Query 046237
Match_columns 137
No_of_seqs 113 out of 350
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 10:02:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046237hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14111 DUF4283: Domain of un 99.8 1.7E-20 3.6E-25 135.6 1.8 71 2-72 67-137 (153)
2 PF14392 zf-CCHC_4: Zinc knuck 99.8 1.2E-19 2.7E-24 109.5 3.9 49 76-125 1-49 (49)
3 PF00098 zf-CCHC: Zinc knuckle 97.5 5.8E-05 1.3E-09 36.2 1.2 17 109-125 2-18 (18)
4 PF13696 zf-CCHC_2: Zinc knuck 95.4 0.0086 1.9E-07 32.8 1.2 18 108-125 9-26 (32)
5 smart00343 ZnF_C2HC zinc finge 94.5 0.016 3.4E-07 29.8 0.7 18 109-126 1-18 (26)
6 PF15288 zf-CCHC_6: Zinc knuck 94.5 0.022 4.8E-07 32.7 1.4 21 108-128 2-24 (40)
7 PF13917 zf-CCHC_3: Zinc knuck 93.1 0.063 1.4E-06 31.2 1.6 19 107-125 4-22 (42)
8 COG5082 AIR1 Arginine methyltr 91.8 0.093 2E-06 39.9 1.5 22 103-124 56-77 (190)
9 COG5082 AIR1 Arginine methyltr 89.6 0.15 3.2E-06 38.9 0.8 16 109-124 99-114 (190)
10 PTZ00368 universal minicircle 84.5 0.53 1.2E-05 33.8 1.3 19 107-125 129-147 (148)
11 KOG0109 RNA-binding protein LA 83.7 1.9 4.2E-05 35.1 4.3 85 41-128 80-181 (346)
12 KOG4400 E3 ubiquitin ligase in 82.5 0.61 1.3E-05 36.7 1.0 25 101-126 138-162 (261)
13 KOG0341 DEAD-box protein abstr 75.5 1 2.3E-05 38.4 0.4 22 108-129 571-592 (610)
14 PTZ00368 universal minicircle 74.9 1.7 3.8E-05 31.1 1.4 19 108-126 104-122 (148)
15 PF14787 zf-CCHC_5: GAG-polypr 73.2 3.1 6.6E-05 23.3 1.8 24 107-130 2-25 (36)
16 COG5222 Uncharacterized conser 72.2 1.8 3.9E-05 35.5 1.0 22 108-129 177-198 (427)
17 COG5179 TAF1 Transcription ini 71.8 2.1 4.6E-05 38.4 1.4 24 107-130 937-962 (968)
18 KOG2044 5'-3' exonuclease HKE1 71.1 3 6.5E-05 38.2 2.2 24 103-126 256-279 (931)
19 PF01194 RNA_pol_N: RNA polyme 66.2 2.9 6.3E-05 26.0 0.8 14 106-119 3-17 (60)
20 PLN00032 DNA-directed RNA poly 65.9 2.7 5.8E-05 27.1 0.6 15 106-120 3-18 (71)
21 KOG2560 RNA splicing factor - 65.2 1.6 3.5E-05 37.5 -0.7 21 108-128 113-133 (529)
22 PF10083 DUF2321: Uncharacteri 65.2 2.8 6.1E-05 31.0 0.7 31 79-115 46-76 (158)
23 PRK04016 DNA-directed RNA poly 64.3 3 6.5E-05 26.2 0.6 13 106-118 3-16 (62)
24 COG1644 RPB10 DNA-directed RNA 59.8 3.7 8.1E-05 25.7 0.4 16 106-121 3-19 (63)
25 KOG4400 E3 ubiquitin ligase in 58.3 6.3 0.00014 30.9 1.6 24 106-129 163-186 (261)
26 COG4306 Uncharacterized protei 57.5 3.5 7.5E-05 29.7 0.0 15 101-116 63-77 (160)
27 KOG3497 DNA-directed RNA polym 55.9 4 8.7E-05 25.6 0.1 11 106-116 3-13 (69)
28 COG1998 RPS31 Ribosomal protei 52.0 13 0.00028 22.3 1.9 17 98-114 7-26 (51)
29 smart00647 IBR In Between Ring 49.6 9.6 0.00021 22.7 1.1 18 106-123 47-64 (64)
30 KOG0125 Ataxin 2-binding prote 47.6 16 0.00035 30.4 2.4 37 35-72 92-128 (376)
31 COG1241 MCM2 Predicted ATPase 47.0 85 0.0018 28.6 7.0 72 38-113 82-157 (682)
32 KOG0119 Splicing factor 1/bran 45.9 12 0.00026 32.7 1.4 18 109-126 287-304 (554)
33 KOG0119 Splicing factor 1/bran 43.7 13 0.00029 32.4 1.4 25 108-132 262-286 (554)
34 PF13240 zinc_ribbon_2: zinc-r 41.8 8.7 0.00019 19.1 0.0 10 106-115 12-21 (23)
35 KOG2673 Uncharacterized conser 39.9 15 0.00033 31.7 1.2 18 110-127 131-148 (485)
36 KOG2985 Uncharacterized conser 39.8 7.6 0.00016 31.1 -0.6 24 108-131 82-105 (306)
37 PF13248 zf-ribbon_3: zinc-rib 39.5 9.9 0.00021 19.2 0.0 9 107-115 16-24 (26)
38 PF05515 Viral_NABP: Viral nuc 34.9 17 0.00036 25.9 0.6 20 108-127 63-82 (124)
39 KOG3794 CBF1-interacting corep 32.9 21 0.00045 30.4 0.9 24 108-131 125-150 (453)
40 PF09297 zf-NADH-PPase: NADH p 32.9 20 0.00043 18.9 0.6 12 107-118 3-14 (32)
41 PF14205 Cys_rich_KTR: Cystein 30.2 25 0.00053 21.5 0.7 14 102-115 23-36 (55)
42 PF01485 IBR: IBR domain; Int 29.4 23 0.0005 20.9 0.5 17 107-123 48-64 (64)
43 PF13821 DUF4187: Domain of un 28.5 24 0.00052 21.4 0.4 21 107-127 27-51 (55)
