Query 020450
Match_columns 326
No_of_seqs 174 out of 368
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:28:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02642 R3H_encore_like R3H do 99.9 4.3E-22 9.3E-27 150.8 8.0 63 22-87 1-63 (63)
2 cd06006 R3H_unknown_2 R3H doma 99.6 2.9E-15 6.2E-20 113.3 6.8 58 27-86 2-59 (59)
3 PF01424 R3H: R3H domain; Int 99.6 2.6E-15 5.6E-20 112.1 6.5 62 23-87 2-63 (63)
4 smart00393 R3H Putative single 99.5 7.3E-15 1.6E-19 115.0 4.4 72 13-87 8-79 (79)
5 cd02646 R3H_G-patch R3H domain 99.5 4.8E-14 1E-18 105.3 6.3 57 27-86 2-58 (58)
6 cd02641 R3H_Smubp-2_like R3H d 99.5 6.4E-14 1.4E-18 105.8 7.0 58 27-86 2-60 (60)
7 cd02636 R3H_sperm-antigen R3H 99.5 6.1E-14 1.3E-18 106.7 6.7 58 28-87 3-61 (61)
8 cd02325 R3H R3H domain. The na 99.5 8.3E-14 1.8E-18 99.5 6.6 59 26-86 1-59 (59)
9 cd02643 R3H_NF-X1 R3H domain o 99.4 2.1E-13 4.6E-18 106.7 6.4 67 16-85 4-73 (74)
10 PF12752 SUZ: SUZ domain; Int 99.3 1.4E-12 3.1E-17 98.0 4.8 46 111-156 2-59 (59)
11 KOG2953 mRNA-binding protein E 99.3 2.6E-12 5.7E-17 128.1 6.6 162 6-170 94-270 (432)
12 cd02640 R3H_NRF R3H domain of 99.3 7.1E-12 1.5E-16 95.0 6.7 57 28-86 3-60 (60)
13 cd06007 R3H_DEXH_helicase R3H 99.3 7.1E-12 1.5E-16 94.7 6.4 56 28-86 3-59 (59)
14 cd02644 R3H_jag R3H domain fou 99.0 1.9E-09 4.2E-14 83.1 6.8 60 24-86 6-66 (67)
15 cd02645 R3H_AAA R3H domain of 98.6 1E-07 2.3E-12 72.4 7.3 40 46-85 20-59 (60)
16 cd02638 R3H_unknown_1 R3H doma 98.4 7E-07 1.5E-11 68.5 5.9 56 29-85 4-60 (62)
17 cd02639 R3H_RRM R3H domain of 98.3 3.5E-07 7.5E-12 69.6 2.1 54 31-86 6-60 (60)
18 COG1847 Jag Predicted RNA-bind 97.4 0.00037 8E-09 64.8 6.8 59 25-86 148-207 (208)
19 KOG1952 Transcription factor N 97.1 0.00075 1.6E-08 73.1 5.4 95 5-102 804-903 (950)
20 cd02637 R3H_PARN R3H domain of 94.4 0.15 3.3E-06 39.4 6.3 56 29-87 4-63 (65)
21 PF08110 Antimicrobial15: Ocel 56.2 8.3 0.00018 23.4 1.5 12 294-305 7-18 (19)
22 KOG4060 Uncharacterized conser 40.2 15 0.00032 33.5 1.2 25 47-72 62-86 (176)
23 PF06262 DUF1025: Possibl zinc 26.4 39 0.00085 28.0 1.5 16 57-72 75-90 (97)
24 PF05572 Peptidase_M43: Pregna 26.2 44 0.00095 29.5 1.9 23 52-75 66-88 (154)
No 1
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.87 E-value=4.3e-22 Score=150.85 Aligned_cols=63 Identities=37% Similarity=0.712 Sum_probs=59.0
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEec
Q 020450 22 SKHLVLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILERC 87 (326)
Q Consensus 22 DR~fLLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~KT 87 (326)
||+|||+||++|++||+++.. ..++|||||||+|+|||+||+||||.|+++|+| +|+|+|+||
T Consensus 1 dr~~~l~~E~~i~~Fi~~~~~--~~~~f~pm~sy~RllvH~la~~~gL~s~s~~~~-~r~vvv~kt 63 (63)
T cd02642 1 DRLFVLKLEKDLLAFIKDSTR--QSLELPPMNSYYRLLAHRVAQYYGLDHNVDNSG-GKCVIVNKT 63 (63)
T ss_pred CchHHHHHHHHHHHHHhCCCC--CeeEcCCCCcHHHHHHHHHHHHhCCeeEeecCC-ceEEEEEeC
Confidence 799999999999999999853 359999999999999999999999999999988 899999986
No 2
>cd06006 R3H_unknown_2 R3H domain of a group of fungal proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.59 E-value=2.9e-15 Score=113.26 Aligned_cols=58 Identities=28% Similarity=0.485 Sum_probs=53.6
