Query psy6232
Match_columns 100
No_of_seqs 55 out of 57
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 21:10:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2571|consensus 98.9 2.9E-10 6.3E-15 102.2 0.3 96 1-96 141-238 (862)
2 KOG1098|consensus 53.2 9.3 0.0002 35.3 2.0 38 42-79 166-203 (780)
3 KOG1228|consensus 34.4 20 0.00042 29.3 1.0 28 64-91 170-200 (256)
4 PF10236 DAP3: Mitochondrial r 30.4 15 0.00033 29.2 -0.2 51 44-94 45-103 (309)
5 KOG3218|consensus 19.6 32 0.00069 27.4 -0.3 18 52-69 137-154 (208)
6 KOG4263|consensus 18.1 1.1E+02 0.0023 25.7 2.4 25 39-63 128-152 (299)
7 PF08430 Fork_head_N: Forkhead 15.9 59 0.0013 23.8 0.4 10 86-95 119-128 (136)
8 PF08171 Mad3_BUB1_II: Mad3/BU 15.6 74 0.0016 21.2 0.8 23 78-100 43-68 (68)
9 PF01191 RNA_pol_Rpb5_C: RNA p 15.1 35 0.00077 22.8 -0.9 23 52-74 3-25 (74)
10 COG1902 NemA NADH:flavin oxido 15.0 77 0.0017 26.4 0.9 18 77-94 172-191 (363)
No 1
>KOG2571|consensus
Probab=98.89 E-value=2.9e-10 Score=102.16 Aligned_cols=96 Identities=24% Similarity=0.156 Sum_probs=89.8
Q ss_pred CCCCCCCCccccccCCCCce-eccCCC-cccHHHHHHHHHHHHHHHHHHHhHHHhhhccCcccccccccccccccccchh
Q psy6232 1 MCGLRNDDPCFFQNSIPDYL-FFVSPS-IYFLDDFILKQHAWVWLLWLLSQTWITLHIWTPKCERLATTEKLFVRPMYDA 78 (100)
Q Consensus 1 ~C~~r~~d~C~f~~~iPdyL-F~~~p~-~~~l~~f~~~~~~w~WLlWllSQ~Wit~HiW~p~~eRLA~tEkLFv~p~Y~~ 78 (100)
.|.+|..|||.-+|.++|+. .+.++. ..++.+|......|.|+.|+.||.|.+.|.|++++++.+++|+++..|+|.|
T Consensus 141 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 220 (862)
T KOG2571|consen 141 NAILRQSDPCERRGFLSDESLKPKLSKTFESLKLFILDYQLWESLIDLDSGSWRGYTDMNTANKRKMPNEGLTRAPRYIG 220 (862)
T ss_pred cchhccCCcccccccccccCCCCCCCccccchhccccchhhhccCcccccccchheeeccccccccccccCCccCceeee
Confidence 37889999999999999998 999984 4577999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhccccccccc
Q psy6232 79 LLIDQSMSLNRRCDDEKD 96 (100)
Q Consensus 79 ~liDQsl~lNRrr~d~~~ 96 (100)
..++|++++++++.+...
