Query 041609
Match_columns 71
No_of_seqs 105 out of 288
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 08:56:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041609.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041609hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14392 zf-CCHC_4: Zinc knuck 99.8 1.8E-21 3.9E-26 108.0 3.2 47 24-70 1-48 (49)
2 PF00098 zf-CCHC: Zinc knuckle 97.1 0.0002 4.3E-09 32.3 1.0 16 55-70 2-17 (18)
3 PF13696 zf-CCHC_2: Zinc knuck 94.8 0.0093 2E-07 30.6 0.3 18 54-71 9-26 (32)
4 smart00343 ZnF_C2HC zinc finge 94.1 0.022 4.7E-07 27.1 0.6 16 55-70 1-16 (26)
5 PF15288 zf-CCHC_6: Zinc knuck 91.8 0.078 1.7E-06 28.4 0.8 16 55-70 3-20 (40)
6 COG5082 AIR1 Arginine methyltr 90.8 0.1 2.2E-06 36.3 0.7 18 53-70 60-77 (190)
7 COG5082 AIR1 Arginine methyltr 87.0 0.28 6.1E-06 34.1 0.8 16 54-69 98-113 (190)
8 PF13917 zf-CCHC_3: Zinc knuck 85.5 0.45 9.7E-06 25.6 1.0 18 53-70 4-21 (42)
9 KOG4400 E3 ubiquitin ligase in 84.0 0.48 1E-05 33.3 0.9 25 45-70 136-160 (261)
10 PTZ00368 universal minicircle 81.7 0.74 1.6E-05 29.6 1.0 18 53-70 129-146 (148)
11 COG4306 Uncharacterized protei 77.8 0.78 1.7E-05 30.7 0.2 16 45-61 61-76 (160)
12 PF10083 DUF2321: Uncharacteri 73.8 1.8 3.9E-05 29.4 1.1 18 43-61 59-76 (158)
13 COG5222 Uncharacterized conser 73.6 1.3 2.8E-05 33.5 0.5 17 54-70 177-193 (427)
14 PTZ00368 universal minicircle 72.0 1.6 3.4E-05 28.1 0.5 16 55-70 105-120 (148)
15 smart00647 IBR In Between Ring 70.5 2.4 5.1E-05 22.9 0.9 17 53-69 48-64 (64)
16 KOG0341 DEAD-box protein abstr 69.8 1.9 4.2E-05 33.9 0.6 16 55-70 572-587 (610)
17 KOG4400 E3 ubiquitin ligase in 66.4 2.3 5E-05 29.8 0.4 19 52-70 91-109 (261)
18 KOG2560 RNA splicing factor - 65.7 1.5 3.2E-05 34.6 -0.7 17 54-70 113-129 (529)
19 KOG2044 5'-3' exonuclease HKE1 65.7 3.9 8.5E-05 34.2 1.6 30 41-70 248-277 (931)
20 KOG0109 RNA-binding protein LA 64.8 8.2 0.00018 29.0 3.0 50 22-71 117-178 (346)
21 PF14205 Cys_rich_KTR: Cystein 64.0 3.2 6.9E-05 23.6 0.6 16 46-61 21-36 (55)
22 PRK04016 DNA-directed RNA poly 59.2 4.1 8.8E-05 23.7 0.5 13 52-64 3-16 (62)
23 PF01194 RNA_pol_N: RNA polyme 58.4 4.6 9.9E-05 23.3 0.6 11 52-62 3-13 (60)
24 PF14787 zf-CCHC_5: GAG-polypr 52.9 7.3 0.00016 20.4 0.8 18 53-70 2-19 (36)
25 PF01485 IBR: IBR domain; Int 50.4 7.2 0.00016 20.8 0.6 17 53-69 48-64 (64)
26 KOG0119 Splicing factor 1/bran 49.7 7.9 0.00017 30.8 0.9 17 55-71 287-303 (554)
27 COG5179 TAF1 Transcription ini 49.4 7 0.00015 32.4 0.5 17 54-70 938-956 (968)
28 PF00567 TUDOR: Tudor domain; 47.9 14 0.0003 21.4 1.6 50 14-63 65-121 (121)
29 COG1644 RPB10 DNA-directed RNA 47.3 7.9 0.00017 22.6 0.4 14 52-65 3-17 (63)
30 cd00258 GM2-AP GM2 activator p 45.2 46 0.001 22.6 3.9 38 11-48 30-67 (162)
31 PF13240 zinc_ribbon_2: zinc-r 42.6 8.9 0.00019 17.7 0.1 9 53-61 13-21 (23)
32 cd01488 Uba3_RUB Ubiquitin act 40.8 41 0.00089 24.5 3.4 34 26-60 258-291 (291)
33 PF13248 zf-ribbon_3: zinc-rib 40.2 10 0.00022 17.8 0.1 8 54-61 17-24 (26)
34 PF00339 Arrestin_N: Arrestin 39.0 31 0.00068 20.9 2.2 38 3-40 3-41 (149)
35 PF04521 Viral_P18: ssRNA posi 37.3 16 0.00034 23.8 0.7 14 50-63 25-39 (120)
36 TIGR03831 YgiT_finger YgiT-typ 37.3 26 0.00057 17.5 1.5 18 45-62 23-41 (46)
37 PF14599 zinc_ribbon_6: Zinc-r 36.7 39 0.00084 19.3 2.2 36 27-62 17-57 (61)
38 COG1198 PriA Primosomal protei 35.9 25 0.00053 29.0 1.7 26 45-70 454-479 (730)
39 COG1998 RPS31 Ribosomal protei 35.8 22 0.00047 19.9 1.0 17 44-60 7-26 (51)
40 PF02150 RNA_POL_M_15KD: RNA p 34.4 18 0.00039 18.2 0.5 9 54-62 2-10 (35)
41 smart00661 RPOL9 RNA polymeras 34.3 17 0.00038 18.9 0.5 8 55-62 2-9 (52)
42 PF08095 Toxin_25: Hefutoxin f 32.7 3.8 8.2E-05 19.1 -2.0 13 58-70 7-19 (22)
43 PF01315 Ald_Xan_dh_C: Aldehyd 31.1 20 0.00044 22.0 0.5 11 43-53 101-111 (111)
44 KOG3362 Predicted BBOX Zn-fing 31.0 18 0.00039 24.5 0.2 13 52-64 117-129 (156)
45 PF11741 AMIN: AMIN domain; I 30.9 83 0.0018 17.8 3.1 17 18-34 68-84 (95)
46 cd00029 C1 Protein kinase C co 30.3 32 0.0007 17.3 1.1 16 45-61 4-19 (50)
47 PLN03024 Putative EG45-like do 29.9 23 0.00049 22.9 0.5 25 23-50 100-124 (125)
48 PF14803 Nudix_N_2: Nudix N-te 29.7 26 0.00055 17.8 0.6 13 50-62 19-31 (34)
49 PF09297 zf-NADH-PPase: NADH p 26.8 25 0.00055 17.0 0.3 11 54-64 4-14 (32)
50 PF06463 Mob_synth_C: Molybden 26.5 27 0.00058 22.2 0.4 10 54-63 70-79 (128)
51 KOG2907 RNA polymerase I trans 26.2 18 0.00039 23.4 -0.4 11 52-62 6-16 (116)
52 PF05515 Viral_NABP: Viral nuc 26.0 38 0.00082 22.1 1.1 17 55-71 64-80 (124)
53 KOG2673 Uncharacterized conser 25.2 34 0.00074 27.0 0.9 16 56-71 131-146 (485)
54 KOG0696 Serine/threonine prote 25.2 31 0.00068 27.7 0.7 18 43-60 46-63 (683)
55 PF08772 NOB1_Zn_bind: Nin one 24.8 28 0.00061 20.6 0.3 11 51-61 22-32 (73)
56 KOG4399 C2HC-type Zn-finger pr 23.7 37 0.00081 25.3 0.8 19 53-71 261-279 (325)
57 KOG3591 Alpha crystallins [Pos 23.7 1.5E+02 0.0032 20.0 3.7 32 19-50 73-104 (173)