44 COG5049 XRN1 5'-3' exonuclease 28.1 26 0.00057 32.2 0.8 27 104-130 247-273 (953)
45 PF02591 DUF164: Putative zinc 27.3 26 0.00056 20.8 0.4 10 107-116 46-55 (56)
46 PF06869 DUF1258: Protein of u 26.1 31 0.00067 27.6 0.8 29 106-134 17-46 (258)
47 KOG4399 C2HC-type Zn-finger pr 24.4 34 0.00073 27.7 0.7 20 107-126 261-280 (325)
48 KOG0309 Conserved WD40 repeat- 24.4 45 0.00097 31.0 1.5 23 98-120 1033-1055(1081)
49 PF14803 Nudix_N_2: Nudix N-te 24.1 28 0.0006 19.0 0.1 12 105-116 20-31 (34)
50 TIGR02024 FtcD glutamate formi 23.4 38 0.00082 27.7 0.8 57 8-64 142-204 (298)
51 KOG3362 Predicted BBOX Zn-fing 22.9 31 0.00067 25.3 0.2 13 106-118 117-129 (156)
52 COG1047 SlpA FKBP-type peptidy 22.9 1.4E+02 0.003 22.4 3.7 25 61-85 104-129 (174)
53 smart00661 RPOL9 RNA polymeras 22.8 39 0.00084 19.3 0.6 10 108-117 1-10 (52)
54 PF10102 DUF2341: Domain of un 22.2 96 0.0021 20.4 2.5 14 36-49 28-41 (89)
55 PF06689 zf-C4_ClpX: ClpX C4-t 22.0 37 0.0008 19.1 0.4 9 108-116 2-10 (41)
56 cd00729 rubredoxin_SM Rubredox 21.0 71 0.0015 17.2 1.4 25 109-133 4-31 (34)
57 KOG0107 Alternative splicing f 20.9 52 0.0011 25.1 1.1 18 108-125 101-118 (195)
58 PF14605 Nup35_RRM_2: Nup53/35 20.6 1.1E+02 0.0023 18.0 2.2 31 39-71 1-31 (53)
59 COG2098 Uncharacterized protei 20.5 3.1E+02 0.0068 19.2 5.1 41 39-79 24-66 (116)
60 PF08772 NOB1_Zn_bind: Nin one 20.3 42 0.00091 21.6 0.4 12 104-115 21-32 (73)
61 PF02824 TGS: TGS domain; Int 20.3 90 0.002 18.7 1.9 43 47-89 13-57 (60)
No 1
>PF14111 DUF4283: Domain of unknown function (DUF4283)
Probab=99.79 E-value=1.7e-20 Score=135.63 Aligned_cols=71 Identities=30% Similarity=0.485 Sum_probs=69.8
Q ss_pred chhhhccCCCEEEcCCEEEEecCCCCCCCcccccceeeeeeeecCCCcccchhhHHhhhccccccEEEeee
Q 046237 2 DQRRILCTRPWSFNRCLFVLTEPTGIGDFSKQNLNFCSFWIQLHKLPLMSMTKVVGLLFGSMIGEVEEVDK 72 (137)
Q Consensus 2 D~~~Vl~~gPW~~~~~~lil~~w~~~~~~~~~~l~~~~vWVri~~LP~~~~~~~~~~~Ig~~iG~~l~vD~ 72 (137)
|+++|+++|||+|+|+.+++++|+|++++++..++++++||||+|||+.||+++++.+||+.+|+++++|.
T Consensus 67 d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~ 137 (153)
T PF14111_consen 67 DRQRVLKGGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDE 137 (153)
T ss_pred ceeEEEecccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEc
Confidence 88999999999999999999999999999999999999999999999999999999999999999999996
No 2
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=99.78 E-value=1.2e-19 Score=109.53 Aligned_cols=49 Identities=47% Similarity=0.891 Sum_probs=46.6
Q ss_pred eeecCCCceeEEEeecCCcceEEEEEEeeccCccccCCcccccCCCcCCC
Q 046237 76 INITRPLMRGLTVQLEGEENLSTVEVYYERLPDFCFQRGRIGHVFRECPY 125 (137)
Q Consensus 76 idv~kPL~~~v~i~~~~~~~~~~~~v~YE~lp~fC~~Cg~iGH~~~~C~~ 125 (137)
||+++||.+.+.+++++ |+..+++|+|||||.||++||.+||+.++|++
T Consensus 1 id~~kPL~~~i~v~~~~-g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 1 IDVSKPLRREIKVKFPE-GESFWVKVKYERLPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred CCCCCcccceEEEEeCC-CcEEEEEEEECCcChhhcCCCCcCcCHhHcCC
Confidence 68999999999999886 78999999999999999999999999999985
No 3
>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=97.47 E-value=5.8e-05 Score=36.18 Aligned_cols=17 Identities=47% Similarity=1.095 Sum_probs=15.7
Q ss_pred cccCCcccccCCCcCCC
Q 046237 109 FCFQRGRIGHVFRECPY 125 (137)
Q Consensus 109 fC~~Cg~iGH~~~~C~~ 125 (137)
-|++||..||..++||.
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 59999999999999984
No 4
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=95.37 E-value=0.0086 Score=32.77 Aligned_cols=18 Identities=33% Similarity=0.859 Sum_probs=17.2
Q ss_pred ccccCCcccccCCCcCCC
Q 046237 108 DFCFQRGRIGHVFRECPY 125 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~ 125 (137)
+.|..|+.-||..+.||.
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 589999999999999999
No 5
>smart00343 ZnF_C2HC zinc finger.
