Query psy7862
Match_columns 101
No_of_seqs 101 out of 244
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 20:44:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7862hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3503|consensus 100.0 2.1E-36 4.5E-41 200.3 3.5 63 38-100 1-63 (64)
2 PF04135 Nop10p: Nucleolar RNA 100.0 4.4E-30 9.6E-35 163.9 4.7 51 40-90 1-53 (53)
3 COG2260 Predicted Zn-ribbon RN 99.9 1.3E-26 2.8E-31 151.7 4.2 57 38-95 1-58 (59)
4 PRK13130 H/ACA RNA-protein com 99.9 1.3E-24 2.8E-29 139.7 4.3 47 46-92 8-55 (56)
5 TIGR00354 polC DNA polymerase, 81.6 0.77 1.7E-05 43.8 1.5 46 36-85 621-667 (1095)
6 COG1998 RPS31 Ribosomal protei 52.4 15 0.00033 23.8 2.4 27 40-67 5-32 (51)
7 PF09068 EF-hand_2: EF hand; 41.3 20 0.00044 25.6 1.8 13 77-89 16-28 (127)
8 PF14261 DUF4351: Domain of un 29.4 36 0.00077 21.6 1.4 13 83-95 14-26 (59)
9 PF04707 PRELI: PRELI-like fam 28.8 68 0.0015 23.1 2.9 42 17-58 54-95 (157)
10 TIGR03735 PRTRC_A PRTRC system 23.9 41 0.00088 26.3 1.1 14 64-77 142-155 (192)
11 PF13043 DUF3903: Domain of un 23.9 64 0.0014 20.0 1.7 13 79-91 11-23 (40)
12 COG0248 GppA Exopolyphosphatas 23.5 1.8E+02 0.0039 25.4 5.0 32 4-35 123-154 (492)
13 PF03552 Cellulose_synt: Cellu 22.2 64 0.0014 29.9 2.1 40 49-90 66-107 (720)
14 PF04749 PLAC8: PLAC8 family; 20.1 82 0.0018 20.1 1.8 13 79-91 68-80 (106)
No 1
>KOG3503|consensus
Probab=100.00 E-value=2.1e-36 Score=200.33 Aligned_cols=63 Identities=73% Similarity=1.225 Sum_probs=62.0
Q ss_pred eEEEEEeCCCCceeeeecccCCCCCCccccCCCCCCCCCccHHHHHHHHHHhCCCCCCCCCCC
Q psy7862 38 MYLMYYLGEDGKRVYTLKKVDPAGNPTVSAHPARFSPDDKYSRERITILRRFGLLRTQQPASA 100 (101)
Q Consensus 38 M~L~yyl~e~gc~vYTLk~~CP~G~~T~saHPARFSPdDKYskYR~~LKkr~glLptq~~~~~ 100 (101)
|||||||||+|+++||||++.|.|+.|.+|||||||||||||++|+.||||||+||||+|+++
T Consensus 1 M~L~y~lne~g~rvYTlKk~~p~G~~T~saHPARFSPdDKySrqR~tlKKRFgll~tQ~p~~~ 63 (64)
T KOG3503|consen 1 MFLMYYLNENGKRVYTLKKVSPSGEQTLSAHPARFSPDDKYSRQRITLKKRFGLLPTQKPKPV 63 (64)
T ss_pred CeeEEEECCCCcEEEEEeecCCCCceecccCccccCccccccceeeeehhhhccccccCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999876
No 2
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=99.96 E-value=4.4e-30 Score=163.89 Aligned_cols=51 Identities=63% Similarity=1.035 Sum_probs=46.6
Q ss_pred EEEEe-CCCCceeeeecccCCC-CCCccccCCCCCCCCCccHHHHHHHHHHhC
Q psy7862 40 LMYYL-GEDGKRVYTLKKVDPA-GNPTVSAHPARFSPDDKYSRERITILRRFG 90 (101)
Q Consensus 40 L~yyl-~e~gc~vYTLk~~CP~-G~~T~saHPARFSPdDKYskYR~~LKkr~g 90 (101)
|||++ ++++|++|||++.||. |++|.+|||||||||||||+|||+||+|||
T Consensus 1 m~~~~r~c~~~~~YTLk~~cp~cG~~T~~ahPaRFSPdDky~~yRi~lKkrfg 53 (53)
T PF04135_consen 1 MRYYIRKCPGCRVYTLKDKCPPCGGPTESAHPARFSPDDKYSKYRIALKKRFG 53 (53)
T ss_dssp -EEEEEECTTTCEEESSSBBTTTSSBSEESSSSSS-TTTTTCHHHHHHHHHH-
T ss_pred CCcccccCCCCCcEeCCCccCCCCCCCcCCcCCCCCCCCccHHHHHHHHhhcC
