Query 032322
Match_columns 143
No_of_seqs 94 out of 96
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 12:34:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032322.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032322hhsearch_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 5.1E-16 1.1E-20 106.1 2.8 53 33-91 4-57 (57)
2 PF03763 Remorin_C: Remorin, C 99.5 1.6E-14 3.4E-19 107.7 5.2 50 94-143 3-52 (111)
3 PF03763 Remorin_C: Remorin, C 81.7 2.8 6.1E-05 31.5 4.2 32 92-123 23-54 (111)
4 PF07352 Phage_Mu_Gam: Bacteri 59.6 35 0.00075 25.9 5.8 53 81-133 14-66 (149)
5 PF03250 Tropomodulin: Tropomo 31.0 50 0.0011 26.6 2.7 30 75-106 57-86 (147)
6 PF07352 Phage_Mu_Gam: Bacteri 29.6 1.3E+02 0.0027 22.9 4.6 38 104-141 15-52 (149)
7 PF12856 Apc9: Anaphase-promot 26.5 51 0.0011 24.8 2.0 23 95-117 44-66 (100)
8 cd07663 BAR_SNX5 The Bin/Amphi 25.7 3.3E+02 0.0072 22.8 6.8 46 84-131 116-161 (218)
9 KOG2962 Prohibitin-related mem 24.8 1.2E+02 0.0025 27.1 4.1 41 80-120 225-267 (322)
10 cd07662 BAR_SNX6 The Bin/Amphi 23.2 2.2E+02 0.0047 24.1 5.3 47 83-131 115-161 (218)
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=99.59 E-value=5.1e-16 Score=106.08 Aligned_cols=53 Identities=55% Similarity=0.683 Sum_probs=46.5
Q ss_pred CCChhhhhcccCCCCCCCCCCCCcceeeeccC-CCchhhhcccccCCCCchhHHHHHHHH
Q 032322 33 NNDVAEEKAVTQLHDQEKPVDDSKALAVVDQT-PDSAKKKISGEKKISGSHDRDVALAEV 91 (143)
Q Consensus 33 ~kdvaeEkav~P~p~~~~~~ddsKAl~vvek~-~~~~~~~~~~~k~~~gs~drD~~Larv 91 (143)
++|++++++++|||. +.+.||||||++|++. ++++. +|+++||+|||++|+||
T Consensus 4 ~~dva~ek~~~PpP~-~~k~ddSKAl~vVek~~~epa~-----eK~s~GS~dRDa~LA~v 57 (57)
T PF03766_consen 4 AKDVAEEKSVIPPPA-EEKPDDSKALVVVEKKVPEPAE-----EKPSEGSIDRDAALARV 57 (57)
T ss_pred chhhccccCCCCCCC-CCCCCccceEEEeeccCCCccc-----cccCCCcchhhhhhhcC
Confidence 489999999998886 6778999999999986 56776 78899999999999985
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=99.51 E-value=1.6e-14 Score=107.66 Aligned_cols=50 Identities=42% Similarity=0.666 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHhhHhHHHhhhhhhhhHHHHhhhhhcC
Q 032322 94 EKRESFIKAWEESEKTKAENKAQKKLSAVAAWENSKKASLEAKLKKIEVT 143 (143)
Q Consensus 94 EKR~s~IkAWEE~EKaK~~nra~k~~s~I~aWEn~kKAk~EAelkKiEek 143 (143)
+.+.++|.+||++|++|+.|||++++++|++|||+||+++|++|+++|.+
T Consensus 3 ~~~~a~a~aWe~ae~aK~~~r~~ree~~I~aWEn~qkaKaea~m~k~E~k 52 (111)
T PF03763_consen 3 EEVEAKADAWEEAEKAKINNRYEREEAKIQAWENLQKAKAEAEMRKIEEK 52 (111)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999999999999999999999999999999963
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=81.71 E-value=2.8 Score=31.46 Aligned_cols=32 Identities=34% Similarity=0.493 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHhhhhhHHHHHHHhhHhHH
Q 032322 92 EKEKRESFIKAWEESEKTKAENKAQKKLSAVA 123 (143)
Q Consensus 92 e~EKR~s~IkAWEE~EKaK~~nra~k~~s~I~ 123 (143)
-+++..+-|.+||...|+|++....+.+.++.
T Consensus 23 r~~ree~~I~aWEn~qkaKaea~m~k~E~klE 54 (111)
T PF03763_consen 23 RYEREEAKIQAWENLQKAKAEAEMRKIEEKLE 54 (111)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677899999999999999998888877653
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=59.56 E-value=35 Score=25.91 Aligned_cols=53 Identities=23% Similarity=0.351 Sum_probs=39.4
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhHhHHHhhhhhhhhH
Q 032322 81 SHDRDVALAEVEKEKRESFIKAWEESEKTKAENKAQKKLSAVAAWENSKKASL 133 (143)
Q Consensus 81 s~drD~~Larve~EKR~s~IkAWEE~EKaK~~nra~k~~s~I~aWEn~kKAk~ 133 (143)
.++|....-......+.+.|+.|-+++...+.++...-...|+.|=...+...