Probab=94.53 E-value=0.016 Score=29.81 Aligned_cols=18 Identities=39% Similarity=1.032 Sum_probs=15.9
Q ss_pred cccCCcccccCCCcCCCC
Q 046237 109 FCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 109 fC~~Cg~iGH~~~~C~~~ 126 (137)
.|+.||..||..++|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999843
No 6
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.52 E-value=0.022 Score=32.69 Aligned_cols=21 Identities=29% Similarity=0.546 Sum_probs=17.3
Q ss_pred ccccCCcccccCC--CcCCCCCC
Q 046237 108 DFCFQRGRIGHVF--RECPYLKS 128 (137)
Q Consensus 108 ~fC~~Cg~iGH~~--~~C~~~~~ 128 (137)
.-|..||.+||.. +.||.-..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~ 24 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCW 24 (40)
T ss_pred ccccccccccccccCccCCCCCC
Confidence 3599999999987 78998763
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=93.09 E-value=0.063 Score=31.16 Aligned_cols=19 Identities=37% Similarity=0.606 Sum_probs=17.3
Q ss_pred CccccCCcccccCCCcCCC
Q 046237 107 PDFCFQRGRIGHVFRECPY 125 (137)
Q Consensus 107 p~fC~~Cg~iGH~~~~C~~ 125 (137)
...|..|+..||-..+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4689999999999999995
No 8
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=91.79 E-value=0.093 Score=39.90 Aligned_cols=22 Identities=36% Similarity=0.845 Sum_probs=13.7
Q ss_pred eeccCccccCCcccccCCCcCC
Q 046237 103 YERLPDFCFQRGRIGHVFRECP 124 (137)
Q Consensus 103 YE~lp~fC~~Cg~iGH~~~~C~ 124 (137)
+-.--.+|++||..||..++||
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccccchhcccCcccccCC
Confidence 3334456666666666666666
No 9
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=89.64 E-value=0.15 Score=38.86 Aligned_cols=16 Identities=38% Similarity=0.995 Sum_probs=11.8
Q ss_pred cccCCcccccCCCcCC
Q 046237 109 FCFQRGRIGHVFRECP 124 (137)
Q Consensus 109 fC~~Cg~iGH~~~~C~ 124 (137)
.|++||..||..+.|+
T Consensus 99 ~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 99 KCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccCccccccC
Confidence 4567788888888883
No 10
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=84.53 E-value=0.53 Score=33.82 Aligned_cols=19 Identities=37% Similarity=0.973 Sum_probs=14.9
Q ss_pred CccccCCcccccCCCcCCC
Q 046237 107 PDFCFQRGRIGHVFRECPY 125 (137)
Q Consensus 107 p~fC~~Cg~iGH~~~~C~~ 125 (137)
+..|++||..||..++||.
T Consensus 129 ~~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 129 DKTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CCccccCCCcCcccccCCC
Confidence 4688888888888888875
No 11
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=83.66 E-value=1.9 Score=35.13 Aligned_cols=85 Identities=18% Similarity=0.247 Sum_probs=58.5
Q ss_pred eeeecCCCcccchhhHHhhhccccccEEEeee-----eeEeeecCCCceeE---E-EeecCCcceEEEEEEeeccC----
Q 046237 41 WIQLHKLPLMSMTKVVGLLFGSMIGEVEEVDK-----GVKINITRPLMRGL---T-VQLEGEENLSTVEVYYERLP---- 107 (137)
Q Consensus 41 WVri~~LP~~~~~~~~~~~Ig~~iG~~l~vD~-----rV~idv~kPL~~~v---~-i~~~~~~~~~~~~v~YE~lp---- 107 (137)
=+.+.|+.....+.+ +++.=..-|.+++.|. -|.+|...-....+ . -++. |...-+++.=-||.
T Consensus 80 kl~vgNis~tctn~E-lRa~fe~ygpviecdivkdy~fvh~d~~eda~~air~l~~~~~~--gk~m~vq~stsrlrtapg 156 (346)
T KOG0109|consen 80 KLHVGNISPTCTNQE-LRAKFEKYGPVIECDIVKDYAFVHFDRAEDAVEAIRGLDNTEFQ--GKRMHVQLSTSRLRTAPG 156 (346)
T ss_pred ccccCCCCccccCHH-HhhhhcccCCceeeeeecceeEEEEeeccchHHHHhcccccccc--cceeeeeeeccccccCCC
Confidence 345778888888877 4555567799999987 34455433322221 0 1223 56677778777775
Q ss_pred ----ccccCCcccccCCCcCCCCCC
Q 046237 108 ----DFCFQRGRIGHVFRECPYLKS 128 (137)
Q Consensus 108 ----~fC~~Cg~iGH~~~~C~~~~~ 128 (137)
--|+.||+-||-+++||....
T Consensus 157 mgDq~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 157 MGDQSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred CCCHHHheeccccccccccCCccCC
Confidence 479999999999999998764
No 12
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=82.53 E-value=0.61 Score=36.69 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=19.7
Q ss_pred EEeeccCccccCCcccccCCCcCCCC
Q 046237 101 VYYERLPDFCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 101 v~YE~lp~fC~~Cg~iGH~~~~C~~~ 126 (137)
+.+.+- .+||.||..||...+|+..
T Consensus 138 ~~~~~~-~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 138 VDGPKP-AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCC-CccCCCCcCCcchhhCCCC
Confidence 344444 6799999999999999955
No 13
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=75.49 E-value=1 Score=38.37 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=19.4
Q ss_pred ccccCCcccccCCCcCCCCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYLKSS 129 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~~~ 129 (137)
.-|.+||-+||-...||+..+-
T Consensus 571 kGCayCgGLGHRItdCPKle~~ 592 (610)
T KOG0341|consen 571 KGCAYCGGLGHRITDCPKLEAQ 592 (610)
T ss_pred cccccccCCCcccccCchhhhh
Confidence 5799999999999999998643
No 14
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=74.94 E-value=1.7 Score=31.12 Aligned_cols=19 Identities=37% Similarity=0.915 Sum_probs=13.5
Q ss_pred ccccCCcccccCCCcCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~ 126 (137)
..|+.||..||..++|+..
T Consensus 104 ~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 104 RACYNCGGEGHISRDCPNA 122 (148)
T ss_pred hhhcccCcCCcchhcCCCc
Confidence 3577777777777777764
No 15
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=73.17 E-value=3.1 Score=23.29 Aligned_cols=24 Identities=25% Similarity=0.366 Sum_probs=14.2
Q ss_pred CccccCCcccccCCCcCCCCCCCC
Q 046237 107 PDFCFQRGRIGHVFRECPYLKSSP 130 (137)
Q Consensus 107 p~fC~~Cg~iGH~~~~C~~~~~~~ 130 (137)
|..|..||+=.|-.++|.-.....
