Query 043522
Match_columns 84
No_of_seqs 101 out of 238
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 05:54:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043522.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043522hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15288 zf-CCHC_6: Zinc knuck 96.9 0.00051 1.1E-08 37.4 1.5 20 61-80 2-23 (40)
2 PF00098 zf-CCHC: Zinc knuckle 96.7 0.0013 2.7E-08 30.0 1.5 17 62-78 2-18 (18)
3 PF13696 zf-CCHC_2: Zinc knuck 94.9 0.013 2.8E-07 30.5 0.9 21 60-80 8-28 (32)
4 PF14392 zf-CCHC_4: Zinc knuck 92.7 0.047 1E-06 30.3 0.6 19 60-78 31-49 (49)
5 COG5179 TAF1 Transcription ini 90.9 0.16 3.4E-06 42.3 2.1 26 55-80 932-959 (968)
6 smart00343 ZnF_C2HC zinc finge 90.3 0.15 3.2E-06 24.5 0.9 18 62-79 1-18 (26)
7 PF13917 zf-CCHC_3: Zinc knuck 86.2 0.41 8.9E-06 26.2 1.1 19 60-78 4-22 (42)
8 COG5082 AIR1 Arginine methyltr 79.6 1.2 2.6E-05 31.7 1.5 16 61-76 98-113 (190)
9 PTZ00368 universal minicircle 62.6 5.3 0.00011 26.3 1.6 21 60-80 77-97 (148)
10 PF13717 zinc_ribbon_4: zinc-r 59.9 5.8 0.00013 20.6 1.1 13 57-69 22-34 (36)
11 PF02178 AT_hook: AT hook moti 59.1 4.2 9.1E-05 16.9 0.4 9 36-44 2-10 (13)
12 PF13719 zinc_ribbon_5: zinc-r 58.3 6.6 0.00014 20.3 1.2 12 57-68 22-33 (37)
13 COG5082 AIR1 Arginine methyltr 56.0 5.9 0.00013 28.2 1.0 18 60-77 60-77 (190)
14 PRK14890 putative Zn-ribbon RN 54.8 5.2 0.00011 23.4 0.5 18 60-78 36-53 (59)
15 PTZ00368 universal minicircle 52.3 9.2 0.0002 25.1 1.4 18 61-78 104-121 (148)
16 PRK14892 putative transcriptio 48.2 20 0.00043 22.9 2.4 10 59-68 20-29 (99)
17 PHA00689 hypothetical protein 47.0 9.6 0.00021 21.9 0.7 13 60-72 17-29 (62)
18 KOG3116 Predicted C3H1-type Zn 46.8 3.9 8.5E-05 28.4 -1.0 22 58-79 25-46 (177)
19 PF05634 APO_RNA-bind: APO RNA 46.7 18 0.0004 26.0 2.3 22 59-80 97-123 (204)
20 KOG0782 Predicted diacylglycer 44.8 5.5 0.00012 33.4 -0.7 25 55-79 271-295 (1004)
21 KOG0341 DEAD-box protein abstr 44.4 10 0.00022 30.6 0.7 22 59-80 569-590 (610)
22 smart00384 AT_hook DNA binding 43.5 15 0.00033 18.1 1.1 10 36-45 2-11 (26)
23 PF12647 RNHCP: RNHCP domain; 41.4 18 0.00038 23.0 1.4 15 59-73 66-80 (92)
24 KOG4400 E3 ubiquitin ligase in 41.2 15 0.00033 26.4 1.2 19 61-79 144-162 (261)
25 KOG2044 5'-3' exonuclease HKE1 40.3 12 0.00026 32.1 0.7 20 60-79 260-279 (931)
26 KOG0119 Splicing factor 1/bran 38.6 18 0.00038 29.5 1.3 19 61-79 286-304 (554)
27 KOG3794 CBF1-interacting corep 38.0 16 0.00034 29.0 0.9 21 60-80 124-146 (453)
28 TIGR02098 MJ0042_CXXC MJ0042 f 36.6 25 0.00055 17.7 1.3 9 60-68 25-33 (38)
29 PLN00111 accumulation of photo 34.2 34 0.00073 27.0 2.2 22 59-80 119-145 (399)
30 PF08086 Toxin_17: Ergtoxin fa 33.7 5.1 0.00011 21.5 -1.7 12 66-77 24-35 (41)
31 PF12353 eIF3g: Eukaryotic tra 33.7 34 0.00073 22.5 1.9 21 58-79 104-124 (128)
32 PRK09335 30S ribosomal protein 29.9 54 0.0012 20.9 2.2 9 60-68 20-28 (95)