Q ss_pred HHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 27 LSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 27 LkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
.++|+.|..||+|... ..+.|||||+++|.+||+||++|||.++|+|.+++|+|+|.|
T Consensus 2 ~~~E~~l~~fv~d~~~--~~~~f~pM~~~~R~~vHdla~~~gl~SeS~d~Ep~R~V~v~k 59 (59)
T cd06006 2 QQIESTLRKFINDKSK--RSLRFPPMRSPQRAFIHELAKDYGLYSESQDPEPKRSVFVKK 59 (59)
T ss_pred hhHHHHHHHHHhCCCC--CceeCCCCCHHHHHHHHHHHHHcCCeeEecCCCCCcEEEEeC
Confidence 5799999999999753 359999999999999999999999999999999999999975
No 3
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=99.59 E-value=2.6e-15 Score=112.15 Aligned_cols=62 Identities=32% Similarity=0.680 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEec
Q 020450 23 KHLVLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILERC 87 (326)
Q Consensus 23 R~fLLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~KT 87 (326)
|.+|+++++.+++|+.++.. .+.|||||+|+|++||++|++|||.|.|.|+|+.|+|+|+||
T Consensus 2 ~~~l~~~~~~~~~~~~~~~~---~~~f~pm~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~k~ 63 (63)
T PF01424_consen 2 REELEKIEEKLIEFFLSSGE---SLEFPPMNSFERKLIHELAEYYGLKSKSEGEGPNRRVVVSKT 63 (63)
T ss_dssp HHHHHHHHHHHHHHHHHCSS---EEEEEC--SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEEES
T ss_pred hHHHHHHHHHHHHHHHcCCC---EEEECCCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEEeC
Confidence 67889999999999976653 599999999999999999999999999999999999999986
No 4
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=99.52 E-value=7.3e-15 Score=115.01 Aligned_cols=72 Identities=26% Similarity=0.530 Sum_probs=64.3
Q ss_pred HHHHhcCCchhHHHHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEec
Q 020450 13 AFLVKDNLPSKHLVLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILERC 87 (326)
Q Consensus 13 ~~~lk~npkDR~fLLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~KT 87 (326)
++..+-.++.+.+|.+++.++.+|+..... .+.|||||+|+|.+||++|+.|||.|.|.|.|+.|+|+|+++
T Consensus 8 ~d~~~~~~~~~~~l~~~~~~~~~~v~~~~~---~~~~~pm~~~~R~~iH~~a~~~~l~s~S~g~g~~R~vvv~~~ 79 (79)
T smart00393 8 LDALSYRPRRREELIELELEIARFVKSTKE---SVELPPMNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79 (79)
T ss_pred EECCccCHHHHHHHHHHHHHHHHHHhccCC---eEEcCCCCHHHHHHHHHHHHHcCCEEEEEcCCCCcEEEEEeC
Confidence 334445788999999999999999987753 499999999999999999999999999999999999999874
No 5
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.49 E-value=4.8e-14 Score=105.29 Aligned_cols=57 Identities=26% Similarity=0.535 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 27 LSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 27 LkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
-.++++|..|+.++. ..+.||||++++|.+||+||+.|||.+.|.|.|++|+|+|+|
T Consensus 2 ~~i~~~i~~F~~~~~---~~~~fppm~~~~R~~vH~lA~~~~L~S~S~G~g~~R~v~v~k 58 (58)
T cd02646 2 EDIKDEIEAFLLDSR---DSLSFPPMDKHGRKTIHKLANCYNLKSKSRGKGKKRFVTVTK 58 (58)
T ss_pred hHHHHHHHHHHhCCC---ceEecCCCCHHHHHHHHHHHHHcCCcccccccCCceEEEEEC
