Query psy3121
Match_columns 190
No_of_seqs 34 out of 36
Neff 1.7
Searched_HMMs 46136
Date Fri Aug 16 16:59:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1595|consensus 100.0 8.5E-35 1.8E-39 266.9 3.2 97 88-186 13-121 (528)
2 KOG1595|consensus 71.5 2.8 6.1E-05 40.4 2.2 73 102-188 196-277 (528)
3 PF08596 Lgl_C: Lethal giant l 61.5 3.7 8E-05 36.7 0.9 43 29-80 80-127 (395)
4 PF15443 DUF4630: Domain of un 50.9 12 0.00027 31.3 2.3 45 123-172 86-134 (156)
5 PF14804 Jag_N: Jag N-terminus 44.0 16 0.00035 24.8 1.6 28 19-46 11-38 (52)
6 smart00356 ZnF_C3H1 zinc finge 24.6 44 0.00094 18.2 1.0 20 153-174 5-24 (27)
7 PF13465 zf-H2C2_2: Zinc-finge 23.8 46 0.001 19.1 1.0 8 119-126 10-17 (26)
8 PF02963 EcoRI: Restriction en 23.6 39 0.00085 30.3 1.1 27 119-145 144-170 (257)
9 PF00642 zf-CCCH: Zinc finger 22.2 15 0.00032 21.5 -1.3 10 180-189 10-19 (27)
10 COG1210 GalU UDP-glucose pyrop 19.8 36 0.00079 30.9 0.1 22 57-78 23-46 (291)
No 1
>KOG1595|consensus
Probab=100.00 E-value=8.5e-35 Score=266.90 Aligned_cols=97 Identities=68% Similarity=1.244 Sum_probs=92.1
Q ss_pred eeeccccccchhhhhhhhccccCchhhcccccCCCceeeeecccCcccccCCcccCCCCCccCCceeeeeccCCcccCCC
Q psy3121 88 ICLMGILCLKVPRYLKEFRVEQCPLFLQHKCTQHRPFTCFHWHFMNQRRRRPVRKRDGSFNYSPDTYCTKYDETTGLCPD 167 (190)
Q Consensus 88 ~~~~~~~~~~~~~YLkeFRveqCplF~QhkC~qHRPyTCF~WHF~NQRRRRPvr~~DGtFNYSPDVYCskYDE~TG~CP~ 167 (190)
-|+.+.+++++++||||||+|| |+|+||||.|||||+||+|||.||||||||+++|||||||+|+||++|+|.||+||+
T Consensus 13 s~~~e~~~~~~~~~~k~~~~e~-~~~~~~~~~~~r~~~~~k~~~~~qR~~~~v~~~~Gs~~~~~~i~~~~~~e~~~~C~~ 91 (528)
T KOG1595|consen 13 SCLSEFEAPNDYAYLKEFRVEQ-PLFLQHKCLQHRPFVCFKWHFLNQRRRRPVARRDGSFNYSPDIYCTKYDEVTGICPD 91 (528)
T ss_pred hcchhhccccHHHHHHHHHHhc-hhhhhhhhcccccchhhhhhhhccccccchhhhcCccccccceeecchhhccccCCC
Confidence 4566899999999999999999 999999999999999999999999999999999999999999999999999999999
Q ss_pred CC------------CCCceEeeeeccccCCC
Q psy3121 168 GD------------DPDTYCTKYDETTGLCP 186 (190)
Q Consensus 168 GD------------terkYhlRYyk~TGsCp 186 (190)
|| .|++|||+||| |+.|.