33 PF14787 zf-CCHC_5: GAG-polypr 29.3 38 0.00083 17.9 1.2 20 61-80 3-22 (36)
34 KOG2560 RNA splicing factor - 27.0 16 0.00034 29.6 -0.7 20 60-79 112-131 (529)
35 PF10122 Mu-like_Com: Mu-like 25.3 43 0.00094 19.0 1.1 16 60-75 24-39 (51)
36 PLN00186 ribosomal protein S26 25.2 71 0.0015 20.8 2.2 10 60-69 20-29 (109)
37 PRK12286 rpmF 50S ribosomal pr 24.8 74 0.0016 18.1 2.0 19 59-77 26-44 (57)
38 PF05129 Elf1: Transcription e 24.8 33 0.00071 20.9 0.6 10 59-68 45-54 (81)
39 PF05741 zf-nanos: Nanos RNA b 24.3 34 0.00074 19.6 0.5 19 60-78 33-54 (55)
40 PTZ00172 40S ribosomal protein 23.5 80 0.0017 20.6 2.2 10 60-69 20-29 (108)
41 COG5222 Uncharacterized conser 23.3 37 0.00081 26.3 0.8 21 60-80 176-196 (427)
42 COG4888 Uncharacterized Zn rib 21.6 75 0.0016 20.6 1.8 8 60-67 22-29 (104)
43 KOG3214 Uncharacterized Zn rib 21.1 63 0.0014 21.0 1.4 29 39-67 2-30 (109)
44 PRK11675 LexA regulated protei 20.3 56 0.0012 20.6 1.0 10 35-44 17-26 (90)
No 1
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=96.92 E-value=0.00051 Score=37.44 Aligned_cols=20 Identities=30% Similarity=0.689 Sum_probs=17.8
Q ss_pred eeCCccCcCCCCc--CCCCCCC
Q 043522 61 VRCSNFEEWGHNV--RTCKVDK 80 (84)
Q Consensus 61 ~~Cs~C~~~GHn~--~tC~~~~ 80 (84)
++|..|+++||.+ ++||+..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 6999999999997 7999865
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=96.66 E-value=0.0013 Score=29.96 Aligned_cols=17 Identities=41% Similarity=0.706 Sum_probs=15.7
Q ss_pred eCCccCcCCCCcCCCCC
Q 043522 62 RCSNFEEWGHNVRTCKV 78 (84)
Q Consensus 62 ~Cs~C~~~GHn~~tC~~ 78 (84)
+|-+|++.||..+.|++
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 69999999999999984
No 3
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.87 E-value=0.013 Score=30.49 Aligned_cols=21 Identities=24% Similarity=0.563 Sum_probs=18.9
Q ss_pred eeeCCccCcCCCCcCCCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKVDK 80 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~~~ 80 (84)
...|-+|++.||....|+.+.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCEeecCCCCCccHhHCCCCC
Confidence 479999999999999999853
No 4
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=92.66 E-value=0.047 Score=30.28 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=17.2
Q ss_pred eeeCCccCcCCCCcCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKV 78 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~ 78 (84)
...|..|+..||....|+.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 5689999999999999974
No 5
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=90.93 E-value=0.16 Score=42.28 Aligned_cols=26 Identities=19% Similarity=0.410 Sum_probs=20.7
Q ss_pred cccCCeeeCCccCcCCCCc--CCCCCCC
Q 043522 55 FKRSSSVRCSNFEEWGHNV--RTCKVDK 80 (84)
Q Consensus 55 sk~~~~~~Cs~C~~~GHn~--~tC~~~~ 80 (84)
.|+-++.+|+.|+|.||-+ +.||+-.