Confidence 57888 9999999999999997 999999999999999999999999999997
No 3
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.3e-26 Score=151.71 Aligned_cols=57 Identities=40% Similarity=0.596 Sum_probs=52.9
Q ss_pred eEEEEEeCCCCceeeeecccCCC-CCCccccCCCCCCCCCccHHHHHHHHHHhCCCCCC
Q psy7862 38 MYLMYYLGEDGKRVYTLKKVDPA-GNPTVSAHPARFSPDDKYSRERITILRRFGLLRTQ 95 (101)
Q Consensus 38 M~L~yyl~e~gc~vYTLk~~CP~-G~~T~saHPARFSPdDKYskYR~~LKkr~glLptq 95 (101)
|.+++....+ |++|||++.||. |+.|.+||||||||||||+|||++||+++++++.|
T Consensus 1 M~~~~rkC~~-cg~YTLke~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~~~~~~ 58 (59)
T COG2260 1 MKSLIRKCPK-CGRYTLKEKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLGLLPNQ 58 (59)
T ss_pred CcchhhcCcC-CCceeecccCCCCCCccccCCCCCCCccchHHHHHHHHHHHhccccCC
Confidence 6677777765 999999999998 99999999999999999999999999999999986
No 4
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=99.90 E-value=1.3e-24 Score=139.74 Aligned_cols=47 Identities=43% Similarity=0.649 Sum_probs=44.3
Q ss_pred CCCceeeeecccCCC-CCCccccCCCCCCCCCccHHHHHHHHHHhCCC
Q psy7862 46 EDGKRVYTLKKVDPA-GNPTVSAHPARFSPDDKYSRERITILRRFGLL 92 (101)
Q Consensus 46 e~gc~vYTLk~~CP~-G~~T~saHPARFSPdDKYskYR~~LKkr~glL 92 (101)
...|++|||++.||. |++|.+|||||||||||||+|||+||||.++-
T Consensus 8 C~~CgvYTLk~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~~~ 55 (56)
T PRK13130 8 CPKCGVYTLKEICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKRRKLN 55 (56)
T ss_pred CCCCCCEEccccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHHHhhcC
Confidence 568999999999997 99999999999999999999999999998863
No 5
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=81.60 E-value=0.77 Score=43.75 Aligned_cols=46 Identities=11% Similarity=-0.096 Sum_probs=32.6
Q ss_pred cceEEEEEeCCCCceeeeecccCCC-CCCccccCCCCCCCCCccHHHHHHH
Q psy7862 36 ITMYLMYYLGEDGKRVYTLKKVDPA-GNPTVSAHPARFSPDDKYSRERITI 85 (101)
Q Consensus 36 ~~M~L~yyl~e~gc~vYTLk~~CP~-G~~T~saHPARFSPdDKYskYR~~L 85 (101)
+.+.++. ...|+.||++..||+ |+.|..+||.+.+- |--..|++++
T Consensus 621 vev~~RK---CPkCG~yTlk~rCP~CG~~Te~~~pc~~~i-~l~~~~~~A~ 667 (1095)
T TIGR00354 621 VEIAIRK---CPQCGKESFWLKCPVCGELTEQLYYGKRKV-DLRELYEEAI 667 (1095)
T ss_pred EEEEEEE---CCCCCcccccccCCCCCCccccccceeEEe-cHHHHHHHHH
Confidence 3445555 789999999999995 99999999995432 2223444443
No 6
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=52.42 E-value=15 Score=23.79 Aligned_cols=27 Identities=33% Similarity=0.415 Sum_probs=18.6
Q ss_pred EEEEeCCCCceeeeecccCCC-CCCcccc
Q psy7862 40 LMYYLGEDGKRVYTLKKVDPA-GNPTVSA 67 (101)
Q Consensus 40 L~yyl~e~gc~vYTLk~~CP~-G~~T~sa 67 (101)
+.||-.+++. +=.+++.||. |.-++-|
T Consensus 5 ~~yY~v~~~k-v~rk~~~CPrCG~gvfmA 32 (51)
T COG1998 5 LKYYEVDDEK-VKRKNRFCPRCGPGVFMA 32 (51)
T ss_pred eeEEEEcCCc-EEEccccCCCCCCcchhh
Confidence 4677766655 7778888997 7545444