Confidence 468999999999885 359999999999999999999999999999999999999986
No 6
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=99.49 E-value=6.4e-14 Score=105.80 Aligned_cols=58 Identities=36% Similarity=0.679 Sum_probs=53.3
Q ss_pred HHHHHHHHHHhcCCCCCCcceecCC-CChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 27 LSMEEALVNFLQDDNSADGVLELEP-MDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 27 LkLEe~I~~FIqd~~~~~~sleFPP-MNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
.++++.|.+||+++... .+.||| ||+++|++||+||+.|||.|+|.|.|++|+|+|.|
T Consensus 2 ~~~~~~i~~F~~~~~~~--~l~F~p~ls~~eR~~vH~lA~~~gL~s~S~G~g~~R~v~v~k 60 (60)
T cd02641 2 KHLKAMVKAFMKDPKAT--ELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60 (60)
T ss_pred hhHHHHHHHHHcCCCcC--cEECCCCCCHHHHHHHHHHHHHcCCceEeeCCCCceEEEeeC
Confidence 46899999999998743 499999 99999999999999999999999999999999975
No 7
>cd02636 R3H_sperm-antigen R3H domain of a group of metazoan proteins that is related to the sperm-associated antigen 7. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.49 E-value=6.1e-14 Score=106.70 Aligned_cols=58 Identities=31% Similarity=0.554 Sum_probs=52.9
Q ss_pred HHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCC-cceEEEEEec
Q 020450 28 SMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEG-VDRHLILERC 87 (326)
Q Consensus 28 kLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG-~~R~VVI~KT 87 (326)
++|+.+..||+|+..+ ..+|||||+|+|.+||++|+..||.++|.|+| ++|+|||++.
T Consensus 3 ~~e~~~~~f~~d~~~~--~~~l~pM~~~eRkivHDv~~~~Gl~S~S~Geee~~R~VVv~~k 61 (61)
T cd02636 3 SMEKEVSKFIKDSVRT--REKFQPMDKVERSIVHDVAEVAGLTSFSFGEDEVDRYVMIFKK 61 (61)
T ss_pred hHHHHHHHHhhccccc--ccccCCCCHHHHHHHHHHHHhcCceeEecCCCCCceEEEEecC
Confidence 6899999999998643 48999999999999999999999999999976 9999999863
No 8
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.48 E-value=8.3e-14 Score=99.45 Aligned_cols=59 Identities=41% Similarity=0.692 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 26 VLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 26 LLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
+.++|+.|..|+++.... .+.|||||+|+|++||++|++|||.+++.|.|..|+|+|.+
T Consensus 1 ~~~~~~~l~~f~~~~~~~--~~~~~p~~~~~R~~vH~la~~~~L~s~s~g~~~~r~v~i~~ 59 (59)
T cd02325 1 REEREEELEAFAKDAAGK--SLELPPMNSYERKLIHDLAEYYGLKSESEGEGPNRRVVITK 59 (59)
T ss_pred ChHHHHHHHHHHHhhcCC--eEEcCCCCHHHHHHHHHHHHHCCCEEEEecCCCCcEEEEeC
Confidence 367999999999998422 59999999999999999999999999999999999999974
No 9
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.43 E-value=2.1e-13 Score=106.72 Aligned_cols=67 Identities=22% Similarity=0.416 Sum_probs=58.5
Q ss_pred HhcCCchhHHHHHHHHHHHHHhcCCCC---CCcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEE
Q 020450 16 VKDNLPSKHLVLSMEEALVNFLQDDNS---ADGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILE 85 (326)
Q Consensus 16 lk~npkDR~fLLkLEe~I~~FIqd~~~---~~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~ 85 (326)
.++|+ .|+.++|+.|..|+.+... +...+.|||||+|+|.+||.||++|||.++|.|+|+.|+|||.
