Query 011951
Match_columns 474
No_of_seqs 164 out of 207
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:01:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011951.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011951hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04782 DUF632: Protein of un 100.0 2.6E-33 5.5E-38 283.3 6.5 110 328-473 1-110 (312)
2 PF04783 DUF630: Protein of un 100.0 1.7E-29 3.7E-34 198.7 8.0 60 1-60 1-60 (60)
3 PF06600 DUF1140: Protein of u 40.8 19 0.00041 31.9 1.9 16 448-463 73-88 (107)
4 PF06404 PSK: Phytosulfokine p 39.2 23 0.00049 30.1 2.1 11 31-42 64-74 (81)
5 KOG2675 Adenylate cyclase-asso 37.0 97 0.0021 34.1 6.9 25 36-60 183-207 (480)
6 PF12408 DUF3666: Ribose-5-pho 30.9 38 0.00083 26.2 2.0 25 326-350 4-28 (48)
7 PF06989 BAALC_N: BAALC N-term 28.1 24 0.00052 27.4 0.5 11 1-11 1-11 (53)
8 PF08629 PDE8: PDE8 phosphodie 20.3 15 0.00032 28.5 -1.9 7 1-7 1-7 (52)
9 COG4817 DNA-binding ferritin-l 18.2 1.4E+02 0.003 26.9 3.3 30 325-354 44-75 (111)
10 PF09225 Endonuc-PvuII: Restri 17.1 97 0.0021 29.0 2.2 23 436-462 108-131 (155)
No 1
>PF04782 DUF632: Protein of unknown function (DUF632); InterPro: IPR006867 This conserved region contains a leucine zipper-like domain. The proteins are found only in plants and their functions are unknown.
Probab=99.98 E-value=2.6e-33 Score=283.35 Aligned_cols=110 Identities=41% Similarity=0.700 Sum_probs=92.1
Q ss_pred chHHHHHHHHHHHHHHHhcCCchhhhhhccccCCCcccccccccchhhHHHHhhhccCCCCCCCCCcccccccceeeeee
Q 011951 328 DFFSSMKDIELLFIKASDSGKEVPRMLEANKLHFRPIFEEKDSDSMASTILKACFSCGEDPPQVQEEPVQTDVKYLTWHR 407 (474)
Q Consensus 328 dl~ev~keIe~~F~rA~~sg~eVs~mLE~~k~~y~~~~~~~~~~~~~s~~~~~~~~c~~~~~~~~~~~~~~~~k~~~w~r 407 (474)
||++||||||++|+|||+||+|||+||||||++|++.|..... ...+..++++.|+|+|
T Consensus 1 dl~ev~kei~~~F~kAs~sg~eVs~lLE~~k~~~~~~~~~~~~---------------------~~~~s~~~~~~~~w~~ 59 (312)
T PF04782_consen 1 DLLEVVKEIDDYFLKASESGKEVSRLLEAGKIHYHSNFSDLKG---------------------KVDHSSRVLSPISWSR 59 (312)
T ss_pred CHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCCCCCcccccccc---------------------cccchhhhccccccCC
Confidence 7899999999999999999999999999999999998876211 1112335578889998
Q ss_pred ccccCCCCCCCCCCCCCCcccccccCCccccccccccchhhHHHHHHHHHHHHHHHhhhccccccC
Q 011951 408 TTSSRSSSSRNPLGANSKDDVEDLTGDIFDSIHMISSSHASTLDRLYAWERKLYDEVKVKSDVGSD 473 (474)
Q Consensus 408 s~Ss~sssSr~pl~~~~~~d~~~~~~d~~ee~~m~sgShsSTLdRLyaWEkKLYdEVKa~E~ir~~ 473 (474)
+.+|+ ..+...++.+++||++|||+||||||||||||||+|||++|+||++
T Consensus 60 s~~s~---------------~~~~~~~~~~~~~~~~gshssTLdkLyaWEKKLY~EVKa~E~~r~~ 110 (312)
T PF04782_consen 60 SSSSR---------------ISNSDSDFDEEECMGSGSHSSTLDKLYAWEKKLYDEVKAEEKLRIE 110 (312)
T ss_pred CCCCc---------------ccccccCcCcccCcccchHHHHHHHHHHHHHHHHHHHHccHHHHHH
Confidence 86654 1233456778899999999999999999999999999999999975
No 2
>PF04783 DUF630: Protein of unknown function (DUF630); InterPro: IPR006868 This region is sometimes found at the N terminus of putative plant bZIP proteins IPR006867 from INTERPRO. The function of this conserved region is not known.
