Query psy4569
Match_columns 88
No_of_seqs 116 out of 187
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 20:21:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4028|consensus 100.0 1.3E-29 2.8E-34 171.4 6.2 87 2-88 83-175 (175)
2 PF07162 B9-C2: Ciliary basal 99.9 6.8E-26 1.5E-30 156.2 8.2 77 2-78 85-168 (168)
3 KOG4027|consensus 99.8 7.1E-21 1.5E-25 131.5 7.0 86 3-88 93-185 (187)
4 KOG4446|consensus 99.2 5E-12 1.1E-16 97.1 2.9 78 2-79 311-402 (471)
5 PF10058 DUF2296: Predicted in 40.5 15 0.00032 20.9 0.9 18 32-49 1-18 (54)
6 PF10572 UPF0556: Uncharacteri 34.3 14 0.0003 25.8 0.1 27 22-48 75-105 (158)
7 PF10405 BHD_3: Rad4 beta-hair 33.3 8.7 0.00019 23.3 -0.9 24 65-88 17-40 (76)
8 PF10908 DUF2778: Protein of u 25.4 40 0.00086 22.3 1.1 53 19-73 29-97 (120)
9 PTZ00090 40S ribosomal protein 24.0 68 0.0015 23.7 2.1 27 39-65 93-124 (233)
10 KOG2314|consensus 22.5 39 0.00085 28.3 0.7 50 24-75 497-566 (698)
11 COG0602 NrdG Organic radical a 20.6 24 0.00051 25.1 -0.8 48 26-74 52-114 (212)
No 1
>KOG4028|consensus
Probab=99.96 E-value=1.3e-29 Score=171.41 Aligned_cols=87 Identities=43% Similarity=0.701 Sum_probs=85.3
Q ss_pred cccccceeeeeeceEe---CCCc--EEEeceeecC-HHHHHhhceecCCceecCCceeeeCCCceeEEEEEeeEEEEEEe
Q psy4569 2 HDEFTRQFLGGGPQLK---SPDL--VYTGLDRYRG-MHDEFTRQFLGGGPQLKSPDLVYTGLDRYRLHTEAMGCVHLELS 75 (88)
Q Consensus 2 ~D~~gr~~~~GYg~~~---~pG~--~~~~~wRP~~-~~~~l~~~f~Gg~pel~d~~~v~~~~~R~~l~t~s~G~V~l~l~ 75 (88)
+|.|||..+.|||+|+ +||. +.|+||||+| |++++...|+||+|||...|.++++++|+++.+.+.|+|++++|
T Consensus 83 ~dnfgr~eiagyg~~~lpsspgkh~la~~~wrp~gswreel~~~~vggg~ql~~~~ai~~~a~r~ki~s~a~g~v~~ei~ 162 (175)
T KOG4028|consen 83 HDNFGRCEIAGYGFCHLPSSPGKHQLACGCWRPKGSWREELAHAFVGGGLQLLHGDAIEDGADREKIHSAAAGTVHFEIG 162 (175)
T ss_pred cCcccceeecccceEeccCCCCcceecccccCCCCcHHHHHHHHHhcCCceeeccccccCchhhheeeeeccceEEEEEe
Confidence 6999999999999999 7898 9999999999 99999999999999999999999999999999999999999999
Q ss_pred eeecCccccCccC
Q psy4569 76 IILRNFDKYGIEA 88 (88)
Q Consensus 76 v~~r~f~k~Gv~~ 88 (88)
+++|||++|||+|
T Consensus 163 ii~knf~rygi~c 175 (175)
T KOG4028|consen 163 IILKNFDRYGIEC 175 (175)
T ss_pred eeehhhhhhcccC
Confidence 9999999999998
No 2
>PF07162 B9-C2: Ciliary basal body-associated, B9 protein; InterPro: IPR010796 Proteins in this entry include the MSK1 protein (Q9NXB0 from SWISSPROT) and other known or predicted flagellar basal body proteome components [] or cilia-containing species. Although the function is unknown, a cilia-specific role has been suggested for the poorly characterised B9 domain [, , ]. Mutations in MSK1 have been shown to cause Meckel syndrome type 1, a severe foetal development disorder that has been reported in most populations.
