Query 048387
Match_columns 134
No_of_seqs 91 out of 111
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 09:02:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048387hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2491 Nuclear matrix protein 100.0 8.6E-54 1.9E-58 382.1 6.3 133 2-134 85-237 (674)
2 PF11957 efThoc1: THO complex 100.0 1.2E-50 2.6E-55 353.0 6.9 134 1-134 9-153 (491)
3 cd01479 Sec24-like Sec24-like: 34.5 18 0.00038 29.3 0.7 56 26-89 86-142 (244)
4 COG2707 Predicted membrane pro 32.9 13 0.00028 29.3 -0.2 18 84-101 37-54 (151)
5 PF06720 Phi-29_GP16_7: Bacter 28.4 43 0.00093 25.6 1.9 33 14-47 85-117 (130)
6 PF14688 DUF4461: Domain of un 20.0 35 0.00077 29.2 0.0 47 50-103 45-97 (313)
7 cd05171 PIKKc_ATM Ataxia telan 19.6 44 0.00094 27.7 0.5 38 57-98 47-84 (279)
8 COG5509 Uncharacterized small 19.3 1.3E+02 0.0028 20.6 2.7 61 7-70 5-65 (65)
9 PF12335 SBF2: Myotubularin pr 18.6 2.6E+02 0.0056 23.0 4.8 33 57-90 83-115 (225)
10 PF12422 Condensin2nSMC: Conde 18.3 2E+02 0.0044 21.7 3.9 39 57-95 114-152 (152)
No 1
>KOG2491 consensus Nuclear matrix protein [Nuclear structure]
Probab=100.00 E-value=8.6e-54 Score=382.06 Aligned_cols=133 Identities=48% Similarity=0.850 Sum_probs=126.6
Q ss_pred eeeecccCcccchhHHHHHHHHhcccCHHHHHHHHhhhhcchhhhhhhhhcccchhHHHHHHHHHHHHhcccCCcchhhH
Q 048387 2 VLYLCEKEHVEGGMIFQLLEDLTEMSTMKNCKDIFGYIESKQDILGKLELFARGKLVMLRTCNQLLRRLSKANDVVFCGR 81 (134)
Q Consensus 2 ~l~~~~~~~~~~~~~f~lleDl~d~~ti~~c~~~f~~vEsr~~~~~~~~~~~~~kl~lLR~cN~LLRRLSks~dt~fcGR 81 (134)
|..++.+|+|+.++||++|+|++|++|+++|.+||+|||+|+..|++..++.+|||+||||||||||||||++||+||||
T Consensus 85 v~~~~~~~~cs~~~Pf~lLeDl~dm~tl~eCkkiF~yvE~~~~~~K~~~f~~~~kn~lLR~cNdLLRRLSrt~ntvFCGR 164 (674)
T KOG2491|consen 85 VINGVTEGICSASTPFVLLEDLLDMSTLDECKKIFTYVEKNVATWKSNTFFAAGKNVLLRMCNDLLRRLSRTQNTVFCGR 164 (674)
T ss_pred HHHhhhHhhhcCCccHHHHHHHHhhhhHHHHHHHHHHHHHhHHHHccchhhhcccchhHHHHHHHHHHHhhcccceehHH
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCccccccccccccCCCcccccCCCCC--------------------CCccChHHHHhhhcCC
Q 048387 82 ILMFLAHFFPLSERSAVNIKGVFNTSNETKYEKDPPD--------------------GIPVDFNFYKTFWSLQ 134 (134)
Q Consensus 82 Il~FLs~~fpl~erSglN~~g~fn~~n~T~~e~~~~~--------------------~~~id~~~Y~~FWsLQ 134 (134)
|++|||++|||+||||+|++|+||++|||.|+..+.+ .++|||++|++|||||
T Consensus 165 I~lfLsrfFPlsErSG~Nl~g~fN~~nvt~fg~~e~d~~~~~~e~~et~~~e~~~~~~ikvd~~lY~~FWSLQ 237 (674)
T KOG2491|consen 165 IQLFLSRFFPLSERSGLNLQGQFNLENVTVFGTNEQDSTLGDVEEGETGDEEAPTTCSIKVDYNLYRKFWSLQ 237 (674)
T ss_pred HHHHHHHhCCchhccccchhcccccccceecccccccccccccCCCCcccccCCCcccccccHHHHHHHHHHH
Confidence 9999999999999999999999999999999876421 2679999999999998
No 2
>PF11957 efThoc1: THO complex subunit 1 transcription elongation factor; InterPro: IPR021861 The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm.
