Query psy1508
Match_columns 119
No_of_seqs 110 out of 549
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 20:00:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1508hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4471|consensus 100.0 3.1E-45 6.8E-50 312.1 6.2 117 2-118 439-556 (717)
2 KOG1089|consensus 100.0 4.9E-41 1.1E-45 286.4 7.3 117 2-118 410-530 (573)
3 PF06602 Myotub-related: Myotu 99.9 5.4E-28 1.2E-32 197.6 6.7 56 2-57 297-352 (353)
4 KOG1090|consensus 99.9 3.8E-25 8.2E-30 197.3 4.3 104 3-107 1333-1453(1732)
5 PF12578 3-PAP: Myotubularin-a 96.8 0.00026 5.6E-09 51.6 -0.7 40 76-115 60-102 (142)
6 PF12575 DUF3753: Protein of u 54.2 3.7 8.1E-05 27.0 -0.2 22 36-57 1-22 (72)
7 PHA02692 hypothetical protein; 48.2 4.9 0.00011 26.3 -0.4 22 36-57 1-22 (70)
8 PHA02975 hypothetical protein; 47.3 5.3 0.00012 26.0 -0.3 22 36-57 1-22 (69)
9 PHA02844 putative transmembran 45.1 6.3 0.00014 26.1 -0.2 22 36-57 1-22 (75)
10 PHA02819 hypothetical protein; 43.8 6 0.00013 25.9 -0.5 22 36-57 1-22 (71)
11 PHA03054 IMV membrane protein; 43.5 6 0.00013 26.0 -0.5 22 36-57 1-22 (72)
12 PHA02650 hypothetical protein; 42.3 7.5 0.00016 26.1 -0.2 22 36-57 1-22 (81)
13 PF04661 Pox_I3: Poxvirus I3 s 37.5 21 0.00045 28.8 1.6 15 3-17 97-111 (262)
14 PHA03068 DNA-binding phosphopr 37.5 21 0.00045 28.9 1.6 16 3-18 107-122 (270)
15 PF09569 RE_ScaI: ScaI restric 28.3 65 0.0014 24.8 2.9 39 9-47 10-48 (191)
No 1
>KOG4471|consensus
Probab=100.00 E-value=3.1e-45 Score=312.15 Aligned_cols=117 Identities=57% Similarity=1.020 Sum_probs=114.7
Q ss_pred CcCchHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHhccccccccCcCCHHHHHHHhhCCCCcccccccccccccccCC
Q psy1508 2 KGSPVFLQLIDAVWQVTTMFRHAFEFNEHFLITILDHLYSCRFGTFLFNSDRERNQENMKQRTVSLWSYINSSLDLYKNP 81 (119)
Q Consensus 2 E~SPiFlqFLDcV~Ql~~q~P~~FEFn~~~L~~L~d~~~s~~fgtFl~n~e~eR~~~~~~~~t~SlW~~~~~~~~~f~N~ 81 (119)
|+||||||||||||||+||||+||||||.||+.|+||+|||+||||||||||||.+.++.++|.|+|+++++..+.|.||
T Consensus 439 drsPVFLQwlDcV~Ql~rqfP~aFEFne~fLi~i~dh~ySClFGTFLcN~ekeR~~~~i~~~t~slWs~l~s~~~~f~Np 518 (717)
T KOG4471|consen 439 DRSPVFLQWLDCVWQLMRQFPCAFEFNEAFLIKIVDHLYSCLFGTFLCNSEKEREKEDITERTGSLWSYLNSSLSNFCNP 518 (717)
T ss_pred ccCchhHHHHHHHHHHHHhCCcccccCHHHHHHHHHHHHHhhhhhhhcCCHHHHhhcCcccchhhHHHHHhhcchhhcCc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCC-CceeccCCcCCceechhhccccCCCCCCCCC
Q psy1508 82 LYFPQL-HVLEPIASMRHIKLWKGLYCRWNPSMRAQRE 118 (119)
Q Consensus 82 ~Y~~~~-~~l~p~~~~~~~~lW~~~y~R~~~~~~~~~~ 118 (119)
+|.+.+ .||+|.++++.+.||.+||+||++++.++++
T Consensus 519 ~y~~~s~~vL~Pvas~r~l~LW~~~ylrw~~~~~~~~~ 556 (717)
T KOG4471|consen 519 FYDPSSNGVLYPVASVRALELWVQYYLRWNPPMEPQEP 556 (717)
T ss_pred ccCchhcccccchHhhhchhhceeeeeccCCCCCCCCc
Confidence 999988 9999999999999999999999999999876
No 2
>KOG1089|consensus
Probab=100.00 E-value=4.9e-41 Score=286.37 Aligned_cols=117 Identities=44% Similarity=0.859 Sum_probs=112.3
Q ss_pred CcCchHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHhccccccccCcCCHHHHHHHhhCCCCcccccccccccccccCC
Q psy1508 2 KGSPVFLQLIDAVWQVTTMFRHAFEFNEHFLITILDHLYSCRFGTFLFNSDRERNQENMKQRTVSLWSYINSSLDLYKNP 81 (119)
Q Consensus 2 E~SPiFlqFLDcV~Ql~~q~P~~FEFn~~~L~~L~d~~~s~~fgtFl~n~e~eR~~~~~~~~t~SlW~~~~~~~~~f~N~ 81 (119)
|.||||+|||||||||++|||++|||||+||+.|++|+|+|+|||||+||||||.+.++..+|.|+|+++.+++++|+||