T Consensus 4 ~~~~~---~~~~~vE~~l~~la~~~~~~~~~~~~~~l~PM~~~eR~iIH~la~~~~l~S~S~G~ep~R~VvI~ 73 (74)
T cd02643 4 AKKDP---KFVKDVEKDLIELVESVNKGKQTSRSHSFPPMNREKRRIVHELAEHFGIESVSYDQEPKRNVVAT 73 (74)
T ss_pred HHHCH---HHHHHHHHHHHHHHHHHHhccccCCeeECCCCCHHHHHHHHHHHhhCCCEEEecCCCCCceEEEe
Confidence 44556 8999999999999997421 1236899999999999999999999999999999999999996
No 10
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=99.33 E-value=1.4e-12 Score=98.01 Aligned_cols=46 Identities=33% Similarity=0.439 Sum_probs=35.8
Q ss_pred CccccccccCCCCCc------------CCCCCCCCCCCHHHHHHHHHHHHHhhcCCCC
Q 020450 111 TTSHQILRRKEAPPV------------LKIQSPSGEHSLAEREAAYLAARERIFSMDA 156 (326)
Q Consensus 111 ~p~~~ImkR~~~s~~------------~ks~~~~~~kS~EEREeeY~rAReRIF~~~~ 156 (326)
.|+++||||+..... .........+|+||||++|++||+|||++++
T Consensus 2 ~p~~~IlkRp~~~~~~~~~~~~~~~~~~~~~~~~~~kSlEERE~eY~~AR~RIFg~~~ 59 (59)
T PF12752_consen 2 KPKRKILKRPSKGSSSSDSGSSGSSPNSSSRKKRPSKSLEEREAEYAEARARIFGSSE 59 (59)
T ss_pred CCCCeEecCCCCCCCcccccccccCCCcccccccccCCHHHHHHHHHHHHHHHhCCCC
Confidence 468999999743321 1223568999999999999999999999763
No 11
>KOG2953 consensus mRNA-binding protein Encore [RNA processing and modification]
Probab=99.30 E-value=2.6e-12 Score=128.11 Aligned_cols=162 Identities=20% Similarity=0.188 Sum_probs=126.0
Q ss_pred ccHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCCCcceecCCC-ChHHHHHHHHHHHHhCCeeeeec------CCc
Q 020450 6 FAMVEELAFLVKDNLPSKHLVLSMEEALVNFLQDDNSADGVLELEPM-DSYNRLLLHRLADIFGFAHESVG------EGV 78 (326)
Q Consensus 6 ~dl~efL~~~lk~npkDR~fLLkLEe~I~~FIqd~~~~~~sleFPPM-NSYqRlLVHrLAeyyGL~heS~g------eG~ 78 (326)
....-|+++.+ +||+.|..|+++|.+|..|+++...+ .++||++ .+|.|++.|++|+.|||...... .+.
