Query psy5284
Match_columns 180
No_of_seqs 162 out of 895
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 22:39:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5284.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5284hhsearch_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 99.9 1.2E-23 2.7E-28 148.6 5.5 82 3-88 1-82 (84)
2 smart00692 DM3 Zinc finger dom 99.7 2.5E-18 5.3E-23 115.0 2.6 59 22-87 1-59 (59)
3 COG5189 SFP1 Putative transcri 31.5 14 0.0003 33.0 -0.4 24 2-25 349-372 (423)
4 PF13300 DUF4078: Domain of un 28.1 57 0.0012 23.5 2.4 25 17-41 30-54 (88)
5 KOG3496|consensus 17.6 71 0.0015 22.1 1.1 34 2-40 29-62 (72)
6 PF08653 DASH_Dam1: DASH compl 14.5 2E+02 0.0043 19.1 2.6 25 153-177 11-35 (58)
7 cd01238 PH_Tec Tec pleckstrin 14.5 1.7E+02 0.0038 20.9 2.6 21 21-41 85-105 (106)
8 KOG0229|consensus 11.8 1.4E+02 0.0031 27.5 1.7 24 154-179 266-289 (420)
9 PF09236 AHSP: Alpha-haemoglob 10.4 2.1E+02 0.0046 20.6 1.9 22 155-178 62-83 (89)
10 PF02805 Ada_Zn_binding: Metal 10.1 2.6E+02 0.0057 18.9 2.2 21 4-24 27-47 (66)
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=99.89 E-value=1.2e-23 Score=148.63 Aligned_cols=82 Identities=35% Similarity=0.791 Sum_probs=60.0
Q ss_pred cceeeccCCCCccCCCCeEEEecCCChhHHHHHHHHhccccCCcccCCCCCceeeccCCccCCCcccCCCCcccCCCcee
Q psy5284 3 PSCCVPTCKLMRNNSEKLSYHEIPSKEPLRTNWIKQIGILTGNKFWQPTSESAVVCSKHFIEPDFVETPLRRRLKPTSVP 82 (180)
Q Consensus 3 ~~C~V~gC~n~~~k~~~isff~FPkd~~~r~~Wi~~~~~~~~~~~~~p~~~~~~VCs~HF~~~~f~~~~~~~~Lk~~AVP 82 (180)
++|+|+||.+......+++||+||+|++++++|++++++.. .+.+... .+||+.||++++|.....+++|+++|||
T Consensus 1 r~C~v~~C~~~~~~~~~~~f~~fP~d~~~~~~W~~~~~~~~---~~~~~~~-~~ICs~HF~~~~~~~~~~~~~L~~~AVP 76 (84)
T PF05485_consen 1 RKCCVPGCSNSSSRKPGVSFFRFPKDPERRKKWLKACGRED---WWKPTKN-SRICSRHFEPDDFRRSSKRRRLKPDAVP 76 (84)
T ss_dssp --ETSSSTTTSTCCTTSS-EEE--SSHHHHHHHHHHHTSTC---G-GTSTT-SEEEGGGSTGGGBSTTTSSSSB-TT---
T ss_pred CEEEeccCcCCCeeCCCeEEEECCCCHHHHHHHHHHhcccc---cccccCC-ccchhhhCchhhcccccCCCcCCCCCCC
Confidence 57999999666666789999999999999999999999953 2345554 8999999999999766889999999999
Q ss_pred ecccCC
Q psy5284 83 SVFYMM 88 (180)
Q Consensus 83 tlf~~~ 88 (180)
|||++.
T Consensus 77 tl~~~~ 82 (84)
T PF05485_consen 77 TLFLPP 82 (84)
T ss_dssp CCC---
T ss_pred cCcCCC
Confidence 999864
No 2
>smart00692 DM3 Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK.