Probab=99.96 E-value=1.7e-29 Score=198.67 Aligned_cols=60 Identities=55% Similarity=0.927 Sum_probs=59.0
Q ss_pred CCCCcccccchHHHHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhhccCC
Q 011951 1 MGVSSSKLEEDKALQLCRERKKFVRQALDGRCSLAATHVMYVQSLRNTGTALRKFVEPEG 60 (474)
Q Consensus 1 MGc~~Sk~d~~~av~~CkeRk~~~k~Av~~R~~lAaaH~~Y~~SL~~~g~aL~~f~~~e~ 60 (474)
|||++||+|++|+|++|||||+|||+||++||+||+||++|++|||+||.||++|+++|+
T Consensus 1 MGC~~SK~d~eeaV~~CkeRkr~~k~Av~~R~~lAaaH~aY~~SLr~~g~aL~~F~~~et 60 (60)
T PF04783_consen 1 MGCSQSKLDDEEAVSLCKERKRLMKQAVDARYALAAAHAAYIQSLRNVGAALRQFAEGET 60 (60)
T ss_pred CCCCcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999999999999999999999983
No 3
>PF06600 DUF1140: Protein of unknown function (DUF1140); InterPro: IPR009520 This entry is represented by Bacteriophage bIL286, Orf36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown.
Probab=40.75 E-value=19 Score=31.91 Aligned_cols=16 Identities=38% Similarity=0.922 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHHHHHH
Q 011951 448 STLDRLYAWERKLYDE 463 (474)
Q Consensus 448 STLdRLyaWEkKLYdE 463 (474)
--|||||-|-.||.+|
T Consensus 73 ~e~Dr~~~Ws~kLHQd 88 (107)
T PF06600_consen 73 AEIDRLFHWSSKLHQD 88 (107)
T ss_pred HHHHHHhhHHHHHHHH
Confidence 4689999999999987
No 4
>PF06404 PSK: Phytosulfokine precursor protein (PSK); InterPro: IPR009438 This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis [].; GO: 0008083 growth factor activity, 0008283 cell proliferation, 0005576 extracellular region
Probab=39.19 E-value=23 Score=30.05 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=9.3
Q ss_pred hHHHHHHHHHHH
Q 011951 31 RCSLAATHVMYV 42 (474)
Q Consensus 31 R~~lAaaH~~Y~ 42 (474)
|..|| ||.+||
T Consensus 64 RRtL~-AHlDYI 74 (81)
T PF06404_consen 64 RRTLA-AHLDYI 74 (81)
T ss_pred HHHHH-HHhhhe
Confidence 45888 999998
No 5
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=36.99 E-value=97 Score=34.09 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCC
Q 011951 36 ATHVMYVQSLRNTGTALRKFVEPEG 60 (474)
Q Consensus 36 aaH~~Y~~SL~~~g~aL~~f~~~e~ 60 (474)
.-|+.++++++.+=.-|+.|+..+.
T Consensus 183 ~~hveWvKa~l~l~~eL~~YVk~hh 207 (480)
T KOG2675|consen 183 PRHVEWVKAYLALFLELQAYVKEHH 207 (480)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4599999999999999999998775
No 6
>PF12408 DUF3666: Ribose-5-phosphate isomerase ; InterPro: IPR022133 This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with PF02502 from PFAM. There are two completely conserved residues (D and F) that may be functionally important. ; PDB: 3ONO_A 3C5Y_N 2PPW_A.
