Query psy5060
Match_columns 145
No_of_seqs 123 out of 777
Neff 5.5
Searched_HMMs 46136
Date Sat Aug 17 00:43:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5060.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5060hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05485 THAP: THAP domain; I 99.8 5E-21 1.1E-25 131.4 6.2 73 7-81 10-83 (84)
2 smart00692 DM3 Zinc finger dom 99.8 1.1E-19 2.4E-24 118.9 3.1 57 17-78 1-58 (59)
3 PF13300 DUF4078: Domain of un 27.3 70 0.0015 22.6 2.7 24 12-35 30-53 (88)
4 PF15129 FAM150: FAM150 family 20.4 37 0.0008 25.5 0.2 34 16-53 57-90 (123)
5 cd01238 PH_Tec Tec pleckstrin 14.8 2.1E+02 0.0045 20.1 3.0 24 13-36 82-105 (106)
6 cd01237 Unc112 Unc-112 pleckst 13.9 1.3E+02 0.0029 22.0 1.8 16 22-37 87-102 (106)
7 PF13030 DUF3891: Protein of u 11.5 56 0.0012 26.5 -0.9 43 10-53 66-108 (221)
8 CHL00039 psbF photosystem II p 9.7 1.1E+02 0.0023 18.6 0.1 10 70-79 19-28 (39)
9 PF13790 DUF4182: Domain of un 9.4 1.7E+02 0.0036 17.8 0.9 24 106-129 5-29 (38)
10 TIGR01333 cyt_b559_beta cytoch 9.3 1.1E+02 0.0024 18.9 0.1 10 70-79 23-32 (43)
No 1
>PF05485 THAP: THAP domain; InterPro: IPR006612 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. The THAP domain is an ~90-residue domain restricted to animals, which is shared between the THAP family of cellular DNA-binding proteins, and transposases from mobile genomic parasites. The defined THAP domain includes: a C2CH signature (consensus: C-x(2,4)-C-x(35,50)-C-x(2)-H); three additional key residues that are strictly conserved in all THAP domains that have been found to date (THAP1 amino acids P26, W36, F58); a C-terminal AVPTIF box; and several other conserved amino acid positions with distinct physicochemical properties (e.g. hydrophobic and polar). The THAP domain can be found in one or more copies and can be associated with other domains, such as the C2H2-type zinc finger. The THAP domain is supposed to be a DNA-binding domain (DBD) [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding; PDB: 3KDE_C 2D8R_A 2JM3_A 2KO0_A 2JTG_A 2L1G_A.
Probab=99.84 E-value=5e-21 Score=131.40 Aligned_cols=73 Identities=45% Similarity=0.814 Sum_probs=54.5
Q ss_pred ccccCCCCcEEEeCCCChHHHHHHHHHhhcCCC-CcCCCceeccccCCcCccccccccCCcccCCCceecccCCCC
Q psy5060 7 NSLFWTSSTKFGRFPEDKLRRKQWCIAMKRDKW-KPSKHSKICSAHFTEDSFETNAWSERKKLSDTAVPSIFTFPD 81 (145)
Q Consensus 7 n~~~k~~~vsfhrFPkD~~rr~kWi~~~~r~~~-~p~k~~~VCS~HF~~~~f~~~~~~~r~~Lk~~AVPTIF~~~~ 81 (145)
|+...+.+++||+||+|++++++|+++|++.++ .+...++|||+||++++|.. ...+.+|++|||||||+.++
T Consensus 10 ~~~~~~~~~~f~~fP~d~~~~~~W~~~~~~~~~~~~~~~~~ICs~HF~~~~~~~--~~~~~~L~~~AVPtl~~~~~ 83 (84)
T PF05485_consen 10 NSSSRKPGVSFFRFPKDPERRKKWLKACGREDWWKPTKNSRICSRHFEPDDFRR--SSKRRRLKPDAVPTLFLPPE 83 (84)
T ss_dssp TSTCCTTSS-EEE--SSHHHHHHHHHHHTSTCG-GTSTTSEEEGGGSTGGGBST--TTSSSSB-TT---CCC----
T ss_pred CCCeeCCCeEEEECCCCHHHHHHHHHHhcccccccccCCccchhhhCchhhccc--ccCCCcCCCCCCCcCcCCCC
Confidence 356678899999999999999999999999887 77889999999999999944 34568999999999998654
No 2
>smart00692 DM3 Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK.