58 PF02591 DUF164: Putative zinc 23.6 32 0.0007 18.6 0.3 10 53-62 46-55 (56)
59 PF00130 C1_1: Phorbol esters/ 23.5 94 0.002 16.0 2.2 11 51-61 9-19 (53)
60 PF11405 Inhibitor_I67: Bromel 23.1 33 0.00072 18.0 0.3 17 45-61 7-23 (41)
61 PF14149 YhfH: YhfH-like prote 22.8 21 0.00045 18.7 -0.5 13 49-61 8-21 (37)
62 smart00109 C1 Protein kinase C 22.6 65 0.0014 15.9 1.4 11 51-61 9-19 (49)
63 PF06869 DUF1258: Protein of u 21.8 27 0.00059 25.4 -0.2 18 53-70 18-35 (258)
64 PF11875 DUF3395: Domain of un 21.5 42 0.00092 22.0 0.7 37 23-62 84-121 (151)
No 1
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=99.83 E-value=1.8e-21 Score=108.00 Aligned_cols=47 Identities=40% Similarity=0.837 Sum_probs=45.0
Q ss_pred eeCCCCCccceeccc-CcceEEEEEEeCCCccccccccceecCCCcCC
Q 041609 24 VDLSGPLPNSVMVEL-PDDCILVKVMYENLPLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 24 iDl~kpL~~~i~ve~-~g~~~~v~v~YE~LP~fC~~Cg~iGH~~~~C~ 70 (71)
||+++||++++.|+. +|+.++++|+|||||.||++||.+||+.++|+
T Consensus 1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcC
Confidence 699999999999997 58899999999999999999999999999997
No 2
>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=97.15 E-value=0.0002 Score=32.27 Aligned_cols=16 Identities=44% Similarity=1.043 Sum_probs=15.0
Q ss_pred ccccccceecCCCcCC
Q 041609 55 KCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~ 70 (71)
-|+.||..||...+|+
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 4999999999999997
No 3
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.81 E-value=0.0093 Score=30.60 Aligned_cols=18 Identities=33% Similarity=0.728 Sum_probs=16.2
Q ss_pred cccccccceecCCCcCCC
Q 041609 54 LKCIVCGNIGHDRTQCQR 71 (71)
Q Consensus 54 ~fC~~Cg~iGH~~~~C~~ 71 (71)
+.|..|+.-||.+++|+.
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 479999999999999973
No 4
>smart00343 ZnF_C2HC zinc finger.
Probab=94.05 E-value=0.022 Score=27.06 Aligned_cols=16 Identities=44% Similarity=1.003 Sum_probs=14.6
Q ss_pred ccccccceecCCCcCC
Q 041609 55 KCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~ 70 (71)
.|+.||..||...+|+
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4899999999999996
No 5
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=91.83 E-value=0.078 Score=28.44 Aligned_cols=16 Identities=50% Similarity=1.173 Sum_probs=13.1
Q ss_pred ccccccceecCC--CcCC
Q 041609 55 KCIVCGNIGHDR--TQCQ 70 (71)
Q Consensus 55 fC~~Cg~iGH~~--~~C~ 70 (71)
-|..||.+||.. ..|+
T Consensus 3 kC~~CG~~GH~~t~k~CP 20 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCP 20 (40)
T ss_pred cccccccccccccCccCC
Confidence 599999999985 5565
No 6
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=90.77 E-value=0.1 Score=36.30 Aligned_cols=18 Identities=39% Similarity=0.864 Sum_probs=16.4
Q ss_pred ccccccccceecCCCcCC
Q 041609 53 PLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~ 70 (71)
-.+|++||..||...+|+
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 358999999999999997
No 7
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=86.97 E-value=0.28 Score=34.10 Aligned_cols=16 Identities=44% Similarity=1.014 Sum_probs=15.0
Q ss_pred cccccccceecCCCcC
Q 041609 54 LKCIVCGNIGHDRTQC 69 (71)
Q Consensus 54 ~fC~~Cg~iGH~~~~C 69 (71)
..|++||..||...+|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 6899999999999999
No 8
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=85.49 E-value=0.45 Score=25.60 Aligned_cols=18 Identities=33% Similarity=0.861 Sum_probs=16.1
Q ss_pred ccccccccceecCCCcCC
Q 041609 53 PLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~ 70 (71)
-..|..|+..||...+|+
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 357999999999999997
No 9
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=84.00 E-value=0.48 Score=33.26 Aligned_cols=25 Identities=32% Similarity=0.542 Sum_probs=20.0
Q ss_pred EEEEeCCCccccccccceecCCCcCC
Q 041609 45 VKVMYENLPLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 45 v~v~YE~LP~fC~~Cg~iGH~~~~C~ 70 (71)
..+.+.+- .+|+.||..||...+|+
T Consensus 136 ~~~~~~~~-~~Cy~Cg~~GH~s~~C~ 160 (261)
T KOG4400|consen 136 DPVDGPKP-AKCYSCGEQGHISDDCP 160 (261)
T ss_pred ccccCCCC-CccCCCCcCCcchhhCC
Confidence 34555555 78999999999999997
No 10
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=81.68 E-value=0.74 Score=29.64 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=12.1
Q ss_pred ccccccccceecCCCcCC
Q 041609 53 PLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~ 70 (71)
+..|+.|+..||...+|+
T Consensus 129 ~~~C~~Cg~~gH~~~dCp 146 (148)
T PTZ00368 129 DKTCYNCGQTGHLSRDCP 146 (148)
T ss_pred CCccccCCCcCcccccCC
Confidence 346777777777777665
No 11
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.80 E-value=0.78 Score=30.65 Aligned_cols=16 Identities=38% Similarity=0.663 Sum_probs=12.9
Q ss_pred EEEEeCCCccccccccc
Q 041609 45 VKVMYENLPLKCIVCGN 61 (71)
Q Consensus 45 v~v~YE~LP~fC~~Cg~ 61 (71)
+-=.|| .|.||++||.