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d~~ 25 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTDVD 25 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCCCC
T ss_pred CccCcccCCCcchhhhhhhhhccc
Confidence 567999999999999998765443
No 16
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.21 E-value=1.8 Score=35.47 Aligned_cols=22 Identities=27% Similarity=0.745 Sum_probs=19.5
Q ss_pred ccccCCcccccCCCcCCCCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYLKSS 129 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~~~ 129 (137)
+.|+.||.-||-...||.....
T Consensus 177 Y~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 177 YVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred eeEEecCCCCchhhcCCCCCCC
Confidence 6999999999999999987643
No 17
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=71.84 E-value=2.1 Score=38.35 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=19.0
Q ss_pred CccccCCcccccC--CCcCCCCCCCC
Q 046237 107 PDFCFQRGRIGHV--FRECPYLKSSP 130 (137)
Q Consensus 107 p~fC~~Cg~iGH~--~~~C~~~~~~~ 130 (137)
..-|.+||.+||- .+.||.-.++-
T Consensus 937 tr~C~nCGQvGHmkTNK~CP~f~s~~ 962 (968)
T COG5179 937 TRTCGNCGQVGHMKTNKACPKFSSKD 962 (968)
T ss_pred ceecccccccccccccccCccccCCC
Confidence 4689999999995 57899866543
No 18
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=71.10 E-value=3 Score=38.22 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=20.7
Q ss_pred eeccCccccCCcccccCCCcCCCC
Q 046237 103 YERLPDFCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 103 YE~lp~fC~~Cg~iGH~~~~C~~~ 126 (137)
+..-|.-|+.||..||..++|.-.
T Consensus 256 ~P~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 256 FPNKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred cCCCcccchhhcccCCcHhhcCCc
Confidence 356677899999999999999876
No 19
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=66.16 E-value=2.9 Score=26.04 Aligned_cols=14 Identities=36% Similarity=0.930 Sum_probs=9.1
Q ss_pred cCccccCCccc-ccC
Q 046237 106 LPDFCFQRGRI-GHV 119 (137)
Q Consensus 106 lp~fC~~Cg~i-GH~ 119 (137)
+|..||+||.+ ||.
T Consensus 3 iPVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNK 17 (60)
T ss_dssp -SSS-STTTSBTCGH
T ss_pred CceecCCCCCChhHh
Confidence 58899999974 443
No 20
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=65.92 E-value=2.7 Score=27.07 Aligned_cols=15 Identities=33% Similarity=0.948 Sum_probs=11.2
Q ss_pred cCccccCCccc-ccCC
Q 046237 106 LPDFCFQRGRI-GHVF 120 (137)
Q Consensus 106 lp~fC~~Cg~i-GH~~ 120 (137)
+|.-||+||.+ ||.-
T Consensus 3 iPVRCFTCGkvig~~w 18 (71)
T PLN00032 3 IPVRCFTCGKVIGNKW 18 (71)
T ss_pred CceeecCCCCCcHHHH
Confidence 58899999974 5543
No 21
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=65.24 E-value=1.6 Score=37.54 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=18.5
Q ss_pred ccccCCcccccCCCcCCCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYLKS 128 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~~ 128 (137)
-+|-+||-+||..+.|-.+-.
T Consensus 113 GACeNCGAmtHk~KDCmERPR 133 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCMERPR 133 (529)
T ss_pred hhhhhhhhhhcchHHHhhcch
Confidence 599999999999999987653
No 22
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=65.18 E-value=2.8 Score=30.97 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=20.5
Q ss_pred cCCCceeEEEeecCCcceEEEEEEeeccCccccCCcc
Q 046237 79 TRPLMRGLTVQLEGEENLSTVEVYYERLPDFCFQRGR 115 (137)
Q Consensus 79 ~kPL~~~v~i~~~~~~~~~~~~v~YE~lp~fC~~Cg~ 115 (137)
+.|++....+ +..+.+...|+ .|.||++||.
T Consensus 46 ~~~IrG~y~v-----~gv~~~g~~~~-~PsYC~~CGk 76 (158)
T PF10083_consen 46 STPIRGDYHV-----EGVFGLGGHYE-APSYCHNCGK 76 (158)
T ss_pred CCCCCCceec-----CCeeeeCCCCC-CChhHHhCCC
Confidence 4455555433 12344557888 9999999997
No 23
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=64.30 E-value=3 Score=26.16 Aligned_cols=13 Identities=31% Similarity=0.869 Sum_probs=10.4
Q ss_pred cCccccCCccc-cc
Q 046237 106 LPDFCFQRGRI-GH 118 (137)
Q Consensus 106 lp~fC~~Cg~i-GH 118 (137)
+|.-||+||++ ||
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 58899999974 55
No 24
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=59.84 E-value=3.7 Score=25.72 Aligned_cols=16 Identities=44% Similarity=1.020 Sum_probs=11.9
Q ss_pred cCccccCCcc-cccCCC
Q 046237 106 LPDFCFQRGR-IGHVFR 121 (137)
Q Consensus 106 lp~fC~~Cg~-iGH~~~ 121 (137)
.|..||+||. +||.-.
T Consensus 3 iPiRCFsCGkvi~~~w~ 19 (63)
T COG1644 3 IPVRCFSCGKVIGHKWE 19 (63)
T ss_pred CceEeecCCCCHHHHHH
Confidence 5889999996 566543
No 25
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=58.35 E-value=6.3 Score=30.91 Aligned_cols=24 Identities=38% Similarity=0.794 Sum_probs=21.4
Q ss_pred cCccccCCcccccCCCcCCCCCCC
Q 046237 106 LPDFCFQRGRIGHVFRECPYLKSS 129 (137)
Q Consensus 106 lp~fC~~Cg~iGH~~~~C~~~~~~ 129 (137)
.+..|+.|+..||...+|+.....
