Query psy15631
Match_columns 213
No_of_seqs 111 out of 237
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 17:39:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0527|consensus 99.5 5.9E-15 1.3E-19 134.1 5.4 37 2-38 108-144 (331)
2 cd01389 MATA_HMG-box MATA_HMG- 98.4 1.2E-07 2.6E-12 67.7 2.8 31 2-32 47-77 (77)
3 KOG0528|consensus 98.2 8.1E-07 1.8E-11 85.5 2.7 37 1-37 370-406 (511)
4 cd01388 SOX-TCF_HMG-box SOX-TC 97.7 2.2E-05 4.7E-10 55.6 2.2 26 2-27 47-72 (72)
5 KOG3248|consensus 91.6 0.19 4.1E-06 48.1 3.6 28 2-29 237-264 (421)
6 smart00398 HMG high mobility g 91.6 0.1 2.3E-06 34.9 1.4 24 2-25 47-70 (70)
7 PF00505 HMG_box: HMG (high mo 89.8 0.066 1.4E-06 36.4 -0.8 24 2-25 46-69 (69)
8 cd00084 HMG-box High Mobility 85.5 0.57 1.2E-05 30.9 1.7 21 2-22 46-66 (66)
9 PF12336 SOXp: SOX transcripti 70.7 1.6 3.5E-05 33.9 0.4 13 26-38 1-13 (84)
10 cd01390 HMGB-UBF_HMG-box HMGB- 48.8 13 0.00028 24.7 1.7 19 2-20 46-64 (66)
11 PF09011 HMG_box_2: HMG-box do 41.7 18 0.00039 25.5 1.6 19 2-20 50-68 (73)
12 PF12108 SF3a60_bindingd: Spli 35.5 36 0.00079 21.7 2.1 18 5-23 11-28 (28)
No 1
>KOG0527|consensus
Probab=99.54 E-value=5.9e-15 Score=134.05 Aligned_cols=37 Identities=73% Similarity=1.137 Sum_probs=34.9
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCCCCC
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQS 38 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~~~~ 38 (213)
||+||||||||||++||++|||||||||||+|+....
T Consensus 108 EKrPFi~EAeRLR~~HmkehPdYKYRPRRKkk~~~~~ 144 (331)
T KOG0527|consen 108 EKRPFVDEAERLRAQHMKEYPDYKYRPRRKKKKRPKL 144 (331)
T ss_pred hhccHHHHHHHHHHHHHHhCCCccccccccccccccc
Confidence 8999999999999999999999999999999887764
No 2
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=98.45 E-value=1.2e-07 Score=67.72 Aligned_cols=31 Identities=35% Similarity=0.629 Sum_probs=29.4
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCcccCCCCC
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP 32 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~ 32 (213)
||.+|.++|++++++|+++||+|+|+|||+.
T Consensus 47 eK~~y~~~A~~~k~~~~~~~p~Yky~p~~~~ 77 (77)
T cd01389 47 VKAYYKELAEEEKERHAREYPDYKYTPRKSS 77 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCcccCCCCC
Confidence 6899999999999999999999999999974
No 3
>KOG0528|consensus
Probab=98.19 E-value=8.1e-07 Score=85.49 Aligned_cols=37 Identities=38% Similarity=0.790 Sum_probs=33.7
Q ss_pred CCcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCCCC
Q psy15631 1 MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQ 37 (213)
Q Consensus 1 ~EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~~~ 37 (213)
.||+||++|-.||..+|+++|||||||||-|+.|..+
T Consensus 370 ~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPKRTCvvd 406 (511)
T KOG0528|consen 370 TEKQPYYEEQARLSKLHLEKYPDYRYKPRPKRTCVVD 406 (511)
T ss_pred ccccchHHHHHHHHHhhhccCcccccCCCCCceeeec
Confidence 3899999999999999999999999999988877553
No 4
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=97.70 E-value=2.2e-05 Score=55.62 Aligned_cols=26 Identities=58% Similarity=1.088 Sum_probs=24.9
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCccc
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYKYr 27 (213)
||.+|.++|++++++|+++||||||+
T Consensus 47 eK~~y~~~a~~~k~~y~~~~p~y~y~ 72 (72)
T cd01388 47 EKQPYYEEAKKLKELHMKLYPDYKWR 72 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence 68999999999999999999999996
No 5
>KOG3248|consensus
Probab=91.58 E-value=0.19 Score=48.07 Aligned_cols=28 Identities=25% Similarity=0.492 Sum_probs=24.8
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCcccCC
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPR 29 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYKYrPR 29 (213)
|..-|+|.|++.|+.||+.||+|.-|-+
T Consensus 237 EQAKYyElArKerqlH~qlYP~WSARdN 264 (421)
T KOG3248|consen 237 EQAKYYELARKERQLHMQLYPGWSARDN 264 (421)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcchhhh
Confidence 5678999999999999999999986665
No 6
>smart00398 HMG high mobility group.