T Consensus 61 lg~dye-~psfchncgs 76 (160)
T COG4306 61 LGGDYE-PPSFCHNCGS 76 (160)
T ss_pred cCCCCC-CcchhhcCCC
Confidence 445687 8999999996
No 12
>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=73.75 E-value=1.8 Score=29.39 Aligned_cols=18 Identities=33% Similarity=0.599 Sum_probs=14.4
Q ss_pred EEEEEEeCCCccccccccc
Q 041609 43 ILVKVMYENLPLKCIVCGN 61 (71)
Q Consensus 43 ~~v~v~YE~LP~fC~~Cg~ 61 (71)
+.+.-.|+ .|.||++||.
T Consensus 59 ~~~g~~~~-~PsYC~~CGk 76 (158)
T PF10083_consen 59 FGLGGHYE-APSYCHNCGK 76 (158)
T ss_pred eeeCCCCC-CChhHHhCCC
Confidence 34556788 9999999996
No 13
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.58 E-value=1.3 Score=33.47 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=16.0
Q ss_pred cccccccceecCCCcCC
Q 041609 54 LKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 54 ~fC~~Cg~iGH~~~~C~ 70 (71)
+.|+.||.-||-+++|+
T Consensus 177 Y~CyRCGqkgHwIqnCp 193 (427)
T COG5222 177 YVCYRCGQKGHWIQNCP 193 (427)
T ss_pred eeEEecCCCCchhhcCC
Confidence 58999999999999997
No 14
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=72.02 E-value=1.6 Score=28.08 Aligned_cols=16 Identities=38% Similarity=0.929 Sum_probs=10.2
Q ss_pred ccccccceecCCCcCC
Q 041609 55 KCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~ 70 (71)
.|+.|+.-||..++|+
T Consensus 105 ~C~~Cg~~gH~~~~C~ 120 (148)
T PTZ00368 105 ACYNCGGEGHISRDCP 120 (148)
T ss_pred hhcccCcCCcchhcCC
Confidence 5666666666666664
No 15
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=70.46 E-value=2.4 Score=22.88 Aligned_cols=17 Identities=24% Similarity=0.397 Sum_probs=14.4
Q ss_pred ccccccccceecCCCcC
Q 041609 53 PLKCIVCGNIGHDRTQC 69 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C 69 (71)
-.||+.|+...|....|
T Consensus 48 ~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 48 FSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CeECCCCCCcCCCCCCC
Confidence 45899999999987766
No 16
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=69.84 E-value=1.9 Score=33.90 Aligned_cols=16 Identities=44% Similarity=1.132 Sum_probs=15.2
Q ss_pred ccccccceecCCCcCC
Q 041609 55 KCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~ 70 (71)
=|..||-+||.+.+|+
T Consensus 572 GCayCgGLGHRItdCP 587 (610)
T KOG0341|consen 572 GCAYCGGLGHRITDCP 587 (610)
T ss_pred ccccccCCCcccccCc
Confidence 5999999999999997
No 17
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=66.43 E-value=2.3 Score=29.83 Aligned_cols=19 Identities=32% Similarity=0.833 Sum_probs=16.3
Q ss_pred CccccccccceecCCCcCC
Q 041609 52 LPLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 52 LP~fC~~Cg~iGH~~~~C~ 70 (71)
....|++|+..||...+|+
T Consensus 91 ~~~~c~~C~~~gH~~~~c~ 109 (261)
T KOG4400|consen 91 IAAACFNCGEGGHIERDCP 109 (261)
T ss_pred cchhhhhCCCCccchhhCC
Confidence 4569999999999999886
No 18
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=65.71 E-value=1.5 Score=34.56 Aligned_cols=17 Identities=29% Similarity=0.726 Sum_probs=15.6
Q ss_pred cccccccceecCCCcCC
Q 041609 54 LKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 54 ~fC~~Cg~iGH~~~~C~ 70 (71)
.+|-+||-+||..+.|.
T Consensus 113 GACeNCGAmtHk~KDCm 129 (529)
T KOG2560|consen 113 GACENCGAMTHKVKDCM 129 (529)
T ss_pred hhhhhhhhhhcchHHHh
Confidence 58999999999999994
No 19
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=65.70 E-value=3.9 Score=34.20 Aligned_cols=30 Identities=33% Similarity=0.870 Sum_probs=24.6
Q ss_pred ceEEEEEEeCCCccccccccceecCCCcCC
Q 041609 41 DCILVKVMYENLPLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 41 ~~~~v~v~YE~LP~fC~~Cg~iGH~~~~C~ 70 (71)
+...-++.+.+-|.-|+.||..||..++|.