Probab=99.72 E-value=2.5e-18 Score=114.96 Aligned_cols=59 Identities=27% Similarity=0.456 Sum_probs=49.6
Q ss_pred EEecCCChhHHHHHHHHhccccCCcccCCCCCceeeccCCccCCCcccCCCCcccCCCceeecccC
Q psy5284 22 YHEIPSKEPLRTNWIKQIGILTGNKFWQPTSESAVVCSKHFIEPDFVETPLRRRLKPTSVPSVFYM 87 (180)
Q Consensus 22 ff~FPkd~~~r~~Wi~~~~~~~~~~~~~p~~~~~~VCs~HF~~~~f~~~~~~~~Lk~~AVPtlf~~ 87 (180)
||+||+|++++++|+++|+... .+.+.. +.+|||+||+++||. ++++|+++||||||++
T Consensus 1 ff~FP~d~~~~~~W~~~~~~~~---~~~~~~-~~~vCs~HF~~~~~~---~~~~L~~~AvPt~~l~ 59 (59)
T smart00692 1 LFRFPKDPELLKKWEHNLRLSP---DEKKLK-NSRICSRHFEPECFG---KRRRLKPGAVPTLELG 59 (59)
T ss_pred CCCCccCHHHHHHHHHHhCCCc---cccCCC-CCCcchhhCCHhHhC---CccccCCCCCccccCC
Confidence 6999999999999999999843 333444 489999999999995 4568999999999973
No 3
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=31.45 E-value=14 Score=33.04 Aligned_cols=24 Identities=33% Similarity=0.627 Sum_probs=20.7
Q ss_pred CcceeeccCCCCccCCCCeEEEec
Q psy5284 2 PPSCCVPTCKLMRNNSEKLSYHEI 25 (180)
Q Consensus 2 ~~~C~V~gC~n~~~k~~~isff~F 25 (180)
|.+|-|+||...+....|+.+|+.
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred eecCCCCCchhhhccccchhhhhh
Confidence 468999999999988888888875
No 4
>PF13300 DUF4078: Domain of unknown function (DUF4078)
Probab=28.14 E-value=57 Score=23.47 Aligned_cols=25 Identities=8% Similarity=0.213 Sum_probs=19.6
Q ss_pred CCCeEEEecCCChhHHHHHHHHhcc
Q psy5284 17 SEKLSYHEIPSKEPLRTNWIKQIGI 41 (180)
Q Consensus 17 ~~~isff~FPkd~~~r~~Wi~~~~~ 41 (180)
..|+.||.|.+|+..|++=+..+..
T Consensus 30 ~~Gvgfy~FS~Dee~R~~qme~L~~ 54 (88)
T PF13300_consen 30 THGVGFYAFSKDEEERQEQMEELEE 54 (88)
T ss_pred HHcceeeecCCCHHHHHHHHHHHHH
Confidence 4689999999998888776666543
No 5
>KOG3496|consensus
Probab=17.57 E-value=71 Score=22.06 Aligned_cols=34 Identities=18% Similarity=0.390 Sum_probs=22.5
Q ss_pred CcceeeccCCCCccCCCCeEEEecCCChhHHHHHHHHhc
Q psy5284 2 PPSCCVPTCKLMRNNSEKLSYHEIPSKEPLRTNWIKQIG 40 (180)
Q Consensus 2 ~~~C~V~gC~n~~~k~~~isff~FPkd~~~r~~Wi~~~~ 40 (180)
++-||+ |.-+..-.+...++ .+++.+.+||++=.
T Consensus 29 ~KpCCa--CpetK~~RDaCIle---~gee~C~~lIEahk 62 (72)
T KOG3496|consen 29 PKPCCA--CPETKKARDACILE---NGEEKCGKLIEAHK 62 (72)
T ss_pred CCcccc--CCchhhhhhhHhhh---cCHHHHHHHHHHHH
Confidence 356888 88876533333333 77889999998743
No 6
>PF08653 DASH_Dam1: DASH complex subunit Dam1; InterPro: IPR013962 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=14.50 E-value=2e+02 Score=19.08 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=18.7
Q ss_pred hhHHHHHhhhhhHHHHHHHHhhccc
Q psy5284 153 KKFLEMLQLNLEMLEVANHFLADYS 177 (180)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (180)
+|.|+.++.|.+.|.....=|++||
T Consensus 11 ~D~~~~L~~n~~~L~~ihesL~~FN 35 (58)
T PF08653_consen 11 SDSMETLDKNMEQLNQIHESLSDFN 35 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778888888888877766666654
No 7
>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=14.45 E-value=1.7e+02 Score=20.94 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=16.3
Q ss_pred EEEecCCChhHHHHHHHHhcc
Q psy5284 21 SYHEIPSKEPLRTNWIKQIGI 41 (180)
Q Consensus 21 sff~FPkd~~~r~~Wi~~~~~ 41 (180)
.||-+..+++-++.|+++|+.