Probab=100.00 E-value=1.2e-50 Score=353.04 Aligned_cols=134 Identities=49% Similarity=0.905 Sum_probs=125.2
Q ss_pred CeeeecccCc--ccchhHHHHHHHHhcccCHHHHHHHHhhhhcchhhhhhhhhcccchhH-HHHHHHHHHHHhcccCCcc
Q 048387 1 IVLYLCEKEH--VEGGMIFQLLEDLTEMSTMKNCKDIFGYIESKQDILGKLELFARGKLV-MLRTCNQLLRRLSKANDVV 77 (134)
Q Consensus 1 i~l~~~~~~~--~~~~~~f~lleDl~d~~ti~~c~~~f~~vEsr~~~~~~~~~~~~~kl~-lLR~cN~LLRRLSks~dt~ 77 (134)
|++++++.+. |++++||.|+||+||++||+.|+.+|+|||+|+++|+++.++.+||+. +|||||+|||||||++|++
T Consensus 9 ~~~~~~~~~~~~~~~~~~f~L~edl~d~~ti~~c~~~F~y~Esr~~~~~~~~~~~~~k~~~lLR~cN~LLrRLSrt~~~~ 88 (491)
T PF11957_consen 9 LVLILSENEISPCDWALPFFLLEDLLDSLTIPDCEKVFWYVESRRERFKAGNFFQRGKNLVLLRMCNELLRRLSRTQDTV 88 (491)
T ss_pred HHHHHHHhcccccccccHHHHHHHHHhhCcHHHHHHHHHHHhccHHHHhcccccccCcccccHHHHHHHHHHHHhcccHH
Confidence 4678899999 999999999999999999999999999999999999999999999966 9999999999999999999
Q ss_pred hhhHHHHHHHhhcCCCccccccccccccCCCcccccCCC--------CCCCccChHHHHhhhcCC
Q 048387 78 FCGRILMFLAHFFPLSERSAVNIKGVFNTSNETKYEKDP--------PDGIPVDFNFYKTFWSLQ 134 (134)
Q Consensus 78 fcGRIl~FLs~~fpl~erSglN~~g~fn~~n~T~~e~~~--------~~~~~id~~~Y~~FWsLQ 134 (134)
|||||++|||++|||+||||+|++|+||++|+|.||.+. .+..++||+||++||+||
T Consensus 89 fcGRi~~FLs~~fPl~ErSg~Nl~g~fn~~n~T~~~~~~~~~~~~~~~~~~~~D~~~Y~~FW~LQ 153 (491)
T PF11957_consen 89 FCGRILIFLSQLFPLSERSGVNLRGEFNVENVTTFEEQEEGEDEDADSDKMQIDYNLYPKFWSLQ 153 (491)
T ss_pred HHHHHHHHHHHHCCCcccccCcccccccccccccccccccccCccCccccccccHHHHHHHHHHH
Confidence 999999999999999999999999999999999999211 234579999999999998
No 3
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=34.48 E-value=18 Score=29.28 Aligned_cols=56 Identities=13% Similarity=0.275 Sum_probs=40.1
Q ss_pred ccCHHHHHHHH-hhhhcchhhhhhhhhcccchhHHHHHHHHHHHHhcccCCcchhhHHHHHHHhh
Q 048387 26 MSTMKNCKDIF-GYIESKQDILGKLELFARGKLVMLRTCNQLLRRLSKANDVVFCGRILMFLAHF 89 (134)
Q Consensus 26 ~~ti~~c~~~f-~~vEsr~~~~~~~~~~~~~kl~lLR~cN~LLRRLSks~dt~fcGRIl~FLs~~ 89 (134)
..++++|++.+ +.+|+-...+.+..-.++|=-.-|+.+..+|+ ..-|||++|.+..
T Consensus 86 lv~l~e~~~~i~~lL~~L~~~~~~~~~~~~c~G~Al~~A~~lL~--------~~GGkIi~f~s~~ 142 (244)
T cd01479 86 LVNLKESRQVIEDLLDQIPEMFQDTKETESALGPALQAAFLLLK--------ETGGKIIVFQSSL 142 (244)
T ss_pred eecHHHHHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHH--------hcCCEEEEEeCCC
Confidence 36789999877 66666555554443344555788999999999 2359999999854
No 4
>COG2707 Predicted membrane protein [Function unknown]
Probab=32.91 E-value=13 Score=29.28 Aligned_cols=18 Identities=39% Similarity=0.676 Sum_probs=15.7
Q ss_pred HHHHhhcCCCcccccccc
Q 048387 84 MFLAHFFPLSERSAVNIK 101 (134)
Q Consensus 84 ~FLs~~fpl~erSglN~~ 101 (134)
.+|.++||+-||.|+|+.
