Query psy4075
Match_columns 67
No_of_seqs 82 out of 84
Neff 2.8
Searched_HMMs 46136
Date Sat Aug 17 00:41:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4075.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4075hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4109|consensus 99.5 5.1E-15 1.1E-19 100.7 2.4 38 30-67 52-89 (116)
2 PF05186 Dpy-30: Dpy-30 motif; 98.7 1.7E-08 3.7E-13 57.4 3.0 25 43-67 1-25 (42)
3 KOG4109|consensus 67.8 1.7 3.7E-05 30.0 -0.0 27 41-67 4-30 (116)
4 PF11414 Suppressor_APC: Adeno 47.3 11 0.00024 24.1 1.1 14 54-67 17-30 (84)
5 PF12460 MMS19_C: RNAPII trans 23.8 66 0.0014 24.3 2.1 23 39-61 351-375 (415)
6 PF11210 DUF2996: Protein of u 22.4 95 0.0021 21.4 2.5 22 41-62 4-25 (119)
7 PF09230 DFF40: DNA fragmentat 22.2 67 0.0015 24.4 1.9 18 50-67 171-188 (230)
8 PF02985 HEAT: HEAT repeat; I 21.9 60 0.0013 16.0 1.1 10 52-61 1-10 (31)
9 PF10941 DUF2620: Protein of u 19.7 61 0.0013 22.4 1.1 12 50-61 106-117 (117)
10 PF03130 HEAT_PBS: PBS lyase H 17.8 1.2E+02 0.0027 14.7 1.8 13 49-61 14-26 (27)
No 1
>KOG4109|consensus
Probab=99.52 E-value=5.1e-15 Score=100.68 Aligned_cols=38 Identities=55% Similarity=0.919 Sum_probs=35.7
Q ss_pred CCCCCCCCCCCCchhHHHHhhhHHHHHHHHHHHHhhcC
Q psy4075 30 PGLKKPRLDLHALPTRQYLDQTVVPILLAALTQLTKER 67 (67)
Q Consensus 30 ~~~~~~~~~l~sLP~RqYLdqTVVPiLLqGL~~LaKER 67 (67)
+..++++.+++++|+|||||+||+||||+||.+|||+|
T Consensus 52 a~~~k~k~~v~~~ptRqYLdqtVaPiLL~Gm~~lA~~r 89 (116)
T KOG4109|consen 52 ANQQKPKEDVNSMPTRQYLDQTVAPILLQGMAALAKER 89 (116)
T ss_pred hhhcCccccccCCchhhhcccchhHHHHHHHHHHHhhC
Confidence 44579999999999999999999999999999999998
No 2
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=98.68 E-value=1.7e-08 Score=57.37 Aligned_cols=25 Identities=56% Similarity=0.913 Sum_probs=22.6
Q ss_pred hhHHHHhhhHHHHHHHHHHHHhhcC
Q psy4075 43 PTRQYLDQTVVPILLAALTQLTKER 67 (67)
Q Consensus 43 P~RqYLdqTVVPiLLqGL~~LaKER 67 (67)
|.|+||+++|+|+|.+||.+++|+|
T Consensus 1 p~r~YL~~~v~p~L~~gL~~l~~~r 25 (42)
T PF05186_consen 1 PARQYLKETVGPVLTEGLAELAKER 25 (42)
T ss_dssp -HHHHHHHHTHHHHHHHHHHHHHH-
T ss_pred CHHHHHHHHhHHHHHHHHHHHHHHC
Confidence 7899999999999999999999997
No 3
>KOG4109|consensus
Probab=67.81 E-value=1.7 Score=29.96 Aligned_cols=27 Identities=30% Similarity=0.612 Sum_probs=23.8
Q ss_pred CchhHHHHhhhHHHHHHHHHHHHhhcC
Q psy4075 41 ALPTRQYLDQTVVPILLAALTQLTKER 67 (67)
Q Consensus 41 sLP~RqYLdqTVVPiLLqGL~~LaKER 67 (67)
+-|-|+|++..+-|.|+.|++.+|+-|
T Consensus 4 ~~pa~~~~~~~et~~l~ng~s~~a~n~ 30 (116)
T KOG4109|consen 4 SSPARQYLPEAETPVLLNGMSIAARNP 30 (116)
T ss_pred cccccccCccccchhhhhhhhhhccCC
Confidence 457799999999999999999998754
No 4
>PF11414 Suppressor_APC: Adenomatous polyposis coli tumour suppressor protein; PDB: 1M5I_A.
Probab=47.26 E-value=11 Score=24.09 Aligned_cols=14 Identities=36% Similarity=0.517 Sum_probs=12.1
Q ss_pred HHHHHHHHHHhhcC
Q psy4075 54 PILLAALTQLTKER 67 (67)
Q Consensus 54 PiLLqGL~~LaKER 67 (67)
-+||+||+.+.|+|
T Consensus 17 d~LLqgLe~~Er~r 30 (84)
T PF11414_consen 17 DVLLQGLEMEERER 30 (84)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHH
Confidence 47999999999876
No 5
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=23.80 E-value=66 Score=24.31 Aligned_cols=23 Identities=35% Similarity=0.668 Sum_probs=17.2
Q ss_pred CCCchhHHHHh--hhHHHHHHHHHH
Q psy4075 39 LHALPTRQYLD--QTVVPILLAALT 61 (67)
Q Consensus 39 l~sLP~RqYLd--qTVVPiLLqGL~ 61 (67)
++.+|..-|+. .+++|+|+|+|.
