Query psy3211
Match_columns 84
No_of_seqs 104 out of 341
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:11:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3211hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00372 Hemocyanin_M: Hemocya 100.0 5.8E-40 1.3E-44 249.1 4.9 75 7-81 46-125 (278)
2 KOG2203|consensus 36.1 17 0.00036 32.2 0.9 22 59-80 277-298 (772)
3 PF03494 Beta-APP: Beta-amyloi 35.6 13 0.00027 21.5 0.0 15 21-35 10-24 (39)
4 cd07278 PX_RICS_like The phosp 30.8 33 0.00071 24.0 1.5 14 64-78 83-96 (114)
5 PF00747 Viral_DNA_bp: ssDNA b 28.1 32 0.0007 31.9 1.3 18 66-83 433-452 (1122)
6 PHA03367 single-stranded DNA b 27.2 39 0.00085 31.4 1.7 18 66-83 411-430 (1115)
7 PHA03362 single-stranded bindi 25.2 44 0.00095 31.3 1.7 18 66-83 457-476 (1189)
8 cd07299 PX_TCGAP The phosphoin 24.3 51 0.0011 23.1 1.5 14 64-78 82-95 (113)
9 PF02843 GARS_C: Phosphoribosy 23.2 40 0.00088 21.7 0.8 13 25-37 81-93 (93)
10 cd07298 PX_RICS The phosphoino 20.4 67 0.0015 22.5 1.5 12 66-78 86-97 (115)
No 1
>PF00372 Hemocyanin_M: Hemocyanin, copper containing domain; InterPro: IPR000896 Haemocyanins are copper-containing oxygen transport proteins found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases [], but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit []. Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases []. Larval storage proteins (LSP) [] are proteins from the hemolymph of insects, which may serve as a store of amino acids for synthesis of adult proteins. There are two classes of LSP's, arylphorins, which are rich in aromatic amino acids, and methionine-rich LSP's. LSP's forms hexameric complexes. LSP's are structurally related to arthropods hemocyanins. This entry represents the copper-containg domain that usually occurs in the centre of haemocyanin proteins.; GO: 0005344 oxygen transporter activity, 0006810 transport; PDB: 1HCY_A 1HC1_C 3IXV_E 3IXW_L 3GWJ_F 3HHS_A 1NOL_A 1LLA_A 1OXY_A 1LL1_A.
Probab=100.00 E-value=5.8e-40 Score=249.14 Aligned_cols=75 Identities=35% Similarity=0.567 Sum_probs=68.1
Q ss_pred EEEEecCCCCCCC-CCCceeceehhhhchhHHHHHHHhhCCCCCC----CCCcccchhhhHHHHHHHHHHHhhhhhcCCC
Q psy3211 7 SLYFDDKSSSGLQ-EQEDYLEYYRHDLGINLFHYHWHEANPFAGN----LVGNHRRGESFYYMHQQMLARQSYGLECGVH 81 (84)
Q Consensus 7 ~~~i~~nyt~~~~-~~e~~LsYFtEDigLN~yy~~~h~~yP~w~~----~~~~~RrGElf~y~hqQllARY~LERlSn~~ 81 (84)
.++||+|||++.. ++|++||||||||||||||++||++||+|+. +..|+||||+||||||||||||+|||||||.