Probab=30.93 E-value=38 Score=26.24 Aligned_cols=25 Identities=28% Similarity=0.430 Sum_probs=18.3
Q ss_pred CcchHHHHHHHHHHHHHHHhcCCch
Q 011951 326 SKDFFSSMKDIELLFIKASDSGKEV 350 (474)
Q Consensus 326 ~rdl~ev~keIe~~F~rA~~sg~eV 350 (474)
.||+++++|+|+..|+|.+=+|..-
T Consensus 4 ~k~ll~iLk~iDqdLvK~AisGe~F 28 (48)
T PF12408_consen 4 YKDLLDILKAIDQDLVKTAISGERF 28 (48)
T ss_dssp S--HHHHHHHS-HHHHHHHT-SHHH
T ss_pred hhhHHHHHHHhCHHHHHHHhccHHH
Confidence 4799999999999999999887543
No 7
>PF06989 BAALC_N: BAALC N-terminus; InterPro: IPR009728 This entry represents the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic) is highly conserved among mammals, but is absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions [].; GO: 0005737 cytoplasm
Probab=28.06 E-value=24 Score=27.40 Aligned_cols=11 Identities=27% Similarity=0.435 Sum_probs=8.7
Q ss_pred CCCCcccccch
Q 011951 1 MGVSSSKLEED 11 (474)
Q Consensus 1 MGc~~Sk~d~~ 11 (474)
|||..|+.|.-
T Consensus 1 mgcggsradai 11 (53)
T PF06989_consen 1 MGCGGSRADAI 11 (53)
T ss_pred CCCCccccccc
Confidence 89999987653
No 8
>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=20.29 E-value=15 Score=28.53 Aligned_cols=7 Identities=43% Similarity=0.596 Sum_probs=2.9
Q ss_pred CCCCccc
Q 011951 1 MGVSSSK 7 (474)
Q Consensus 1 MGc~~Sk 7 (474)
|||+.|-
T Consensus 1 mgcapsi 7 (52)
T PF08629_consen 1 MGCAPSI 7 (52)
T ss_pred CCcCCcE
Confidence 4444443
No 9
>COG4817 DNA-binding ferritin-like protein (Dps family) [General function prediction only]
Probab=18.20 E-value=1.4e+02 Score=26.94 Aligned_cols=30 Identities=30% Similarity=0.420 Sum_probs=23.8
Q ss_pred CCcchHH--HHHHHHHHHHHHHhcCCchhhhh
Q 011951 325 ASKDFFS--SMKDIELLFIKASDSGKEVPRML 354 (474)
Q Consensus 325 ~~rdl~e--v~keIe~~F~rA~~sg~eVs~mL 354 (474)
++.+..+ ++++|=+.|.-|+..|++|..+|
T Consensus 44 g~t~~~~~~Il~~iLelfE~aaadgk~v~dv~ 75 (111)
T COG4817 44 GPTGWNEMKILGNILELFEEAAADGKEVTDVL 75 (111)
T ss_pred CcchhHHHHHHHHHHHHHHHHHhccccHHHHh
Confidence 5555555 88888888999999998888776
No 10
>PF09225 Endonuc-PvuII: Restriction endonuclease PvuII; InterPro: IPR015306 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the type II restriction endonuclease PvuII, which recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3 []. ; PDB: 1H56_B 1EYU_A 3KSK_B 1F0O_A 1PVI_B 1PVU_B 3PVI_A 1K0Z_B 1NI0_A 2PVI_A ....
Probab=17.12 E-value=97 Score=29.02 Aligned_cols=23 Identities=30% Similarity=0.718 Sum_probs=16.3
Q ss_pred cccccccccchhhHHHHHHH-HHHHHHH
Q 011951 436 FDSIHMISSSHASTLDRLYA-WERKLYD 462 (474)
Q Consensus 436 ~ee~~m~sgShsSTLdRLya-WEkKLYd 462 (474)
.+-+||. ..-|+.+|. ||+|+|.
T Consensus 108 ~~iY~l~----p~~lE~~y~~WE~kw~~ 131 (155)
T PF09225_consen 108 QEIYKLT----PEDLEPFYDKWERKWYS 131 (155)
T ss_dssp EEEEEE-----HHHHHHHHHHHHHHHHH
T ss_pred hhhhhcC----HHHhHHHHHHHHHHHHh
Confidence 3445555 567889884 9999996
Done!