Query psy3618
Match_columns 136
No_of_seqs 109 out of 139
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 21:11:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3618.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3618hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06991 Prp19_bind: Splicing 100.0 8.9E-45 1.9E-49 300.9 5.8 120 1-121 151-276 (276)
2 KOG1425|consensus 100.0 2.4E-40 5.2E-45 287.5 5.0 123 1-123 300-429 (430)
3 cd07322 PriL_PriS_Eukaryotic E 20.5 60 0.0013 28.8 1.5 45 31-78 257-303 (390)
4 PF03531 SSrecog: Structure-sp 19.9 25 0.00055 29.2 -0.8 12 70-81 201-212 (222)
5 KOG1425|consensus 17.7 78 0.0017 29.2 1.7 39 1-40 229-268 (430)
6 KOG4188|consensus 15.8 74 0.0016 25.9 0.9 32 57-88 9-42 (159)
7 cd04498 hPOT1_OB2 hPOT1_OB2: A 13.9 76 0.0016 24.2 0.5 23 7-30 70-92 (123)
8 PF00436 SSB: Single-strand bi 13.2 95 0.0021 20.6 0.8 19 7-25 58-76 (104)
9 PF09020 YopE_N: YopE, N termi 11.3 68 0.0015 24.7 -0.4 13 55-67 110-122 (126)
10 COG4492 PheB ACT domain-contai 10.8 93 0.002 25.1 0.2 13 53-65 12-24 (150)
No 1
>PF06991 Prp19_bind: Splicing factor, Prp19-binding domain; InterPro: IPR009730 This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix [].
Probab=100.00 E-value=8.9e-45 Score=300.87 Aligned_cols=120 Identities=56% Similarity=0.864 Sum_probs=110.8
Q ss_pred CchhhhhhHHHHhh------hccccchhcccccCCCCCCccchhhhhhccCCCCcccccccccccchhhhhhccCcCCCc
Q psy3618 1 MVEDEVRAEDAKNR------IKNGEEARLEDVNTDDENDEDSEEDILKRDFSSATLDDHFDKTVLPKVMQVKNFGRSGRT 74 (136)
Q Consensus 1 ~~~~~~~~~~~~~~------~k~g~~~~l~~~~~~d~~~~~~~e~I~kRD~s~pt~eD~vdk~~LPkvMQvRnfGK~GrT 74 (136)
|-+.|.++++..+. -.+|...|||+|.|.+.+-++..++||+|||++||++|+||+++|||||||||||++|||
T Consensus 151 mteEEr~~ed~~~~k~~~~~~~k~k~~fmQKyyHkGaF~~d~~~~i~~RD~~~~t~~d~~dk~~LPk~mqvr~fGk~grt 230 (276)
T PF06991_consen 151 MTEEERRAEDRENPKQIENKKEKGKMKFMQKYYHKGAFFQDEEDEIYKRDFSAPTGEDKFDKSLLPKVMQVRNFGKSGRT 230 (276)
T ss_pred cCHHHHHHHHHhhhhhhhccccccchhhhhhcccccccccchHHHHhhccccccchHhhhhHHhchHHHhhhhhccccCc
Confidence 45667777776542 248999999999999999999888999999999999999999999999999999999999
Q ss_pred ccccccCCcCCCCCCCCccccchhhhhhhhhhcCCccccCCCccccC
Q psy3618 75 KYSHLVDQDTTQFDSPWLSETSQNHKFHLNQAAGMKQVFVKPSLSKR 121 (136)
Q Consensus 75 KyThL~dEDTT~~d~~W~~~~~~~~Kf~~~k~gGmkq~FdrPs~kKk 121 (136)
|||||++||||+|+++|++.++++.+| .+++|||+++|+||++|||
T Consensus 231 KythL~~eDTt~~~~~w~~~~~~~~~~-~~~~~g~~~~fd~p~~kk~ 276 (276)
T PF06991_consen 231 KYTHLVDEDTTRFDSPWSQESAQNAKF-KNKAAGMKQVFDRPSKKKK 276 (276)
T ss_pred cccccccccccccCCcccccchHHHHH-HHhcccccccccCccccCC
Confidence 999999999999999999999999999 7899999999999999875
No 2
>KOG1425|consensus
Probab=100.00 E-value=2.4e-40 Score=287.53 Aligned_cols=123 Identities=54% Similarity=0.817 Sum_probs=113.7
Q ss_pred CchhhhhhHHHHh------hhccccchhcccccCCCCCCccchhh-hhhccCCCCcccccccccccchhhhhhccCcCCC
Q psy3618 1 MVEDEVRAEDAKN------RIKNGEEARLEDVNTDDENDEDSEED-ILKRDFSSATLDDHFDKTVLPKVMQVKNFGRSGR 73 (136)
Q Consensus 1 ~~~~~~~~~~~~~------~~k~g~~~~l~~~~~~d~~~~~~~e~-I~kRD~s~pt~eD~vdk~~LPkvMQvRnfGK~Gr 73 (136)
|-|.|-|+++-+| .-++|---|||+|-|.+-+=-+++++ |+||||++||++|+|||++||||||||||||+||
T Consensus 300 MteEERr~~lrknpkv~tnk~~KgkykFLQKYYHkGAFf~de~de~V~KRDfseaT~ed~~dKtILPKvMQVKnFgragr 379 (430)
T KOG1425|consen 300 MTEEERRAELRKNPKVSTNKAKKGKYKFLQKYYHKGAFFLDEDDEIVLKRDFSEATLEDHLDKTILPKVMQVKNFGRAGR 379 (430)