T Consensus 46 ~~vi~~nyt~~~~~~~E~~LsYFtEDIGLNs~~~~~h~~yP~w~~~~~~~~~kdRrGElfyY~h~QlLARY~lERlSngL 125 (278)
T PF00372_consen 46 PVVIPANYTGWYTQNPEQKLSYFTEDIGLNSYYYYWHLVYPFWMNGEEYGLNKDRRGELFYYMHQQLLARYYLERLSNGL 125 (278)
T ss_dssp EEEEESTSSSGTTSSGGGGGHHHHT-HHHHHHHHHHHHHS-TTBSSHHHSSHHTTHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred eeEEeccccccccCChhHhHHHHhhcccHHHHHHHHHhcCcccccccccccccccchhhhHHHHHHHHHHHHHHHhccCC
Confidence 5899999999855 8999999999999999999999999999983 5789999999999999999999999999984
No 2
>KOG2203|consensus
Probab=36.09 E-value=17 Score=32.21 Aligned_cols=22 Identities=9% Similarity=-0.117 Sum_probs=18.0
Q ss_pred hhhHHHHHHHHHHHhhhhhcCC
Q psy3211 59 ESFYYMHQQMLARQSYGLECGV 80 (84)
Q Consensus 59 Elf~y~hqQllARY~LERlSn~ 80 (84)
.|=+=.||||+|++.+|-++|-
T Consensus 277 DLDLPtqqvlvAt~rceEIanE 298 (772)
T KOG2203|consen 277 DLDLPTQQVLVATVRCEEIANE 298 (772)
T ss_pred CCCCchhhhHHhhhhHHHHHHH
Confidence 3445689999999999998874
No 3
>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=35.61 E-value=13 Score=21.54 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=12.8
Q ss_pred CCceeceehhhhchh
Q psy3211 21 QEDYLEYYRHDLGIN 35 (84)
Q Consensus 21 ~e~~LsYFtEDigLN 35 (84)
..+||-+|.||+|-|
T Consensus 10 ~~~klvf~aEDvgSN 24 (39)
T PF03494_consen 10 YHKKLVFLAEDVGSN 24 (39)
T ss_dssp CCCCCCCCCCCCSSS
T ss_pred EeeEEEEEhhHcCCC
Confidence 467999999999966
No 4
>cd07278 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and d
Probab=30.82 E-value=33 Score=24.02 Aligned_cols=14 Identities=14% Similarity=-0.033 Sum_probs=11.0
Q ss_pred HHHHHHHHHhhhhhc
Q psy3211 64 MHQQMLARQSYGLEC 78 (84)
Q Consensus 64 ~hqQllARY~LERlS 78 (84)
+-.|||++| |||||
T Consensus 83 ~~~~~l~~Y-L~RlS 96 (114)
T cd07278 83 NLHQVLSDY-LKRLS 96 (114)
T ss_pred HHHHHHHHH-HHHHH
Confidence 457888886 88988
No 5
>PF00747 Viral_DNA_bp: ssDNA binding protein; InterPro: IPR000635 Although the overall picture of Human cytomegalovirus (HHV-5) DNA synthesis appears typical of the Herpesviruses, some novel features are emerging. Six herpesvirus-group-common genes encode proteins that likely constitute the replication fork machinery, including a two-subunit DNA polymerase, a helicas-primase complex and a single-stranded DNA-binding protein []. The Human herpesvirus 1 (HHV-1) single-strand DNA-binding protein ICP8 is a 128kDa zinc metalloprotein. Photoaffinity labeling has shown that the region encompassing residues 368-902 contains the single-strand DNA-binding site of ICP8 []. The HHHV-1 UL5, UL8, and UL52 genes encode an essential heterotrimeric DNA helicase-primase that is responsible for concomitant DNA unwinding and primer synthesis at the viral DNA replication fork. ICP8 may stimulate DNA unwinding and enable bypass of cisplatin damaged DNA by recruiting the helicase-primase to the DNA [].; GO: 0003697 single-stranded DNA binding, 0006260 DNA replication, 0042025 host cell nucleus; PDB: 1URJ_A.
