Query psy11577
Match_columns 89
No_of_seqs 101 out of 252
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 22:03:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11577.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11577hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07815 SRPBCC_PITP Lipid-bind 99.9 5.9E-25 1.3E-29 169.8 4.2 61 28-88 109-169 (251)
2 cd08889 SRPBCC_PITPNM1-2_like 99.9 7.4E-25 1.6E-29 170.1 4.1 61 28-88 111-171 (260)
3 cd08890 SRPBCC_PITPNC1_like Li 99.9 8.9E-25 1.9E-29 168.9 4.4 61 28-88 108-168 (250)
4 cd08888 SRPBCC_PITPNA-B_like L 99.9 9.2E-25 2E-29 169.4 4.4 61 28-88 110-171 (258)
5 PF02121 IP_trans: Phosphatidy 99.9 2.8E-24 6.1E-29 165.7 1.8 61 28-88 111-171 (254)
6 KOG3668|consensus 99.9 2.6E-23 5.7E-28 161.9 4.7 61 28-88 112-172 (269)
7 PF15484 DUF4642: Domain of un 44.7 14 0.0003 27.6 1.4 21 52-72 130-150 (156)
8 PF08114 PMP1_2: ATPase proteo 26.9 28 0.00061 21.0 0.5 12 2-13 29-40 (43)
9 PF02731 SKIP_SNW: SKIP/SNW do 17.8 2.1E+02 0.0046 21.2 3.7 29 51-88 17-45 (158)
10 TIGR02617 tnaA_trp_ase tryptop 17.0 99 0.0022 26.6 2.0 36 40-81 32-79 (467)
No 1
>cd07815 SRPBCC_PITP Lipid-binding SRPBCC domain of Class I and Class II Phosphatidylinositol Transfer Proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the phosphatidylinositol transfer protein (PITP) family of lipid transfer proteins. This family of proteins includes Class 1 PITPs (PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator and related proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2, PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and related proteins). The PITP family belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns
Probab=99.90 E-value=5.9e-25 Score=169.81 Aligned_cols=61 Identities=46% Similarity=0.645 Sum_probs=60.0
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|.+|+|+++|||+||+++|++|+|++||||+|++++++|+++|||++|+|.||||||
T Consensus 109 IET~h~~d~g~~eNv~~L~~~~L~~ReV~~IDIa~d~~~~~dYk~eeDp~~f~S~kTgRGP 169 (251)
T cd07815 109 IESMHKPDLGTQENAHNLSAEQLAQRKVVVIDIANDSVASKDYKPEEDPKLFKSKKTGRGP 169 (251)
T ss_pred EEEEEcCCCCCcccccCCCHHHHhCcEEEEEeccCCCCCcccCCcccCCchhcccccCCCC
Confidence 5799999999999999999999999999999999999999999999999999999999999
No 2
>cd08889 SRPBCC_PITPNM1-2_like Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs). This subgroup includes an N-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class II phosphatidylinositol transfer protein (PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal domain-interacting receptor2) and PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related proteins. These are membrane associated multidomain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Ablation of the mouse gene en
Probab=99.90 E-value=7.4e-25 Score=170.07 Aligned_cols=61 Identities=38% Similarity=0.529 Sum_probs=59.9
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|++|+|+++|||+||+++|++|+|++||||+|+|++++|+++|||++|+|+||||||
T Consensus 111 IET~h~~d~g~~eNv~~L~~~~L~~ReV~~IDIa~d~v~~~dYk~eeDP~~f~S~kTgRGP 171 (260)
T cd08889 111 IETYYFDDAGEQENVFNLSPAELRQRIIDFIDIVKDPVPGSDYKAEEDPKLYVSEKTGRGP 171 (260)
T ss_pred EEEEEcCCCCCccccccCCHHHhhCceEEEEeccCCCCCccccCcccCcchhcccccCCCC
Confidence 4799999999999999999999999999999999999999999999999999999999999
No 3
>cd08890 SRPBCC_PITPNC1_like Lipid-binding SRPBCC domain of mammalian PITPNC1,and related proteins (Class IIB PITPs). This subgroup includes the N-terminal SRPBCC (START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of mammalian Class IIB phosphatidylinositol transfer protein (PITP), PITPNC1/RdgBbeta, and related proteins. These are metazoan proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Mammalian PITPNC1 contains an amino-terminal SRPBCC PITP-like domain and a short carboxyl-terminal domain. It is a cytoplasmic protein, and is ubiquitously