T Consensus 248 F~IlRE~~~P~~~~~C~~cgq~gh~~~dc~ 277 (931)
T KOG2044|consen 248 FSILREEFFPNKPRRCFLCGQTGHEAKDCE 277 (931)
T ss_pred eEEeeeeecCCCcccchhhcccCCcHhhcC
Confidence 334446667889999999999999999995
No 20
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=64.84 E-value=8.2 Score=29.01 Aligned_cols=50 Identities=22% Similarity=0.384 Sum_probs=34.6
Q ss_pred EEeeCCCCCccce----ecccCcceEEEEEEeCCCc--------cccccccceecCCCcCCC
Q 041609 22 VDVDLSGPLPNSV----MVELPDDCILVKVMYENLP--------LKCIVCGNIGHDRTQCQR 71 (71)
Q Consensus 22 V~iDl~kpL~~~i----~ve~~g~~~~v~v~YE~LP--------~fC~~Cg~iGH~~~~C~~ 71 (71)
|.+|....-...| .-+.+|+...|.+.=-+|. .-|..||.-||-.++|+.
T Consensus 117 vh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtapgmgDq~~cyrcGkeghwskEcP~ 178 (346)
T KOG0109|consen 117 VHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPGMGDQSGCYRCGKEGHWSKECPV 178 (346)
T ss_pred EEEeeccchHHHHhcccccccccceeeeeeeccccccCCCCCCHHHheeccccccccccCCc
Confidence 3444544444433 2234577777888887774 469999999999999984
No 21
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=63.97 E-value=3.2 Score=23.63 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=13.0
Q ss_pred EEEeCCCccccccccc
Q 041609 46 KVMYENLPLKCIVCGN 61 (71)
Q Consensus 46 ~v~YE~LP~fC~~Cg~ 61 (71)
+-+-+++|.||..|+.
T Consensus 21 DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 21 DTVLKNFPLYCPKCKQ 36 (55)
T ss_pred CceeccccccCCCCCc
Confidence 3456899999999985
No 22
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=59.16 E-value=4.1 Score=23.68 Aligned_cols=13 Identities=31% Similarity=1.288 Sum_probs=10.0
Q ss_pred Cccccccccce-ec
Q 041609 52 LPLKCIVCGNI-GH 64 (71)
Q Consensus 52 LP~fC~~Cg~i-GH 64 (71)
.|--||+||.+ ||
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 58899999963 44
No 23
>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=58.35 E-value=4.6 Score=23.30 Aligned_cols=11 Identities=36% Similarity=1.494 Sum_probs=7.5
Q ss_pred Cccccccccce
Q 041609 52 LPLKCIVCGNI 62 (71)
Q Consensus 52 LP~fC~~Cg~i 62 (71)
.|--||+||.+
T Consensus 3 iPVRCFTCGkv 13 (60)
T PF01194_consen 3 IPVRCFTCGKV 13 (60)
T ss_dssp -SSS-STTTSB
T ss_pred CceecCCCCCC
Confidence 57889999964
No 24
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=52.88 E-value=7.3 Score=20.38 Aligned_cols=18 Identities=33% Similarity=0.623 Sum_probs=11.5
Q ss_pred ccccccccceecCCCcCC
Q 041609 53 PLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~ 70 (71)
|.-|..|+.=.|-.++|.
T Consensus 2 ~~~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECR 19 (36)
T ss_dssp --C-TTTSSSCS-TTT--
T ss_pred CccCcccCCCcchhhhhh
Confidence 567999999999999995
No 25
>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=50.40 E-value=7.2 Score=20.83 Aligned_cols=17 Identities=29% Similarity=0.714 Sum_probs=12.6
Q ss_pred ccccccccceecCCCcC
Q 041609 53 PLKCIVCGNIGHDRTQC 69 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C 69 (71)
-.||+.|+..-|....|
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 35899999988886655
No 26
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=49.69 E-value=7.9 Score=30.81 Aligned_cols=17 Identities=35% Similarity=0.993 Sum_probs=14.2
Q ss_pred ccccccceecCCCcCCC
Q 041609 55 KCIVCGNIGHDRTQCQR 71 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~~ 71 (71)
.|.+||-+||...+|+.
T Consensus 287 ~c~~cg~~gH~~~dc~~ 303 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKV 303 (554)
T ss_pred cccccCCcccccccCCC
Confidence 78888888888888874
No 27
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=49.35 E-value=7 Score=32.37 Aligned_cols=17 Identities=35% Similarity=0.942 Sum_probs=13.4
Q ss_pred cccccccceecCC--CcCC
Q 041609 54 LKCIVCGNIGHDR--TQCQ 70 (71)
Q Consensus 54 ~fC~~Cg~iGH~~--~~C~ 70 (71)
.-|.+||.+||.. +.||
T Consensus 938 r~C~nCGQvGHmkTNK~CP 956 (968)
T COG5179 938 RTCGNCGQVGHMKTNKACP 956 (968)
T ss_pred eecccccccccccccccCc
Confidence 4799999999974 4454
No 28
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=47.88 E-value=14 Score=21.43 Aligned_cols=50 Identities=20% Similarity=0.379 Sum_probs=31.5
Q ss_pred ccceEEEEEEeeCCCCCccceecccCc-------ceEEEEEEeCCCcccccccccee
Q 041609 14 YGYYVRILVDVDLSGPLPNSVMVELPD-------DCILVKVMYENLPLKCIVCGNIG 63 (71)
Q Consensus 14 ~g~yaRV~V~iDl~kpL~~~i~ve~~g-------~~~~v~v~YE~LP~fC~~Cg~iG 63 (71)
-|.+-|..|..+.......--.|+-.. ....+.-++..+|..+..|.+-|
T Consensus 65 ~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~~~~~~P~~a~~~~L~g 121 (121)
T PF00567_consen 65 DGRWYRAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPPEFASLPPQAIKCKLAG 121 (121)
T ss_dssp TSEEEEEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--HHHCSSSSSCEEEEET-
T ss_pred CCceeeEEEEEecccceeEEEEEecCceEEEcHHHhhhhCHHHhhCChhhEEEEEcC
Confidence 367889988777777666655554321 23445566777899998888755
No 29
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=47.34 E-value=7.9 Score=22.59 Aligned_cols=14 Identities=50% Similarity=1.483 Sum_probs=10.5
Q ss_pred Cccccccccc-eecC
Q 041609 52 LPLKCIVCGN-IGHD 65 (71)
Q Consensus 52 LP~fC~~Cg~-iGH~ 65 (71)
.|--||+||. |||.
T Consensus 3 iPiRCFsCGkvi~~~ 17 (63)
T COG1644 3 IPVRCFSCGKVIGHK 17 (63)
T ss_pred CceEeecCCCCHHHH
Confidence 5788999996 4553
No 30
>cd00258 GM2-AP GM2 activator protein (GM2-AP) is a non-enzymatic lysosomal protein that acts as cofactor in the sequential degradation of gangliosides. GM2A is an essential cofactor for beta-hexosaminidase A (Hex A) in the enzymatic hydrolysis of GM2 ganglioside to GM3. Mutation of the gene results in the AB variant of Tay-Sachs disease. GM2-AP and similar proteins belong to the ML domain family.