Probab=99.78 E-value=1.1e-19 Score=118.87 Aligned_cols=57 Identities=35% Similarity=0.584 Sum_probs=50.7
Q ss_pred EEeCCCChHHHHHHHHHhhcCC-CCcCCCceeccccCCcCccccccccCCcccCCCceecccC
Q psy5060 17 FGRFPEDKLRRKQWCIAMKRDK-WKPSKHSKICSAHFTEDSFETNAWSERKKLSDTAVPSIFT 78 (145)
Q Consensus 17 fhrFPkD~~rr~kWi~~~~r~~-~~p~k~~~VCS~HF~~~~f~~~~~~~r~~Lk~~AVPTIF~ 78 (145)
||+||+|++++++|+++|++.. +.+.+..+|||+||+++||.. +++|++|||||||+
T Consensus 1 ff~FP~d~~~~~~W~~~~~~~~~~~~~~~~~vCs~HF~~~~~~~-----~~~L~~~AvPt~~l 58 (59)
T smart00692 1 LFRFPKDPELLKKWEHNLRLSPDEKKLKNSRICSRHFEPECFGK-----RRRLKPGAVPTLEL 58 (59)
T ss_pred CCCCccCHHHHHHHHHHhCCCccccCCCCCCcchhhCCHhHhCC-----ccccCCCCCccccC
Confidence 7999999999999999999864 346789999999999999964 35899999999997
No 3
>PF13300 DUF4078: Domain of unknown function (DUF4078)
Probab=27.32 E-value=70 Score=22.65 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=19.6
Q ss_pred CCCcEEEeCCCChHHHHHHHHHhh
Q psy5060 12 TSSTKFGRFPEDKLRRKQWCIAMK 35 (145)
Q Consensus 12 ~~~vsfhrFPkD~~rr~kWi~~~~ 35 (145)
+.|+.||.|..|.+.+++=+..+.
T Consensus 30 ~~Gvgfy~FS~Dee~R~~qme~L~ 53 (88)
T PF13300_consen 30 THGVGFYAFSKDEEERQEQMEELE 53 (88)
T ss_pred HHcceeeecCCCHHHHHHHHHHHH
Confidence 568999999999988887666654
No 4
>PF15129 FAM150: FAM150 family
Probab=20.38 E-value=37 Score=25.48 Aligned_cols=34 Identities=24% Similarity=0.407 Sum_probs=25.2
Q ss_pred EEEeCCCChHHHHHHHHHhhcCCCCcCCCceeccccCC
Q psy5060 16 KFGRFPEDKLRRKQWCIAMKRDKWKPSKHSKICSAHFT 53 (145)
Q Consensus 16 sfhrFPkD~~rr~kWi~~~~r~~~~p~k~~~VCS~HF~ 53 (145)
..=-||.|..+..++++.+.. |-..+--|++||.
T Consensus 57 ~~ei~prdl~~k~kfi~h~tg----pl~fs~~c~k~f~ 90 (123)
T PF15129_consen 57 RVEIVPRDLRMKDKFIKHLTG----PLYFSPKCSKHFH 90 (123)
T ss_pred ceeeccccchhHHHHHHHhCC----ceeeCHHHHHHHH
Confidence 345588999999999887663 4445667999996
No 5
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few dis
Probab=14.84 E-value=2.1e+02 Score=20.06 Aligned_cols=24 Identities=25% Similarity=0.404 Sum_probs=18.4
Q ss_pred CCcEEEeCCCChHHHHHHHHHhhc
Q psy5060 13 SSTKFGRFPEDKLRRKQWCIAMKR 36 (145)
Q Consensus 13 ~~vsfhrFPkD~~rr~kWi~~~~r 36 (145)
.+-.||-+-.+++-+..|+.+++.