Probab=99.90 E-value=8.9e-25 Score=168.89 Aligned_cols=61 Identities=39% Similarity=0.445 Sum_probs=59.8
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|.+|+|+++|||+||+++|++|+|++||||+|+|++++|++++||++|+|.||||||
T Consensus 108 IET~h~~d~g~~eN~~~L~~~~L~~ReV~~IDIa~d~v~~~dYk~eeDp~~f~S~kTgRGP 168 (250)
T cd08890 108 IETKYEDNKGKSENCIFLSEAELSEREVCHLDIAYDEIPEKYYKEEEDPKYFKSEKTGRGP 168 (250)
T ss_pred EEEEEcCCCCCccccccCCHHHhcCceEEEEecccCCCCcccCCcccCCccccccccCCCC
Confidence 4789999999999999999999999999999999999999999999999999999999999
No 4
>cd08888 SRPBCC_PITPNA-B_like Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cy
Probab=99.90 E-value=9.2e-25 Score=169.41 Aligned_cols=61 Identities=46% Similarity=0.628 Sum_probs=59.6
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCC-CCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDP-VSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~-i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|.+|+|+++|||+||+++|++|+|++||||+|+ |++++|+++|||++|+|+||||||
T Consensus 110 IET~h~~d~g~~eNv~~L~~e~L~~ReV~~IDIa~d~~~~~~dYk~eeDP~~f~S~kTgRGP 171 (258)
T cd08888 110 IETWHKPDLGTQENVHNLDPEEWKEVEVVYIDIADRSQVDPKDYKADEDPAKFQSEKTGRGP 171 (258)
T ss_pred EEEEEcCCCCCccccccCCHHHHhCcEEEEEecccCCcCCcccCCcccCcccccccccCCCC
Confidence 5799999999999999999999999999999999999 599999999999999999999999
No 5
>PF02121 IP_trans: Phosphatidylinositol transfer protein; InterPro: IPR001666 Phosphatidylinositol transfer protein (PITP) is a ubiquitous cytosolic protein, thought to be involved in transport of phospholipids from their site of synthesis in the endoplasmic reticulum and Golgi to other cell membranes []. More recently, PITP has been shown to be an essential component of the polyphosphoinositide synthesis machinery and is hence required for proper signalling by epidermal growth factor and f-Met-Leu-Phe, as well as for exocytosis. The role of PITP in polyphosphoinositide synthesis may also explain its involvement in intracellular vesicular traffic [].; GO: 0006810 transport, 0005622 intracellular; PDB: 1T27_A 1KCM_A 2A1L_A 1UW5_C.
Probab=99.89 E-value=2.8e-24 Score=165.67 Aligned_cols=61 Identities=51% Similarity=0.713 Sum_probs=42.8
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|.+|+|+++|||+||+++|++|+|++||||+|++++++|+++|||++|+|+||||||
T Consensus 111 IET~~~~d~G~~eNv~~L~~~~lk~reV~~IDI~~d~i~~~dyk~~eDp~~f~S~ktgRGP 171 (254)
T PF02121_consen 111 IETMHKPDNGTSENVFNLSPEELKKREVVFIDIANDPISPKDYKEEEDPTKFKSKKTGRGP 171 (254)
T ss_dssp EEEEEESSSS--TTTT---HHHHTTSEEEEE-TTGGGS-CCC--GGG-CCC---TTT----
T ss_pred EEEEEcCCCCCcCcccCCCHHHhcCceEEEEEecCCcccccccCcccCchheEecCCCCCC
Confidence 3789999999999999999999999999999999999999999999999999999999999
No 6
>KOG3668|consensus
Probab=99.88 E-value=2.6e-23 Score=161.91 Aligned_cols=61 Identities=43% Similarity=0.621 Sum_probs=59.9
Q ss_pred cccccCCCCCCCCCcCCCCcccccceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 28 AGEFGPEELPGFGLVHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 28 ~~~~~~~D~G~~ENVf~Ls~~eLk~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|+|.+|+|+++|||+|++++|++|+|++||||+|+|++.+|++++||++|+|.||||||
T Consensus 112 IeT~~~~d~G~~eNvf~l~~~~~~~rei~~IDIa~d~v~~~dyk~eeDP~~f~s~kTgRGp 172 (269)
T KOG3668|consen 112 IETIYLDDAGTQENVFGLDPEDLNQREIVFIDIADDPVPPNDYKAEEDPKLFQSEKTGRGP 172 (269)