T Consensus 94 ~~~dy~~ve~~-qnpR~~~~lsR~El~~~~~~Q~~~~q--qt~~q~~~ts~~~~~~~rvaq~y~l~T~~~p~~~~~~~p~ 170 (432)
T KOG2953|consen 94 QAVDYFLVEAL-QNPRHRLTLSRKELDIQCQFQGPVQQ--QTEFQNYPTSYLRLAAHRVAQHYGLATTGEPSYISGIDPY 170 (432)
T ss_pred hcccHHHHhhh-hcchhhhhhhcccchhhhhhcCcccc--cccCCCccccchhhhhcccccccccccccccccccccCch
Confidence 34567999999 58999999999999999999999865 4899997 89999999999999999886432 344
Q ss_pred ceEEEEEecCCCCCCchhhhhhhhccC--CCCCCCccccccccCCCCCcC--CCC---CCCCCCCHHHHHHHHHHHHHhh
Q 020450 79 DRHLILERCSETSIPSILVSDILWQYG--EPQSLTTSHQILRRKEAPPVL--KIQ---SPSGEHSLAEREAAYLAARERI 151 (326)
Q Consensus 79 ~R~VVI~KTp~TriP~~~LSElv~~~~--~~~~~~p~~~ImkR~~~s~~~--ks~---~~~~~kS~EEREeeY~rAReRI 151 (326)
..++++.|+.+.+.|...+.++..... +.-.+.-+..|--|+...... ++. ......|+|||+++|..||.||
T Consensus 171 eqR~l~~k~~~s~~P~~~~~~~P~ssp~~~~~~~~~~~~~sp~p~~g~G~~~~~p~~~~~~~~~S~~~~kq~yd~~r~r~ 250 (432)
T KOG2953|consen 171 EQRILVTKTGESRFPGVSLSEIPVSSPSSNGWSEQRKGDISPRPTSGGGVSLSSPSNPQVTLLRSVEERKQEYDKARGRI 250 (432)
T ss_pred hccccccccccccCCchhhccccccCccccccccccccccCCCCCCCCcccccCCcCCCccccccchhhhhhhhhhhccc
Confidence 467789999999999999998876421 222334455677777644322 221 2347789999999999999999
Q ss_pred cCCCCCC-CCCCCCCCCcch
Q 020450 152 FSMDART-VAEPVRQKPRSV 170 (326)
Q Consensus 152 F~~~~~~-~~dt~s~~~R~v 170 (326)
|+..... .+|+.++-+++.
T Consensus 251 g~~~~~~~s~Dss~q~~p~~ 270 (432)
T KOG2953|consen 251 GSKPVTNDSKDSSSQQPPQN 270 (432)
T ss_pred cCccccccCcccccccCCcc
Confidence 9987765 778887766664
No 12
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.29 E-value=7.1e-12 Score=94.99 Aligned_cols=57 Identities=25% Similarity=0.542 Sum_probs=51.8
Q ss_pred HHHHHHHHHhcCCCCCCcceecCC-CChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 28 SMEEALVNFLQDDNSADGVLELEP-MDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 28 kLEe~I~~FIqd~~~~~~sleFPP-MNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
.+++.|.+|+++.... .+.||| |++++|.+||++|..+||.|.|.|.|.+|+|+|+|
T Consensus 3 ~~~~~i~~F~~s~~~~--~l~f~p~lt~~eR~~vH~~a~~~gL~s~S~G~g~~R~v~v~k 60 (60)
T cd02640 3 DYRQIIQNYAHSDDIR--DMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60 (60)
T ss_pred hHHHHHHHHHcCCccc--eEEcCCCCCHHHHHHHHHHHHHcCCceeeEeCCCCeEEEEeC
Confidence 4789999999987543 499999 99999999999999999999999999999999975
No 13
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.28 E-value=7.1e-12 Score=94.74 Aligned_cols=56 Identities=27% Similarity=0.516 Sum_probs=51.5
Q ss_pred HHHHHHHHHhcCCCCCCcceecCC-CChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 28 SMEEALVNFLQDDNSADGVLELEP-MDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 28 kLEe~I~~FIqd~~~~~~sleFPP-MNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
.+++.|.+|+++. .. .+.||| |++++|.+||++|..+||.|.|.|.|..|+|+|+|
T Consensus 3 ~i~~~i~~F~~~~-~~--~l~Fpp~ls~~eR~~vH~~a~~~gL~s~S~G~g~~R~v~v~K 59 (59)
T cd06007 3 AINKALEDFRASD-NE--EYEFPSSLTNHERAVIHRLCRKLGLKSKSKGKGSNRRLSVYK 59 (59)
T ss_pred cHHHHHHHHHcCc-cc--EEEcCCCCCHHHHHHHHHHHHHcCCCceeecCCCCeEEEEeC
Confidence 4788999999988 33 499999 99999999999999999999999999999999986
No 14
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.95 E-value=1.9e-09 Score=83.11 Aligned_cols=60 Identities=23% Similarity=0.408 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHhC-CeeeeecCCcceEEEEEe
Q 020450 24 HLVLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIFG-FAHESVGEGVDRHLILER 86 (326)
Q Consensus 24 ~fLLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyyG-L~heS~geG~~R~VVI~K 86 (326)
.-|..|-+.+.+.+..... .+.|+|||+|+|.+||.+++.|+ |.++|.|+|++|+|||..