No 7
>PF09068 EF-hand_2: EF hand; InterPro: IPR015153 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=41.28 E-value=20 Score=25.58 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=11.3
Q ss_pred ccHHHHHHHHHHh
Q psy7862 77 KYSRERITILRRF 89 (101)
Q Consensus 77 KYskYR~~LKkr~ 89 (101)
||+.||-++|-|+
T Consensus 16 rfsaYRtA~KLR~ 28 (127)
T PF09068_consen 16 RFSAYRTAMKLRF 28 (127)
T ss_dssp SSHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHH
Confidence 7999999988775
No 8
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=29.40 E-value=36 Score=21.55 Aligned_cols=13 Identities=38% Similarity=0.588 Sum_probs=10.9
Q ss_pred HHHHHHhCCCCCC
Q psy7862 83 ITILRRFGLLRTQ 95 (101)
Q Consensus 83 ~~LKkr~glLptq 95 (101)
|.|++|||-||..
T Consensus 14 RlL~rrFG~lp~~ 26 (59)
T PF14261_consen 14 RLLTRRFGELPPE 26 (59)
T ss_pred HHHHHHcCCCCHH
Confidence 5699999999864
No 9
>PF04707 PRELI: PRELI-like family; InterPro: IPR006797 These proteins contain a conserved region found in the yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. GFP-tagged MSF1 localizes to mitochondria and is required for wild-type respiratory growth []. This region is also found in a number of other eukaryotic proteins. The PRELI/MSF1 domain is an eukaryotic protein module which occurs in stand-alone form in several proteins, including the human PRELI protein and the yeast MSF1 protein, and as an amino-terminal domain in an orthologous group of proteins typified by human SEC14L1, which is conserved in all animals. In this group of proteins, the PRELI/MSF1 domain co-occurs with the CRAL-TRIO (see PDOC50191 from PROSITEDOC) and the GOLD domains (see PDOC50866 from PROSITEDOC). The PRELI/MSF1 domain is approximately 170 residues long and is predicted to assume a globular alpha + beta fold with six beta strands and four alpha helices. It has been suggested that the PRELI/MSF1 domain may have a function associated with cellular membrane [].
Probab=28.83 E-value=68 Score=23.11 Aligned_cols=42 Identities=14% Similarity=0.029 Sum_probs=31.9
Q ss_pred ccCCCcceEEeeccCCCCccceEEEEEeCCCCceeeeecccC
Q psy7862 17 LTGGSDQVYLIEYFPYFPLITMYLMYYLGEDGKRVYTLKKVD 58 (101)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~M~L~yyl~e~gc~vYTLk~~C 58 (101)
|.|+.+.+|++|.-=.-+-.+...++.-|..-+...++.+.|
T Consensus 54 l~g~~~~~~~~E~S~vD~~~k~l~~~t~Nls~~~~~~v~E~~ 95 (157)
T PF04707_consen 54 LIGVDSECYIIEESIVDPKNKTLTTKTRNLSFSSFLSVEETC 95 (157)
T ss_pred HhCcCceEEEEEEEEEECCCCEEEEEEEEcccCceeEEEEEE
Confidence 578788899999765556666667777788777777777776
No 10
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=23.92 E-value=41 Score=26.27 Aligned_cols=14 Identities=29% Similarity=0.301 Sum_probs=11.1
Q ss_pred ccccCCCCCCCCCc
Q psy7862 64 TVSAHPARFSPDDK 77 (101)
Q Consensus 64 T~saHPARFSPdDK 77 (101)
.-..+||+||++|.