T Consensus 82 ~~r~~yl~A~s~~er~~WI~ai~~ 105 (106)
T cd01238 82 DEGTLYVFAPTEELRKRWIKALKQ 105 (106)
T ss_pred CCCeEEEEcCCHHHHHHHHHHHHh
Confidence 344677677788889999999864
No 6
>cd01237 Unc112 Unc-112 pleckstrin homology (PH) domain. Unc-112 pleckstrin homology (PH) domain. Unc-112 and related proteins contain two FERM domains with a PH domain between them. Both the PH and FERM domains have a PH-like fold. The FERM domains are likely responsible for the role of Unc-112 in organizing beta-integrin. The specific role of the Unc-112 PH domain is not known, but it is predicted to be involved in mediating membrane interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=13.92 E-value=1.3e+02 Score=21.98 Aligned_cols=16 Identities=13% Similarity=0.397 Sum_probs=13.3
Q ss_pred CChHHHHHHHHHhhcC
Q psy5060 22 EDKLRRKQWCIAMKRD 37 (145)
Q Consensus 22 kD~~rr~kWi~~~~r~ 37 (145)
.+++.+.+|+++|+.+
T Consensus 87 dsEeqya~Wmaa~rla 102 (106)
T cd01237 87 DNEKQYAKWMAACRLA 102 (106)
T ss_pred CCHHHHHHHHHHHHHh
Confidence 3568889999999975
No 7
>PF13030 DUF3891: Protein of unknown function (DUF3891)
Probab=11.48 E-value=56 Score=26.51 Aligned_cols=43 Identities=14% Similarity=0.237 Sum_probs=30.2
Q ss_pred cCCCCcEEEeCCCChHHHHHHHHHhhcCCCCcCCCceeccccCC
Q psy5060 10 FWTSSTKFGRFPEDKLRRKQWCIAMKRDKWKPSKHSKICSAHFT 53 (145)
Q Consensus 10 ~k~~~vsfhrFPkD~~rr~kWi~~~~r~~~~p~k~~~VCS~HF~ 53 (145)
..|...+|.-+|.+ .....|..-+....-...--..+||.|+.
T Consensus 66 ~~g~P~~F~~~p~~-~~~~~~~~gi~~~~~~~~yaaLL~S~H~~ 108 (221)
T PF13030_consen 66 ETGAPYDFMDYPLQ-EKLAFYRRGIDEAEQKSPYAALLCSMHYS 108 (221)
T ss_pred ccCCccchhhCChh-HHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 45778899999944 56688888877642222235789999984
No 8
>CHL00039 psbF photosystem II protein VI
Probab=9.66 E-value=1.1e+02 Score=18.63 Aligned_cols=10 Identities=40% Similarity=0.786 Sum_probs=7.6
Q ss_pred CCceecccCC
Q psy5060 70 DTAVPSIFTF 79 (145)
Q Consensus 70 ~~AVPTIF~~ 79 (145)
.-||||+|..
T Consensus 19 ~lavPtvffl 28 (39)
T CHL00039 19 GLAVPTVFFL 28 (39)
T ss_pred cccCCceeec
Confidence 3589999874
No 9
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=9.43 E-value=1.7e+02 Score=17.77 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=15.4
Q ss_pred hccCccccccCCCCe-eeeecccce
Q psy5060 106 VCKTSKAWFENPGSQ-FTFLYHFCR 129 (145)
Q Consensus 106 ~~~~~~~~~~~~~sq-~~~~~~~~~ 129 (145)
+|.+=+..++-.++. +..+|+.|.
T Consensus 5 vCq~C~~~Id~~e~ekV~~lYg~C~ 29 (38)
T PF13790_consen 5 VCQHCNETIDHFETEKVTTLYGKCG 29 (38)
T ss_pred EeccccceeeeecCCcEEEEEEECC
Confidence 444444555555556 889999885
No 10
>TIGR01333 cyt_b559_beta cytochrome b559, beta subunit. This model describes the beta subunit of cytochrome b559, about 40 residues in length. It is homologous to the N-terminal half of the alpha subunit, a protein of about 83 residues. Cytochrome b559 is associated with photosystem II.
Probab=9.30 E-value=1.1e+02 Score=18.89 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=7.6
Q ss_pred CCceecccCC
Q psy5060 70 DTAVPSIFTF 79 (145)
Q Consensus 70 ~~AVPTIF~~ 79 (145)
--||||+|..
T Consensus 23 ~lavPtVffl 32 (43)
T TIGR01333 23 ALAIPTVFFF 32 (43)
T ss_pred cccCCceeec
Confidence 3589999874
Done!