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~~ 186 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQKS 186 (261)
T ss_pred CCCccccCCCcceecccCCccccc
Confidence 388999999999999999988754
No 26
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.47 E-value=3.5 Score=29.68 Aligned_cols=15 Identities=40% Similarity=0.711 Sum_probs=11.9
Q ss_pred EEeeccCccccCCccc
Q 046237 101 VYYERLPDFCFQRGRI 116 (137)
Q Consensus 101 v~YE~lp~fC~~Cg~i 116 (137)
=.|| .|.||.+||.-
T Consensus 63 ~dye-~psfchncgs~ 77 (160)
T COG4306 63 GDYE-PPSFCHNCGSR 77 (160)
T ss_pred CCCC-CcchhhcCCCC
Confidence 3566 89999999963
No 27
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=55.90 E-value=4 Score=25.59 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=9.3
Q ss_pred cCccccCCccc
Q 046237 106 LPDFCFQRGRI 116 (137)
Q Consensus 106 lp~fC~~Cg~i 116 (137)
+|..||.||++
T Consensus 3 iPiRCFtCGKv 13 (69)
T KOG3497|consen 3 IPIRCFTCGKV 13 (69)
T ss_pred eeeEeeecccc
Confidence 57889999975
No 28
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=51.96 E-value=13 Score=22.31 Aligned_cols=17 Identities=35% Similarity=0.425 Sum_probs=12.4
Q ss_pred EEEEEe---eccCccccCCc
Q 046237 98 TVEVYY---ERLPDFCFQRG 114 (137)
Q Consensus 98 ~~~v~Y---E~lp~fC~~Cg 114 (137)
+++++. .++..||..||
T Consensus 7 yY~v~~~kv~rk~~~CPrCG 26 (51)
T COG1998 7 YYEVDDEKVKRKNRFCPRCG 26 (51)
T ss_pred EEEEcCCcEEEccccCCCCC
Confidence 455555 45678999999
No 29
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=49.61 E-value=9.6 Score=22.66 Aligned_cols=18 Identities=28% Similarity=0.340 Sum_probs=14.4
Q ss_pred cCccccCCcccccCCCcC
Q 046237 106 LPDFCFQRGRIGHVFREC 123 (137)
Q Consensus 106 lp~fC~~Cg~iGH~~~~C 123 (137)
-..||+.|+.-.|....|
T Consensus 47 ~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 47 GFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CCeECCCCCCcCCCCCCC
Confidence 356899999999987665
No 30
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=47.57 E-value=16 Score=30.35 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=29.1
Q ss_pred cceeeeeeeecCCCcccchhhHHhhhccccccEEEeee
Q 046237 35 LNFCSFWIQLHKLPLMSMTKVVGLLFGSMIGEVEEVDK 72 (137)
Q Consensus 35 l~~~~vWVri~~LP~~~~~~~~~~~Ig~~iG~~l~vD~ 72 (137)
-+..|=-+.+.|+|+.|+..+...+.+ +.|++++|+-
T Consensus 92 s~~~pkRLhVSNIPFrFRdpDL~aMF~-kfG~VldVEI 128 (376)
T KOG0125|consen 92 SKDTPKRLHVSNIPFRFRDPDLRAMFE-KFGKVLDVEI 128 (376)
T ss_pred CCCCCceeEeecCCccccCccHHHHHH-hhCceeeEEE
Confidence 344566788899999999999666665 5699999976
No 31
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=46.98 E-value=85 Score=28.58 Aligned_cols=72 Identities=17% Similarity=0.126 Sum_probs=44.6
Q ss_pred eeeeeeecCCCcccchhhHHhhhc-cccccEEEeeeee-EeeecCCCceeEEEeecCCcceEEEEEEe--eccCccccCC
Q 046237 38 CSFWIQLHKLPLMSMTKVVGLLFG-SMIGEVEEVDKGV-KINITRPLMRGLTVQLEGEENLSTVEVYY--ERLPDFCFQR 113 (137)
Q Consensus 38 ~~vWVri~~LP~~~~~~~~~~~Ig-~~iG~~l~vD~rV-~idv~kPL~~~v~i~~~~~~~~~~~~v~Y--E~lp~fC~~C 113 (137)
-.+++++.++|..+ ..+.|. +.+|+.+.++..| +..--+|......+.-.+=|....+.+.- ...|.+|.+|
T Consensus 82 ~~~~~~~~~~~~~~----~iR~l~s~~igkLV~v~GiV~r~s~v~p~~~~~~~~C~~Cg~~~~~~~~~~~~~~~~~C~~~ 157 (682)
T COG1241 82 KKIHVRFKNLPNRL----SIRELRSEHIGKLVSVEGIVTRASEVRPRLKKAVFECPKCGREVEVEQSEFRVEPPRECENC 157 (682)
T ss_pred cceEEEecCCcCCc----ChhhCchhhCCcEEEEEEEEEecccccceeEEEEEEcCCCCCEEEEEeccccccCCccCCCc
Confidence 56899999999997 455555 8999999998733 23344455544444444323333322221 2366789888
No 32
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=45.86 E-value=12 Score=32.67 Aligned_cols=18 Identities=28% Similarity=0.606 Sum_probs=16.6
Q ss_pred cccCCcccccCCCcCCCC
Q 046237 109 FCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 109 fC~~Cg~iGH~~~~C~~~ 126 (137)
.|+.||-+||....|+..
T Consensus 287 ~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCcccccccCCCc
Confidence 899999999999999987
No 33
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=43.74 E-value=13 Score=32.36 Aligned_cols=25 Identities=32% Similarity=0.503 Sum_probs=22.2
Q ss_pred ccccCCcccccCCCcCCCCCCCCCc
Q 046237 108 DFCFQRGRIGHVFRECPYLKSSPTN 132 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~~~~~~ 132 (137)
.+|..||.-||..-.|+.+.+.-+|
T Consensus 262 ~~c~~cg~~~H~q~~cp~r~~~~~n 286 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGRIPNTTN 286 (554)
T ss_pred ccccccCCCccccccCCcccccccc
Confidence 6999999999999999999766665
No 34
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.76 E-value=8.7 Score=19.08 Aligned_cols=10 Identities=30% Similarity=0.547 Sum_probs=7.4
Q ss_pred cCccccCCcc
Q 046237 106 LPDFCFQRGR 115 (137)
Q Consensus 106 lp~fC~~Cg~ 115 (137)
--.||.+||.
T Consensus 12 ~~~fC~~CG~ 21 (23)
T PF13240_consen 12 DAKFCPNCGT 21 (23)
T ss_pred cCcchhhhCC
Confidence 3468999984
No 35
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=39.92 E-value=15 Score=31.68 Aligned_cols=18 Identities=39% Similarity=0.861 Sum_probs=16.9
Q ss_pred ccCCcccccCCCcCCCCC
Q 046237 110 CFQRGRIGHVFRECPYLK 127 (137)
Q Consensus 110 C~~Cg~iGH~~~~C~~~~ 127 (137)
||+||-.-|+.+.|+.+.
