Query psy12694
Match_columns 112
No_of_seqs 43 out of 45
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 17:15:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4218|consensus 99.6 2E-16 4.2E-21 135.3 5.6 34 1-36 93-126 (475)
2 TIGR01602 PY-rept-46 Plasmodiu 54.0 3.6 7.8E-05 26.4 -0.3 16 4-19 3-18 (46)
3 PF09689 PY_rept_46: Plasmodiu 42.3 7.8 0.00017 24.9 -0.1 15 4-18 3-17 (46)
4 COG3474 Cytochrome c2 [Energy 40.9 14 0.00029 28.3 0.9 10 2-11 49-58 (135)
5 PRK06341 single-stranded DNA-b 34.8 36 0.00079 26.1 2.5 16 95-110 151-166 (166)
6 PF10562 CaM_bdg_C0: Calmoduli 20.5 1.2E+02 0.0026 17.8 2.3 14 11-24 2-15 (29)
7 PF10405 BHD_3: Rad4 beta-hair 19.2 41 0.00089 22.8 0.2 8 5-12 3-10 (76)
8 PF09452 Mvb12: ESCRT-I subuni 15.2 54 0.0012 23.6 0.0 18 5-22 8-25 (91)
9 PF02234 CDI: Cyclin-dependent 12.9 81 0.0018 19.7 0.4 7 5-11 1-7 (51)
10 PF15086 UPF0542: Uncharacteri 12.8 1.9E+02 0.0041 20.2 2.2 18 13-30 50-67 (74)
No 1
>KOG4218|consensus
Probab=99.64 E-value=2e-16 Score=135.29 Aligned_cols=34 Identities=62% Similarity=0.916 Sum_probs=30.7
Q ss_pred CCCCCCCCCcchhhHHHHHHHHHHHhhhhhhhhhcc
Q psy12694 1 MRGGRNKFGPMYKRDRARKLQMMRQRQIAVQTLQRA 36 (112)
Q Consensus 1 MRGGRNKFGPmYKRDRA~k~Q~~~qr~ia~~~l~~s 36 (112)
|||||||||||||||||+|||+. .+|..++++.|
T Consensus 93 MRGGRNKFGpmYKrDRAlkqQkk--AqirAng~KlE 126 (475)
T KOG4218|consen 93 MRGGRNKFGPMYKRDRALKQQKK--AQIRANGIKLE 126 (475)
T ss_pred hcccccccCchhhhhHHHHHHHH--HHhhhcceeee
Confidence 89999999999999999999984 56777888888
No 2
>TIGR01602 PY-rept-46 Plasmodium yoelii repeat of length 46. This repeat is found in only 2 genes in Plasmodium yoelii, in each of these genes it is repeated 9 times. It is found in no other organism.
Probab=53.98 E-value=3.6 Score=26.38 Aligned_cols=16 Identities=38% Similarity=0.789 Sum_probs=13.6
Q ss_pred CCCCCCcchhhHHHHH
Q psy12694 4 GRNKFGPMYKRDRARK 19 (112)
Q Consensus 4 GRNKFGPmYKRDRA~k 19 (112)
-|.||-.|||||.--|
T Consensus 3 KkSkF~sMFKrDK~dk 18 (46)
T TIGR01602 3 KRSRFPTMFKKDKKDK 18 (46)
T ss_pred ccchhhHHHhcccccc
Confidence 4789999999998754
No 3
>PF09689 PY_rept_46: Plasmodium yoelii repeat (PY_rept_46); InterPro: IPR006489 This repeat is found in the products of only 2 genes in Plasmodium yoelii, in each of these proteins it is repeated 9 times. It is found in no other organism.
