGHiARNCPaPK 442 (463)
..|||||..-|..++||.|+
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~ 148 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPF 148 (485)
T ss_pred ccccccCCCCCccccCCCcc
Confidence 44999999999999999985
No 31
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=53.99 E-value=9 Score=37.36 Aligned_cols=21 Identities=29% Similarity=0.684 Sum_probs=18.2
Q ss_pred CCcccccccCCCCcccccccC
Q 012460 420 WNSETCSNCGKENHTAATCKM 440 (463)
Q Consensus 420 kg~IKCFNCGKEGHiARNCPa 440 (463)
.+.+-|++||+.||+.++|..
T Consensus 98 ~g~~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 98 RGRGFCYRCGERGHIGRNCKD 118 (195)
T ss_pred ccccccccCCCcccccccccc
Confidence 455669999999999999988
No 32
>KOG3070 consensus Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis]
Probab=53.34 E-value=9.6 Score=37.54 Aligned_cols=40 Identities=20% Similarity=0.527 Sum_probs=26.0
Q ss_pred ccccccCCCCccc----ccccCCCCCCCceecCCCcccccCCCC
Q 012460 423 ETCSNCGKENHTA----ATCKMQKQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 423 IKCFNCGKEGHiA----RNCPaPKK~KgCfkCGk~GH~AKDCPq 462 (463)
..|+.||+.+|.. +.|...+....|+.|+..||.+..|.+
T Consensus 174 ~~~~~~g~~~~~~~~~~r~~~g~r~~~~~~~~~~~g~~~~~~~e 217 (235)
T KOG3070|consen 174 VSGRACGGAGAAQRPPVRKCGGYRPASLCYTCGEPGHVADGCEE 217 (235)
T ss_pred cccccccccccccCCCCcccccCCCcccccccCccccccccccc
Confidence 3446677777533 225555544568888888888888865
No 33
>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=44.31 E-value=11 Score=33.92 Aligned_cols=20 Identities=20% Similarity=0.601 Sum_probs=17.3
Q ss_pred CcccccccCCCCcccccccCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP 441 (463)
..+.|..|+ ..|+...||-.
T Consensus 105 ~~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 105 SKVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred ceEEeCCCC-CCcccccCCcc
Confidence 579999997 78999999964
No 34
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=41.31 E-value=13 Score=40.51 Aligned_cols=17 Identities=41% Similarity=1.198 Sum_probs=15.7
Q ss_pred CceecCCCcccccCCCC
Q 012460 446 PCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 446 gCfkCGk~GH~AKDCPq 462 (463)
.||+||..-|-.++||.
T Consensus 130 ~CFNC~g~~hsLrdC~r 146 (485)
T KOG2673|consen 130 PCFNCGGTPHSLRDCPR 146 (485)
T ss_pred cccccCCCCCccccCCC
Confidence 49999999999999986
No 35
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=38.94 E-value=18 Score=39.42 Aligned_cols=47 Identities=11% Similarity=0.017 Sum_probs=28.6
Q ss_pred HhhhhccCCCCcccccccccccccCCCCCCccccccccccCCccccCc
Q 012460 320 TTATITGANDGVKSVEMNNLYSLRLEDDKPLSDMRLGRRVEDTVSVGP 367 (463)
Q Consensus 320 ~TllVQNANpDcKSi~~~~LkaLgpe~~~tLemMTaCqGVgGgv~~gP 367 (463)
++++--|..+|+++|. --++++++-.-..--|=+-.|-|.-..++-|
T Consensus 336 DRmiDmGFEddir~iF-~~FK~QRQTLLFSATMP~KIQ~FAkSALVKP 382 (610)
T KOG0341|consen 336 DRMIDMGFEDDIRTIF-SFFKGQRQTLLFSATMPKKIQNFAKSALVKP 382 (610)
T ss_pred HHHhhccchhhHHHHH-HHHhhhhheeeeeccccHHHHHHHHhhcccc
Confidence 5666778889999882 3366776633222125556676665555555
No 36
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=25.81 E-value=30 Score=40.09 Aligned_cols=21 Identities=29% Similarity=0.724 Sum_probs=18.4
Q ss_pred CcccccccCCCCcccccccCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ 441 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP 441 (463)
....||-||+.||.+.+|...