T ss_pred ccHHHHHHHHhhCcccccccccchhHHHHHHHHhccccccCcchhhHHhhccccccccccccccccccceeecccccccc
Confidence 5567777777664 46788889999999999998777777 9999999999999999999999999999999999
Q ss_pred cccccccCCcCCCCCCCCccccchhhhhhhhhhcCCccccCCCccccCCC
Q psy3618 74 TKYSHLVDQDTTQFDSPWLSETSQNHKFHLNQAAGMKQVFVKPSLSKRKP 123 (136)
Q Consensus 74 TKyThL~dEDTT~~d~~W~~~~~~~~Kf~~~k~gGmkq~FdrPs~kKkk~ 123 (136)
||||||++||||.|++||+..++++.||+.+++||+.++|++|..||+|+
T Consensus 380 TK~THLvneDTT~~~s~W~~~~~~n~kf~~~raGg~r~~fd~p~sKKrK~ 429 (430)
T KOG1425|consen 380 TKWTHLVNEDTTDFDSPWYSESNLNLKFNKKRAGGDRPVFDRPLSKKRKT 429 (430)
T ss_pred cceeeeccccccccCCcccCCCchHhHHHHHhccCCccccCCccchhccC
Confidence 99999999999999999999999999999999999999999999988875
No 3
>cd07322 PriL_PriS_Eukaryotic Eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of
Probab=20.45 E-value=60 Score=28.78 Aligned_cols=45 Identities=20% Similarity=0.448 Sum_probs=33.4
Q ss_pred CCCccchhhhhhccCCCCcccccccccccchhhhhh-ccCcC-CCccccc
Q psy3618 31 ENDEDSEEDILKRDFSSATLDDHFDKTVLPKVMQVK-NFGRS-GRTKYSH 78 (136)
Q Consensus 31 ~~~~~~~e~I~kRD~s~pt~eD~vdk~~LPkvMQvR-nfGK~-GrTKyTh 78 (136)
.+.-++.-.+++.-|+-+...|.+||+. ..||| ++|+. |++.|+=
T Consensus 257 Gl~~~e~l~~~~~~ftk~~~~~~f~k~~---~Y~irH~yG~eG~~~~Y~p 303 (390)
T cd07322 257 GLSLEEALKFWRSEFTKKMDADKFDKEY---AYNIRHNYGKEGKRANYTP 303 (390)
T ss_pred CCCHHHHHHHHHHhhcccCCcchhhhhh---HhhhhhhccccCCCCCCCC
Confidence 3444556677888898776678999875 68999 59998 4588864
No 4
>PF03531 SSrecog: Structure-specific recognition protein (SSRP1); InterPro: IPR000969 Human structure-specific recognition protein, SSRP1, [] binds specifically to DNA modified with the anti-cancer drug cisplatin. An 81kDa protein is predicted, containing several highly-charged domains and a stretch of 75 residues that share 47% identity with a portion of the high mobility group (HMG) protein HMG1. This HMG box probably constitutes the structure recognition element for cisplatin-modified DNA, the probable recognition motif being the local duplex unwinding and bending that occurs on formation of intra-strand cross-links []. SSRP1 is the human homologue of a recently identified mouse protein that binds to recombination signal sequences []. These sequences have been postulated to form stem-loop structures, further implicating local bends and unwinding in DNA as a recognition target for HMG-box proteins. A Drosophila melanogaster cDNA encoding an HMG-box-containing protein has also been isolated [, ]. This protein shares 50% sequence identity with human SSRP1. In vitro binding studies using Drosophila SSRP showed that the protein binds to single-stranded DNA and RNA, with highest affinity for nucleotides G and U. Comparison of the predicted amino acid sequences among SSRP family members reveals 48% identity, with structural conservation in the C terminus of the HMG box, as well as domains of highly charged residues. The most highly conserved regions lie in the poorly understood N terminus, suggesting that this portion of the protein is critical for its function []. This entry contains Pob3 Q04636 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p (IPR013953 from INTERPRO)-Pob3p) []. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 3F5R_A 2GCL_B 2GCJ_D.