Probab=28.13 E-value=32 Score=31.92 Aligned_cols=18 Identities=28% Similarity=0.117 Sum_probs=10.6
Q ss_pred HHHHHH--HhhhhhcCCCCC
Q psy3211 66 QQMLAR--QSYGLECGVHLG 83 (84)
Q Consensus 66 qQllAR--Y~LERlSn~~~~ 83 (84)
-||||| |||||.+.+..|
T Consensus 433 PqlLAr~~~YLerc~~~~~~ 452 (1122)
T PF00747_consen 433 PQLLARLCYYLERCDHYKSG 452 (1122)
T ss_dssp HHHHHHHHHHHTT----S--
T ss_pred HHHHHHHHHHHHHhhccccC
Confidence 499999 799999988765
No 6
>PHA03367 single-stranded DNA binding protein; Provisional
Probab=27.21 E-value=39 Score=31.41 Aligned_cols=18 Identities=22% Similarity=0.084 Sum_probs=15.4
Q ss_pred HHHHHH--HhhhhhcCCCCC
Q psy3211 66 QQMLAR--QSYGLECGVHLG 83 (84)
Q Consensus 66 qQllAR--Y~LERlSn~~~~ 83 (84)
-||||| |||||.+.+..|
T Consensus 411 PqLLAr~~~YLerc~~~~s~ 430 (1115)
T PHA03367 411 PQLLARYCYYLQFCQHQKSS 430 (1115)
T ss_pred HHHHHHHHHHHHHhhccccC
Confidence 499999 799999988765
No 7
>PHA03362 single-stranded binding protein UL29; Provisional
Probab=25.21 E-value=44 Score=31.33 Aligned_cols=18 Identities=28% Similarity=0.145 Sum_probs=15.5
Q ss_pred HHHHHH--HhhhhhcCCCCC
Q psy3211 66 QQMLAR--QSYGLECGVHLG 83 (84)
Q Consensus 66 qQllAR--Y~LERlSn~~~~ 83 (84)
-||||| |||||.+.+..|
T Consensus 457 PqLlAr~~~YLeRc~~~~~~ 476 (1189)
T PHA03362 457 PQLLARLLFYLERCDAGAFG 476 (1189)
T ss_pred HHHHHHHHHHHHHhhccccC
Confidence 489999 799999988775
No 8
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=24.28 E-value=51 Score=23.06 Aligned_cols=14 Identities=7% Similarity=0.048 Sum_probs=10.7
Q ss_pred HHHHHHHHHhhhhhc
Q psy3211 64 MHQQMLARQSYGLEC 78 (84)
Q Consensus 64 ~hqQllARY~LERlS 78 (84)
+-.|||++| |+|||
T Consensus 82 ~~~~~l~~Y-L~RlS 95 (113)
T cd07299 82 ILTPLLSEY-LNRLT 95 (113)
T ss_pred HHHHHHHHH-HHHHH
Confidence 357888886 88887
No 9
>PF02843 GARS_C: Phosphoribosylglycinamide synthetase, C domain; InterPro: IPR020560 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the C-domain, which is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005480 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 2YW2_B 2YYA_A 3MJF_A 2IP4_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A 2YRW_A 2YS7_A ....
Probab=23.24 E-value=40 Score=21.69 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=8.0
Q ss_pred eceehhhhchhHH
Q psy3211 25 LEYYRHDLGINLF 37 (84)
Q Consensus 25 LsYFtEDigLN~y 37 (84)
=.|||.|||.-++
T Consensus 81 g~~yR~DIG~~al 93 (93)
T PF02843_consen 81 GMFYRKDIGHRAL 93 (93)
T ss_dssp TEE--STTTHHHH
T ss_pred CCEEcCccChhhC
Confidence 3689999997653
No 10
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=20.43 E-value=67 Score=22.50 Aligned_cols=12 Identities=25% Similarity=0.099 Sum_probs=10.2
Q ss_pred HHHHHHHhhhhhc
Q psy3211 66 QQMLARQSYGLEC 78 (84)
Q Consensus 66 qQllARY~LERlS 78 (84)
.|||++| |+|||
T Consensus 86 ~~~l~~Y-L~RlS 97 (115)
T cd07298 86 TQMLMAY-LSRLS 97 (115)
T ss_pred HHHHHHH-HHHHH
Confidence 8888986 88987
Done!