T Consensus 932 GRK~Ttr~C~nCGQvGHmkTNK~CP~f~ 959 (968)
T COG5179 932 GRKNTTRTCGNCGQVGHMKTNKACPKFS 959 (968)
T ss_pred CCCCcceecccccccccccccccCcccc
Confidence 4455689999999999987 5888753
No 6
>smart00343 ZnF_C2HC zinc finger.
Probab=90.28 E-value=0.15 Score=24.51 Aligned_cols=18 Identities=33% Similarity=0.661 Sum_probs=15.5
Q ss_pred eCCccCcCCCCcCCCCCC
Q 043522 62 RCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 62 ~Cs~C~~~GHn~~tC~~~ 79 (84)
.|.+|++.||..+.|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 488999999999999843
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=86.23 E-value=0.41 Score=26.17 Aligned_cols=19 Identities=32% Similarity=0.576 Sum_probs=17.4
Q ss_pred eeeCCccCcCCCCcCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKV 78 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~ 78 (84)
...|-+|.+.||-..-|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 5799999999999999994
No 8
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=79.60 E-value=1.2 Score=31.68 Aligned_cols=16 Identities=44% Similarity=0.785 Sum_probs=9.5
Q ss_pred eeCCccCcCCCCcCCC
Q 043522 61 VRCSNFEEWGHNVRTC 76 (84)
Q Consensus 61 ~~Cs~C~~~GHn~~tC 76 (84)
..|.+|++.||-.+-|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 4555666666666666
No 9
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=62.64 E-value=5.3 Score=26.30 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=15.2
Q ss_pred eeeCCccCcCCCCcCCCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKVDK 80 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~~~ 80 (84)
...|.+|++.||..+.|+...
T Consensus 77 ~~~C~~Cg~~GH~~~~C~~~~ 97 (148)
T PTZ00368 77 PRSCYNCGQTGHISRECPNRA 97 (148)
T ss_pred CcccCcCCCCCcccccCCCcc
Confidence 356888888888888887643
No 10
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.86 E-value=5.8 Score=20.56 Aligned_cols=13 Identities=31% Similarity=0.560 Sum_probs=9.9
Q ss_pred cCCeeeCCccCcC
Q 043522 57 RSSSVRCSNFEEW 69 (84)
Q Consensus 57 ~~~~~~Cs~C~~~ 69 (84)
.|..++|++|+..
T Consensus 22 ~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 22 KGRKVRCSKCGHV 34 (36)
T ss_pred CCcEEECCCCCCE
Confidence 4458999999863
No 11
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=59.06 E-value=4.2 Score=16.90 Aligned_cols=9 Identities=44% Similarity=0.959 Sum_probs=3.1
Q ss_pred CCCCCCCcc
Q 043522 36 RTTGRPQTK 44 (84)
Q Consensus 36 r~~GRPkk~ 44 (84)
+..|||+|.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 457999865
No 12
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=58.33 E-value=6.6 Score=20.35 Aligned_cols=12 Identities=25% Similarity=0.526 Sum_probs=9.4
Q ss_pred cCCeeeCCccCc
Q 043522 57 RSSSVRCSNFEE 68 (84)
Q Consensus 57 ~~~~~~Cs~C~~ 68 (84)
.+..++|++|+.