T Consensus 6 ~~L~~~A~~~a~~v~~tg~---~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G~~~~R~vvI~~ 66 (67)
T cd02644 6 ETLIRLAERAAEKVRRTGK---PVKLEPMNAYERRIIHDALANDEDVETESEGEGPYRRVVISP 66 (67)
T ss_pred HHHHHHHHHHHHHHHHHCC---eeEeCCCCHHHHHHHHHHHHhCCCceEEeecCCCCeEEEEEe
Confidence 3466677777777777653 49999999999999999999777 999999999999999975
No 15
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=98.65 E-value=1e-07 Score=72.35 Aligned_cols=40 Identities=33% Similarity=0.474 Sum_probs=38.4
Q ss_pred ceecCCCChHHHHHHHHHHHHhCCeeeeecCCcceEEEEE
Q 020450 46 VLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDRHLILE 85 (326)
Q Consensus 46 sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~ 85 (326)
..+|.|||+|.|.++|++.+.|||.++|.|+|+.|+|+|.
T Consensus 20 ~veL~Pm~~~eRri~H~~v~~~~l~s~S~G~ep~RrvvI~ 59 (60)
T cd02645 20 PVELLPRSAYIRRLQHDLVERYQLRSESFGSEPNRRLRIL 59 (60)
T ss_pred eEEcCCCCHHHHHHHHHHHHHCCCeEEEecCCCCcEEEEe
Confidence 3899999999999999999999999999999999999996
No 16
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.39 E-value=7e-07 Score=68.47 Aligned_cols=56 Identities=32% Similarity=0.425 Sum_probs=47.3
Q ss_pred HHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHH-HHhCCeeeeecCCcceEEEEE
Q 020450 29 MEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLA-DIFGFAHESVGEGVDRHLILE 85 (326)
Q Consensus 29 LEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLA-eyyGL~heS~geG~~R~VVI~ 85 (326)
+.+++.-|++..... ..+.|+|||+|.|.+||... ++-++.++|.|+|+.|+|||.
T Consensus 4 ~~~~~~~f~~~~~~~-r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G~ep~RrVVI~ 60 (62)
T cd02638 4 VSEELEIFLLSFQRY-RVLLFPPLNSRRRYLIHQTVENRFLLSTFSVGEGWARRTVVC 60 (62)
T ss_pred hHHHHHHHHHhcccC-CeEecCCCChHHHHHHHHHHhcCCCceEEEccCCCCcEEEEe
Confidence 567777898876543 36999999999999999865 567899999999999999986
No 17
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.29 E-value=3.5e-07 Score=69.60 Aligned_cols=54 Identities=26% Similarity=0.420 Sum_probs=45.8
Q ss_pred HHHHHHhcCCCCCCcceecCC-CChHHHHHHHHHHHHhCCeeeeecCCcceEEEEEe
Q 020450 31 EALVNFLQDDNSADGVLELEP-MDSYNRLLLHRLADIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 31 e~I~~FIqd~~~~~~sleFPP-MNSYqRlLVHrLAeyyGL~heS~geG~~R~VVI~K 86 (326)
.+|.-|..+.... .+.||| +++.+|.+||.||..+||.|.+.|.|..|.|+|+|
T Consensus 6 sqlllFkdd~~~~--eL~Fp~~ls~~eRriih~la~~lGL~~~s~G~g~~R~v~v~k 60 (60)
T cd02639 6 SQLLLFKDDRMRD--ELAFPSSLSPAERRIVHLLASRLGLNHVSDGTGERRQVQITK 60 (60)
T ss_pred eeEEEEecCCCce--EEEcCCCCCHHHHHHHHHHHHHcCCceEEeCCCceEEEeecC
Confidence 3445577776643 499999 79999999999999999999999999999999875
No 18
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=97.41 E-value=0.00037 Score=64.84 Aligned_cols=59 Identities=22% Similarity=0.378 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHH-HHhCCeeeeecCCcceEEEEEe
Q 020450 25 LVLSMEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLA-DIFGFAHESVGEGVDRHLILER 86 (326)
Q Consensus 25 fLLkLEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLA-eyyGL~heS~geG~~R~VVI~K 86 (326)
.|.+|-+.+-.=+.... ..+.++||++|.|.+||..- ++-|+.++|.|+|+.|+|||..