T Consensus 351 l~~vP~~vl~~~l~~LlPLLlqsL~ 375 (415)
T PF12460_consen 351 LKNVPKSVLLPELPTLLPLLLQSLS 375 (415)
T ss_pred HhhCCHHHHHHHHHHHHHHHHHHhC
Confidence 45667666665 379999999985
No 6
>PF11210 DUF2996: Protein of unknown function (DUF2996); InterPro: IPR021374 This family of proteins has no known function.
Probab=22.39 E-value=95 Score=21.43 Aligned_cols=22 Identities=23% Similarity=0.517 Sum_probs=19.3
Q ss_pred CchhHHHHhhhHHHHHHHHHHH
Q psy4075 41 ALPTRQYLDQTVVPILLAALTQ 62 (67)
Q Consensus 41 sLP~RqYLdqTVVPiLLqGL~~ 62 (67)
.=|..+|+++-++|-|-++|+.
T Consensus 4 dKPF~efi~ed~lPaL~~~l~~ 25 (119)
T PF11210_consen 4 DKPFPEFIEEDFLPALKKALEK 25 (119)
T ss_pred CCCHHHHHHHhhhHHHHHHHHH
Confidence 3488999999999999999875
No 7
>PF09230 DFF40: DNA fragmentation factor 40 kDa; InterPro: IPR015311 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. DNA fragmentation factor (DFF) is a complex of the DNase DFF40 (CAD) and its chaperone/inhibitor DFF45 (ICAD-L). In its inactive form, DFF is a heterodimer composed of a 45kDa chaperone inhibitor subunit (DFF45 or ICAD), and a 40kDa latent endonuclease subunit (DFF40 or CAD). Upon caspase-3 cleavage of DFF45, DFF40 forms active endonuclease homo-oligomers. It is activated during apoptosis to induce DNA fragmentation. DNA binding by DFF is mediated by the nuclease subunit, which can also form stable DNA complexes after release from DFF [, ]. The nuclease subunit is inhibited in DNA cleavage but not in DNA binding []. DFF45 can also be cleaved and inactivated by caspase-7 but not by caspase-6 and caspase-8. The cleaved DFF45 fragments dissociate from DFF40, allowing DFF40 to oligomerise, forming a large complex that cleaves DNA by introducing double strand breaks. Histone H1 confers DNA binding ability to DFF and stimulates the nuclease activity of DFF40 [].; GO: 0016787 hydrolase activity, 0006309 DNA fragmentation involved in apoptotic nuclear change, 0005634 nucleus, 0005737 cytoplasm; PDB: 1V0D_A.
Probab=22.21 E-value=67 Score=24.38 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHHHHhhcC
Q psy4075 50 QTVVPILLAALTQLTKER 67 (67)
Q Consensus 50 qTVVPiLLqGL~~LaKER 67 (67)
.||+|-|+++++.+.+.|
T Consensus 171 RtIlP~l~~ai~~~~~~~ 188 (230)
T PF09230_consen 171 RTILPTLVEAIKECQDGR 188 (230)
T ss_dssp TTHHHHHHHHHHH---SS
T ss_pred hhHHHHHHHHHHHhhccc
Confidence 589999999999876543
No 8
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=21.87 E-value=60 Score=16.00 Aligned_cols=10 Identities=50% Similarity=0.876 Sum_probs=7.0
Q ss_pred HHHHHHHHHH
Q psy4075 52 VVPILLAALT 61 (67)
Q Consensus 52 VVPiLLqGL~ 61 (67)
++|.|+++|+
T Consensus 1 llp~l~~~l~ 10 (31)
T PF02985_consen 1 LLPILLQLLN 10 (31)
T ss_dssp HHHHHHHHHT
T ss_pred CHHHHHHHcC
Confidence 4788887764
No 9
>PF10941 DUF2620: Protein of unknown function DUF2620; InterPro: IPR021238 This is a bacterial family of proteins with unknown function.
Probab=19.74 E-value=61 Score=22.36 Aligned_cols=12 Identities=50% Similarity=0.891 Sum_probs=9.8
Q ss_pred hhHHHHHHHHHH
Q psy4075 50 QTVVPILLAALT 61 (67)
Q Consensus 50 qTVVPiLLqGL~ 61 (67)
++|||+|+++|.
T Consensus 106 e~vvP~l~~~l~ 117 (117)
T PF10941_consen 106 EQVVPVLIKALK 117 (117)
T ss_pred HHHHHHHHHHhC
Confidence 578999998873
No 10
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=17.78 E-value=1.2e+02 Score=14.71 Aligned_cols=13 Identities=38% Similarity=0.703 Sum_probs=10.0
Q ss_pred hhhHHHHHHHHHH
Q psy4075 49 DQTVVPILLAALT 61 (67)
Q Consensus 49 dqTVVPiLLqGL~ 61 (67)
|...+|.|+++|+
T Consensus 14 d~~ai~~L~~~L~ 26 (27)
T PF03130_consen 14 DPRAIPALIEALE 26 (27)
T ss_dssp SHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhc
Confidence 4677888888875
Done!