Probab=99.93 E-value=6.8e-26 Score=156.18 Aligned_cols=77 Identities=31% Similarity=0.522 Sum_probs=74.0
Q ss_pred cccccceeeeeeceEe---CCCc--EEEeceee-cC-HHHHHhhceecCCceecCCceeeeCCCceeEEEEEeeEEEEEE
Q psy4569 2 HDEFTRQFLGGGPQLK---SPDL--VYTGLDRY-RG-MHDEFTRQFLGGGPQLKSPDLVYTGLDRYRLHTEAMGCVHLEL 74 (88)
Q Consensus 2 ~D~~gr~~~~GYg~~~---~pG~--~~~~~wRP-~~-~~~~l~~~f~Gg~pel~d~~~v~~~~~R~~l~t~s~G~V~l~l 74 (88)
+|.|||+.+.|||+++ +||. ++++|||| .+ +.+++++||+|++|||.|+++++++++|++|+|+|+|+|+|+|
T Consensus 85 ~D~~gr~~~~GYG~~~lP~~pG~h~~~v~~wrP~~~s~~~~l~~~f~G~~pel~d~~~~~~~~~R~~l~t~s~G~V~v~l 164 (168)
T PF07162_consen 85 LDSWGRDRVEGYGFCHLPTQPGRHEVEVPTWRPVSGSIRQELRSFFVGGRPELVDPDFIASGESRFGLRTESSGSVKVRL 164 (168)
T ss_pred EcccCCeEEeEEeEEEeCCCCceEEEEEEEEeecCCCHHHHhhhheecCCceEcCcchhcCcccccCcEEEeeeEEEEEE
Confidence 5999999999999999 7898 99999999 66 9999999999999999999999999999999999999999999
Q ss_pred eeee
Q psy4569 75 SIIL 78 (88)
Q Consensus 75 ~v~~ 78 (88)
||++
T Consensus 165 ~vi~ 168 (168)
T PF07162_consen 165 NVII 168 (168)
T ss_pred EEeC
Confidence 9985
No 3
>KOG4027|consensus
Probab=99.84 E-value=7.1e-21 Score=131.51 Aligned_cols=86 Identities=19% Similarity=0.249 Sum_probs=82.6
Q ss_pred ccccceeeeeeceEe---CCCc--EEEeceeecC--HHHHHhhceecCCceecCCceeeeCCCceeEEEEEeeEEEEEEe
Q psy4569 3 DEFTRQFLGGGPQLK---SPDL--VYTGLDRYRG--MHDEFTRQFLGGGPQLKSPDLVYTGLDRYRLHTEAMGCVHLELS 75 (88)
Q Consensus 3 D~~gr~~~~GYg~~~---~pG~--~~~~~wRP~~--~~~~l~~~f~Gg~pel~d~~~v~~~~~R~~l~t~s~G~V~l~l~ 75 (88)
|-+|++.+.|||.+| .||. +.++++-|+. .+|++.+||.+..||+.||++++++++|+.++|+|.|.|.++||
T Consensus 93 d~~G~d~v~GYg~~hiP~~pgrh~~~vp~f~Pe~~s~~q~~tswl~rr~pE~~DPkv~a~~~gr~~~r~~s~G~v~l~~n 172 (187)
T KOG4027|consen 93 DHSGKDCVTGYGMLHIPTEPGRHVCRVPCFLPEPSSTVQQLTSWLRRRNPEFVDPKVPANADGRYACRTSSKGYVDLEIN 172 (187)
T ss_pred CcCCcceeeeeeeEecCcCCCceeEEEeeEecCCHHHHHHHHHHHHhcCccccCCccccccCCceEEEeeccceEEEEEe
Confidence 678999999999999 7888 9999999999 99999999999999999999999999999999999999999999
Q ss_pred eeecCccccCccC
Q psy4569 76 IILRNFDKYGIEA 88 (88)
Q Consensus 76 v~~r~f~k~Gv~~ 88 (88)
+++|++.|+||+.