T Consensus 22 ~~~~vrC~~C~~ 33 (37)
T PF13719_consen 22 GGRKVRCPKCGH 33 (37)
T ss_pred CCcEEECCCCCc
Confidence 345899999985
No 13
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=56.00 E-value=5.9 Score=28.17 Aligned_cols=18 Identities=33% Similarity=0.543 Sum_probs=16.7
Q ss_pred eeeCCccCcCCCCcCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCK 77 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~ 77 (84)
...|-+|+|.||-++-||
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 468999999999999999
No 14
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.77 E-value=5.2 Score=23.42 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=12.5
Q ss_pred eeeCCccCcCCCCcCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKV 78 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~ 78 (84)
..||.+|.++| |..+||+
T Consensus 36 I~RC~~CRk~~-~~Y~CP~ 53 (59)
T PRK14890 36 IYRCEKCRKQS-NPYTCPK 53 (59)
T ss_pred EeechhHHhcC-CceECCC
Confidence 57788888887 4556654
No 15
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=52.32 E-value=9.2 Score=25.13 Aligned_cols=18 Identities=33% Similarity=0.488 Sum_probs=10.9
Q ss_pred eeCCccCcCCCCcCCCCC
Q 043522 61 VRCSNFEEWGHNVRTCKV 78 (84)
Q Consensus 61 ~~Cs~C~~~GHn~~tC~~ 78 (84)
..|-+|++.||..+.|+.
T Consensus 104 ~~C~~Cg~~gH~~~~C~~ 121 (148)
T PTZ00368 104 RACYNCGGEGHISRDCPN 121 (148)
T ss_pred hhhcccCcCCcchhcCCC
Confidence 356666666666666654
No 16
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=48.18 E-value=20 Score=22.86 Aligned_cols=10 Identities=10% Similarity=0.355 Sum_probs=7.5
Q ss_pred CeeeCCccCc
Q 043522 59 SSVRCSNFEE 68 (84)
Q Consensus 59 ~~~~Cs~C~~ 68 (84)
+...|..|+.
T Consensus 20 t~f~CP~Cge 29 (99)
T PRK14892 20 KIFECPRCGK 29 (99)
T ss_pred cEeECCCCCC
Confidence 4788888883
No 17
>PHA00689 hypothetical protein
Probab=47.00 E-value=9.6 Score=21.89 Aligned_cols=13 Identities=23% Similarity=0.445 Sum_probs=10.8
Q ss_pred eeeCCccCcCCCC
Q 043522 60 SVRCSNFEEWGHN 72 (84)
Q Consensus 60 ~~~Cs~C~~~GHn 72 (84)
.++|.+|+..|-.
T Consensus 17 avtckrcgktglr 29 (62)
T PHA00689 17 AVTCKRCGKTGLR 29 (62)
T ss_pred eeehhhccccCce
Confidence 6899999988754
No 18
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=46.85 E-value=3.9 Score=28.41 Aligned_cols=22 Identities=36% Similarity=0.557 Sum_probs=19.0
Q ss_pred CCeeeCCccCcCCCCcCCCCCC
Q 043522 58 SSSVRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 58 ~~~~~Cs~C~~~GHn~~tC~~~ 79 (84)
+.-++|-.|.|+||=-+-|++.
T Consensus 25 ~~~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 25 GSSARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred ccchhHHHHHhhccceeeecCc
Confidence 3468999999999999999875
No 19
>PF05634 APO_RNA-bind: APO RNA-binding; InterPro: IPR008512 This family consists of plant APO (accumulation of photosystem 1) proteins.
Probab=46.68 E-value=18 Score=26.00 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=18.8
Q ss_pred CeeeCCcc-----CcCCCCcCCCCCCC
Q 043522 59 SSVRCSNF-----EEWGHNVRTCKVDK 80 (84)
Q Consensus 59 ~~~~Cs~C-----~~~GHn~~tC~~~~ 80 (84)
....|+.| +..||..+||....
T Consensus 97 pV~~C~~C~EVHVG~~GH~irtC~g~k 123 (204)
T PF05634_consen 97 PVKACGYCPEVHVGPVGHKIRTCGGFK 123 (204)
T ss_pred eeeecCCCCCeEECCCcccccccCCCC
Confidence 47899999 45899999999876
No 20
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=44.83 E-value=5.5 Score=33.36 Aligned_cols=25 Identities=24% Similarity=0.191 Sum_probs=20.0
Q ss_pred cccCCeeeCCccCcCCCCcCCCCCC
Q 043522 55 FKRSSSVRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 55 sk~~~~~~Cs~C~~~GHn~~tC~~~ 79 (84)
+|.-..+.||.|+|.-|++-||=+.
