Query psy15739
Match_columns 95
No_of_seqs 104 out of 135
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:09:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15739.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15739hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1555|consensus 99.9 7.3E-26 1.6E-30 181.1 5.9 90 2-93 177-267 (316)
2 cd08069 MPN_RPN11_CSN5 Mov34/M 99.8 1.2E-19 2.6E-24 140.5 5.7 85 7-94 153-237 (268)
3 PF13012 MitMem_reg: Maintenan 99.1 2.7E-11 5.8E-16 81.7 -0.0 76 6-93 1-81 (115)
4 cd08065 MPN_eIF3h Mpr1p, Pad1p 95.2 0.093 2E-06 40.7 7.0 44 15-58 144-187 (266)
5 KOG1554|consensus 65.7 2.6 5.5E-05 35.0 0.6 32 33-64 220-251 (347)
6 PF07152 YaeQ: YaeQ protein; 45.2 24 0.00051 26.6 2.8 26 29-54 16-44 (174)
7 PF11074 DUF2779: Domain of un 36.7 1.4E+02 0.0029 21.1 5.5 61 20-92 58-118 (130)
8 PF13210 DUF4018: Domain of un 35.9 13 0.00028 28.6 0.2 19 6-24 146-167 (192)
9 PF08629 PDE8: PDE8 phosphodie 29.7 24 0.00052 22.1 0.6 9 6-14 24-32 (52)
10 PF08295 Sin3_corepress: Sin3 21.8 76 0.0017 21.8 2.0 53 30-90 32-92 (101)
11 PF03909 BSD: BSD domain ; I 21.5 1.8E+02 0.0038 17.6 3.4 34 57-93 2-35 (62)
12 PF02762 Cbl_N3: CBL proto-onc 21.2 46 0.00099 22.8 0.8 20 19-38 58-77 (86)
No 1
>KOG1555|consensus
Probab=99.92 E-value=7.3e-26 Score=181.08 Aligned_cols=90 Identities=44% Similarity=0.536 Sum_probs=87.3
Q ss_pred cccCCCCcccccccccccc-hhHHHHHhhcCCceeeeeeeeeCCHHHHHHHhhhcccccccCCCccchHHHHhhhHHHHH
Q psy15739 2 MVLGQEPRQTTSNLGHLQK-HSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVN 80 (95)
Q Consensus 2 ~m~gqEPRQTTSNiGhL~K-PSiqAlihGLnr~YYSi~I~yrk~~lEqkMLlnLhKk~W~~gL~l~~~~~~~~~N~~~v~ 80 (95)
++.|+||||||||+||+.+ ||+|+++||+| |||++.|.||+++.|++|++|+|+++|.++ ...+|.++.+.|++.+.
T Consensus 177 ~~~~~eprqtts~~~~m~~~~s~q~~~~g~n-~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~-~~~~y~e~~k~~~~~~~ 254 (316)
T KOG1555|consen 177 ISPGGEPRQTTSNGGHMDMQESLQEDIHGLN-RYYRIEIPLHVLPYEQLMLLNVPLKSWKSL-QDVLYEEKLKAYLQSVP 254 (316)
T ss_pred ccCCCCCccccccccccccchhHHhHhhccC-ceEEEEeeEEechhhhhchhccchhhhhhc-chhhHHHHHHHhhhhhh
Confidence 5789999999999999999 99999999999 999999999999999999999999999999 99999999999999999
Q ss_pred HHHHHHHHHhcCC
Q psy15739 81 DMLELAKHYNKGK 93 (95)
Q Consensus 81 ~m~~La~~Y~k~i 93 (95)
.|.+|++.|++.+
T Consensus 255 ~~~sL~~~~N~~~ 267 (316)
T KOG1555|consen 255 SMKSLSKVYNKVC 267 (316)
T ss_pred HHHhHHHHHHHHH
Confidence 9999999999764
No 2
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.79 E-value=1.2e-19 Score=140.54 Aligned_cols=85 Identities=46% Similarity=0.754 Sum_probs=82.4
Q ss_pred CCcccccccccccchhHHHHHhhcCCceeeeeeeeeCCHHHHHHHhhhcccccccCCCccchHHHHhhhHHHHHHHHHHH