Probab=45.16 E-value=46 Score=22.62 Aligned_cols=38 Identities=18% Similarity=0.081 Sum_probs=28.2
Q ss_pred CCcccceEEEEEEeeCCCCCccceecccCcceEEEEEE
Q 041609 11 ERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVM 48 (71)
Q Consensus 11 ~~~~g~yaRV~V~iDl~kpL~~~i~ve~~g~~~~v~v~ 48 (71)
....--.|.+-+..+|+.||.-.+.|+++-.-+|++|=
T Consensus 30 pg~~tvs~~~~~~~~lsSp~~~~l~v~k~v~g~Wi~iP 67 (162)
T cd00258 30 PGDLTVSTVGSTSVPLSSPLKVILTLEKEVAGLWMKIP 67 (162)
T ss_pred CCcEEEEEEEEEeeEcCCCcEEEEEEEeecccEEEEcc
Confidence 33344467888889999999999999987555676654
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.61 E-value=8.9 Score=17.75 Aligned_cols=9 Identities=33% Similarity=0.748 Sum_probs=6.7
Q ss_pred ccccccccc
Q 041609 53 PLKCIVCGN 61 (71)
Q Consensus 53 P~fC~~Cg~ 61 (71)
-.||.+||.
T Consensus 13 ~~fC~~CG~ 21 (23)
T PF13240_consen 13 AKFCPNCGT 21 (23)
T ss_pred CcchhhhCC
Confidence 358888885
No 32
>cd01488 Uba3_RUB Ubiquitin activating enzyme (E1) subunit UBA3. UBA3 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins. consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. UBA3 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2.
Probab=40.83 E-value=41 Score=24.49 Aligned_cols=34 Identities=26% Similarity=0.298 Sum_probs=24.9
Q ss_pred CCCCCccceecccCcceEEEEEEeCCCcccccccc
Q 041609 26 LSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCG 60 (71)
Q Consensus 26 l~kpL~~~i~ve~~g~~~~v~v~YE~LP~fC~~Cg 60 (71)
.+.+|..-.+...++-.....++||+.|. |..|+
T Consensus 258 ~~~~~~n~~~~~g~~g~~~~~~~~~~~~~-c~~c~ 291 (291)
T cd01488 258 CYENLNNYLMYNGVDGCYTYTFEHERKED-CPVCS 291 (291)
T ss_pred cccCCCceEEEecCCceEEEEEEEeeCCC-CCCCC
Confidence 34456556666665557789999999998 88885
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.19 E-value=10 Score=17.80 Aligned_cols=8 Identities=38% Similarity=0.796 Sum_probs=5.8
Q ss_pred cccccccc
Q 041609 54 LKCIVCGN 61 (71)
Q Consensus 54 ~fC~~Cg~ 61 (71)
.||.+||.
T Consensus 17 ~fC~~CG~ 24 (26)
T PF13248_consen 17 KFCPNCGA 24 (26)
T ss_pred ccChhhCC
Confidence 47888874
No 34
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=39.04 E-value=31 Score=20.89 Aligned_cols=38 Identities=21% Similarity=0.107 Sum_probs=25.4
Q ss_pred ccccccccCCcccceEEEEEEeeCCCCCcc-ceecccCc
Q 041609 3 HGIYLTTKERTYGYYVRILVDVDLSGPLPN-SVMVELPD 40 (71)
Q Consensus 3 ~~iD~~t~~~~~g~yaRV~V~iDl~kpL~~-~i~ve~~g 40 (71)
+.+|....-..-|+.++-.|.+.+++|+.- .|.|...|
T Consensus 3 I~ld~~~~~y~~Ge~I~G~V~l~~~~~~~i~~i~v~l~G 41 (149)
T PF00339_consen 3 IELDNPKPVYFPGEVISGKVVLELSKPIKIKSIKVRLKG 41 (149)
T ss_dssp EEES-SEEEEESS--EEEEEEECTTT-TTTSEEEEEEEE
T ss_pred EEECCCCCEECCCCEEEEEEEEEECCccceeEEEEEEEE
Confidence 456656666677999999999999999865 55666555
No 35
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=37.29 E-value=16 Score=23.81 Aligned_cols=14 Identities=29% Similarity=0.354 Sum_probs=11.5
Q ss_pred CCCccccc-ccccee
Q 041609 50 ENLPLKCI-VCGNIG 63 (71)
Q Consensus 50 E~LP~fC~-~Cg~iG 63 (71)
=+||.||. +|||+-
T Consensus 25 C~Ln~~~G~~CGMpa 39 (120)
T PF04521_consen 25 CRLNSFCGVSCGMPA 39 (120)
T ss_pred ecCCCCCCcCCCCcc
Confidence 47999987 899973
No 36
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=37.27 E-value=26 Score=17.53 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=13.8
Q ss_pred EEEEeCCCcc-ccccccce
Q 041609 45 VKVMYENLPL-KCIVCGNI 62 (71)
Q Consensus 45 v~v~YE~LP~-fC~~Cg~i 62 (71)
-.+..+++|. +|..||..
T Consensus 23 ~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 23 ELIVIENVPALVCPQCGEE 41 (46)
T ss_pred EEEEEeCCCccccccCCCE
Confidence 4566788886 79999964
No 37
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=36.65 E-value=39 Score=19.31 Aligned_cols=36 Identities=28% Similarity=0.459 Sum_probs=13.4
Q ss_pred CCCCccc-----eecccCcceEEEEEEeCCCccccccccce
Q 041609 27 SGPLPNS-----VMVELPDDCILVKVMYENLPLKCIVCGNI 62 (71)
Q Consensus 27 ~kpL~~~-----i~ve~~g~~~~v~v~YE~LP~fC~~Cg~i 62 (71)
+.|++.. ++|--++-.-.-++.|-+|...|.+||..