T Consensus 271 sKEivAisCSWCKqayH~KvtCFml 295 (1004)
T KOG0782|consen 271 SKEIVAISCSWCKQAYHLKVTCFML 295 (1004)
T ss_pred cccEEEEEehHHHHHhhcchhhhhh
Confidence 3333578999999999999999654
No 21
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=44.36 E-value=10 Score=30.61 Aligned_cols=22 Identities=18% Similarity=0.428 Sum_probs=19.6
Q ss_pred CeeeCCccCcCCCCcCCCCCCC
Q 043522 59 SSVRCSNFEEWGHNVRTCKVDK 80 (84)
Q Consensus 59 ~~~~Cs~C~~~GHn~~tC~~~~ 80 (84)
...-|.-|++.||.-.-||+..
T Consensus 569 ~~kGCayCgGLGHRItdCPKle 590 (610)
T KOG0341|consen 569 GEKGCAYCGGLGHRITDCPKLE 590 (610)
T ss_pred CccccccccCCCcccccCchhh
Confidence 4678999999999999999875
No 22
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=43.50 E-value=15 Score=18.08 Aligned_cols=10 Identities=40% Similarity=0.803 Sum_probs=7.8
Q ss_pred CCCCCCCccc
Q 043522 36 RTTGRPQTKK 45 (84)
Q Consensus 36 r~~GRPkk~R 45 (84)
|..|||+|..
T Consensus 2 RkRGRPrK~~ 11 (26)
T smart00384 2 RKRGRPRKAP 11 (26)
T ss_pred CCCCCCCCCC
Confidence 5679998774
No 23
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=41.38 E-value=18 Score=22.96 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=13.4
Q ss_pred CeeeCCccCcCCCCc
Q 043522 59 SSVRCSNFEEWGHNV 73 (84)
Q Consensus 59 ~~~~Cs~C~~~GHn~ 73 (84)
..++|.+|+....|+
T Consensus 66 iiHrC~~Cg~l~~Nr 80 (92)
T PF12647_consen 66 IIHRCTRCGELRSNR 80 (92)
T ss_pred EEEecCCCCCcccCC
Confidence 489999999999995
No 24
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=41.21 E-value=15 Score=26.38 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=17.1
Q ss_pred eeCCccCcCCCCcCCCCCC
Q 043522 61 VRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 61 ~~Cs~C~~~GHn~~tC~~~ 79 (84)
+.|-.|++.||...-|+.+
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 6899999999999999954
No 25
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=40.32 E-value=12 Score=32.11 Aligned_cols=20 Identities=25% Similarity=0.528 Sum_probs=18.0
Q ss_pred eeeCCccCcCCCCcCCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~~ 79 (84)
..+|-.|+|+||+..-|...
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred cccchhhcccCCcHhhcCCc
Confidence 46799999999999999876
No 26
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=38.64 E-value=18 Score=29.52 Aligned_cols=19 Identities=32% Similarity=0.501 Sum_probs=17.0
Q ss_pred eeCCccCcCCCCcCCCCCC
Q 043522 61 VRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 61 ~~Cs~C~~~GHn~~tC~~~ 79 (84)
..|..|+.+||+..-|+..
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 3899999999999999877
No 27
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=37.97 E-value=16 Score=29.01 Aligned_cols=21 Identities=38% Similarity=0.849 Sum_probs=17.8
Q ss_pred eeeCCccCcCCCCc--CCCCCCC
Q 043522 60 SVRCSNFEEWGHNV--RTCKVDK 80 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~--~tC~~~~ 80 (84)
.|+|=+|+.+||-. +-||.-.