T Consensus 92 ~~~~C~~~g~s~~~~e~~~hL~~~k-~~~~~ 121 (528)
T KOG1595|consen 92 GDEHCAVLGRSVGDTERTYHLRYYK-TLPCV 121 (528)
T ss_pred CcccchhcccccCCcceeEeccccc-cccCc
Confidence 65 58999999999 88874
No 2
>KOG1595|consensus
Probab=71.51 E-value=2.8 Score=40.36 Aligned_cols=73 Identities=27% Similarity=0.487 Sum_probs=53.3
Q ss_pred hhhhccccCchhhcccccCCCceeeeecc-cCcccccCCcccCCCCCccCCceeeeeccCCcccCCCCC--------CCC
Q psy3121 102 LKEFRVEQCPLFLQHKCTQHRPFTCFHWH-FMNQRRRRPVRKRDGSFNYSPDTYCTKYDETTGLCPDGD--------DPD 172 (190)
Q Consensus 102 LkeFRveqCplF~QhkC~qHRPyTCF~WH-F~NQRRRRPvr~~DGtFNYSPDVYCskYDE~TG~CP~GD--------ter 172 (190)
|-+|.|++|+==.- |-=+.|=+-| =.|-|||-|-| |-|+-. =|..+-. |.|..|| .|-
T Consensus 196 My~fKir~C~R~~s-----hDwteCPf~HpgEkARRRDPRk-----yhYs~t-pCPefrk--G~C~rGD~CEyaHgvfEc 262 (528)
T KOG1595|consen 196 MYSFKIRRCSRPRS-----HDWTECPFAHPGEKARRRDPRK-----YHYSST-PCPEFRK--GSCERGDSCEYAHGVFEC 262 (528)
T ss_pred EEeeeecccCCccC-----CCcccCCccCCCcccccCCccc-----ccccCc-cCccccc--CCCCCCCccccccceehh
Confidence 45789999986533 4457788899 67777776654 788864 4877766 9999999 566
Q ss_pred ceEeeeeccccCCCCC
Q psy3121 173 TYCTKYDETTGLCPDG 188 (190)
Q Consensus 173 kYhlRYyk~TGsCp~g 188 (190)
-+|=-=|+ |-.|-||
T Consensus 263 wLHPa~YR-T~~CkDg 277 (528)
T KOG1595|consen 263 WLHPARYR-TRKCKDG 277 (528)
T ss_pred hcCHHHhc-cccccCC
Confidence 66655677 7788776
No 3
>PF08596 Lgl_C: Lethal giant larvae(Lgl) like, C-terminal; InterPro: IPR013905 The Lethal giant larvae (Lgl) tumour suppressor protein is conserved from yeast to mammals. The Lgl protein functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface []. The N-terminal half of Lgl members contains WD40 repeats (see IPR001680 from INTERPRO), while the C-terminal half appears specific to the protein []. ; PDB: 2OAJ_A.
Probab=61.51 E-value=3.7 Score=36.75 Aligned_cols=43 Identities=30% Similarity=0.611 Sum_probs=27.6
Q ss_pred ceEEEE---EEEeecccceeehhhhHHHHHhhcCcceeeeeec--CCcchhhhhhhh
Q psy3121 29 TIVEIN---VEVLEHSNIGLVSQATTYALLKIAQPREILALVD--GPSIQFQETIKL 80 (190)
Q Consensus 29 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~ 80 (190)
++++.+ |..|.+||||+|.-| --.--|+++| ||.|-|++.|+-
T Consensus 80 ~l~~~~~g~vtal~~S~iGFvaig---------y~~G~l~viD~RGPavI~~~~i~~ 127 (395)
T PF08596_consen 80 TLLDAKQGPVTALKNSDIGFVAIG---------YESGSLVVIDLRGPAVIYNENIRE 127 (395)
T ss_dssp EEE---S-SEEEEEE-BTSEEEEE---------ETTSEEEEEETTTTEEEEEEEGGG
T ss_pred hheeccCCcEeEEecCCCcEEEEE---------ecCCcEEEEECCCCeEEeeccccc
Confidence 455554 789999999999533 3333456665 899888877765
No 4
>PF15443 DUF4630: Domain of unknown function (DUF4630)
Probab=50.93 E-value=12 Score=31.32 Aligned_cols=45 Identities=36% Similarity=0.628 Sum_probs=24.0
Q ss_pred ceeeeecccCcccccCCcccCCCCCccCC-ceeeeeccC---CcccCCCCCCCC
Q psy3121 123 PFTCFHWHFMNQRRRRPVRKRDGSFNYSP-DTYCTKYDE---TTGLCPDGDDPD 172 (190)
Q Consensus 123 PyTCF~WHF~NQRRRRPvr~~DGtFNYSP-DVYCskYDE---~TG~CP~GDter 172 (190)
+|.||-|- |||.-|.+|-+++-+| .--.+.-.| -|-++||||=|+
T Consensus 86 ll~CfsWg-----rrrrrK~~~~~s~~~p~qd~~qd~EEelaLt~i~PNGdCed 134 (156)
T PF15443_consen 86 LLQCFSWG-----RRRRRKNPDASSSSSPAQDHLQDPEEELALTAIFPNGDCED 134 (156)
T ss_pred eeeccCcC-----ccccccCccccccCCcccccccCchhcceeeeeccCCcccc
Confidence 57899994 4444456666665333 222222222 135677777554
No 5
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=44.02 E-value=16 Score=24.82 Aligned_cols=28 Identities=29% Similarity=0.498 Sum_probs=17.8
Q ss_pred hHHHHhhhhcceEEEEEEEeecccceee
Q psy3121 19 VDKAMHALSSTIVEINVEVLEHSNIGLV 46 (190)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (190)
+++|...|....-++++||++..+=|+.