T Consensus 410 e~SPvF~qFLDcvwQl~~QfP~~FEFne~fLi~L~~h~ys~qfGtFl~NsekeR~e~~~~~kt~slW~~~~~~~~~f~Np 489 (573)
T KOG1089|consen 410 EESPVFLQFLDCVWQLLEQFPCAFEFNERFLIKLHEHAYSSQFGTFLGNSEKERRELNLSEKTTSLWDYLLPRKEEFVNP 489 (573)
T ss_pred ccCcHHHHHHHHHHHHHhhCCcceehhHHHHHHHHHhhHHhhhccccccCHHHHHHhcccccceehHHhHhhhhhhhcCc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCceeccCCcCC----ceechhhccccCCCCCCCCC
Q psy1508 82 LYFPQLHVLEPIASMRH----IKLWKGLYCRWNPSMRAQRE 118 (119)
Q Consensus 82 ~Y~~~~~~l~p~~~~~~----~~lW~~~y~R~~~~~~~~~~ 118 (119)
+|+|...++.|..++.. +++|.++|.||++++.++.+
T Consensus 490 ly~~~~~~~~~~l~P~~~~~~l~~W~~~y~r~d~~~~~~~~ 530 (573)
T KOG1089|consen 490 LYDPRYLVIWPILAPQTATLSLQVWSSLYERWDEGLSPRTP 530 (573)
T ss_pred cccccccceeeccCcccccchhHHHHHHHHhhccCCCcccc
Confidence 99999999888777777 99999999999998888765
No 3
>PF06602 Myotub-related: Myotubularin-like phosphatase domain; InterPro: IPR010569 This family represents a region within eukaryotic myotubularin-related proteins that is sometimes found with IPR004182 from INTERPRO. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate []. Mutations in gene encoding myotubularin-related proteins have been associated with disease [].; GO: 0016791 phosphatase activity, 0016311 dephosphorylation; PDB: 1M7R_B 1LW3_A 1ZVR_A 1ZSQ_A 2YF0_A.
Probab=99.94 E-value=5.4e-28 Score=197.63 Aligned_cols=56 Identities=61% Similarity=1.051 Sum_probs=49.1
Q ss_pred CcCchHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHhccccccccCcCCHHHHHH
Q psy1508 2 KGSPVFLQLIDAVWQVTTMFRHAFEFNEHFLITILDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 2 E~SPiFlqFLDcV~Ql~~q~P~~FEFn~~~L~~L~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
|.||||+|||||||||++|||++|||||.||++|+||+|||+|||||+|||+||.+
T Consensus 297 ~~sPvFl~FLDcV~ql~~q~P~~FEFne~~L~~l~~~~~s~~fgtFl~n~e~eR~~ 352 (353)
T PF06602_consen 297 ERSPVFLQFLDCVWQLLRQFPTAFEFNESLLIFLADHSYSGRFGTFLFNSEKEREE 352 (353)
T ss_dssp C---HHHHHHHHHHHHHHHSTTT-SB-HHHHHHHHHHHCCTSSTTT-SSSHHHHHH
T ss_pred ccccchhHHHHHHHHHHHhCCCceecCHHHHHHHHHHHhcCCCCccccCCHHHhcc
Confidence 78999999999999999999999999999999999999999999999999999975
No 4
>KOG1090|consensus
Probab=99.91 E-value=3.8e-25 Score=197.31 Aligned_cols=104 Identities=36% Similarity=0.679 Sum_probs=94.1
Q ss_pred cCchHHHHHHHHHHHHHhcCCCCccCHHHHHHHHHHhccccccccCcCCHHHHHHHhh-------------CCCCccccc
Q psy1508 3 GSPVFLQLIDAVWQVTTMFRHAFEFNEHFLITILDHLYSCRFGTFLFNSDRERNQENM-------------KQRTVSLWS 69 (119)
Q Consensus 3 ~SPiFlqFLDcV~Ql~~q~P~~FEFn~~~L~~L~d~~~s~~fgtFl~n~e~eR~~~~~-------------~~~t~SlW~ 69 (119)
.||+|+||||||+|+.+|||+|||||.-||.+|++|..||+|.|||+|||.||.+.++ +..|.|+|+
T Consensus 1333 fsPsFlqFLDcVhQi~~QfPmaFEFs~FYl~FLaYHsvs~rFRTFl~Dce~eR~esg~~~~ek~er~~~p~nr~~~svwe 1412 (1732)
T KOG1090|consen 1333 FSPSFLQFLDCVHQISQQFPMAFEFSYFYLSFLAYHSVSGRFRTFLLDCEEERIESGLLYEEKGERRGQPLNRATISVWE 1412 (1732)
T ss_pred cCchHHHHHHHHHHHHHhccchhhhHHHHHHHHhhhccchhhhhhhccccHHhhhhhhhHHhhccccCCCcccccchHHH
Confidence 5899999999999999999999999999999999999999999999999999998764 234679999
Q ss_pred ccccc---cccccCCCCCCCC-CceeccCCcCCceechhhcc
Q psy1508 70 YINSS---LDLYKNPLYFPQL-HVLEPIASMRHIKLWKGLYC 107 (119)
Q Consensus 70 ~~~~~---~~~f~N~~Y~~~~-~~l~p~~~~~~~~lW~~~y~ 107 (119)
+|... ...|.|.+|.|.+ .+++|..++.++++| .+|.