T Consensus 131 CFNC~g~~hsLrdC~rp~ 148 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPF 148 (485)
T ss_pred ccccCCCCCccccCCCcc
Confidence 899999999999999876
No 36
>KOG2985 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.79 E-value=7.6 Score=31.10 Aligned_cols=24 Identities=29% Similarity=0.549 Sum_probs=19.5
Q ss_pred ccccCCcccccCCCcCCCCCCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYLKSSPT 131 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~~~~~ 131 (137)
.-|..||..||....|.....-+.
T Consensus 82 g~ckRcg~~ghl~fqcRn~~~vke 105 (306)
T KOG2985|consen 82 GSCKRCGRVGHLTFQCRNFLSVKE 105 (306)
T ss_pred cchhhccccchhhHHHhhhhhccc
Confidence 579999999999999987654443
No 37
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.46 E-value=9.9 Score=19.25 Aligned_cols=9 Identities=33% Similarity=0.741 Sum_probs=6.7
Q ss_pred CccccCCcc
Q 046237 107 PDFCFQRGR 115 (137)
Q Consensus 107 p~fC~~Cg~ 115 (137)
-.||.+||.
T Consensus 16 ~~fC~~CG~ 24 (26)
T PF13248_consen 16 AKFCPNCGA 24 (26)
T ss_pred cccChhhCC
Confidence 468888884
No 38
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=34.87 E-value=17 Score=25.90 Aligned_cols=20 Identities=30% Similarity=0.492 Sum_probs=16.8
Q ss_pred ccccCCcccccCCCcCCCCC
Q 046237 108 DFCFQRGRIGHVFRECPYLK 127 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~~~ 127 (137)
..|+.||.+=|....|+...
T Consensus 63 ~~C~~CG~~l~~~~~C~~~~ 82 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRRNT 82 (124)
T ss_pred CccccccceeecCCcCCCcc
Confidence 57999999999888899543
No 39
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=32.91 E-value=21 Score=30.36 Aligned_cols=24 Identities=33% Similarity=0.640 Sum_probs=18.5
Q ss_pred ccccCCcccccC--CCcCCCCCCCCC
Q 046237 108 DFCFQRGRIGHV--FRECPYLKSSPT 131 (137)
Q Consensus 108 ~fC~~Cg~iGH~--~~~C~~~~~~~~ 131 (137)
.-|-.|+.+||. .++||.-.....
T Consensus 125 VrC~kChkwGH~n~DreCplf~~~~~ 150 (453)
T KOG3794|consen 125 VRCLKCHKWGHINTDRECPLFGKSMN 150 (453)
T ss_pred eeEEeecccccccCCccCcchhhccc
Confidence 459999999996 578998765443
No 40
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=32.88 E-value=20 Score=18.89 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=6.4
Q ss_pred CccccCCccccc
Q 046237 107 PDFCFQRGRIGH 118 (137)
Q Consensus 107 p~fC~~Cg~iGH 118 (137)
..||..||---+
T Consensus 3 ~rfC~~CG~~t~ 14 (32)
T PF09297_consen 3 HRFCGRCGAPTK 14 (32)
T ss_dssp TSB-TTT--BEE
T ss_pred CcccCcCCcccc
Confidence 579999997543
No 41
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.17 E-value=25 Score=21.50 Aligned_cols=14 Identities=14% Similarity=0.441 Sum_probs=11.6
Q ss_pred EeeccCccccCCcc
Q 046237 102 YYERLPDFCFQRGR 115 (137)
Q Consensus 102 ~YE~lp~fC~~Cg~ 115 (137)
.-++.|.||..|..
T Consensus 23 ~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 23 VLKNFPLYCPKCKQ 36 (55)
T ss_pred eeccccccCCCCCc
Confidence 45789999999975
No 42
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=29.38 E-value=23 Score=20.85 Aligned_cols=17 Identities=35% Similarity=0.712 Sum_probs=11.3
Q ss_pred CccccCCcccccCCCcC
Q 046237 107 PDFCFQRGRIGHVFREC 123 (137)
Q Consensus 107 p~fC~~Cg~iGH~~~~C 123 (137)
..||+.|+.--|....|
T Consensus 48 ~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 48 TEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp SEECSSSTSESCTTS-H
T ss_pred CcCccccCcccCCCCCC
Confidence 46788888877775544
No 43
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=28.50 E-value=24 Score=21.38 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=15.4
Q ss_pred CccccCCcccccCC----CcCCCCC
Q 046237 107 PDFCFQRGRIGHVF----RECPYLK 127 (137)
Q Consensus 107 p~fC~~Cg~iGH~~----~~C~~~~ 127 (137)
..||+.||.-=-+. ++||=..
