Query 011479
Match_columns 484
No_of_seqs 51 out of 53
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 01:49:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011479.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011479hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03494 Beta-APP: Beta-amyloi 22.0 59 0.0013 24.9 1.5 11 363-373 22-32 (39)
2 PHA01732 proline-rich protein 21.0 1.6E+02 0.0034 26.3 4.1 7 60-66 61-67 (94)
3 KOG3671 Actin regulatory prote 15.8 1.6E+03 0.036 25.6 14.7 52 261-324 442-493 (569)
4 PF00164 Ribosom_S12_S23: Ribo 15.5 1.5E+02 0.0033 27.3 3.0 38 432-470 62-102 (122)
5 cd00102 IPT Immunoglobulin-lik 13.1 1.6E+02 0.0035 22.7 2.1 20 355-374 15-36 (89)
6 KOG3671 Actin regulatory prote 12.3 7.3E+02 0.016 28.2 7.4 8 14-21 369-376 (569)
7 KOG1924 RhoA GTPase effector D 11.1 6E+02 0.013 30.6 6.5 7 432-438 827-833 (1102)
8 COG4815 Uncharacterized protei 11.0 2.1E+02 0.0046 27.2 2.6 33 337-369 60-92 (145)
9 cd01180 IPT_plexin_repeat1 Fir 10.8 1.5E+02 0.0033 24.6 1.5 18 354-371 14-31 (94)
10 KOG1690 emp24/gp25L/p24 family 10.4 1.3E+02 0.0028 30.3 1.0 64 281-352 27-91 (215)
No 1
>PF03494 Beta-APP: Beta-amyloid peptide (beta-APP); InterPro: IPR013803 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. This entry represents the amyloid-beta peptide (A-beta), which originates as a breakdown product from the cleavage of amyloid-beta precursor protein (APP, or A4), an integral, glycosylated membrane brain protein. More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein [].; GO: 0005488 binding, 0016021 integral to membrane; PDB: 2LMQ_F 3JTI_B 2LMO_B 3MOQ_D 2LNQ_E 2LMP_G 2BEG_B 1AMC_A 3OW9_B 3U0T_F ....
Probab=22.04 E-value=59 Score=24.94 Aligned_cols=11 Identities=45% Similarity=0.903 Sum_probs=9.4
Q ss_pred ccCcceeEEEe
Q 011479 363 GENKGAFMEVI 373 (484)
Q Consensus 363 GENKGAtMev~ 373 (484)
|.||||++.|-
T Consensus 22 gSNKGAIIGLM 32 (39)
T PF03494_consen 22 GSNKGAIIGLM 32 (39)
T ss_dssp SSSSSEEEEEE
T ss_pred CCCCceEEEEE
Confidence 89999998764
No 2
>PHA01732 proline-rich protein
Probab=20.99 E-value=1.6e+02 Score=26.35 Aligned_cols=7 Identities=43% Similarity=0.515 Sum_probs=4.6
Q ss_pred Ccccccc
Q 011479 60 AVGVSSV 66 (484)
Q Consensus 60 a~gvaSv 66 (484)
+.|+|||
T Consensus 61 a~gTasL 67 (94)
T PHA01732 61 AGGTASL 67 (94)
T ss_pred ccCccee
Confidence 3677775
No 3
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=15.84 E-value=1.6e+03 Score=25.57 Aligned_cols=52 Identities=21% Similarity=0.295 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCCCCcCCCCCCCCCCCccccceEEeecccCCCCCCCCCCCCCCCCCCCCCCc
Q 011479 261 ATAPPPSPLTLPPPQFTSKAETQPTIPAETEQKTVLVQTRSEKPKSWFNGTGNHFDETHKPSSY 324 (484)
Q Consensus 261 ~tapPPSpLtLPps~~ks~~e~e~kip~~~eqktvlvqk~~~~pKp~~~~~~~~~~~t~~~s~~ 324 (484)
...|||+.+++|+.-.-. +.|-.+.++--|. .....+++-+.++-|++++.-
T Consensus 442 gppPPP~~~~~Pp~~aga------~aPp~p~~~~al~------~~i~~G~ql~~ve~t~~~~~d 493 (569)
T KOG3671|consen 442 GPPPPPSAPIAPPQGAGA------AAPPAPPARPALL------DAIAPGGQLKKVETTALSSGD 493 (569)
T ss_pred CCCCCCCccCCCCCccCC------CCCCCCCCccccc------cccCccccccceeeccCcCcc
Confidence 345667777788743321 1122222222222 233455666667767766533
No 4
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=15.46 E-value=1.5e+02 Score=27.28 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=29.8
Q ss_pred ceeee---ccccceeecceEeeccccCCCCccEEEeccCCCC
Q 011479 432 MGAFM---NSNVQGVNNSIVFHSSCSHHDPGVHLSLSRKPSG 470 (484)
Q Consensus 432 i~ayv---NSNVQ~VNNSil~~SSc~~~DPGVHl~ls~k~~g 470 (484)
+.||| ..|+|. |+-+|+.+-.-.+=|||++.+-++..|
T Consensus 62 v~AyIPg~Ghnlqe-hs~VLVrGgrv~DlPGVkykvVRG~~D 102 (122)
T PF00164_consen 62 VTAYIPGEGHNLQE-HSVVLVRGGRVGDLPGVKYKVVRGVYD 102 (122)
T ss_dssp EEEEC-SSSCCSTT-TSEEEEEEESBTTSTTECEEBETTSTT
T ss_pred EEEEecCCcccccc-cceEEEeccccCCCCceEEEEEeeccc
Confidence 67886 577776 666788887778889999999987643
No 5
>cd00102 IPT Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers.