T Consensus 17 ~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SY 57 (61)
T PF14599_consen 17 ATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSY 57 (61)
T ss_dssp -----------EEEEEESSS--EEEEE--TT----TTTS--
T ss_pred hCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCc
Confidence 4455542 45544553334589999999999999964
No 38
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=35.94 E-value=25 Score=28.98 Aligned_cols=26 Identities=19% Similarity=0.396 Sum_probs=15.7
Q ss_pred EEEEeCCCccccccccceecCCCcCC
Q 041609 45 VKVMYENLPLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 45 v~v~YE~LP~fC~~Cg~iGH~~~~C~ 70 (71)
..+--..=-.+|++||.-...-..|+
T Consensus 454 lt~H~~~~~L~CH~Cg~~~~~p~~Cp 479 (730)
T COG1198 454 LTLHKATGQLRCHYCGYQEPIPQSCP 479 (730)
T ss_pred eEEecCCCeeEeCCCCCCCCCCCCCC
Confidence 33333334557888877766666665
No 39
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.78 E-value=22 Score=19.92 Aligned_cols=17 Identities=29% Similarity=0.356 Sum_probs=12.4
Q ss_pred EEEEEeC---CCcccccccc
Q 041609 44 LVKVMYE---NLPLKCIVCG 60 (71)
Q Consensus 44 ~v~v~YE---~LP~fC~~Cg 60 (71)
+++|+.| ++-.||..||
T Consensus 7 yY~v~~~kv~rk~~~CPrCG 26 (51)
T COG1998 7 YYEVDDEKVKRKNRFCPRCG 26 (51)
T ss_pred EEEEcCCcEEEccccCCCCC
Confidence 4566663 4567999999
No 40
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=34.42 E-value=18 Score=18.24 Aligned_cols=9 Identities=44% Similarity=0.969 Sum_probs=6.7
Q ss_pred cccccccce
Q 041609 54 LKCIVCGNI 62 (71)
Q Consensus 54 ~fC~~Cg~i 62 (71)
.||..||.+
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 489999875
No 41
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.27 E-value=17 Score=18.94 Aligned_cols=8 Identities=50% Similarity=1.178 Sum_probs=5.9
Q ss_pred ccccccce
Q 041609 55 KCIVCGNI 62 (71)
Q Consensus 55 fC~~Cg~i 62 (71)
||..||.+
T Consensus 2 FCp~Cg~~ 9 (52)
T smart00661 2 FCPKCGNM 9 (52)
T ss_pred CCCCCCCc
Confidence 78888765
No 42
>PF08095 Toxin_25: Hefutoxin family; InterPro: IPR012630 This family consists of the hefutoxins that are found in the venom of the scorpion Heterometrus fulvipes (Indian black scorpion). These toxins, kappa-hefutoxin1 and kappa-hefutoxin2, exhibit no homology to any known toxins. The hefutoxins are potassium channel toxins [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1HP9_A.
Probab=32.69 E-value=3.8 Score=19.13 Aligned_cols=13 Identities=38% Similarity=0.951 Sum_probs=9.9
Q ss_pred cccceecCCCcCC
Q 041609 58 VCGNIGHDRTQCQ 70 (71)
Q Consensus 58 ~Cg~iGH~~~~C~ 70 (71)
+|-.-||....|+
T Consensus 7 scwk~g~deetck 19 (22)
T PF08095_consen 7 SCWKAGHDEETCK 19 (22)
T ss_dssp HHHHHHS-TTHHH
T ss_pred HHHHccCcHHHHH
Confidence 6888899998885
No 43
>PF01315 Ald_Xan_dh_C: Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; InterPro: IPR000674 Aldehyde oxidase (1.2.3.1 from EC) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (1.1.1.204 from EC) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.1.3.22 from EC) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1N63_E 1N60_B 1ZXI_E 1N5W_E 1N62_B 1N61_E 3AN1_B 2E3T_A 1WYG_A 2W3R_D ....
Probab=31.07 E-value=20 Score=22.04 Aligned_cols=11 Identities=73% Similarity=1.005 Sum_probs=5.6
Q ss_pred EEEEEEeCCCc
Q 041609 43 ILVKVMYENLP 53 (71)
Q Consensus 43 ~~v~v~YE~LP 53 (71)
..++|+||.||
T Consensus 101 ~~V~V~Ye~lp 111 (111)
T PF01315_consen 101 ELVKVEYEELP 111 (111)
T ss_dssp HT-EEEEEE--
T ss_pred cCcEEEeEeCC
Confidence 35777888776
No 44
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=31.04 E-value=18 Score=24.49 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=9.9
Q ss_pred Cccccccccceec
Q 041609 52 LPLKCIVCGNIGH 64 (71)
Q Consensus 52 LP~fC~~Cg~iGH 64 (71)
+-.||..||.++-
T Consensus 117 ~r~fCaVCG~~S~ 129 (156)
T KOG3362|consen 117 LRKFCAVCGYDSK 129 (156)
T ss_pred cchhhhhcCCCch
Confidence 3369999998764
No 45
>PF11741 AMIN: AMIN domain; InterPro: IPR021731 This N-terminal domain of various bacterial protein families is crucial for the targetting of periplasmic or extracellular proteins to specific regions of the bacterial envelope. AMIN is derived from the N-terminal domain of AmiC, an N-acetylmuramoyl-l-alanine amidase of Escherichia coli which localises to the septal ring during division and plays a key role in the separation of daughter cells. The AMIN domain is present in several protein families besides amidases suggesting that AMIN may represent a general targetting determinant involved in the localisation of periplasmic protein complexes []. ; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity
Probab=30.92 E-value=83 Score=17.78 Aligned_cols=17 Identities=35% Similarity=0.505 Sum_probs=10.2
Q ss_pred EEEEEEeeCCCCCccce
Q 041609 18 VRILVDVDLSGPLPNSV 34 (71)
Q Consensus 18 aRV~V~iDl~kpL~~~i 34 (71)
-+++|.+||.++....+
T Consensus 68 ~~~Rvvi~l~~~~~y~~ 84 (95)
T PF11741_consen 68 DTVRVVIDLKGPASYKV 84 (95)
T ss_pred CEEEEEEEcCCCcccee
Confidence 35566666776666633
No 46
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=30.35 E-value=32 Score=17.34 Aligned_cols=16 Identities=31% Similarity=0.573 Sum_probs=9.7
Q ss_pred EEEEeCCCccccccccc
Q 041609 45 VKVMYENLPLKCIVCGN 61 (71)
Q Consensus 45 v~v~YE~LP~fC~~Cg~ 61 (71)
+...|. .|.+|..|+.