T Consensus 148 ~L~~LA~~~A~rV~~tg---~~v~L~pM~~~ERkIVH~~l~~~~~V~T~SeG~ep~R~vVV~~ 207 (208)
T COG1847 148 TLIKLAERAAERVLETG---RSVELEPMPPFERKIVHTALSANPGVETYSEGEEPNRRVVVRP 207 (208)
T ss_pred HHHHHHHHHHHHHHhhC---CeeecCCCCHHHHHHHHHHHHhcCCcceeecCCCCceEEEEec
Confidence 44444444444443333 35999999999999999965 6678999999999999999974
No 19
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=97.05 E-value=0.00075 Score=73.09 Aligned_cols=95 Identities=21% Similarity=0.318 Sum_probs=77.8
Q ss_pred cccHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCC----CcceecCCCChHHHHHHHHHHHHhCCeeeeecCCcce
Q 020450 5 QFAMVEELAFLVKDNLPSKHLVLSMEEALVNFLQDDNSA----DGVLELEPMDSYNRLLLHRLADIFGFAHESVGEGVDR 80 (326)
Q Consensus 5 g~dl~efL~~~lk~npkDR~fLLkLEe~I~~FIqd~~~~----~~sleFPPMNSYqRlLVHrLAeyyGL~heS~geG~~R 80 (326)
.+-+-++|.+..+.++ +|+..+|++++.|+...... ..+..||+|+-..|.+||.+|+.|+|...+.+..+.|
T Consensus 804 ~~~~~e~~~e~~r~~~---~f~~sv~~e~~~lv~~~~~~~~~~~k~~~~p~ms~~~rr~vh~~~e~~~l~~~sa~~~pkr 880 (950)
T KOG1952|consen 804 LSKFSESLKEDARKDL---KFVKSVEKELEFLVELVKRGKNYSKKSHSFPPMSRDKRRLVHELAEVFGLESVSADSEPKR 880 (950)
T ss_pred hhhhhHHHHHHHHhch---hhhccchhhhHHHHHHHhhcccccccccccCchhHHHHHHHHhhhhccCCcccccCCCccc
Confidence 4567788888888777 89999999998887654311 2357899999999999999999999999999988889
Q ss_pred EEEEEecCCC-CCCchhhhhhhh
Q 020450 81 HLILERCSET-SIPSILVSDILW 102 (326)
Q Consensus 81 ~VVI~KTp~T-riP~~~LSElv~ 102 (326)
.+|++....+ ..|...+++++.
T Consensus 881 ~~v~t~ir~~s~~~~~~~~~~~~ 903 (950)
T KOG1952|consen 881 NVVVTAIRGKSVFPATTITGVLN 903 (950)
T ss_pred ceeeEeecccccCchhhHHHHHH
Confidence 9999987765 567777777775
No 20
>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=94.44 E-value=0.15 Score=39.45 Aligned_cols=56 Identities=27% Similarity=0.484 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCCCCcceecCCCChHHHHHHHHHHHHh---CCeeeeec-CCcceEEEEEec
Q 020450 29 MEEALVNFLQDDNSADGVLELEPMDSYNRLLLHRLADIF---GFAHESVG-EGVDRHLILERC 87 (326)
Q Consensus 29 LEe~I~~FIqd~~~~~~sleFPPMNSYqRlLVHrLAeyy---GL~heS~g-eG~~R~VVI~KT 87 (326)
+.+.|.+|+++... .+.++|||+|+|.|++...... |+.-+... +...+.|++.+.