T Consensus 173 vv~k~arKlgy~t 185 (187)
T KOG4027|consen 173 VVIKCARKLGYST 185 (187)
T ss_pred eeehhhHhhcccc
Confidence 9999999999973
No 4
>KOG4446|consensus
Probab=99.23 E-value=5e-12 Score=97.05 Aligned_cols=78 Identities=23% Similarity=0.221 Sum_probs=70.3
Q ss_pred cccccceeeeeeceEe---CCCc--EEEeceeecC--HHHHHhhceecCCceecCCceeeeC-------CCceeEEEEEe
Q psy4569 2 HDEFTRQFLGGGPQLK---SPDL--VYTGLDRYRG--MHDEFTRQFLGGGPQLKSPDLVYTG-------LDRYRLHTEAM 67 (88)
Q Consensus 2 ~D~~gr~~~~GYg~~~---~pG~--~~~~~wRP~~--~~~~l~~~f~Gg~pel~d~~~v~~~-------~~R~~l~t~s~ 67 (88)
+|.|+|..+.|||.-. +||. ..+.+|||.+ |..+|+++|+||+-++.|.++.-.+ .+|+..+|+++
T Consensus 311 vD~WqR~rieGYg~~~vplTpg~~t~~I~lwrpi~lgtva~L~r~FIGGsq~~dd~syf~~p~S~~~eRl~r~g~rteTT 390 (471)
T KOG4446|consen 311 VDYWQRQRIEGYGSGYVPLTPGKSTSKIHLWRPISLGTVASLYRMFIGGSQAIDDISYFGTPKSSSLERLGRDGQRTETT 390 (471)
T ss_pred hhhhhhhhccccceeEEecCCCCCcceeEEeeeeccCcHHHHHHHhhcchhhcchhhhcCCCchhhhhhhccCCCcccce
Confidence 6999999999999877 8888 9999999999 9999999999999999988876543 48999999999
Q ss_pred eEEEEEEeeeec
Q psy4569 68 GCVHLELSIILR 79 (88)
Q Consensus 68 G~V~l~l~v~~r 79 (88)
|+|.++|..+.+
T Consensus 391 Gti~~Rl~~lqq 402 (471)
T KOG4446|consen 391 GTIAIRLLPLQQ 402 (471)
T ss_pred eeEEEEEehhhh
Confidence 999999987664
No 5
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=40.48 E-value=15 Score=20.91 Aligned_cols=18 Identities=28% Similarity=0.420 Sum_probs=14.5
Q ss_pred HHHHHhhceecCCceecC
Q psy4569 32 MHDEFTRQFLGGGPQLKS 49 (88)
Q Consensus 32 ~~~~l~~~f~Gg~pel~d 49 (88)
|++++.+.++|+.|+..+
T Consensus 1 W~Dki~d~L~G~d~~~~~ 18 (54)
T PF10058_consen 1 WFDKILDVLLGDDPTSPS 18 (54)
T ss_pred ChHHHHHHHhCCCCcccc
Confidence 679999999999994433
No 6
>PF10572 UPF0556: Uncharacterised protein family UPF0556; InterPro: IPR018887 This family of proteins has no known function.
Probab=34.30 E-value=14 Score=25.77 Aligned_cols=27 Identities=15% Similarity=0.167 Sum_probs=22.2
Q ss_pred EEEeceeecC----HHHHHhhceecCCceec
Q psy4569 22 VYTGLDRYRG----MHDEFTRQFLGGGPQLK 48 (88)
Q Consensus 22 ~~~~~wRP~~----~~~~l~~~f~Gg~pel~ 48 (88)
..|..|||++ +..++..-+.|+..+..
T Consensus 75 ~sC~I~RPqgkSYL~F~qFkaev~G~ki~y~ 105 (158)
T PF10572_consen 75 YSCIIWRPQGKSYLFFTQFKAEVKGAKIEYA 105 (158)
T ss_pred eEEEEECCCCCcEEEEEEEEEEEecceeeee
Confidence 7899999998 67788888888877764
No 7
>PF10405 BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR018328 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=33.28 E-value=8.7 Score=23.34 Aligned_cols=24 Identities=38% Similarity=0.571 Sum_probs=15.8
Q ss_pred EEeeEEEEEEeeeecCccccCccC
Q psy4569 65 EAMGCVHLELSIILRNFDKYGIEA 88 (88)
Q Consensus 65 ~s~G~V~l~l~v~~r~f~k~Gv~~ 88 (88)
...|.|+|++.-+.+-.+++||||
T Consensus 17 ~P~G~vhi~~~~~~~~a~~l~Idy 40 (76)
T PF10405_consen 17 LPEGCVHIKLPGIEKVAKKLGIDY 40 (76)
T ss_dssp S-TTEEEEE-TTHHHHHHHTT---
T ss_pred CCCceEEEecccHHHHHHHcCCcE
Confidence 456899999888888888888875
No 8
>PF10908 DUF2778: Protein of unknown function (DUF2778); InterPro: IPR021225 This is a bacterial family of uncharacterised proteins.
Probab=25.38 E-value=40 Score=22.28 Aligned_cols=53 Identities=25% Similarity=0.368 Sum_probs=32.9
Q ss_pred CCcEEEeceeecC-HHHHHhhceecCCce--------ecCCceeeeCCCc--eeEE-----EEEeeEEEEE
Q psy4569 19 PDLVYTGLDRYRG-MHDEFTRQFLGGGPQ--------LKSPDLVYTGLDR--YRLH-----TEAMGCVHLE 73 (88)
Q Consensus 19 pG~~~~~~wRP~~-~~~~l~~~f~Gg~pe--------l~d~~~v~~~~~R--~~l~-----t~s~G~V~l~ 73 (88)
||. +--..||.| +...+++++.+ ..+ ..|.+...++..| |+|+ ..|.|+|.+.