T Consensus 85 ~~yl~A~s~~er~~WI~ai~~ 105 (106)
T cd01238 85 TLYVFAPTEELRKRWIKALKQ 105 (106)
T ss_pred eEEEEcCCHHHHHHHHHHHHh
Confidence 456566678889999999864
No 8
>KOG0229|consensus
Probab=11.77 E-value=1.4e+02 Score=27.47 Aligned_cols=24 Identities=42% Similarity=0.570 Sum_probs=20.5
Q ss_pred hHHHHHhhhhhHHHHHHHHhhccccC
Q psy5284 154 KFLEMLQLNLEMLEVANHFLADYSLL 179 (180)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 179 (180)
.||+.|+.|-|.|+-++| -|||||
T Consensus 266 ~l~~ql~~Dce~Le~~~I--MDYSLL 289 (420)
T KOG0229|consen 266 ALLKQLKRDCEFLESLKI--MDYSLL 289 (420)
T ss_pred HHHHHHHHHHHHHHHhcc--hhhhhe
Confidence 389999999999998886 489887
No 9
>PF09236 AHSP: Alpha-haemoglobin stabilising protein; InterPro: IPR015317 Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle []. ; GO: 0030492 hemoglobin binding, 0006457 protein folding, 0020027 hemoglobin metabolic process, 0030097 hemopoiesis, 0050821 protein stabilization; PDB: 1Y01_A 1XZY_A 3OVU_A 1W0A_A 3IA3_C 1Z8U_A 1W0B_A 1W09_A.
Probab=10.38 E-value=2.1e+02 Score=20.59 Aligned_cols=22 Identities=45% Similarity=0.590 Sum_probs=16.0
Q ss_pred HHHHHhhhhhHHHHHHHHhhcccc
Q psy5284 155 FLEMLQLNLEMLEVANHFLADYSL 178 (180)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~ 178 (180)
-|+.+|..++- ++|-||+.|.+
T Consensus 62 Alqel~qeL~t--la~pFL~Kyr~ 83 (89)
T PF09236_consen 62 ALQELQQELNT--LANPFLAKYRA 83 (89)
T ss_dssp HHHHHHHHHHH--HHHHHHHHHHH
T ss_pred HHHHHHHHHHH--HHHHHHHHHHH
Confidence 67777775554 47999998864
No 10
>PF02805 Ada_Zn_binding: Metal binding domain of Ada; InterPro: IPR004026 The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site [, ]. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex [].; GO: 0003677 DNA binding, 0008168 methyltransferase activity, 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent; PDB: 1WPK_A 1ZGW_A 1EYF_A 1ADN_A 1U8B_A.
Probab=10.13 E-value=2.6e+02 Score=18.91 Aligned_cols=21 Identities=19% Similarity=0.629 Sum_probs=12.9
Q ss_pred ceeeccCCCCccCCCCeEEEe
Q psy5284 4 SCCVPTCKLMRNNSEKLSYHE 24 (180)
Q Consensus 4 ~C~V~gC~n~~~k~~~isff~ 24 (180)
-+|-|+|.++..+..++.||.
T Consensus 27 IycrPsC~ar~p~~~nv~ff~ 47 (66)
T PF02805_consen 27 IYCRPSCPARKPKRENVVFFD 47 (66)
T ss_dssp EEE-TT-SSS-S-SCCEEEES
T ss_pred EEecCccccCCCCCceeEeeC
Confidence 367799998766667888875
Done!