T Consensus 4 ~~~~~~-~~~~C~~C~~ 19 (50)
T cd00029 4 VRKSFF-KPTFCDVCRK 19 (50)
T ss_pred EEeeCC-CCCChhhcch
Confidence 344454 4777888853
No 47
>PLN03024 Putative EG45-like domain containing protein 1; Provisional
Probab=29.85 E-value=23 Score=22.87 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=17.8
Q ss_pred EeeCCCCCccceecccCcceEEEEEEeC
Q 041609 23 DVDLSGPLPNSVMVELPDDCILVKVMYE 50 (71)
Q Consensus 23 ~iDl~kpL~~~i~ve~~g~~~~v~v~YE 50 (71)
.+|||+|.+..|--...| .+.|+|+
T Consensus 100 ~~DLS~~AF~~iA~~~aG---~v~V~y~ 124 (125)
T PLN03024 100 TLDLSREAFAQIANPVAG---IINIDYI 124 (125)
T ss_pred ceEcCHHHHHHhcCccCC---EEEEEEe
Confidence 588898888888655444 3677775
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.74 E-value=26 Score=17.78 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=8.8
Q ss_pred CCCccccccccce
Q 041609 50 ENLPLKCIVCGNI 62 (71)
Q Consensus 50 E~LP~fC~~Cg~i 62 (71)
++...+|..||.|
T Consensus 19 ~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 19 DRERLVCPACGFI 31 (34)
T ss_dssp SS-EEEETTTTEE
T ss_pred CccceECCCCCCE
Confidence 4556788888876
No 49
>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=26.75 E-value=25 Score=16.99 Aligned_cols=11 Identities=27% Similarity=0.431 Sum_probs=5.7
Q ss_pred cccccccceec
Q 041609 54 LKCIVCGNIGH 64 (71)
Q Consensus 54 ~fC~~Cg~iGH 64 (71)
.||..||..=.
T Consensus 4 rfC~~CG~~t~ 14 (32)
T PF09297_consen 4 RFCGRCGAPTK 14 (32)
T ss_dssp SB-TTT--BEE
T ss_pred cccCcCCcccc
Confidence 58999987543
No 50
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=26.45 E-value=27 Score=22.19 Aligned_cols=10 Identities=30% Similarity=0.610 Sum_probs=4.9
Q ss_pred ccccccccee
Q 041609 54 LKCIVCGNIG 63 (71)
Q Consensus 54 ~fC~~Cg~iG 63 (71)
.||..|+.+=
T Consensus 70 ~FC~~CNRiR 79 (128)
T PF06463_consen 70 PFCSSCNRIR 79 (128)
T ss_dssp --GGG--EEE
T ss_pred CCCCcCCEEE
Confidence 3999999763
No 51
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=26.22 E-value=18 Score=23.41 Aligned_cols=11 Identities=27% Similarity=0.455 Sum_probs=8.8
Q ss_pred Cccccccccce
Q 041609 52 LPLKCIVCGNI 62 (71)
Q Consensus 52 LP~fC~~Cg~i 62 (71)
=+.||..||.|
T Consensus 6 ~~~FC~~CG~l 16 (116)
T KOG2907|consen 6 DLDFCSDCGSL 16 (116)
T ss_pred Ccchhhhhhhh
Confidence 36799999976
No 52
>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=25.99 E-value=38 Score=22.15 Aligned_cols=17 Identities=35% Similarity=1.030 Sum_probs=14.4
Q ss_pred ccccccceecCCCcCCC
Q 041609 55 KCIVCGNIGHDRTQCQR 71 (71)
Q Consensus 55 fC~~Cg~iGH~~~~C~~ 71 (71)
.|+.||.+=|....|++
T Consensus 64 ~C~~CG~~l~~~~~C~~ 80 (124)
T PF05515_consen 64 RCFKCGRYLHNNGNCRR 80 (124)
T ss_pred ccccccceeecCCcCCC
Confidence 59999999888888864
No 53
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=25.21 E-value=34 Score=27.01 Aligned_cols=16 Identities=38% Similarity=0.991 Sum_probs=14.8
Q ss_pred cccccceecCCCcCCC
Q 041609 56 CIVCGNIGHDRTQCQR 71 (71)
Q Consensus 56 C~~Cg~iGH~~~~C~~ 71 (71)
||+|+---|+..+|++
T Consensus 131 CFNC~g~~hsLrdC~r 146 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPR 146 (485)
T ss_pred ccccCCCCCccccCCC
Confidence 7999999999999975
No 54
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=25.18 E-value=31 Score=27.69 Aligned_cols=18 Identities=17% Similarity=0.253 Sum_probs=14.8
Q ss_pred EEEEEEeCCCcccccccc
Q 041609 43 ILVKVMYENLPLKCIVCG 60 (71)
Q Consensus 43 ~~v~v~YE~LP~fC~~Cg 60 (71)
..+..++=+-|.||+||.
T Consensus 46 HkF~aRFFKqPTfCsHCk 63 (683)
T KOG0696|consen 46 HKFIARFFKQPTFCSHCK 63 (683)
T ss_pred ceeeehhccCCchhhhhh
Confidence 346677889999999995
No 55
>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=24.81 E-value=28 Score=20.59 Aligned_cols=11 Identities=36% Similarity=0.610 Sum_probs=4.7
Q ss_pred CCccccccccc
Q 041609 51 NLPLKCIVCGN 61 (71)
Q Consensus 51 ~LP~fC~~Cg~ 61 (71)
---.||..||.
