Query 032220
Match_columns 145
No_of_seqs 76 out of 78
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:12:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03766 Remorin_N: Remorin, N 99.6 3.2E-16 6.9E-21 107.2 3.6 53 35-90 5-57 (57)
2 PF03763 Remorin_C: Remorin, C 99.6 2E-15 4.3E-20 112.7 5.9 53 92-144 2-54 (111)
3 PF03763 Remorin_C: Remorin, C 78.3 9.4 0.0002 28.7 6.1 29 93-121 25-53 (111)
4 PF07352 Phage_Mu_Gam: Bacteri 48.3 70 0.0015 24.3 5.8 38 92-129 26-63 (149)
5 PF07352 Phage_Mu_Gam: Bacteri 42.1 74 0.0016 24.2 5.1 41 103-143 15-55 (149)
6 PF03250 Tropomodulin: Tropomo 30.0 54 0.0012 26.5 2.8 32 72-105 55-86 (147)
7 PF04210 MtrG: Tetrahydrometha 29.2 34 0.00073 24.7 1.4 16 130-145 15-30 (70)
8 PF12856 Apc9: Anaphase-promot 28.8 46 0.001 25.0 2.1 22 94-115 44-65 (100)
9 PF10549 ORF11CD3: ORF11CD3 do 26.4 1.9E+02 0.0041 19.8 4.6 37 107-144 10-51 (57)
10 smart00806 AIP3 Actin interact 22.7 1.8E+02 0.0039 27.1 5.1 52 79-130 349-411 (426)
No 1
>PF03766 Remorin_N: Remorin, N-terminal region ; InterPro: IPR005518 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=99.61 E-value=3.2e-16 Score=107.25 Aligned_cols=53 Identities=62% Similarity=0.965 Sum_probs=46.3
Q ss_pred CCccccCCCCCCCCCCCCCccccceeeeecCCCCCCCCCCCCCCCchhHHHHHHHH
Q 032220 35 KDVADDKTVIPSPPAEDKPEESKALAVVDKAPEAEPPAGEKSTEGSVNRDAVLARV 90 (145)
Q Consensus 35 kdvaeekaviP~p~~~~~~ddsKAl~vvek~~~~~~~~~~k~~~gs~drD~~Larv 90 (145)
+|++++++++|||. +.+.||||||++|++..+. ++.+|+++||+|||++||||
T Consensus 5 ~dva~ek~~~PpP~-~~k~ddSKAl~vVek~~~e--pa~eK~s~GS~dRDa~LA~v 57 (57)
T PF03766_consen 5 KDVAEEKSVIPPPA-EEKPDDSKALVVVEKKVPE--PAEEKPSEGSIDRDAALARV 57 (57)
T ss_pred hhhccccCCCCCCC-CCCCCccceEEEeeccCCC--ccccccCCCcchhhhhhhcC
Confidence 78999999988775 6788999999999986332 78889999999999999986
No 2
>PF03763 Remorin_C: Remorin, C-terminal region ; InterPro: IPR005516 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=99.59 E-value=2e-15 Score=112.71 Aligned_cols=53 Identities=38% Similarity=0.610 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhhhhhhHHhhhhhhhHHHHHHhhhhhcC
Q 032220 92 TEKRISLIRAWEESEKSQAENKAHKKLSSIVSWENSRKAAVEAELKKIEVNVN 144 (145)
Q Consensus 92 ~EKr~slIkAWEEsEKaKaeNka~kk~s~I~aWEnskKA~~EAeLkKiEeklE 144 (145)
.+.+.+.|.|||++|++|+.|||++++++|++|||++|+++|++|+++|++||
T Consensus 2 ~~~~~a~a~aWe~ae~aK~~~r~~ree~~I~aWEn~qkaKaea~m~k~E~klE 54 (111)
T PF03763_consen 2 KEEVEAKADAWEEAEKAKINNRYEREEAKIQAWENLQKAKAEAEMRKIEEKLE 54 (111)
T ss_pred cHHHHhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999999999999999999999999999999999997
No 3
>PF03763 Remorin_C: Remorin, C-terminal region ; InterPro: IPR005516 Remorin binds both simple and complex galaturonides. The N-terminal region of remorin is proline rich, while the C-terminal region has been predicted to form a coiled-coil, that is expected to interact with other macromolecules, most likely DNA. Functional similarities between the behavior of the proteins and viral proteins involved in intercellular communication have been noted [].