Probab=42.32 E-value=7.8 Score=24.94 Aligned_cols=15 Identities=33% Similarity=0.778 Sum_probs=12.6
Q ss_pred CCCCCCcchhhHHHH
Q psy12694 4 GRNKFGPMYKRDRAR 18 (112)
Q Consensus 4 GRNKFGPmYKRDRA~ 18 (112)
-|.+|-.|+|||.--
T Consensus 3 KkSrFpsMFKrdKkD 17 (46)
T PF09689_consen 3 KKSRFPSMFKRDKKD 17 (46)
T ss_pred ccccchHhhhccccc
Confidence 378999999999854
No 4
>COG3474 Cytochrome c2 [Energy production and conversion]
Probab=40.88 E-value=14 Score=28.33 Aligned_cols=10 Identities=60% Similarity=1.165 Sum_probs=8.6
Q ss_pred CCCCCCCCcc
Q psy12694 2 RGGRNKFGPM 11 (112)
Q Consensus 2 RGGRNKFGPm 11 (112)
+||+||+||-
T Consensus 49 ~~g~nkvGP~ 58 (135)
T COG3474 49 KGGPNKVGPH 58 (135)
T ss_pred cCCCCCCCCc
Confidence 5899999994
No 5
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=34.80 E-value=36 Score=26.13 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=12.9
Q ss_pred CCccccCCCCCCCCCC
Q psy12694 95 YSSSYIPSDMEDDVPY 110 (112)
Q Consensus 95 ~~~~~~~~~~~~~~~~ 110 (112)
..++-.-+||.||+||
T Consensus 151 ~~~~~~~~~~~~~~~~ 166 (166)
T PRK06341 151 GGGGNFSRDMDDDIPF 166 (166)
T ss_pred CCCCCccccccccCCC
Confidence 4456678999999997
No 6
>PF10562 CaM_bdg_C0: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; InterPro: IPR018882 This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue [].
Probab=20.53 E-value=1.2e+02 Score=17.83 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=9.7
Q ss_pred chhhHHHHHHHHHH
Q psy12694 11 MYKRDRARKLQMMR 24 (112)
Q Consensus 11 mYKRDRA~k~Q~~~ 24 (112)
+|||-|-+|+.++.
T Consensus 2 aYKkH~~~kqk~~e 15 (29)
T PF10562_consen 2 AYKKHQIRKQKQLE 15 (29)
T ss_pred cchHHHHHHHHHHH
Confidence 69998877655444
No 7
>PF10405 BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR018328 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=19.21 E-value=41 Score=22.76 Aligned_cols=8 Identities=25% Similarity=0.762 Sum_probs=3.5
Q ss_pred CCCCCcch
Q psy12694 5 RNKFGPMY 12 (112)
Q Consensus 5 RNKFGPmY 12 (112)
||+||+.+
T Consensus 3 kN~~GNie 10 (76)
T PF10405_consen 3 KNEYGNIE 10 (76)
T ss_dssp --TTS-EE
T ss_pred CCCCCCEE
Confidence 67777754
No 8
>PF09452 Mvb12: ESCRT-I subunit Mvb12; InterPro: IPR019014 The endosomal sorting complex required for transport (ESCRT) complexes play a critical role in receptor down-regulation and retroviral budding. A new component of the ESCRT-I complex was identified [], multivesicular body sorting factor of 12 kDa (Mvb12), which binds to the coiled-coil domain of the ESCRT-I subunit vacuolar protein sorting 23 (Vps23) []. ; PDB: 2P22_D.
Probab=15.20 E-value=54 Score=23.64 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=7.4
Q ss_pred CCCCCcchhhHHHHHHHH
Q psy12694 5 RNKFGPMYKRDRARKLQM 22 (112)
Q Consensus 5 RNKFGPmYKRDRA~k~Q~ 22 (112)
+||||..|-|-|-.|+++
T Consensus 8 YN~~g~~fP~~~l~kl~~ 25 (91)
T PF09452_consen 8 YNKYGSDFPRERLPKLTV 25 (91)
T ss_dssp EESSSTTS----------
T ss_pred ccccccccchhhcccccC
Confidence 599999999877555553
No 9
>PF02234 CDI: Cyclin-dependent kinase inhibitor; InterPro: IPR003175 Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.; GO: 0004861 cyclin-dependent protein kinase inhibitor activity, 0007050 cell cycle arrest, 0005634 nucleus; PDB: 1H27_E 1JSU_C.
Probab=12.90 E-value=81 Score=19.73 Aligned_cols=7 Identities=71% Similarity=1.388 Sum_probs=1.9
Q ss_pred CCCCCcc
Q psy12694 5 RNKFGPM 11 (112)
Q Consensus 5 RNKFGPm 11 (112)
||-|||.
T Consensus 1 R~LFgp~ 7 (51)
T PF02234_consen 1 RNLFGPV 7 (51)
T ss_dssp --SS---
T ss_pred CCCCCCC
Confidence 7999987
No 10
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=12.85 E-value=1.9e+02 Score=20.24 Aligned_cols=18 Identities=39% Similarity=0.490 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHHhhhhh
Q psy12694 13 KRDRARKLQMMRQRQIAV 30 (112)
Q Consensus 13 KRDRA~k~Q~~~qr~ia~ 30 (112)
+++|..|+|..++.+|+-
T Consensus 50 ~~ere~K~k~Kr~~~i~k 67 (74)
T PF15086_consen 50 KEEREKKKKAKRQANIAK 67 (74)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455666666666666654
Done!