Q psy15739 7 EPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDMLELA 86 (95)
Q Consensus 7 EPRQTTSNiGhL~KPSiqAlihGLnr~YYSi~I~yrk~~lEqkMLlnLhKk~W~~gL~l~~~~~~~~~N~~~v~~m~~La 86 (95)
|||+||||+|++.+|+++ ..+++++.||+|+|.|+++++|+.||.+|+++.|.++|.+.+|.+++ |...++.|.+|+
T Consensus 153 ~~~~~~s~~~~~~~~~~~-~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~~~l~~~~~~~~~--~~~~~~~~~~l~ 229 (268)
T cd08069 153 EPRQTTSNIGHLPKPKIE-DFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVNTLSLSPLLENS--NEYTIKQILDLA 229 (268)
T ss_pred CcccCccccCccCcHHHH-HhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHHHHhhCCchhhhh--hHHHHHHHHHHH
Confidence 799999999999999999 99999999999999999999999999999999999999999998888 999999999999
Q ss_pred HHHhcCCC
Q psy15739 87 KHYNKGKT 94 (95)
Q Consensus 87 ~~Y~k~i~ 94 (95)
+.|++.+.
T Consensus 230 ~~~~~~~~ 237 (268)
T cd08069 230 EKLEKAEQ 237 (268)
T ss_pred HHHHHHHh
Confidence 99998864
No 3
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.05 E-value=2.7e-11 Score=81.66 Aligned_cols=76 Identities=30% Similarity=0.359 Sum_probs=13.4
Q ss_pred CCCcccccccccccchhHHHHHhhcCCceeeeeeeeeCCHHHHHHHhhhcccccccCCCccch----HHHHhhhHHHHHH
Q psy15739 6 QEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDY----NEHCKLNEGTVND 81 (95)
Q Consensus 6 qEPRQTTSNiGhL~KPSiqAlihGLnr~YYSi~I~yrk~~lEqkMLlnLhKk~W~~gL~l~~~----~~~~~~N~~~v~~ 81 (95)
+|||++ ++.+++||++++||| +|. +..+.+++||.+|++..|..+.-++++ .+.+..+...+.+
T Consensus 1 eEaEri----------gv~~l~~~~~~~~~s-~~~-~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~ 68 (115)
T PF13012_consen 1 EEAERI----------GVDHLARGLGDHYYS-SLS-SQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQD 68 (115)
T ss_dssp SHHHHH----------HHHHHHHH--S-----------------------------------------------------
T ss_pred CchHHH----------HHHHHHccCCCcccc-HHH-HHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHH
Confidence 478888 899999999999999 999 999999999999999999999999999 8889999999999
Q ss_pred HHHHHHHH-hcCC
Q psy15739 82 MLELAKHY-NKGK 93 (95)
Q Consensus 82 m~~La~~Y-~k~i 93 (95)
++.++..| .+.+
T Consensus 69 l~~~lp~~~~~~~ 81 (115)
T PF13012_consen 69 LLSSLPKYDPEEF 81 (115)
T ss_dssp -------------
T ss_pred HHHhcccccHHHH
Confidence 99999988 4443
No 4
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=95.23 E-value=0.093 Score=40.69 Aligned_cols=44 Identities=16% Similarity=0.276 Sum_probs=41.1
Q ss_pred cccccchhHHHHHhhcCCceeeeeeeeeCCHHHHHHHhhhcccc
Q psy15739 15 LGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKT 58 (95)
Q Consensus 15 iGhL~KPSiqAlihGLnr~YYSi~I~yrk~~lEqkMLlnLhKk~ 58 (95)
-|++.++++++.-.+.+..|+.|||..+.+.|++.||..|....