T Consensus 11 i~~A~~~l~~~~~~~~~eVi~~g~kGf~ 38 (52)
T PF14804_consen 11 IEKALKELGVPREELEYEVIEEGKKGFF 38 (52)
T ss_dssp HHHHHHHTT--GGGEEEEEEE--B----
T ss_pred HHHHHHHhCCChHHEEEEEEEcCCCcEE
Confidence 5778888888999999999999887765
No 6
>smart00356 ZnF_C3H1 zinc finger.
Probab=24.59 E-value=44 Score=18.17 Aligned_cols=20 Identities=30% Similarity=0.668 Sum_probs=12.4
Q ss_pred eeeeeccCCcccCCCCCCCCce
Q psy3121 153 TYCTKYDETTGLCPDGDDPDTY 174 (190)
Q Consensus 153 VYCskYDE~TG~CP~GDterkY 174 (190)
..|..| .+|.|+.||.-+--
T Consensus 5 ~~C~~~--~~g~C~~g~~C~~~ 24 (27)
T smart00356 5 ELCKFF--KRGYCPYGDRCKFA 24 (27)
T ss_pred CcCcCc--cCCCCCCCCCcCCC
Confidence 357777 34778877755433
No 7
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.76 E-value=46 Score=19.09 Aligned_cols=8 Identities=38% Similarity=1.202 Sum_probs=6.3
Q ss_pred cCCCceee
Q psy3121 119 TQHRPFTC 126 (190)
Q Consensus 119 ~qHRPyTC 126 (190)
++.|||+|
T Consensus 10 ~~~k~~~C 17 (26)
T PF13465_consen 10 TGEKPYKC 17 (26)
T ss_dssp SSSSSEEE
T ss_pred CCCCCCCC
Confidence 46788888
No 8
>PF02963 EcoRI: Restriction endonuclease EcoRI; InterPro: IPR004221 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents restriction endonucleases EcoRI, which requires magnesium as a cofactor. EcoRI recognises the DNA sequence GAATTC and cleaves after G-1 [].; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1ERI_A 1CL8_A 1QRH_A 1QPS_A 1CKQ_A 1QC9_B 1QRI_A 2OXV_A.
Probab=23.64 E-value=39 Score=30.29 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=15.6
Q ss_pred cCCCceeeeecccCcccccCCcccCCC
Q psy3121 119 TQHRPFTCFHWHFMNQRRRRPVRKRDG 145 (190)
Q Consensus 119 ~qHRPyTCF~WHF~NQRRRRPvr~~DG 145 (190)
..|-||.||-|---------+|.||||
T Consensus 144 E~~fPyV~Fl~G~nF~te~~~v~rpdg 170 (257)
T PF02963_consen 144 ESHFPYVCFLEGSNFLTETISVTRPDG 170 (257)
T ss_dssp SSB--EEEEEESTTS-SS-EEEEETTS
T ss_pred cccCceEEEeccCCccccceeeeCCCC
Confidence 468899999985333333456777777
No 9
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=22.24 E-value=15 Score=21.50 Aligned_cols=10 Identities=60% Similarity=1.049 Sum_probs=5.2
Q ss_pred ccccCCCCCC
Q psy3121 180 ETTGLCPDGD 189 (190)
Q Consensus 180 k~TGsCp~gd 189 (190)
..+|.||-||
T Consensus 10 ~~~g~C~~G~ 19 (27)
T PF00642_consen 10 MRTGTCPFGD 19 (27)
T ss_dssp HHTS--TTGG
T ss_pred ccCCccCCCC
Confidence 3378888776
No 10
>COG1210 GalU UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]
Probab=19.80 E-value=36 Score=30.87 Aligned_cols=22 Identities=45% Similarity=0.836 Sum_probs=18.5
Q ss_pred hcCcceeeeeecCCcchh--hhhh
Q psy3121 57 IAQPREILALVDGPSIQF--QETI 78 (190)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~--~~~~ 78 (190)
-|.|.|.|-+||-|.||+ .|.+
T Consensus 23 KaiPKEMLPIvdKP~IqYiVeEa~ 46 (291)
T COG1210 23 KAIPKEMLPIVDKPLIQYIVEEAV 46 (291)
T ss_pred ccCchhhccccCchhHHHHHHHHH
Confidence 478999999999999997 4544
Done!