T Consensus 221 ~~~~~~~~~~~~~~~~~~ 238 (862)
T KOG2571|consen 221 TTLFQSSVLGLIKVALST 238 (862)
T ss_pred ehhhhhhccccchhhhhc
Confidence 999999999999987653
No 2
>KOG1098|consensus
Probab=53.24 E-value=9.3 Score=35.33 Aligned_cols=38 Identities=24% Similarity=0.204 Sum_probs=34.1
Q ss_pred HHHHHHHhHHHhhhccCcccccccccccccccccchhh
Q psy6232 42 WLLWLLSQTWITLHIWTPKCERLATTEKLFVRPMYDAL 79 (100)
Q Consensus 42 WLlWllSQ~Wit~HiW~p~~eRLA~tEkLFv~p~Y~~~ 79 (100)
=|||.++|+.+-+|-+-|-..|.++.|-.||+--|-++
T Consensus 166 ~ll~v~~qLf~kv~~tkp~asr~~saeif~vc~~~l~P 203 (780)
T KOG1098|consen 166 GLLRVFGQLFKKVEATKPAASRSESAEIFVVCLGYLAP 203 (780)
T ss_pred HHHHHHHHHHHHHHhcCChhhhhhccceeeeeecccCc
Confidence 37999999999999999999999999999998777543
No 3
>KOG1228|consensus
Probab=34.43 E-value=20 Score=29.31 Aligned_cols=28 Identities=29% Similarity=0.479 Sum_probs=21.7
Q ss_pred ccccccccccccchhhhhhhhh---hhcccc
Q psy6232 64 LATTEKLFVRPMYDALLIDQSM---SLNRRC 91 (100)
Q Consensus 64 LA~tEkLFv~p~Y~~~liDQsl---~lNRrr 91 (100)
+..+|||||+|-|-.+|++-+. -=|++|
T Consensus 170 lg~s~kLmVTpEYv~fL~~~anekmdeN~kr 200 (256)
T KOG1228|consen 170 LGHSGKLMVTPEYVDFLLNVANEKMDENKKR 200 (256)
T ss_pred cCCCccEEecHHHHHHHHHHHHHHHhhhHHH
Confidence 3479999999999999998663 345554
No 4
>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 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 [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=30.39 E-value=15 Score=29.23 Aligned_cols=51 Identities=20% Similarity=0.322 Sum_probs=35.2
Q ss_pred HHHHHhHHHhhhccCc-----ccccccc---cccccccccchhhhhhhhhhhccccccc
Q psy6232 44 LWLLSQTWITLHIWTP-----KCERLAT---TEKLFVRPMYDALLIDQSMSLNRRCDDE 94 (100)
Q Consensus 44 lWllSQ~Wit~HiW~p-----~~eRLA~---tEkLFv~p~Y~~~liDQsl~lNRrr~d~ 94 (100)
.|-..|=||.+||=.+ .+.=.++ .+.+|.+|+|..-++.+.+..|...-.+
T Consensus 45 ~~A~~~~wiVl~vp~a~~~~~~~~~~~~~~~~~~~~~qP~~a~~~L~~~~~~N~~~L~~ 103 (309)
T PF10236_consen 45 HYARENGWIVLYVPSAQDWVNGTTDYAPSPYNPGLYDQPMYAAKWLKKFLKANEELLKK 103 (309)
T ss_pred HHHHhCCEEEEEcCCHHHHhhCCeeEeeCCCCCCeeecHHHHHHHHHHHHHHhHHHHHh
Confidence 3555778888886332 2221222 4699999999999999999999744333
No 5
>KOG3218|consensus
Probab=19.59 E-value=32 Score=27.44 Aligned_cols=18 Identities=44% Similarity=0.497 Sum_probs=16.8
Q ss_pred HhhhccCccccccccccc
Q psy6232 52 ITLHIWTPKCERLATTEK 69 (100)
Q Consensus 52 it~HiW~p~~eRLA~tEk 69 (100)
||=|.|.|+...|.+.||
T Consensus 137 IT~H~lvPkH~vL~~eEK 154 (208)
T KOG3218|consen 137 ITEHELVPKHQVLTDEEK 154 (208)
T ss_pred ccceeecCceEEcCHHHH
Confidence 788999999999999987
No 6
>KOG4263|consensus
Probab=18.10 E-value=1.1e+02 Score=25.71 Aligned_cols=25 Identities=28% Similarity=0.707 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhHHHhhhccCccccc
Q psy6232 39 AWVWLLWLLSQTWITLHIWTPKCER 63 (100)
Q Consensus 39 ~w~WLlWllSQ~Wit~HiW~p~~eR 63 (100)
+..-|+-+.--.-.|-|.|+|++.|
T Consensus 128 ~ff~li~~fPR~~LtrHFWTpqQr~ 152 (299)
T KOG4263|consen 128 VFFFLIIFFPRLVLTRHFWTPQQRR 152 (299)
T ss_pred HHHHHHHHHHHHHHHHHhCChHhHh
Confidence 3444555666777899999999864
No 7
>PF08430 Fork_head_N: Forkhead N-terminal region; InterPro: IPR013638 The region described in this entry is found towards the N terminus of various eukaryotic fork head/HNF-3-related transcription factors (which contain the IPR001766 from INTERPRO domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumorigenesis []. ; GO: 0008134 transcription factor binding, 0019904 protein domain specific binding
Probab=15.90 E-value=59 Score=23.75 Aligned_cols=10 Identities=40% Similarity=0.537 Sum_probs=8.1
Q ss_pred hhcccccccc
Q psy6232 86 SLNRRCDDEK 95 (100)
Q Consensus 86 ~lNRrr~d~~ 95 (100)
+|||.||+|.