Probab=91.56 E-value=0.1 Score=34.89 Aligned_cols=24 Identities=38% Similarity=0.639 Sum_probs=22.6
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYK 25 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYK 25 (213)
||.+|.++|++.+++|.+++++|+
T Consensus 47 ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 47 EKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999999985
No 7
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=89.76 E-value=0.066 Score=36.35 Aligned_cols=24 Identities=42% Similarity=0.666 Sum_probs=22.3
Q ss_pred CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHPDYK 25 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YPdYK 25 (213)
||.+|.++|++.+++|.+++++|+
T Consensus 46 eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 46 EKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999998885
No 8
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=85.46 E-value=0.57 Score=30.92 Aligned_cols=21 Identities=29% Similarity=0.436 Sum_probs=19.2
Q ss_pred CcchhHHHHHHHHHHHHhhCC
Q psy15631 2 EKRPFIDEAKRLRAMHMKEHP 22 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~YP 22 (213)
||.+|+++|++.+++|.+.+|
T Consensus 46 ~k~~y~~~a~~~~~~y~~~~~ 66 (66)
T cd00084 46 EKKKYEEKAEKDKERYEKEMP 66 (66)
T ss_pred HHHHHHHHHHHHHHHHHHhhC
Confidence 689999999999999998875
No 9
>PF12336 SOXp: SOX transcription factor; InterPro: IPR022097 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with PF00505 from PFAM. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter. ; PDB: 2LE4_A.
Probab=70.71 E-value=1.6 Score=33.89 Aligned_cols=13 Identities=62% Similarity=0.856 Sum_probs=3.8
Q ss_pred ccCCCCCCCCCCC
Q psy15631 26 YRPRRKPKTPGQS 38 (213)
Q Consensus 26 YrPRRK~k~~~~~ 38 (213)
||||||.|.+++.
T Consensus 1 YRPRRKtKtLlKK 13 (84)
T PF12336_consen 1 YRPRRKTKTLLKK 13 (84)
T ss_dssp S-SS--S------
T ss_pred CCCcccchhhhcc
Confidence 8999999988774
No 10
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=48.78 E-value=13 Score=24.72 Aligned_cols=19 Identities=26% Similarity=0.372 Sum_probs=16.5
Q ss_pred CcchhHHHHHHHHHHHHhh
Q psy15631 2 EKRPFIDEAKRLRAMHMKE 20 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~ 20 (213)
||.+|.++|++.+++..++
T Consensus 46 eK~~y~~~a~~~~~~y~~e 64 (66)
T cd01390 46 EKKKYEEKAEKDKERYEKE 64 (66)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 6899999999999988654
No 11
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=41.71 E-value=18 Score=25.47 Aligned_cols=19 Identities=32% Similarity=0.447 Sum_probs=16.7
Q ss_pred CcchhHHHHHHHHHHHHhh
Q psy15631 2 EKRPFIDEAKRLRAMHMKE 20 (213)
Q Consensus 2 EK~PyideAkrLKa~H~k~ 20 (213)
||.+|.++|+.+|++..++
T Consensus 50 EK~~Y~~~A~~~k~~y~~e 68 (73)
T PF09011_consen 50 EKEPYEERAKEDKERYERE 68 (73)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7899999999999987665
No 12
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=35.53 E-value=36 Score=21.67 Aligned_cols=18 Identities=22% Similarity=0.617 Sum_probs=12.9
Q ss_pred hhHHHHHHHHHHHHhhCCC
Q psy15631 5 PFIDEAKRLRAMHMKEHPD 23 (213)
Q Consensus 5 PyideAkrLKa~H~k~YPd 23 (213)
-|+++-+++|+-| ++||+
T Consensus 11 eFY~rlk~Ike~H-rr~Pn 28 (28)
T PF12108_consen 11 EFYERLKEIKEYH-RRYPN 28 (28)
T ss_dssp HHHHHHHHHHHHH-HS--S
T ss_pred HHHHHHHHHHHHH-HhCCC
Confidence 4788888999988 67775
Done!