T Consensus 37 t~L~~~fP~iek~Gi~~G 54 (151)
T COG2707 37 TGLDKFFPLIEKKGLNLG 54 (151)
T ss_pred HhHHHHhhHHHHcCCeee
Confidence 467899999999999974
No 5
>PF06720 Phi-29_GP16_7: Bacteriophage phi-29 early protein GP16.7; InterPro: IPR009595 The early-expressed gene 16.7 is conserved in bacteriophage phi-29 and related phages. It encodes a membrane protein, GP16.7, consisting of an N-terminal transmembrane domain and a C-terminal DNA-binding and dimerisation domain. GP16.7 plays an important role in organising membrane-associated bacteriophage DNA replication [, ]. The C-terminal domain has a similar secondary structure similar to homeodomains, but forms a fundamentally different tertiary structure consisting of a six-helical dimeric fold []. Multimerisation of this dimer leads to efficient DNA binding.; PDB: 2C5R_B 2BNK_A 1ZAE_B.
Probab=28.39 E-value=43 Score=25.64 Aligned_cols=33 Identities=18% Similarity=0.411 Sum_probs=26.4
Q ss_pred hhHHHHHHHHhcccCHHHHHHHHhhhhcchhhhh
Q 048387 14 GMIFQLLEDLTEMSTMKNCKDIFGYIESKQDILG 47 (134)
Q Consensus 14 ~~~f~lleDl~d~~ti~~c~~~f~~vEsr~~~~~ 47 (134)
.+|..++||+. .+-+..=+++..|+|.....|+
T Consensus 85 rIP~DIIEdl~-~~~L~Te~eVmnYiEnqR~~WK 117 (130)
T PF06720_consen 85 RIPSDIIEDLV-NQRLQTEQEVMNYIENQRTYWK 117 (130)
T ss_dssp ---HHHHHHHH-TT--SSHHHHHHHHHHHHHHHH
T ss_pred CCcHHHHHHHH-HHhhhhHHHHHHHHHhhHhHHh
Confidence 57999999999 8888899999999999999997
No 6
>PF14688 DUF4461: Domain of unknown function (DUF4461)
Probab=19.97 E-value=35 Score=29.16 Aligned_cols=47 Identities=30% Similarity=0.460 Sum_probs=33.5
Q ss_pred hhcccch-hHHHHHHHHHHHHhcccC-Ccc----hhhHHHHHHHhhcCCCcccccccccc
Q 048387 50 ELFARGK-LVMLRTCNQLLRRLSKAN-DVV----FCGRILMFLAHFFPLSERSAVNIKGV 103 (134)
Q Consensus 50 ~~~~~~k-l~lLR~cN~LLRRLSks~-dt~----fcGRIl~FLs~~fpl~erSglN~~g~ 103 (134)
..|..|. ..-.|-|=.-|+||++.+ +.. ++|+.++| ++.|||+.-|+
T Consensus 45 i~~~~~w~~~h~~~~L~sL~rL~~a~~~~~~~~~L~G~tvvF-------~~~sGv~~~G~ 97 (313)
T PF14688_consen 45 IRWDCGWNISHRRSCLQSLERLARAQQHPEALDNLKGRTVVF-------GDFSGVSLDGH 97 (313)
T ss_pred EEecCCCchhhHHHHHHHHHHHHhhccchHHHHhcCCCEEEe-------cCCCccCCCCC
Confidence 3556554 333566778899997654 344 78887776 59999999999
No 7
>cd05171 PIKKc_ATM Ataxia telangiectasia mutated (ATM), catalytic domain; The ATM catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. ATM is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). ATM contains a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. ATM is critical in the response to DNA double strand breaks (DSBs) caused by radiation. It is activated at the site of a DSB and phosphorylates key substrates that trigger pathways that regulate DNA repair and cell cycle checkpoints at the G1/S, S phase, and G2/M transi
Probab=19.64 E-value=44 Score=27.70 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHHhcccCCcchhhHHHHHHHhhcCCCccccc