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred CceeeeeCCccCCHHHHHhCCCCCC
Confidence 47999999876665 6677554
No 44
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=28.10 E-value=26 Score=32.16 Aligned_cols=27 Identities=37% Similarity=0.623 Sum_probs=22.4
Q ss_pred eccCccccCCcccccCCCcCCCCCCCC
Q 046237 104 ERLPDFCFQRGRIGHVFRECPYLKSSP 130 (137)
Q Consensus 104 E~lp~fC~~Cg~iGH~~~~C~~~~~~~ 130 (137)
++-..-|..||+-||+..+|+...+.|
T Consensus 247 ~~~k~k~~~~g~t~~~~e~~k~~~~q~ 273 (953)
T COG5049 247 SRRKRKCTKCGRTGHSDEECKVLTHQP 273 (953)
T ss_pred cccccccccccccccchhhhcccccCc
Confidence 345578999999999999999887654
No 45
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=27.25 E-value=26 Score=20.84 Aligned_cols=10 Identities=50% Similarity=0.766 Sum_probs=7.5
Q ss_pred CccccCCccc
Q 046237 107 PDFCFQRGRI 116 (137)
Q Consensus 107 p~fC~~Cg~i 116 (137)
-.+|.+||++
T Consensus 46 i~~Cp~CgRi 55 (56)
T PF02591_consen 46 IVFCPNCGRI 55 (56)
T ss_pred eEECcCCCcc
Confidence 3578888875
No 46
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=26.08 E-value=31 Score=27.57 Aligned_cols=29 Identities=14% Similarity=0.290 Sum_probs=21.0
Q ss_pred cCccccCCcccccCCCcCCCC-CCCCCcee
Q 046237 106 LPDFCFQRGRIGHVFRECPYL-KSSPTNFI 134 (137)
Q Consensus 106 lp~fC~~Cg~iGH~~~~C~~~-~~~~~~~~ 134 (137)
...||-.||...+..+.|..- ..+.-.++
T Consensus 17 ~h~~CN~CG~~~~~~~kC~~c~~~~vakfv 46 (258)
T PF06869_consen 17 THFICNSCGKVVESNEKCSCCGCGPVAKFV 46 (258)
T ss_pred eehhhhhhhhhhccCceeeccCCCccEEEE
Confidence 357999999999999999755 33333333
No 47
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.44 E-value=34 Score=27.66 Aligned_cols=20 Identities=30% Similarity=0.670 Sum_probs=17.3
Q ss_pred CccccCCcccccCCCcCCCC
Q 046237 107 PDFCFQRGRIGHVFRECPYL 126 (137)
Q Consensus 107 p~fC~~Cg~iGH~~~~C~~~ 126 (137)
-.+|+.||.+-|....||.-
T Consensus 261 ~~~C~iC~~~~~~R~~C~~~ 280 (325)
T KOG4399|consen 261 KHGCFICGELDHKRSTCPNI 280 (325)
T ss_pred hcceeeccccccccccCccH
Confidence 36999999999999999863
No 48
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=24.37 E-value=45 Score=30.96 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=18.7
Q ss_pred EEEEEeeccCccccCCcccccCC
Q 046237 98 TVEVYYERLPDFCFQRGRIGHVF 120 (137)
Q Consensus 98 ~~~v~YE~lp~fC~~Cg~iGH~~ 120 (137)
...+.--++-.||..||..||+.
T Consensus 1033 ~C~l~V~gss~~Cg~C~Hv~H~s 1055 (1081)
T KOG0309|consen 1033 ICHLAVRGSSNFCGTCGHVGHTS 1055 (1081)
T ss_pred eEeeEeeccchhhccccccccHH
Confidence 35566678889999999999974
No 49
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=24.11 E-value=28 Score=19.02 Aligned_cols=12 Identities=33% Similarity=0.274 Sum_probs=8.5
Q ss_pred ccCccccCCccc
Q 046237 105 RLPDFCFQRGRI 116 (137)
Q Consensus 105 ~lp~fC~~Cg~i 116 (137)
+...+|..||.+
T Consensus 20 r~R~vC~~Cg~I 31 (34)
T PF14803_consen 20 RERLVCPACGFI 31 (34)
T ss_dssp S-EEEETTTTEE
T ss_pred ccceECCCCCCE
Confidence 556689999876
No 50
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=23.44 E-value=38 Score=27.66 Aligned_cols=57 Identities=7% Similarity=-0.196 Sum_probs=41.0
Q ss_pred cCCCEEEcCCEEEEecCCCCCCCcccccc------eeeeeeeecCCCcccchhhHHhhhcccc
Q 046237 8 CTRPWSFNRCLFVLTEPTGIGDFSKQNLN------FCSFWIQLHKLPLMSMTKVVGLLFGSMI 64 (137)
Q Consensus 8 ~~gPW~~~~~~lil~~w~~~~~~~~~~l~------~~~vWVri~~LP~~~~~~~~~~~Ig~~i 64 (137)
++|=|.-....+-..+|.|++-|+...-+ -..-|+--||+|+.--+.+++++||+.|
T Consensus 142 RrGq~eg~~e~~~~~~~~PD~Gp~~~~p~~Gat~vGAr~~liayNV~L~t~d~~~a~~IAk~v 204 (298)
T TIGR02024 142 RKGQYEALFEKIKDPKWKPDFGPSEFNPKAGATATGARKFLIAFNVNLGTSNLEIAKKIAKAI 204 (298)
T ss_pred hhhhhccchhhccCCCCCCCCCCCCCCCCCCeEEEecCCceEEEEEeecCCCHHHHHHHHHHh
Confidence 34545433334445789999999875321 1356999999999988889999999776
No 51
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=22.94 E-value=31 Score=25.31 Aligned_cols=13 Identities=31% Similarity=0.465 Sum_probs=9.8
Q ss_pred cCccccCCccccc
Q 046237 106 LPDFCFQRGRIGH 118 (137)
Q Consensus 106 lp~fC~~Cg~iGH 118 (137)
+..||..||..+-
T Consensus 117 ~r~fCaVCG~~S~ 129 (156)
T KOG3362|consen 117 LRKFCAVCGYDSK 129 (156)
T ss_pred cchhhhhcCCCch
Confidence 4479999997654
No 52
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=22.90 E-value=1.4e+02 Score=22.45 Aligned_cols=25 Identities=32% Similarity=0.531 Sum_probs=21.1
Q ss_pred ccccccEEEeee-eeEeeecCCCcee
Q 046237 61 GSMIGEVEEVDK-GVKINITRPLMRG 85 (137)
Q Consensus 61 g~~iG~~l~vD~-rV~idv~kPL~~~ 85 (137)
+...|++.+++. ||.+|.+.||-.+
T Consensus 104 ~~~~~~V~~V~~~~V~VDfNHpLAGk 129 (174)
T COG1047 104 GEIPGVVTEVSGDRVTVDFNHPLAGK 129 (174)
T ss_pred ceeeEEEEEEcCCEEEEeCCCcCCCC
Confidence 556899999988 9999999999654
No 53
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.78 E-value=39 Score=19.34 Aligned_cols=10 Identities=30% Similarity=0.650 Sum_probs=6.9
Q ss_pred ccccCCcccc
Q 046237 108 DFCFQRGRIG 117 (137)
Q Consensus 108 ~fC~~Cg~iG 117 (137)
.||..||.+=
T Consensus 1 ~FCp~Cg~~l 10 (52)
T smart00661 1 KFCPKCGNML 10 (52)
T ss_pred CCCCCCCCcc
Confidence 3788887653
No 54
>PF10102 DUF2341: Domain of unknown function (DUF2341); InterPro: IPR018765 This domain of unknown function is found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins.