T Consensus 142 SH~~spA~PS~tD~ 155 (192)
T TIGR03735 142 SHGTGSAFFSETDD 155 (192)
T ss_pred CCCCCCCCCCcccc
Confidence 34567899999996
No 11
>PF13043 DUF3903: Domain of unknown function (DUF3903)
Probab=23.85 E-value=64 Score=20.04 Aligned_cols=13 Identities=38% Similarity=0.578 Sum_probs=11.1
Q ss_pred HHHHHHHHHHhCC
Q psy7862 79 SRERITILRRFGL 91 (101)
Q Consensus 79 skYR~~LKkr~gl 91 (101)
.|-|-.+|+|||-
T Consensus 11 ~kvr~eckrrfgk 23 (40)
T PF13043_consen 11 QKVRAECKRRFGK 23 (40)
T ss_pred HHHHHHHHHHhch
Confidence 4678999999995
No 12
>COG0248 GppA Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]
Probab=23.51 E-value=1.8e+02 Score=25.42 Aligned_cols=32 Identities=31% Similarity=0.380 Sum_probs=23.4
Q ss_pred CCCCcccceeeeeccCCCcceEEeeccCCCCc
Q psy7862 4 SGLPDSVRAHQVDLTGGSDQVYLIEYFPYFPL 35 (101)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (101)
+++|...+.--+|+-|||-..-+|+.+-...+
T Consensus 123 ~~~~~~~~~lv~DIGGGStEl~~g~~~~~~~~ 154 (492)
T COG0248 123 STLPRKGDGLVIDIGGGSTELVLGDNFEIGLL 154 (492)
T ss_pred hcCCCCCCEEEEEecCCeEEEEEecCCcccee
Confidence 45665556677999999999999985554433
No 13
>PF03552 Cellulose_synt: Cellulose synthase; InterPro: IPR005150 Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium spp. More correctly designated as "cellulose synthase catalytic subunits", plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity [].; GO: 0016760 cellulose synthase (UDP-forming) activity, 0030244 cellulose biosynthetic process, 0016020 membrane
Probab=22.17 E-value=64 Score=29.91 Aligned_cols=40 Identities=15% Similarity=0.409 Sum_probs=24.1
Q ss_pred ceeeeecccCCC--CCCccccCCCCCCCCCccHHHHHHHHHHhC
Q psy7862 49 KRVYTLKKVDPA--GNPTVSAHPARFSPDDKYSRERITILRRFG 90 (101)
Q Consensus 49 c~vYTLk~~CP~--G~~T~saHPARFSPdDKYskYR~~LKkr~g 90 (101)
|+.|.++..||+ =+.....+..+-+|+ |.+.|+.+|+++-
T Consensus 66 Ckk~~ie~R~P~~YF~~~~~~~~~~~~~~--f~~e~~~~k~~ye 107 (720)
T PF03552_consen 66 CKKYNIEPRAPEAYFSSKIDPLKDKVQPE--FVKERRAMKREYE 107 (720)
T ss_pred hhccCCccCCHHHHhccCCCcccCCcChh--HHHHHHHHHHHHH
Confidence 456777777775 222223333344444 8899998888764
No 14
>PF04749 PLAC8: PLAC8 family; InterPro: IPR006461 This group of sequences are described by a region of about 170 amino acids. These proteins have highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterised protein. It is common in plants but found also in Homo sapiens (Human), Dictyostelium, and Leishmania; at least 12 distinct members are found in Arabidopsis. Most members of this family contain more than 10 per cent Cys, but no Cys residue is invariant across the family.
Probab=20.15 E-value=82 Score=20.11 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=12.1
Q ss_pred HHHHHHHHHHhCC
Q psy7862 79 SRERITILRRFGL 91 (101)
Q Consensus 79 skYR~~LKkr~gl 91 (101)
...|.++|+|+||
T Consensus 68 ~~~R~~iR~ry~I 80 (106)
T PF04749_consen 68 CSLRQQIRERYGI 80 (106)
T ss_pred hhHHHHHHHHhCC
Confidence 7889999999998
Done!