T Consensus 124 NVrC~kChkwGH~n~DreCplf~ 146 (453)
T KOG3794|consen 124 NVRCLKCHKWGHINTDRECPLFG 146 (453)
T ss_pred eeeEEeecccccccCCccCcchh
Confidence 79999999999985 6888754
No 28
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=36.63 E-value=25 Score=17.71 Aligned_cols=9 Identities=33% Similarity=0.730 Sum_probs=7.9
Q ss_pred eeeCCccCc
Q 043522 60 SVRCSNFEE 68 (84)
Q Consensus 60 ~~~Cs~C~~ 68 (84)
.++|++|+.
T Consensus 25 ~v~C~~C~~ 33 (38)
T TIGR02098 25 KVRCGKCGH 33 (38)
T ss_pred EEECCCCCC
Confidence 689999986
No 29
>PLN00111 accumulation of photosystem one; Provisional
Probab=34.19 E-value=34 Score=26.99 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=19.1
Q ss_pred CeeeCCccCc-----CCCCcCCCCCCC
Q 043522 59 SSVRCSNFEE-----WGHNVRTCKVDK 80 (84)
Q Consensus 59 ~~~~Cs~C~~-----~GHn~~tC~~~~ 80 (84)
....|+-|.+ .||..+||....
T Consensus 119 pV~~C~~C~EVHVG~~GH~irtC~g~k 145 (399)
T PLN00111 119 PVHACKFCSEVHVGKVGHLIRTCRGPG 145 (399)
T ss_pred eeeecCcCCceeECCCCccccccCCcc
Confidence 4789999966 899999999876
No 30
>PF08086 Toxin_17: Ergtoxin family; InterPro: IPR012622 The Ergtoxin (ErgTx) family is a class of peptides from scorpion venom that specifically block ERG (ether-a-go-go-related gene) K+ channels of the nerve, heart and endocrine cells [, , ]. Peptides of the ErgTx family have from 42 to 47 amino acid residues cross-linked by four disulphide bridges. The four disulphide bridges have been assigned as C1-C4, C2-C6, C3-C7 and C5-C8 (see the schematic representation below) []. ErgTxs consist of a triple-stranded beta-sheet and an alpha-helix, as is typical of K+ channel scorpion toxins. There is a large hydrophobic patch on the surface of the toxin, surrounding a central lysine residue located near the beta-hairpin loop between the second and third strands of the beta-sheet. It has been postulated that this hydrophobic patch is likely to form part of the binding surface of the toxin []. Peptides of the ErgTx family possess a Knottin scaffold (see http://knottin.cbs.cnrs.fr). Some proteins known to belong to the ErgTx family are listed below: ErgTx1, ErgTx2 and ErgTx3 from Centruroides elegans (Bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides exilicauda (Bark scorpion). ErgTx1, ErgTx2 and ErgTx3 from Centruroides gracilis (Slenderbrown scorpion) (Florida bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides limpidus limpidus (Mexican scorpion). ErgTx1, ErgTx2, ErgTx3, ErgTx4, ErgTx5 and gamma-KTx 4.12 from Centruroides sculpturatus (Bark scorpion). ErgTx, ErgTx2, ErgTx3, ErgTx4 and ErgTx5 from Centruroides noxius (Mexican scorpion). ; GO: 0019870 potassium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1NE5_A 1PX9_A.
Probab=33.67 E-value=5.1 Score=21.52 Aligned_cols=12 Identities=33% Similarity=0.526 Sum_probs=9.2
Q ss_pred cCcCCCCcCCCC
Q 043522 66 FEEWGHNVRTCK 77 (84)
Q Consensus 66 C~~~GHn~~tC~ 77 (84)
|+..|||.-||-
T Consensus 24 ckkag~~~gtc~ 35 (41)
T PF08086_consen 24 CKKAGHRGGTCV 35 (41)
T ss_dssp HHHHTSS-EEEE
T ss_pred HHHhCCCCceeE
Confidence 688999998884
No 31
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=33.66 E-value=34 Score=22.52 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=18.1
Q ss_pred CCeeeCCccCcCCCCcCCCCCC
Q 043522 58 SSSVRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 58 ~~~~~Cs~C~~~GHn~~tC~~~ 79 (84)
...+.|..|+ -.|.-..||..