Probab=22.17 E-value=96 Score=20.44 Aligned_cols=14 Identities=14% Similarity=0.631 Sum_probs=11.8
Q ss_pred ceeeeeeeecCCCc
Q 046237 36 NFCSFWIQLHKLPL 49 (137)
Q Consensus 36 ~~~~vWVri~~LP~ 49 (137)
...-+||++..+|.
T Consensus 28 ~~A~iWVkvp~i~~ 41 (89)
T PF10102_consen 28 EQALIWVKVPSIPA 41 (89)
T ss_pred CeEEEEEECCCCCC
Confidence 36789999999994
No 55
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=22.04 E-value=37 Score=19.11 Aligned_cols=9 Identities=33% Similarity=0.368 Sum_probs=4.0
Q ss_pred ccccCCccc
Q 046237 108 DFCFQRGRI 116 (137)
Q Consensus 108 ~fC~~Cg~i 116 (137)
..|++||+-
T Consensus 2 ~~CSFCgr~ 10 (41)
T PF06689_consen 2 KRCSFCGRP 10 (41)
T ss_dssp -B-TTT--B
T ss_pred CCccCCCCC
Confidence 479999885
No 56
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.99 E-value=71 Score=17.18 Aligned_cols=25 Identities=24% Similarity=0.465 Sum_probs=12.9
Q ss_pred cccCCccc---ccCCCcCCCCCCCCCce
Q 046237 109 FCFQRGRI---GHVFRECPYLKSSPTNF 133 (137)
Q Consensus 109 fC~~Cg~i---GH~~~~C~~~~~~~~~~ 133 (137)
.|..||.+ .+.-+.||.=.+++..|
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~~~~F 31 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAPKEKF 31 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCchHHc
Confidence 46677765 22334566555544433
No 57
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=20.94 E-value=52 Score=25.06 Aligned_cols=18 Identities=39% Similarity=0.958 Sum_probs=16.3
Q ss_pred ccccCCcccccCCCcCCC
Q 046237 108 DFCFQRGRIGHVFRECPY 125 (137)
Q Consensus 108 ~fC~~Cg~iGH~~~~C~~ 125 (137)
-||..||--||....|..
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 469999999999999987
No 58
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=20.57 E-value=1.1e+02 Score=18.04 Aligned_cols=31 Identities=29% Similarity=0.421 Sum_probs=23.7
Q ss_pred eeeeeecCCCcccchhhHHhhhccccccEEEee
Q 046237 39 SFWIQLHKLPLMSMTKVVGLLFGSMIGEVEEVD 71 (137)
Q Consensus 39 ~vWVri~~LP~~~~~~~~~~~Ig~~iG~~l~vD 71 (137)
+-||-+.|-|.... +.++....+ +|++.+..
T Consensus 1 ~~wI~V~Gf~~~~~-~~vl~~F~~-fGeI~~~~ 31 (53)
T PF14605_consen 1 STWISVSGFPPDLA-EEVLEHFAS-FGEIVDIY 31 (53)
T ss_pred CcEEEEEeECchHH-HHHHHHHHh-cCCEEEEE
Confidence 45999999998765 466778876 89988654
No 59
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.47 E-value=3.1e+02 Score=19.18 Aligned_cols=41 Identities=20% Similarity=0.122 Sum_probs=24.6
Q ss_pred eeeeeecCCCcccchh-hHHhhhcccc-ccEEEeeeeeEeeec
Q 046237 39 SFWIQLHKLPLMSMTK-VVGLLFGSMI-GEVEEVDKGVKINIT 79 (137)
Q Consensus 39 ~vWVri~~LP~~~~~~-~~~~~Ig~~i-G~~l~vD~rV~idv~ 79 (137)
.+.=|+-|.|....|. +..++|-.++ -+|--+|.+|+||.+
T Consensus 24 alyHqf~GtPvs~~~a~~le~aI~esi~~QP~v~daeV~Id~~ 66 (116)
T COG2098 24 ALYHQFVGTPVSPGTAESLEKAIEESIKVQPFVEDAEVKIDRD 66 (116)
T ss_pred hhhhhhcCCcCCccchHHHHHHHHHHHhcCCceeeEEEEeccc
Confidence 3445777888887774 4555555333 344445558888754
No 60
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=20.30 E-value=42 Score=21.59 Aligned_cols=12 Identities=25% Similarity=0.581 Sum_probs=4.8
Q ss_pred eccCccccCCcc
Q 046237 104 ERLPDFCFQRGR 115 (137)
Q Consensus 104 E~lp~fC~~Cg~ 115 (137)
+--..||..||-
T Consensus 21 ~~~k~FCp~CGn 32 (73)
T PF08772_consen 21 DMTKQFCPKCGN 32 (73)
T ss_dssp -SS--S-SSS--
T ss_pred CCCceeCcccCC
Confidence 445579999996
No 61
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=20.25 E-value=90 Score=18.72 Aligned_cols=43 Identities=23% Similarity=0.265 Sum_probs=26.0
Q ss_pred CCcccchhhHHhhhccccccEEEee--eeeEeeecCCCceeEEEe
Q 046237 47 LPLMSMTKVVGLLFGSMIGEVEEVD--KGVKINITRPLMRGLTVQ 89 (137)
Q Consensus 47 LP~~~~~~~~~~~Ig~~iG~~l~vD--~rV~idv~kPL~~~v~i~ 89 (137)
+|-+---.+++..|++.+|+=...- ....+|++.||...-.++
T Consensus 13 ~~~g~T~~d~A~~I~~~l~~~~~~A~Vng~~vdl~~~L~~~d~v~ 57 (60)
T PF02824_consen 13 LPEGSTVLDVAYSIHSSLAKRAVAAKVNGQLVDLDHPLEDGDVVE 57 (60)
T ss_dssp EETTBBHHHHHHHHSHHHHHCEEEEEETTEEEETTSBB-SSEEEE
T ss_pred CCCCCCHHHHHHHHCHHHHhheeEEEEcCEECCCCCCcCCCCEEE
Confidence 4444444577888887777722221 145688899998776554
Done!