Probab=78.29 E-value=9.4 Score=28.71 Aligned_cols=29 Identities=31% Similarity=0.498 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHhhhhh
Q 032220 93 EKRISLIRAWEESEKSQAENKAHKKLSSI 121 (145)
Q Consensus 93 EKr~slIkAWEEsEKaKaeNka~kk~s~I 121 (145)
++..+-|.+||...|+|++....+....+
T Consensus 25 ~ree~~I~aWEn~qkaKaea~m~k~E~kl 53 (111)
T PF03763_consen 25 EREEAKIQAWENLQKAKAEAEMRKIEEKL 53 (111)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999988777766554
No 4
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=48.30 E-value=70 Score=24.31 Aligned_cols=38 Identities=16% Similarity=0.352 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHhhhhhhHHhhhhh
Q 032220 92 TEKRISLIRAWEESEKSQAENKAHKKLSSIVSWENSRK 129 (145)
Q Consensus 92 ~EKr~slIkAWEEsEKaKaeNka~kk~s~I~aWEnskK 129 (145)
...+...|+.|-+++...+.++...-.+.|+.|=...+
T Consensus 26 ~~~~I~~i~~~~~~~~~~l~~~i~~l~~~l~~y~e~~r 63 (149)
T PF07352_consen 26 ANDEIARIKEWYEAEIAPLQNRIEYLEGLLQAYAEANR 63 (149)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
Confidence 34445555666666666666666666666666644443
No 5
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=42.12 E-value=74 Score=24.19 Aligned_cols=41 Identities=17% Similarity=0.326 Sum_probs=35.3
Q ss_pred HHHHHhHHHHHHHHhhhhhhHHhhhhhhhHHHHHHhhhhhc
Q 032220 103 EESEKSQAENKAHKKLSSIVSWENSRKAAVEAELKKIEVNV 143 (145)
Q Consensus 103 EEsEKaKaeNka~kk~s~I~aWEnskKA~~EAeLkKiEekl 143 (145)
-..+.+.+++.++.++..|..|-+...+.+..++..++..|
T Consensus 15 l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~~~l 55 (149)
T PF07352_consen 15 LQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLEGLL 55 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567788899999999999999999999999998887655
No 6
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=29.96 E-value=54 Score=26.45 Aligned_cols=32 Identities=28% Similarity=0.444 Sum_probs=23.1
Q ss_pred CCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Q 032220 72 AGEKSTEGSVNRDAVLARVETEKRISLIRAWEES 105 (145)
Q Consensus 72 ~~~k~~~gs~drD~~Larve~EKr~slIkAWEEs 105 (145)
...|...|.+||+++|.-++.+- .-++-|++.
T Consensus 55 QT~K~pTG~fdRe~Ll~~lekea--~~~~dre~~ 86 (147)
T PF03250_consen 55 QTEKPPTGPFDREALLDYLEKEA--KELKDREDL 86 (147)
T ss_pred ccCCCCCCCcCHHHHHHHHHHHH--HHHHhhhcc
Confidence 34677899999999999997553 334456653
No 7
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=29.19 E-value=34 Score=24.70 Aligned_cols=16 Identities=31% Similarity=0.507 Sum_probs=13.4
Q ss_pred hhHHHHHHhhhhhcCC
Q 032220 130 AAVEAELKKIEVNVNF 145 (145)
Q Consensus 130 A~~EAeLkKiEeklE~ 145 (145)
..+..+|-+||+|+||
T Consensus 15 ~~i~~rLd~iEeKvEf 30 (70)
T PF04210_consen 15 NEIMKRLDEIEEKVEF 30 (70)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4577889999999998
No 8
>PF12856 Apc9: Anaphase-promoting complex subunit 9; InterPro: IPR024274 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain [].The APC can be divided in four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains multiple subunits, including Apc9 []. This entry represents Apc9, one of the subunits of the anaphase-promoting complex.