T Consensus 14 ~l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~~~l~~y~e~~r~e~ 66 (149)
T PF07352_consen 14 ELQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLEGLLQAYAEANRDEL 66 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHhc
Confidence 34555555555667777888888888888888888888888888876655543
No 5
>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=30.99 E-value=50 Score=26.59 Aligned_cols=30 Identities=37% Similarity=0.449 Sum_probs=23.2
Q ss_pred ccCCCCchhHHHHHHHHHHHHHHHHHHHHHHh
Q 032322 75 EKKISGSHDRDVALAEVEKEKRESFIKAWEES 106 (143)
Q Consensus 75 ~k~~~gs~drD~~Larve~EKR~s~IkAWEE~ 106 (143)
.|...|.+||+++|.-++.+. ....-|++.
T Consensus 57 ~K~pTG~fdRe~Ll~~lekea--~~~~dre~~ 86 (147)
T PF03250_consen 57 EKPPTGPFDREALLDYLEKEA--KELKDREDL 86 (147)
T ss_pred CCCCCCCcCHHHHHHHHHHHH--HHHHhhhcc
Confidence 677899999999999997554 344577764
No 6
>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=29.63 E-value=1.3e+02 Score=22.85 Aligned_cols=38 Identities=18% Similarity=0.438 Sum_probs=32.3
Q ss_pred HHhhhhhHHHHHHHhhHhHHHhhhhhhhhHHHHhhhhh
Q 032322 104 EESEKTKAENKAQKKLSAVAAWENSKKASLEAKLKKIE 141 (143)
Q Consensus 104 EE~EKaK~~nra~k~~s~I~aWEn~kKAk~EAelkKiE 141 (143)
-..+.+.+++.+..++..|..|-..+.+.+..++..++
T Consensus 15 l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~ 52 (149)
T PF07352_consen 15 LQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLE 52 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788889999999999999999999998887765
No 7
>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=26.47 E-value=51 Score=24.75 Aligned_cols=23 Identities=43% Similarity=0.410 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHH
Q 032322 95 KRESFIKAWEESEKTKAENKAQK 117 (143)
Q Consensus 95 KR~s~IkAWEE~EKaK~~nra~k 117 (143)
.|.|-|++|+.+|++-+--=|++
T Consensus 44 l~eSkI~~~l~sEra~h~liFhk 66 (100)
T PF12856_consen 44 LRESKIKAWLSSERAAHCLIFHK 66 (100)
T ss_pred HHHHHHHHHHHHHHHhcceeccc
Confidence 78899999999999765544554
No 8
>cd07663 BAR_SNX5 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It
Probab=25.70 E-value=3.3e+02 Score=22.83 Aligned_cols=46 Identities=17% Similarity=0.174 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhHhHHHhhhhhhh
Q 032322 84 RDVALAEVEKEKRESFIKAWEESEKTKAENKAQKKLSAVAAWENSKKA 131 (143)
Q Consensus 84 rD~~Larve~EKR~s~IkAWEE~EKaK~~nra~k~~s~I~aWEn~kKA 131 (143)
||.--+|--.-.|+.....|+.+.++-.-.|. +-..|..||+.++.
T Consensus 116 r~~~A~K~ll~rR~ral~~~e~A~~~L~KaR~--k~kev~~aE~~~~e 161 (218)
T cd07663 116 LNIEAAKDLLYRRARALADYENSNKALDKARL--KSKDVKQAEAHQQE 161 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hhhhHHHHHHHHHH
Confidence 56666777888899999999999977776665 46678889988774
No 9
>KOG2962 consensus Prohibitin-related membrane protease subunits [General function prediction only]
Probab=24.83 E-value=1.2e+02 Score=27.07 Aligned_cols=41 Identities=34% Similarity=0.281 Sum_probs=33.6
Q ss_pred CchhHHHHHHHHHHHHHHHHH--HHHHHhhhhhHHHHHHHhhH
Q 032322 80 GSHDRDVALAEVEKEKRESFI--KAWEESEKTKAENKAQKKLS 120 (143)
Q Consensus 80 gs~drD~~Larve~EKR~s~I--kAWEE~EKaK~~nra~k~~s 120 (143)
.-|..--.|+..++|||.+-| .++-..||+|+++-|++-+.
T Consensus 225 a~I~~qqkl~EKetekr~~eiE~~~~LarekskADAe~Y~a~k 267 (322)
T KOG2962|consen 225 AKILMQQKLMEKETEKRISEIEDAAFLAREKSKADAEYYRALK 267 (322)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHhHhhhhhhccHHHHHHHH
Confidence 346667778889999999998 67888999999999987653
No 10
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=23.15 E-value=2.2e+02 Score=24.12 Aligned_cols=47 Identities=17% Similarity=0.182 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhHhHHHhhhhhhh
Q 032322 83 DRDVALAEVEKEKRESFIKAWEESEKTKAENKAQKKLSAVAAWENSKKA 131 (143)
Q Consensus 83 drD~~Larve~EKR~s~IkAWEE~EKaK~~nra~k~~s~I~aWEn~kKA 131 (143)
-||.--+|--.-.|+.....|+-++++-.-.|.+. ..|..||+.++.
T Consensus 115 ~r~~~A~Kdll~rR~r~l~~~enA~k~L~KaR~~~--kev~~aE~~~~~ 161 (218)
T cd07662 115 LRESQAAKDLLYRRSRSLVDYENANKALDKARAKN--KDVLQAETTQQL 161 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--ChHHHHHHHHHH
Confidence 36777788888999999999999998877777664 778889988763
Done!