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyK 124 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYK 124 (128)
T ss_pred CceEEeCCCC-CCcccccCCcc
Confidence 3589999996 89999999965
No 32
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=29.86 E-value=54 Score=20.90 Aligned_cols=9 Identities=33% Similarity=0.652 Sum_probs=7.9
Q ss_pred eeeCCccCc
Q 043522 60 SVRCSNFEE 68 (84)
Q Consensus 60 ~~~Cs~C~~ 68 (84)
.++|+.|+.
T Consensus 20 ~V~C~nCgr 28 (95)
T PRK09335 20 YVQCDNCGR 28 (95)
T ss_pred cEEeCCCCC
Confidence 799999985
No 33
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.28 E-value=38 Score=17.89 Aligned_cols=20 Identities=15% Similarity=0.220 Sum_probs=12.5
Q ss_pred eeCCccCcCCCCcCCCCCCC
Q 043522 61 VRCSNFEEWGHNVRTCKVDK 80 (84)
Q Consensus 61 ~~Cs~C~~~GHn~~tC~~~~ 80 (84)
--|.+|+.-.|=...|....
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 46999999999999998654
No 34
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=26.97 E-value=16 Score=29.57 Aligned_cols=20 Identities=25% Similarity=0.481 Sum_probs=17.1
Q ss_pred eeeCCccCcCCCCcCCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKVD 79 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~~ 79 (84)
+--|-+|+..||..+.|=..
T Consensus 112 KGACeNCGAmtHk~KDCmER 131 (529)
T KOG2560|consen 112 KGACENCGAMTHKVKDCMER 131 (529)
T ss_pred hhhhhhhhhhhcchHHHhhc
Confidence 56899999999999999543
No 35
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=25.28 E-value=43 Score=18.99 Aligned_cols=16 Identities=19% Similarity=0.434 Sum_probs=13.3
Q ss_pred eeeCCccCcCCCCcCC
Q 043522 60 SVRCSNFEEWGHNVRT 75 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~t 75 (84)
.++|.+|+..-|-+..
T Consensus 24 eIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 24 EIKCPRCKTINHVRAT 39 (51)
T ss_pred EEECCCCCccceEecc
Confidence 7999999998887654
No 36
>PLN00186 ribosomal protein S26; Provisional
Probab=25.24 E-value=71 Score=20.84 Aligned_cols=10 Identities=40% Similarity=0.790 Sum_probs=8.2
Q ss_pred eeeCCccCcC
Q 043522 60 SVRCSNFEEW 69 (84)
Q Consensus 60 ~~~Cs~C~~~ 69 (84)
.++|+.|+..
T Consensus 20 ~V~C~nCgr~ 29 (109)
T PLN00186 20 RIRCSNCGKC 29 (109)
T ss_pred ceeeCCCccc
Confidence 7999999853
No 37
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=24.84 E-value=74 Score=18.12 Aligned_cols=19 Identities=32% Similarity=0.431 Sum_probs=11.8
Q ss_pred CeeeCCccCcCCCCcCCCC
Q 043522 59 SSVRCSNFEEWGHNVRTCK 77 (84)
Q Consensus 59 ~~~~Cs~C~~~GHn~~tC~ 77 (84)
..+.|+.|+++-=.-.-|+
T Consensus 26 ~l~~C~~CG~~~~~H~vC~ 44 (57)
T PRK12286 26 GLVECPNCGEPKLPHRVCP 44 (57)
T ss_pred cceECCCCCCccCCeEECC
Confidence 3688999988543333343
No 38
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.82 E-value=33 Score=20.88 Aligned_cols=10 Identities=20% Similarity=0.378 Sum_probs=5.0
Q ss_pred CeeeCCccCc