Probab=28.77 E-value=46 Score=25.04 Aligned_cols=22 Identities=36% Similarity=0.379 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHhHHHHHHH
Q 032220 94 KRISLIRAWEESEKSQAENKAH 115 (145)
Q Consensus 94 Kr~slIkAWEEsEKaKaeNka~ 115 (145)
.|.|-|++|+.+|++-..-=|+
T Consensus 44 l~eSkI~~~l~sEra~h~liFh 65 (100)
T PF12856_consen 44 LRESKIKAWLSSERAAHCLIFH 65 (100)
T ss_pred HHHHHHHHHHHHHHHhcceecc
Confidence 7899999999999874333344
No 9
>PF10549 ORF11CD3: ORF11CD3 domain; InterPro: IPR018877 This entry represents the carboxy-terminal domain from ORF11 (Q9XJS9 from SWISSPROT), one of the proteins of Pseudomonas phage D3 (Bacteriophage D3). The function of these proteins are unknown [].
Probab=26.41 E-value=1.9e+02 Score=19.75 Aligned_cols=37 Identities=24% Similarity=0.518 Sum_probs=28.8
Q ss_pred HhHHHHHHHHhhhhhh-----HHhhhhhhhHHHHHHhhhhhcC
Q 032220 107 KSQAENKAHKKLSSIV-----SWENSRKAAVEAELKKIEVNVN 144 (145)
Q Consensus 107 KaKaeNka~kk~s~I~-----aWEnskKA~~EAeLkKiEeklE 144 (145)
.+.++-+..|.+++.. .| ..+|..++++++.+++++.
T Consensus 10 ~ac~e~~~~K~~AS~~GrgL~~W-k~~Kp~l~~ki~~l~~~~Q 51 (57)
T PF10549_consen 10 QACAEYKKEKDIASLCGRGLNRW-KWKKPQLEQKIEELEEQLQ 51 (57)
T ss_pred HHHHHHHhHHHHHHHHhHHHHHH-HHhhHHHHHHHHHHHHHhh
Confidence 3556666677776653 59 8999999999999999875
No 10
>smart00806 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization PUBMED:10679021.
Probab=22.73 E-value=1.8e+02 Score=27.09 Aligned_cols=52 Identities=27% Similarity=0.396 Sum_probs=35.8
Q ss_pred Cchh--HHHHHHHHH-----HHHHHHHH----HHHHHHHHhHHHHHHHHhhhhhhHHhhhhhh
Q 032220 79 GSVN--RDAVLARVE-----TEKRISLI----RAWEESEKSQAENKAHKKLSSIVSWENSRKA 130 (145)
Q Consensus 79 gs~d--rD~~Larve-----~EKr~slI----kAWEEsEKaKaeNka~kk~s~I~aWEnskKA 130 (145)
|+.+ ||.+|-.|. +|.|+-.| |+|+-.-..+-.|.|+++|.....=-+-||.
T Consensus 349 g~~~~~kd~VL~EV~aL~PdHEsRLeAIErAEklR~kEle~r~~d~Fq~ELg~FVe~~kLKks 411 (426)
T smart00806 349 GTFNDLKDQVLMEVRALKPDHESRLEAIERAEKLREKELEYRRVDEFEKELGNFVENGKLKKS 411 (426)
T ss_pred CChhHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccCCcccC
Confidence 4455 899998886 79999999 5555444445567789888877654444443
Done!