T ss_pred EEEEEcCCCCCCCCcccCChhhcceeEEEEEEeecCCCCccccCcccCchhheecccccCC
Confidence 4799999999999999999999999999999999999999999999999999999999999
No 7
>PF15484 DUF4642: Domain of unknown function (DUF4642)
Probab=44.68 E-value=14 Score=27.64 Aligned_cols=21 Identities=29% Similarity=0.591 Sum_probs=16.7
Q ss_pred ceeEEeeeccCCCCCCCCCCC
Q psy11577 52 VREVVHIDIGNDPVSAGDYKE 72 (89)
Q Consensus 52 ~REV~~IDIA~D~i~~kdYk~ 72 (89)
.|||++||+.++.-.++.|.-
T Consensus 130 SrEVIVVDLG~e~p~prsYtr 150 (156)
T PF15484_consen 130 SREVIVVDLGKEYPTPRSYTR 150 (156)
T ss_pred eeeEEEEECCCCCCchhhHHH
Confidence 589999999998766666653
No 8
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=26.88 E-value=28 Score=21.00 Aligned_cols=12 Identities=42% Similarity=0.883 Sum_probs=9.6
Q ss_pred chhHHHhhhcCc
Q psy11577 2 KYDKWEKRKKSD 13 (89)
Q Consensus 2 ~~~~~~~~~~~~ 13 (89)
-|.||..|+.+-
T Consensus 29 iYRKw~aRkr~l 40 (43)
T PF08114_consen 29 IYRKWQARKRAL 40 (43)
T ss_pred HHHHHHHHHHHH
Confidence 389999998763
No 9
>PF02731 SKIP_SNW: SKIP/SNW domain; InterPro: IPR004015 SKIP (SKI-interacting protein) is an essential spliceosomal component and transcriptional coregulator, which may provide regulatory coupling of transcription initiation and splicing []. SKIP was identified in a yeast 2-hybrid screen, where it was shown to interact with both the cellular and viral forms of SKI through the highly conserved region on SKIP known as the SNW domain []. SKIP is now known to interact with a number of other proteins as well. SKIP potentiates the activity of important transcription factors, such as vitamin D receptor, CBF1 (RBP-Jkappa), Smad2/3, and MyoD. It works with Ski in overcoming pRb-mediated cell cycle arrest, and it is targeted by the viral transactivators EBNA2 and E7 []. This entry represents the SNW domain.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=17.80 E-value=2.1e+02 Score=21.24 Aligned_cols=29 Identities=34% Similarity=0.548 Sum_probs=22.6
Q ss_pred cceeEEeeeccCCCCCCCCCCCCCCCCCceecccCCCC
Q psy11577 51 KVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGV 88 (89)
Q Consensus 51 k~REV~~IDIA~D~i~~kdYk~eEDPt~F~S~KTGRGP 88 (89)
.+|.|-+++..-||+.+ ..|+..|.-+||
T Consensus 17 ~~RiIk~ve~~~DPl~P---------pkfK~kkv~~~~ 45 (158)
T PF02731_consen 17 KQRIIKMVEKQQDPLEP---------PKFKHKKVPRGP 45 (158)
T ss_pred CeeEEEEEecCCCCCCc---------chhhcccCCCCC
Confidence 68999999999998654 477777777776
No 10
>TIGR02617 tnaA_trp_ase tryptophanase, leader peptide-associated. Members of this family belong to the beta-eliminating lyase family (pfam01212) and act as tryptophanase (L-tryptophan indole-lyase). The tryptophanases of this family, as a rule, are found with a tryptophanase leader peptide (TnaC) encoded upstream. Both tryptophanases (4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are found between trusted and noise cutoffs, but this model captures nearly all tryptophanases for which the leader peptide gene tnaC can be found upstream.
Probab=16.95 E-value=99 Score=26.57 Aligned_cols=36 Identities=19% Similarity=0.162 Sum_probs=24.7
Q ss_pred CCcCCCCcccccceeEEeeeccCCCCCC------------CCCCCCCCCCCcee
Q psy11577 40 GLVHDLPADKLKVREVVHIDIGNDPVSA------------GDYKETEDPAKFKS 81 (89)
Q Consensus 40 ENVf~Ls~~eLk~REV~~IDIA~D~i~~------------kdYk~eEDPt~F~S 81 (89)
-|+|+|..++ ++||+..|.+.. .|=.=-+||+.++-
T Consensus 32 yN~f~l~s~d------V~IDLrSDTgT~apS~~m~aAM~~GDD~Y~gdpSv~~L 79 (467)
T TIGR02617 32 MNPFLLDSED------VFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYAL 79 (467)
T ss_pred CCcccCCCCC------eEEECccCCCCCCCCHHHHHHHHcCCcccccCchHHHH
Confidence 5999987555 389999999764 33333467776644
Done!