T Consensus 119 ~l~R~R~~Kt 128 (136)
T PF08430_consen 119 ALNRARDPKT 128 (136)
T ss_pred ccccccCCcc
Confidence 4999998874
No 8
>PF08171 Mad3_BUB1_II: Mad3/BUB1 homology region 2; InterPro: IPR012572 This domain is required for cell cycle arrest induced by spindle assembly checkpoint (SPC) activation. It is also involved in the nuclear accumulation and kinetochore targeting of proteins Bub1p, Bub3p and Mad3p [].; GO: 0000075 cell cycle checkpoint, 0005634 nucleus; PDB: 2I3T_D 2I3S_F.
Probab=15.59 E-value=74 Score=21.15 Aligned_cols=23 Identities=17% Similarity=0.351 Sum_probs=10.3
Q ss_pred hhhhhhhhhhccc---cccccccccC
Q psy6232 78 ALLIDQSMSLNRR---CDDEKDVKTE 100 (100)
Q Consensus 78 ~~liDQsl~lNRr---r~d~~~i~~e 100 (100)
-.-+++-|||.|. +..++.+|.|
T Consensus 43 E~s~eEiLA~sR~~~y~~~~~~~k~~ 68 (68)
T PF08171_consen 43 EYSLEEILAISRNVYYKKKQKKRKRE 68 (68)
T ss_dssp B--HHHHHHHHTT--SS---------
T ss_pred eecHHHHHHHHhhcchhhhhhcccCC
Confidence 4678999999998 4455555543
No 9
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=15.07 E-value=35 Score=22.77 Aligned_cols=23 Identities=39% Similarity=0.326 Sum_probs=16.6
Q ss_pred HhhhccCcccccccccccccccc
Q psy6232 52 ITLHIWTPKCERLATTEKLFVRP 74 (100)
Q Consensus 52 it~HiW~p~~eRLA~tEkLFv~p 74 (100)
||-|...|+.+.|..+|+-=+.-
T Consensus 3 i~~H~lVPkH~ils~eE~~~lL~ 25 (74)
T PF01191_consen 3 ITKHELVPKHEILSEEEKKELLK 25 (74)
T ss_dssp CTSSTTC-EEEEE-HHHHHHHHH
T ss_pred cccceecCCeEEcCHHHHHHHHH
Confidence 57899999999999999754433
No 10
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=14.97 E-value=77 Score=26.42 Aligned_cols=18 Identities=33% Similarity=0.505 Sum_probs=15.2
Q ss_pred hhhhhhhhhh--hccccccc
Q psy6232 77 DALLIDQSMS--LNRRCDDE 94 (100)
Q Consensus 77 ~~~liDQsl~--lNRrr~d~ 94 (100)
+|-||||.|. -|+|.|+.
T Consensus 172 hGYLi~qFlsp~tN~RtD~Y 191 (363)
T COG1902 172 HGYLLSQFLSPLTNKRTDEY 191 (363)
T ss_pred cchHHHHhcCCccCCCCCcc
Confidence 5789999998 99988864
Done!