Probab=19.94 E-value=25 Score=29.19 Aligned_cols=12 Identities=50% Similarity=0.852 Sum_probs=10.0
Q ss_pred cCCCcccccccC
Q psy3618 70 RSGRTKYSHLVD 81 (136)
Q Consensus 70 K~GrTKyThL~d 81 (136)
|.|||+|-||+-
T Consensus 201 RQGQT~Y~~lV~ 212 (222)
T PF03531_consen 201 RQGQTRYPFLVM 212 (222)
T ss_dssp EETTEEEEEEEE
T ss_pred cccccccccccc
Confidence 679999999874
No 5
>KOG1425|consensus
Probab=17.73 E-value=78 Score=29.17 Aligned_cols=39 Identities=46% Similarity=0.609 Sum_probs=27.5
Q ss_pred Cchhhhh-hHHHHhhhccccchhcccccCCCCCCccchhhh
Q psy3618 1 MVEDEVR-AEDAKNRIKNGEEARLEDVNTDDENDEDSEEDI 40 (136)
Q Consensus 1 ~~~~~~~-~~~~~~~~k~g~~~~l~~~~~~d~~~~~~~e~I 40 (136)
||+.+|. -|-+.+++++ ..|-|.+|.|+|+..+..+.++
T Consensus 229 ~V~Ee~~k~El~~k~~~~-~~a~l~dv~tdDein~~~eYEa 268 (430)
T KOG1425|consen 229 IVEEEVIKKELEEKKTKN-NEALLNDVDTDDEINEEEEYEA 268 (430)
T ss_pred HHHHHHHHHHHHhhcccc-chHHhhcccccccCChHHHHHH
Confidence 4677777 4445555554 6788999999999776655554
No 6
>KOG4188|consensus
Probab=15.75 E-value=74 Score=25.86 Aligned_cols=32 Identities=25% Similarity=0.303 Sum_probs=25.3
Q ss_pred cccchhhhhhccCcCCCccccccc--CCcCCCCC
Q psy3618 57 TVLPKVMQVKNFGRSGRTKYSHLV--DQDTTQFD 88 (136)
Q Consensus 57 ~~LPkvMQvRnfGK~GrTKyThL~--dEDTT~~d 88 (136)
+.||..|-+=++|...||-|..-. .+|++.|.
T Consensus 9 t~lP~e~~~~gl~~~~rTFkrga~~~sgd~ssWt 42 (159)
T KOG4188|consen 9 TTLPPERKVFGLGQQSRTFKRGAREGSGDRSSWT 42 (159)
T ss_pred HhCCchhccccccccchhhhcccccCCCcccccc
Confidence 579999988888877888887766 67777774
No 7
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=13.94 E-value=76 Score=24.24 Aligned_cols=23 Identities=30% Similarity=0.445 Sum_probs=19.4
Q ss_pred hhHHHHhhhccccchhcccccCCC
Q psy3618 7 RAEDAKNRIKNGEEARLEDVNTDD 30 (136)
Q Consensus 7 ~~~~~~~~~k~g~~~~l~~~~~~d 30 (136)
-++-|+. ||.|+-|+|+.||.+-
T Consensus 70 H~~~ar~-lK~GdfV~L~NVhiK~ 92 (123)
T cd04498 70 HVELAKS-LKPGDFVRIYNVHAKS 92 (123)
T ss_pred hHHHHhh-CCCCCEEEEEEEEEEe
Confidence 3567888 9999999999999753
No 8
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=13.24 E-value=95 Score=20.65 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=13.5
Q ss_pred hhHHHHhhhccccchhccc
Q psy3618 7 RAEDAKNRIKNGEEARLED 25 (136)
Q Consensus 7 ~~~~~~~~~k~g~~~~l~~ 25 (136)
.|+.+...+++|..|.++-
T Consensus 58 ~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 58 LAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp HHHHHHHH--TT-EEEEEE
T ss_pred cccccceEEcCCCEEEEEE
Confidence 6888899999999998864
No 9
>PF09020 YopE_N: YopE, N terminal; InterPro: IPR015110 The N-terminal YopE domain targets YopE for secretion from the bacterium and translocation into eukaryotic cells []. ; GO: 0050765 negative regulation of phagocytosis, 0016020 membrane; PDB: 1L2W_L 1HY5_B.
Probab=11.31 E-value=68 Score=24.73 Aligned_cols=13 Identities=46% Similarity=0.516 Sum_probs=10.3
Q ss_pred cccccchhhhhhc
Q psy3618 55 DKTVLPKVMQVKN 67 (136)
Q Consensus 55 dk~~LPkvMQvRn 67 (136)
--+.|||+||--|
T Consensus 110 aaetlpkymqqln 122 (126)
T PF09020_consen 110 AAETLPKYMQQLN 122 (126)
T ss_dssp HHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHh
Confidence 5678999999654
No 10
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=10.81 E-value=93 Score=25.11 Aligned_cols=13 Identities=38% Similarity=0.486 Sum_probs=10.5
Q ss_pred cccccccchhhhh
Q psy3618 53 HFDKTVLPKVMQV 65 (136)
Q Consensus 53 ~vdk~~LPkvMQv 65 (136)
.++.++||++||.
T Consensus 12 LvredvLp~s~~k 24 (150)
T COG4492 12 LVREDVLPDSMQK 24 (150)
T ss_pred EEehhhchHHHHH
Confidence 4589999999874
Done!