Q 048387 57 LVMLRTCNQLLRRLSKANDVVFCGRILMFLAHFFPLSERSAV 98 (134)
Q Consensus 57 l~lLR~cN~LLRRLSks~dt~fcGRIl~FLs~~fpl~erSgl 98 (134)
..++|+.|.+|++=..+..- .+.+-.-.+.||++.+|+
T Consensus 47 mQl~~~~n~il~~~~e~~~r----~l~i~~y~vipls~~~GL 84 (279)
T cd05171 47 EQVFQLVNTLLERNKETRKR----KLRIRTYKVVPLSPRAGI 84 (279)
T ss_pred HHHHHHHHHHHhhChhhhhc----CceeecceEEecCCCceE
Confidence 78999999999976433321 334666789999999995
No 8
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=19.33 E-value=1.3e+02 Score=20.59 Aligned_cols=61 Identities=10% Similarity=0.152 Sum_probs=42.3
Q ss_pred ccCcccchhHHHHHHHHhcccCHHHHHHHHhhhhcchhhhhhhhhcccchhHHHHHHHHHHHHh
Q 048387 7 EKEHVEGGMIFQLLEDLTEMSTMKNCKDIFGYIESKQDILGKLELFARGKLVMLRTCNQLLRRL 70 (134)
Q Consensus 7 ~~~~~~~~~~f~lleDl~d~~ti~~c~~~f~~vEsr~~~~~~~~~~~~~kl~lLR~cN~LLRRL 70 (134)
+++..-+..+-.+.+|-+..+++.+-++=...+-+-+++++....- ++ .----.|.|+||+
T Consensus 5 ded~~kka~~~~i~~d~LsllsV~El~eRIalLq~EIeRlkAe~~k-K~--~srsAAeaLFrr~ 65 (65)
T COG5509 5 DEDAEKKAFGHEIGNDALSLLSVAELEERIALLQAEIERLKAELAK-KK--ASRSAAEALFRRL 65 (65)
T ss_pred cccccccccccccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHh-hh--ccHHHHHHHHhcC
Confidence 4455556667778899999999999998888888888888754322 11 1122457777774
No 9
>PF12335 SBF2: Myotubularin protein ; InterPro: IPR022096 This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with PF02141 from PFAM, PF03456 from PFAM, PF03455 from PFAM. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.
Probab=18.58 E-value=2.6e+02 Score=23.05 Aligned_cols=33 Identities=24% Similarity=0.217 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHHhcccCCcchhhHHHHHHHhhc
Q 048387 57 LVMLRTCNQLLRRLSKANDVVFCGRILMFLAHFF 90 (134)
Q Consensus 57 l~lLR~cN~LLRRLSks~dt~fcGRIl~FLs~~f 90 (134)
..|.|+.|..|+..|...|. ..++.+|=++..|
T Consensus 83 ~~lv~lin~aLq~~s~~dd~-~~Aa~LL~ls~~f 115 (225)
T PF12335_consen 83 DYLVRLINCALQDCSESDDY-GIAAALLPLSTAF 115 (225)
T ss_pred HHHHHHHHHHHHHHHhccch-HHHHHHHHHHHHH
Confidence 68999999999998885554 4566777777777
No 10
>PF12422 Condensin2nSMC: Condensin II non structural maintenance of chromosomes subunit; InterPro: IPR024741 Subunit G2 is a non-SMC subunit of condensin II, which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II [].; GO: 0005634 nucleus
Probab=18.28 E-value=2e+02 Score=21.75 Aligned_cols=39 Identities=21% Similarity=0.318 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHhcccCCcchhhHHHHHHHhhcCCCcc
Q 048387 57 LVMLRTCNQLLRRLSKANDVVFCGRILMFLAHFFPLSER 95 (134)
Q Consensus 57 l~lLR~cN~LLRRLSks~dt~fcGRIl~FLs~~fpl~er 95 (134)
..|+|+..-.|=|.=++.|...+.--...+..+|||-++
T Consensus 114 ~mL~rl~~PiL~r~L~~~n~~Vr~na~~l~~~aFpl~~p 152 (152)
T PF12422_consen 114 EMLLRLYEPILWRALQAANAKVRSNAAALFLDAFPLHDP 152 (152)
T ss_pred HHHHHHHHHHHHHHHcCCCcchhccHHHHHHHHcCCcCc
Confidence 678999999999988888877787778888889999764
Done!