T Consensus 144 ~~~~~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~ 187 (266)
T cd08065 144 EGKFSTESLREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDS 187 (266)
T ss_pred cCCcCHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCC
Confidence 48999999999999999999999999999999999999997753
No 5
>KOG1554|consensus
Probab=65.73 E-value=2.6 Score=34.96 Aligned_cols=32 Identities=44% Similarity=0.746 Sum_probs=29.4
Q ss_pred ceeeeeeeeeCCHHHHHHHhhhcccccccCCC
Q psy15739 33 HYYSISINYRKNELEQKMLLNLHKKTWMDGLS 64 (95)
Q Consensus 33 ~YYSi~I~yrk~~lEqkMLlnLhKk~W~~gL~ 64 (95)
.|||+.|+|-|..++.+.|--|--+-|..-|.
T Consensus 220 ~yysl~isyfks~ld~kll~~Lwnkywv~Tls 251 (347)
T KOG1554|consen 220 QYYSLEISYFKSSLDMKLLELLWNKYWVRTLS 251 (347)
T ss_pred EeeccchhhhhhhhhHHHHHHHHhhhhhcccc
Confidence 69999999999999999999999999996543
No 6
>PF07152 YaeQ: YaeQ protein; InterPro: IPR009822 This family consists of several hypothetical bacterial proteins of around 180 residues in length, which are often known as YaeQ. YaeQ is homologous to RfaH, a specialised transcription elongation protein. YaeQ is known to compensate for loss of RfaH function [].; PDB: 3C0U_B 2OT9_A 2G3W_B.
Probab=45.15 E-value=24 Score=26.62 Aligned_cols=26 Identities=31% Similarity=0.795 Sum_probs=20.9
Q ss_pred hcCCcee---eeeeeeeCCHHHHHHHhhh
Q psy15739 29 GLNRHYY---SISINYRKNELEQKMLLNL 54 (95)
Q Consensus 29 GLnr~YY---Si~I~yrk~~lEqkMLlnL 54 (95)
-++|||| ++.|.-..+|-++.|+..|
T Consensus 16 D~DR~~Y~~~~lTiA~HPSEt~eRmm~Rl 44 (174)
T PF07152_consen 16 DMDRHYYEDHNLTIARHPSETDERMMVRL 44 (174)
T ss_dssp ETTTTEEEEEEEEEEE-TTS-HHHHHHHH
T ss_pred cCCccccccccEEeeCCCCccHHHHHHHH
Confidence 4789998 6889999999999999876
No 7
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=36.69 E-value=1.4e+02 Score=21.12 Aligned_cols=61 Identities=20% Similarity=0.374 Sum_probs=47.4
Q ss_pred chhHHHHHhhcCCceeeeeeeeeCCHHHHHHHhhhcccccccCCCccchHHHHhhhHHHHHHHHHHHHHHhcC
Q psy15739 20 KHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYNKG 92 (95)
Q Consensus 20 KPSiqAlihGLnr~YYSi~I~yrk~~lEqkMLlnLhKk~W~~gL~l~~~~~~~~~N~~~v~~m~~La~~Y~k~ 92 (95)
+..+.+|+.-++..|.++ |.|.+ ..|..-|..|-+- |.+..+.-.....+|++|+.-+.+.
T Consensus 58 ~~~~~~L~~~i~~~~g~i-vvyN~-sfE~~rL~ela~~----------~p~~~~~l~~I~~r~vDL~~~f~~~ 118 (130)
T PF11074_consen 58 RELIEALIKAIGSIYGSI-VVYNK-SFEKTRLKELAEL----------FPDYAEKLNSIIERTVDLLDPFKNH 118 (130)
T ss_pred HHHHHHHHHHhhhhcCeE-EEech-HHHHHHHHHHHHH----------hHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 347899999999998554 56755 3888888777665 7778888888889999998877663
No 8
>PF13210 DUF4018: Domain of unknown function (DUF4018)
Probab=35.90 E-value=13 Score=28.63 Aligned_cols=19 Identities=37% Similarity=0.569 Sum_probs=16.3
Q ss_pred CCCcccc---cccccccchhHH
Q psy15739 6 QEPRQTT---SNLGHLQKHSVQ 24 (95)
Q Consensus 6 qEPRQTT---SNiGhL~KPSiq 24 (95)
.||..|| +|.||+.||.+.