T Consensus 29 ~G~-Y~IvdR~~Gg~~~~~~~~~~~-~~~WFaLyr~D~idD~t~~~gv~Rg~FRLHP~g~~G~S~GCIT~~ 97 (120)
T PF10908_consen 29 PGR-YWIVDRPSGGRLGWLRDWFKD-RSEWFALYRDDKIDDWTFVNGVKRGNFRLHPVGPSGISEGCITFK 97 (120)
T ss_pred CCe-EEEEECCCCCccceeeecccc-ccceeEEeccCCCCCceEECCEEeeeEEEcCCCCCCcccccEeec
Confidence 344 444589998 88888887777 333 2333445566554 4444 3488888775
No 9
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=24.03 E-value=68 Score=23.66 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=20.1
Q ss_pred ceecCCceecCCce-----eeeCCCceeEEEE
Q psy4569 39 QFLGGGPQLKSPDL-----VYTGLDRYRLHTE 65 (88)
Q Consensus 39 ~f~Gg~pel~d~~~-----v~~~~~R~~l~t~ 65 (88)
...||.||+.+.|. |.-+.+||.+...
T Consensus 93 k~~~~~~ef~~~~~~~~~~i~~p~~~f~~vI~ 124 (233)
T PTZ00090 93 KLFGGRPEFHNIDRDKNGLIIEPTDRFMLVIT 124 (233)
T ss_pred hhcCCchhhcccccccCCcEecCCCcEEEEEE
Confidence 35689999998765 6667899986543
No 10
>KOG2314|consensus
Probab=22.48 E-value=39 Score=28.32 Aligned_cols=50 Identities=12% Similarity=0.095 Sum_probs=36.8
Q ss_pred EeceeecC---HHHHHhhceecCCceecCCce-----ee------------eCCCceeEEEEEeeEEEEEEe
Q psy4569 24 TGLDRYRG---MHDEFTRQFLGGGPQLKSPDL-----VY------------TGLDRYRLHTEAMGCVHLELS 75 (88)
Q Consensus 24 ~~~wRP~~---~~~~l~~~f~Gg~pel~d~~~-----v~------------~~~~R~~l~t~s~G~V~l~l~ 75 (88)
.--|-|+| ..-.+.+ .+|..|+.|.|+ ++ .+.+||+....|.+..++...
T Consensus 497 ~vfwsPkG~fvvva~l~s--~~g~l~F~D~~~a~~k~~~~~eh~~at~veWDPtGRYvvT~ss~wrhk~d~G 566 (698)
T KOG2314|consen 497 TVFWSPKGRFVVVAALVS--RRGDLEFYDTDYADLKDTASPEHFAATEVEWDPTGRYVVTSSSSWRHKVDNG 566 (698)
T ss_pred eEEEcCCCcEEEEEEecc--cccceEEEecchhhhhhccCccccccccceECCCCCEEEEeeehhhhccccc
Confidence 34688999 3344444 689999999885 11 235999999999998888764
No 11
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=20.64 E-value=24 Score=25.12 Aligned_cols=48 Identities=19% Similarity=0.273 Sum_probs=32.5
Q ss_pred ceeecC---HHHHHhhc--------eecCCceecCCce--eeeC--CCceeEEEEEeeEEEEEE
Q psy4569 26 LDRYRG---MHDEFTRQ--------FLGGGPQLKSPDL--VYTG--LDRYRLHTEAMGCVHLEL 74 (88)
Q Consensus 26 ~wRP~~---~~~~l~~~--------f~Gg~pel~d~~~--v~~~--~~R~~l~t~s~G~V~l~l 74 (88)
.|++.. +.+++.+. ++||-| +..+++ +..- ...|++..|+.|++.+..
T Consensus 52 ~~~~~~~~~I~~~i~~~~~~~~~V~lTGGEP-~~~~~l~~Ll~~l~~~g~~~~lETngti~~~~ 114 (212)
T COG0602 52 PGTPMSADEILADIKSLGYKARGVSLTGGEP-LLQPNLLELLELLKRLGFRIALETNGTIPVWT 114 (212)
T ss_pred CCCccCHHHHHHHHHhcCCCcceEEEeCCcC-CCcccHHHHHHHHHhCCceEEecCCCCccccc
Confidence 345555 77777763 999999 554333 3222 345889999999998774
Done!