T Consensus 22 ~~k~FCp~CGn 32 (73)
T PF08772_consen 22 MTKQFCPKCGN 32 (73)
T ss_dssp SS--S-SSS--
T ss_pred CCceeCcccCC
Confidence 34469999986
No 56
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=23.68 E-value=37 Score=25.26 Aligned_cols=19 Identities=32% Similarity=1.020 Sum_probs=16.2
Q ss_pred ccccccccceecCCCcCCC
Q 041609 53 PLKCIVCGNIGHDRTQCQR 71 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~~ 71 (71)
-.||+.||.+-|....|++
T Consensus 261 ~~~C~iC~~~~~~R~~C~~ 279 (325)
T KOG4399|consen 261 KHGCFICGELDHKRSTCPN 279 (325)
T ss_pred hcceeeccccccccccCcc
Confidence 3589999999999998874
No 57
>KOG3591 consensus Alpha crystallins [Posttranslational modification, protein turnover, chaperones]
Probab=23.66 E-value=1.5e+02 Score=19.98 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=24.4
Q ss_pred EEEEEeeCCCCCccceecccCcceEEEEEEeC
Q 041609 19 RILVDVDLSGPLPNSVMVELPDDCILVKVMYE 50 (71)
Q Consensus 19 RV~V~iDl~kpL~~~i~ve~~g~~~~v~v~YE 50 (71)
...|.+|+.+-.+.+|.|..+|....|+=+-|
T Consensus 73 ~F~V~lDV~~F~PeEl~Vk~~~~~l~V~gkHe 104 (173)
T KOG3591|consen 73 KFEVNLDVHQFKPEELKVKTDDNTLEVEGKHE 104 (173)
T ss_pred cEEEEEEcccCcccceEEEeCCCEEEEEeeec
Confidence 45788999999999999998776555554444
No 58
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=23.55 E-value=32 Score=18.60 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=6.9
Q ss_pred ccccccccce
Q 041609 53 PLKCIVCGNI 62 (71)
Q Consensus 53 P~fC~~Cg~i 62 (71)
..+|.+||.|
T Consensus 46 i~~Cp~CgRi 55 (56)
T PF02591_consen 46 IVFCPNCGRI 55 (56)
T ss_pred eEECcCCCcc
Confidence 3578888865
No 59
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.49 E-value=94 Score=16.04 Aligned_cols=11 Identities=45% Similarity=0.999 Sum_probs=6.2
Q ss_pred CCccccccccc
Q 041609 51 NLPLKCIVCGN 61 (71)
Q Consensus 51 ~LP~fC~~Cg~ 61 (71)
..|.+|..|+.
T Consensus 9 ~~~~~C~~C~~ 19 (53)
T PF00130_consen 9 SKPTYCDVCGK 19 (53)
T ss_dssp SSTEB-TTSSS
T ss_pred CCCCCCcccCc
Confidence 45667777764
No 60
>PF11405 Inhibitor_I67: Bromelain inhibitor VI; InterPro: IPR022713 Bromelain inhibitor VI is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. ; PDB: 2BI6_H 1BI6_H.
Probab=23.14 E-value=33 Score=17.97 Aligned_cols=17 Identities=24% Similarity=0.485 Sum_probs=7.9
Q ss_pred EEEEeCCCccccccccc
Q 041609 45 VKVMYENLPLKCIVCGN 61 (71)
Q Consensus 45 v~v~YE~LP~fC~~Cg~ 61 (71)
..=.|..-|.||..|+.
T Consensus 7 ctdtysdcpgfcktcka 23 (41)
T PF11405_consen 7 CTDTYSDCPGFCKTCKA 23 (41)
T ss_dssp E----SS--TT-SSEEE
T ss_pred eecccccCchHHHHHHH
Confidence 34468888999999963
No 61
>PF14149 YhfH: YhfH-like protein
Probab=22.75 E-value=21 Score=18.72 Aligned_cols=13 Identities=54% Similarity=1.272 Sum_probs=9.4
Q ss_pred eCCCcc-ccccccc
Q 041609 49 YENLPL-KCIVCGN 61 (71)
Q Consensus 49 YE~LP~-fC~~Cg~ 61 (71)
|.+||. -|..||.
T Consensus 8 frnLp~K~C~~CG~ 21 (37)
T PF14149_consen 8 FRNLPPKKCTECGK 21 (37)
T ss_pred HHhCCCcccHHHHH
Confidence 456774 7888885
No 62
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=22.59 E-value=65 Score=15.92 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=7.5
Q ss_pred CCccccccccc
Q 041609 51 NLPLKCIVCGN 61 (71)
Q Consensus 51 ~LP~fC~~Cg~ 61 (71)
..|.+|..|+.
T Consensus 9 ~~~~~C~~C~~ 19 (49)
T smart00109 9 KKPTKCCVCRK 19 (49)
T ss_pred CCCCCcccccc
Confidence 34778888853
No 63
>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=21.83 E-value=27 Score=25.42 Aligned_cols=18 Identities=22% Similarity=0.731 Sum_probs=15.7
Q ss_pred ccccccccceecCCCcCC
Q 041609 53 PLKCIVCGNIGHDRTQCQ 70 (71)
Q Consensus 53 P~fC~~Cg~iGH~~~~C~ 70 (71)
..||..||...++.+.|.
T Consensus 18 h~~CN~CG~~~~~~~kC~ 35 (258)
T PF06869_consen 18 HFICNSCGKVVESNEKCS 35 (258)
T ss_pred ehhhhhhhhhhccCceee
Confidence 469999999999998884
No 64
>PF11875 DUF3395: Domain of unknown function (DUF3395); InterPro: IPR024586 Chaperone DnaJ was originally characterised from Escherichia coli as a 41 kDa heat shock protein. DnaJ has a modular structure consisting of a J-domain, a proximal G/F-domain, and a distal zinc finger domain, followed by less conserved C-terminal sequences. Since then, a large number of DnaJ-related proteins containing a J-domain have been characterised from a variety of different organisms. In the genome of Arabidopsis thaliana a total of 89 J-domain proteins have been identified []. This entry represents a C-terminal domain found in some eukaryotic DnaJ-like proteins, including member 11 from the subfamily C1 and protein DnaJ 13 from Arabidopsis. This domain is typically between 147 to 176 amino acids in length.
Probab=21.48 E-value=42 Score=22.02 Aligned_cols=37 Identities=27% Similarity=0.258 Sum_probs=24.5
Q ss_pred EeeCCCCCccceecccCcceEEEE-EEeCCCccccccccce
Q 041609 23 DVDLSGPLPNSVMVELPDDCILVK-VMYENLPLKCIVCGNI 62 (71)
Q Consensus 23 ~iDl~kpL~~~i~ve~~g~~~~v~-v~YE~LP~fC~~Cg~i 62 (71)
-||+|-||..-| .++....-. +.-..||.||.-|=..
T Consensus 84 ~iDVTipLq~lV---~dS~L~l~~~~sKs~L~GF~DP~p~~ 121 (151)
T PF11875_consen 84 VIDVTIPLQALV---KDSQLILPEGVSKSGLPGFYDPCPFL 121 (151)
T ss_pred EEEEhhhhhhEe---ecCEEEEcCCCchhhCCCCCCCcccc
Confidence 467888887766 234333334 6778899999998533
Done!