Q 043522 59 SSVRCSNFEE 68 (84)
Q Consensus 59 ~~~~Cs~C~~ 68 (84)
..+.|+.|++
T Consensus 45 ~~~~C~~Cg~ 54 (81)
T PF05129_consen 45 GILSCRVCGE 54 (81)
T ss_dssp EEEEESSS--
T ss_pred EEEEecCCCC
Confidence 3566666654
No 39
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=24.33 E-value=34 Score=19.61 Aligned_cols=19 Identities=21% Similarity=0.478 Sum_probs=7.6
Q ss_pred eeeCCccCcCC---CCcCCCCC
Q 043522 60 SVRCSNFEEWG---HNVRTCKV 78 (84)
Q Consensus 60 ~~~Cs~C~~~G---Hn~~tC~~ 78 (84)
.+.|..|+..| |..+-||+
T Consensus 33 ~y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 33 KYVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp G---TTT---GGG---GGG-TT
T ss_pred cCcCCCCcCcCccccccccCcC
Confidence 58999998754 66777876
No 40
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=23.54 E-value=80 Score=20.58 Aligned_cols=10 Identities=50% Similarity=0.793 Sum_probs=8.2
Q ss_pred eeeCCccCcC
Q 043522 60 SVRCSNFEEW 69 (84)
Q Consensus 60 ~~~Cs~C~~~ 69 (84)
.++|+.|+..
T Consensus 20 ~V~C~nCgr~ 29 (108)
T PTZ00172 20 PVRCSNCGRC 29 (108)
T ss_pred cEEeCCcccc
Confidence 7999999853
No 41
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.34 E-value=37 Score=26.31 Aligned_cols=21 Identities=19% Similarity=0.517 Sum_probs=18.8
Q ss_pred eeeCCccCcCCCCcCCCCCCC
Q 043522 60 SVRCSNFEEWGHNVRTCKVDK 80 (84)
Q Consensus 60 ~~~Cs~C~~~GHn~~tC~~~~ 80 (84)
-+-|=||+|-||-...|+.+.
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~ 196 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQ 196 (427)
T ss_pred ceeEEecCCCCchhhcCCCCC
Confidence 478999999999999999775
No 42
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=21.58 E-value=75 Score=20.57 Aligned_cols=8 Identities=13% Similarity=0.501 Sum_probs=4.2
Q ss_pred eeeCCccC
Q 043522 60 SVRCSNFE 67 (84)
Q Consensus 60 ~~~Cs~C~ 67 (84)
...|.+|+
T Consensus 22 ~FtCp~Cg 29 (104)
T COG4888 22 TFTCPRCG 29 (104)
T ss_pred eEecCccC
Confidence 45555553
No 43
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=21.09 E-value=63 Score=20.99 Aligned_cols=29 Identities=17% Similarity=0.366 Sum_probs=11.7
Q ss_pred CCCCcccccccccccccccCCeeeCCccC
Q 043522 39 GRPQTKKRREADENRAFKRSSSVRCSNFE 67 (84)
Q Consensus 39 GRPkk~R~~~~~E~~~sk~~~~~~Cs~C~ 67 (84)
|+.|.+|+...-+......-+...|-.|.
T Consensus 2 gkRk~K~k~~~k~r~~~~ldt~FnClfcn 30 (109)
T KOG3214|consen 2 GKRKSKRKEPPKERRVEPLDTQFNCLFCN 30 (109)
T ss_pred CcccccccCCchhhhccchheeeccCccc
Confidence 45554444333222222222345555553
No 44
>PRK11675 LexA regulated protein; Provisional
Probab=20.32 E-value=56 Score=20.56 Aligned_cols=10 Identities=50% Similarity=0.853 Sum_probs=8.3
Q ss_pred CCCCCCCCcc
Q 043522 35 IRTTGRPQTK 44 (84)
Q Consensus 35 ~r~~GRPkk~ 44 (84)
.+.+||||.+
T Consensus 17 ~~~~grp~tn 26 (90)
T PRK11675 17 ERRPGRPKTN 26 (90)
T ss_pred CCCCCCCCCC
Confidence 4689999987
Done!