Probab=13.09 E-value=1.6e+02 Score=22.66 Aligned_cols=20 Identities=35% Similarity=0.398 Sum_probs=15.9
Q ss_pred ccEEEEEeccCccee--EEEec
Q 011479 355 GMRVITIAGENKGAF--MEVIR 374 (484)
Q Consensus 355 G~rVITLAGENKGAt--Mev~~ 374 (484)
|-..|||.|+|-+.. ++|.-
T Consensus 15 GGt~itI~G~~f~~~~~~~v~~ 36 (89)
T cd00102 15 GGTEVTITGSNFGSGSNLRVTF 36 (89)
T ss_pred CCeEEEEEEECCCCCCcEEEEE
Confidence 567999999999887 55554
No 6
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=12.28 E-value=7.3e+02 Score=28.19 Aligned_cols=8 Identities=50% Similarity=0.995 Sum_probs=3.2
Q ss_pred cCCCCCCC
Q 011479 14 LPSIGRPA 21 (484)
Q Consensus 14 ~pS~~~~a 21 (484)
.|+-+|+.
T Consensus 369 vPs~ar~P 376 (569)
T KOG3671|consen 369 VPSAARPP 376 (569)
T ss_pred CCCCCCCC
Confidence 34444433
No 7
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=11.15 E-value=6e+02 Score=30.56 Aligned_cols=7 Identities=57% Similarity=1.108 Sum_probs=3.5
Q ss_pred ceeeecc
Q 011479 432 MGAFMNS 438 (484)
Q Consensus 432 i~ayvNS 438 (484)
++-|||+
T Consensus 827 ~GNyMn~ 833 (1102)
T KOG1924|consen 827 VGNYMNS 833 (1102)
T ss_pred Hhccccc
Confidence 3455554
No 8
>COG4815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=11.02 E-value=2.1e+02 Score=27.19 Aligned_cols=33 Identities=21% Similarity=0.404 Sum_probs=0.0
Q ss_pred hhcccccccccCCCCCCCccEEEEEeccCccee
Q 011479 337 AKNGKVHRKQFSSDSDEVGMRVITIAGENKGAF 369 (484)
Q Consensus 337 ske~kg~~k~~ssdSeD~G~rVITLAGENKGAt 369 (484)
.||.-|.++.++.+.-.+|+.||.|.++|+|-+
T Consensus 60 ~rde~g~n~Pfs~~~~a~~LlI~V~de~~~G~F 92 (145)
T COG4815 60 QRDEGGQNQPFSDDGMAAGLLIFVIDEVLRGVF 92 (145)
T ss_pred EeCCCCCcCCCCcccccCeeEEEEEccccceEE
No 9
>cd01180 IPT_plexin_repeat1 First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=10.85 E-value=1.5e+02 Score=24.56 Aligned_cols=18 Identities=33% Similarity=0.353 Sum_probs=0.0
Q ss_pred CccEEEEEeccCcceeEE
Q 011479 354 VGMRVITIAGENKGAFME 371 (484)
Q Consensus 354 ~G~rVITLAGENKGAtMe 371 (484)
.|-..|||-|+|-|+.|+
T Consensus 14 ~GGT~vTI~G~nl~~~~~ 31 (94)
T cd01180 14 EGGTRLTICGSNLGLRKN 31 (94)
T ss_pred CCCEEEEEEEEcCCCCcc
No 10
>KOG1690 consensus emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=10.44 E-value=1.3e+02 Score=30.25 Aligned_cols=64 Identities=27% Similarity=0.225 Sum_probs=0.0
Q ss_pred CCCCCCCCccccceEEeecccCCCCCCCCCCCCCCCCCCCCCCccCcCCcchhhh-hhhcccccccccCCCCC
Q 011479 281 ETQPTIPAETEQKTVLVQTRSEKPKSWFNGTGNHFDETHKPSSYAHRGNHEVHKE-VAKNGKVHRKQFSSDSD 352 (484)
Q Consensus 281 e~e~kip~~~eqktvlvqk~~~~pKp~~~~~~~~~~~t~~~s~~~~~~k~e~~kd-eske~kg~~k~~ssdSe 352 (484)
++|.|-=++-=.|-.|| +-+-+..-|.+.+++..+ +++++-|-.+|| +.|||.+.+++.++..+
T Consensus 27 ~~e~KCF~eelpk~tmv-~G~yk~qlyd~~~~~y~~-------~p~~gm~VeV~e~fdnnh~Vl~q~~ss~G~ 91 (215)
T KOG1690|consen 27 GTEKKCFIEELPKGTMV-TGNYKAQLYDDQLKGYGS-------YPNIGMHVEVKETFDNNHVVLSQQYSSEGD 91 (215)
T ss_pred CCcccchhhhCCCCcEE-Eeeeeeeeecchhccccc-------CCCceEEEEeecCCCCceEEEeecCCCCCc
Done!