T Consensus 4 v~~~i~~fl~s~~~---~l~le~cngf~RkLiyq~l~~~~~~~I~ve~~~~ekk~~~i~~~k~ 63 (65)
T cd02637 4 VIERIEAFLESEED---DLELEPCNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIEKG 63 (65)
T ss_pred HHHHHHHHHhcCcc---cccccccccHHHHHHHHHHHHHccccceeeeeeccccceEEEEeec
Confidence 45677889988632 3999999999999999888654 22222222 444466666654
No 21
>PF08110 Antimicrobial15: Ocellatin family; InterPro: IPR012518 This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus (Argus frog). The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3. These peptides present haemolytic activity against human erythrocytes and are also active against Escherichia coli [].; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region
Probab=56.19 E-value=8.3 Score=23.42 Aligned_cols=12 Identities=67% Similarity=0.808 Sum_probs=10.7
Q ss_pred hhHHHHHHHHhc
Q 020450 294 GAAKRLFAHALG 305 (326)
Q Consensus 294 gaakr~fahal~ 305 (326)
||||.+.||+-+
T Consensus 7 ~AaK~l~~H~a~ 18 (19)
T PF08110_consen 7 GAAKDLLAHAAE 18 (19)
T ss_pred hHHHHHHHHHhc
Confidence 899999999864
No 22
>KOG4060 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.24 E-value=15 Score=33.52 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=22.3
Q ss_pred eecCCCChHHHHHHHHHHHHhCCeee
Q 020450 47 LELEPMDSYNRLLLHRLADIFGFAHE 72 (326)
Q Consensus 47 leFPPMNSYqRlLVHrLAeyyGL~he 72 (326)
++|+.+-|||| +||.+|++++++-+
T Consensus 62 yD~~~lEsYq~-yvH~la~~l~~~V~ 86 (176)
T KOG4060|consen 62 YDMTLLESYQQ-YVHNLANSLSIKVE 86 (176)
T ss_pred cccchHHHHHH-HHHHHHHHcCceeE
Confidence 78999999997 78999999999865
No 23
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=26.45 E-value=39 Score=28.05 Aligned_cols=16 Identities=38% Similarity=0.702 Sum_probs=11.7
Q ss_pred HHHHHHHHHHhCCeee
Q 020450 57 RLLLHRLADIFGFAHE 72 (326)
Q Consensus 57 RlLVHrLAeyyGL~he 72 (326)
.-+||++|.|||+.-+
T Consensus 75 ~tlvhEiah~fG~~~e 90 (97)
T PF06262_consen 75 DTLVHEIAHHFGISDE 90 (97)
T ss_dssp HHHHHHHHHHTT--HH
T ss_pred HHHHHHHHHHcCCCHH
Confidence 4679999999998754
No 24
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=26.15 E-value=44 Score=29.51 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=15.4
Q ss_pred CChHHHHHHHHHHHHhCCeeeeec
Q 020450 52 MDSYNRLLLHRLADIFGFAHESVG 75 (326)
Q Consensus 52 MNSYqRlLVHrLAeyyGL~heS~g 75 (326)
....-|.|+|+|.-|+||.|- ++
T Consensus 66 ~~~~g~TltHEvGH~LGL~Ht-F~ 88 (154)
T PF05572_consen 66 QYNFGKTLTHEVGHWLGLYHT-FG 88 (154)
T ss_dssp TS-SSHHHHHHHHHHTT---T-T-
T ss_pred ccccccchhhhhhhhhccccc-cc
Confidence 455679999999999999996 54
Done!