T Consensus 259 ~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 259 KPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CcccchhhcccCCcHhhcCCc
Confidence 345799999999999999976
No 37
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.35 E-value=58 Score=38.80 Aligned_cols=40 Identities=25% Similarity=0.602 Sum_probs=23.7
Q ss_pred CcccccccCCCCcccccccCC----CCCCCceecCCCcccccCCCC
Q 012460 421 NSETCSNCGKENHTAATCKMQ----KQNKPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP----KK~KgCfkCGk~GH~AKDCPq 462 (463)
+...|..||..+ ....||.= .....|..||..++. ..||+
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~~~~-y~CPK 668 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIEVEE-DECEK 668 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCcCCC-CcCCC
Confidence 456788888876 34566631 122458888777664 34664
No 38
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.15 E-value=54 Score=37.36 Aligned_cols=39 Identities=18% Similarity=0.144 Sum_probs=25.2
Q ss_pred CCCceeeeccCCCceeeeccccccCCCCCCCCcceEEEe
Q 012460 239 KPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVV 277 (463)
Q Consensus 239 ~~~sv~~~e~~~~~~lf~d~~k~~~~~~~~~~~~~~~~~ 277 (463)
-+-|-+.+=..+-.-+.|||--|+.-.+--.|..-.|-|
T Consensus 302 GtRSAlF~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdv 340 (730)
T COG1198 302 GTRSALFLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDV 340 (730)
T ss_pred EechhhcCchhhccEEEEeccccccccCCcCCCcCHHHH
Confidence 345555555666667788887777666666676655544
No 39
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=23.75 E-value=28 Score=28.92 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=10.1
Q ss_pred cccccccCCC-Ccc
Q 012460 422 SETCSNCGKE-NHT 434 (463)
Q Consensus 422 ~IKCFNCGKE-GHi 434 (463)
++.||.||+. ||.
T Consensus 4 PiRCFsCGkvi~~~ 17 (63)
T COG1644 4 PVRCFSCGKVIGHK 17 (63)
T ss_pred ceEeecCCCCHHHH
Confidence 5789999987 553
No 40
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=21.87 E-value=43 Score=36.23 Aligned_cols=18 Identities=22% Similarity=0.637 Sum_probs=13.4
Q ss_pred CCceecCCCcccc--cCCCC
Q 012460 445 KPCFLCGSFKHRW--KNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~A--KDCPq 462 (463)
-.|++|+..||+. ++||-
T Consensus 125 VrC~kChkwGH~n~DreCpl 144 (453)
T KOG3794|consen 125 VRCLKCHKWGHINTDRECPL 144 (453)
T ss_pred eeEEeecccccccCCccCcc
Confidence 3488888888886 45874
No 41
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=20.94 E-value=47 Score=32.59 Aligned_cols=18 Identities=39% Similarity=0.837 Sum_probs=15.5
Q ss_pred CCceecCCCcccccCCCC
Q 012460 445 KPCFLCGSFKHRWKNCKQ 462 (463)
Q Consensus 445 KgCfkCGk~GH~AKDCPq 462 (463)
..|+.||..||+.+.|.+
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 349999999999999964
No 42
>PF08499 PDEase_I_N: 3'5'-cyclic nucleotide phosphodiesterase N-terminal; InterPro: IPR013706 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This domain is found to the N terminus of the calcium/calmodulin-dependent 3'5'-cyclic nucleotide phosphodiesterase domain (IPR002073 from INTERPRO).; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
Probab=20.92 E-value=59 Score=26.61 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=24.6
Q ss_pred CcccccccccccchHHHHHHHHHHhhhhcc
Q 012460 297 DDDKSVSGVSLERSVEDMGKAVQTTATITG 326 (463)
Q Consensus 297 dd~e~~q~LraEqa~qdVknwMt~TllVQN 326 (463)
|.+.=++++..+--+++|.+|+.-|++-|-
T Consensus 4 d~edel~~i~~dsvp~eVr~WLasTFtrq~ 33 (59)
T PF08499_consen 4 DEEDELSEIQSDSVPDEVRDWLASTFTRQV 33 (59)
T ss_pred ChhhhHhhcccccCCHHHHHHHHHHHHhhh
Confidence 455557778888888999999999998876
No 43
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=20.85 E-value=30 Score=33.22 Aligned_cols=22 Identities=27% Similarity=0.644 Sum_probs=19.4
Q ss_pred cccccccCCCCcccccccCCCC
Q 012460 422 SETCSNCGKENHTAATCKMQKQ 443 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPKK 443 (463)
.+.|..|-+-|||...|.+.++
T Consensus 27 ~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred chhHHHHHhhccceeeecCcee
Confidence 4699999999999999998753
No 44
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.33 E-value=43 Score=25.91 Aligned_cols=30 Identities=30% Similarity=0.595 Sum_probs=19.1
Q ss_pred cccccccCCCCcccccccCCCCCCCceecCCCcc
Q 012460 422 SETCSNCGKENHTAATCKMQKQNKPCFLCGSFKH 455 (463)
Q Consensus 422 ~IKCFNCGKEGHiARNCPaPKK~KgCfkCGk~GH 455 (463)
...|..||..... +...+.-.|..||...|
T Consensus 28 Sq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 4679999877544 33333345888887654
No 45
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.14 E-value=51 Score=34.87 Aligned_cols=38 Identities=16% Similarity=0.394 Sum_probs=21.5
Q ss_pred CcccccccCCCCcccccccCC--CCCCCceecCCCccccc
Q 012460 421 NSETCSNCGKENHTAATCKMQ--KQNKPCFLCGSFKHRWK 458 (463)
Q Consensus 421 g~IKCFNCGKEGHiARNCPaP--KK~KgCfkCGk~GH~AK 458 (463)
...+|..|+..|.+...=... .....|-.|+..|++.+
T Consensus 158 ~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i~ 197 (371)
T COG0484 158 DPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKIIK 197 (371)
T ss_pred CCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeECC
Confidence 567899999888543222111 11234666666666654
Done!