T Consensus 146 a~~kdt~d~w~nkG~l~~~~i~ 167 (192)
T PF13210_consen 146 AELKDTDDFWENKGHLKKPQIP 167 (192)
T ss_pred cCccchhHHHHhcCCCCCCcCc
Confidence 4788888 999999999874
No 9
>PF08629 PDE8: PDE8 phosphodiesterase; InterPro: IPR013938 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This region is found at the N terminus of members of PDE8 phosphodiesterase family []. Phosphodiesterase 8 (PDE8) regulates chemotaxis of activated lymphocytes [].
Probab=29.69 E-value=24 Score=22.11 Aligned_cols=9 Identities=56% Similarity=0.748 Sum_probs=7.0
Q ss_pred CCCcccccc
Q psy15739 6 QEPRQTTSN 14 (95)
Q Consensus 6 qEPRQTTSN 14 (95)
-.||||||-
T Consensus 24 ~sP~qTtt~ 32 (52)
T PF08629_consen 24 NSPRQTTTV 32 (52)
T ss_pred CCCCcceee
Confidence 479999864
No 10
>PF08295 Sin3_corepress: Sin3 family co-repressor; InterPro: IPR013194 This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [].
Probab=21.84 E-value=76 Score=21.79 Aligned_cols=53 Identities=19% Similarity=0.251 Sum_probs=33.9
Q ss_pred cCCceeeee--------eeeeCCHHHHHHHhhhcccccccCCCccchHHHHhhhHHHHHHHHHHHHHHh
Q psy15739 30 LNRHYYSIS--------INYRKNELEQKMLLNLHKKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYN 90 (95)
Q Consensus 30 Lnr~YYSi~--------I~yrk~~lEqkMLlnLhKk~W~~gL~l~~~~~~~~~N~~~v~~m~~La~~Y~ 90 (95)
||..|-|.+ +.-|||..|+.|..+=-- --.|+-+-+.|..+|+.+-.|++...
T Consensus 32 LND~wvs~p~~sEd~~f~~~kKnqyEE~lf~~EDe--------R~E~D~~ie~~~~tI~~Le~l~~~i~ 92 (101)
T PF08295_consen 32 LNDTWVSVPSWSEDSSFKAMKKNQYEEALFRCEDE--------RFELDMLIESNRSTIKLLEELQEKIQ 92 (101)
T ss_pred cCCEEEEeCCccccccccchhhhHHHHHHHHhhhh--------hHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 788888877 456899999988653111 11244455667777776666665543
No 11
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=21.55 E-value=1.8e+02 Score=17.56 Aligned_cols=34 Identities=18% Similarity=0.246 Sum_probs=18.0
Q ss_pred cccccCCCccchHHHHhhhHHHHHHHHHHHHHHhcCC
Q psy15739 57 KTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYNKGK 93 (95)
Q Consensus 57 k~W~~gL~l~~~~~~~~~N~~~v~~m~~La~~Y~k~i 93 (95)
..|..+|.++ +..+.-.+.+.+--.|.+.|.+.|
T Consensus 2 ~~~~~~f~~~---~~~e~i~~lL~~~p~l~~~~~~lV 35 (62)
T PF03909_consen 2 ENWDFEFDID---EQTEEIKKLLEEDPNLRKLYNELV 35 (62)
T ss_dssp SSS--S--CH---HHHHHHHHHHHH-HHHHHHHHHCC
T ss_pred cchhhccccc---CCHHHHHHHHHhCHHHHHHHHHhC
Confidence 4688888553 344444455666666777787776
No 12
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=21.23 E-value=46 Score=22.80 Aligned_cols=20 Identities=35% Similarity=0.473 Sum_probs=15.3
Q ss_pred cchhHHHHHhhcCCceeeee
Q psy15739 19 QKHSVQALIHGLNRHYYSIS 38 (95)
Q Consensus 19 ~KPSiqAlihGLnr~YYSi~ 38 (95)
+||-.||||.|-..-||--+
T Consensus 58 nk~L~qaLidG~reG~ylyP 77 (86)
T PF02762_consen 58 NKSLYQALIDGSREGFYLYP 77 (86)
T ss_dssp SS-HHHHHHHHHHTTSS-EE
T ss_pred CchHHHHHHhccccceEECC
Confidence 79999999999888777544
Done!