T Consensus 1413 yI~r~~k~Tp~FyN~lYa~~~s~ilrP~snV~~l~~W-~fyt 1453 (1732)
T KOG1090|consen 1413 YIDRLSKRTPAFYNYLYAPEDSEILRPYSNVSNLKVW-DFYT 1453 (1732)
T ss_pred HHHHhcccChhHHHHhhCcCCcccccccCCcccccee-ccch
Confidence 99863 4679999999998 889999999999999 5554
No 5
>PF12578 3-PAP: Myotubularin-associated protein; InterPro: IPR022587 The proteins in this entry are found in eukaryotes, and are typically between 115 and 138 amino acids in length. This entry contains myotubularin-associated protein 12 (also known as the phosphatidylinositol-3 phosphate 3-phosphatase adapter subunit, 3-PAP). 3-PAP is a catalytically inactive member of the myotubularin gene family, which coprecipitates lipid phosphatidylinositol 3-phosphate-3-phosphatase activity from lysates of human platelets [].
Probab=96.75 E-value=0.00026 Score=51.64 Aligned_cols=40 Identities=30% Similarity=0.605 Sum_probs=31.8
Q ss_pred ccccCCCCC-CC--CCceeccCCcCCceechhhccccCCCCCC
Q psy1508 76 DLYKNPLYF-PQ--LHVLEPIASMRHIKLWKGLYCRWNPSMRA 115 (119)
Q Consensus 76 ~~f~N~~Y~-~~--~~~l~p~~~~~~~~lW~~~y~R~~~~~~~ 115 (119)
.+|.+..+. |. .++|.|.....++++|++||+||.|.+.-
T Consensus 60 ~~~~~~~~~~P~d~~~lL~P~~~~~~i~lW~qcYlRW~P~a~i 102 (142)
T PF12578_consen 60 EQFFRDWFSKPADSHGLLLPLLSGPQIKLWSQCYLRWIPEAQI 102 (142)
T ss_pred HhhccccccCCcccccccccccccccHHHHHHHHHccCcHHHc
Confidence 456666653 32 28999999999999999999999998743
No 6
>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2.
Probab=54.19 E-value=3.7 Score=26.97 Aligned_cols=22 Identities=41% Similarity=0.776 Sum_probs=18.6
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||+|+-++|.|-..
T Consensus 1 MDKLyaaifGvFmss~ddDf~~ 22 (72)
T PF12575_consen 1 MDKLYAAIFGVFMSSSDDDFNN 22 (72)
T ss_pred ChhHHHHHHhhhcCCCHHHHHH
Confidence 3778999999999999987654
No 7
>PHA02692 hypothetical protein; Provisional
Probab=48.19 E-value=4.9 Score=26.27 Aligned_cols=22 Identities=45% Similarity=0.810 Sum_probs=18.3
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MDKLyaaifGVFmss~DdDF~~ 22 (70)
T PHA02692 1 MDKLYAGVFGSFLSNSDEDFEE 22 (70)
T ss_pred ChhHHHHHHHhhcCCCHHHHHH
Confidence 3678999999999999986543
No 8
>PHA02975 hypothetical protein; Provisional
Probab=47.25 E-value=5.3 Score=26.03 Aligned_cols=22 Identities=23% Similarity=0.620 Sum_probs=18.4
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MdKLYaaiFGvFmsS~DdDF~n 22 (69)
T PHA02975 1 MEKLFTGTYGVFLESNDSDFED 22 (69)
T ss_pred ChhHHHHHHHhhcCCChHHHHH
Confidence 3678999999999999987654
No 9
>PHA02844 putative transmembrane protein; Provisional
Probab=45.10 E-value=6.3 Score=26.08 Aligned_cols=22 Identities=36% Similarity=0.742 Sum_probs=18.4
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MDKLYaaiFGVFmsS~DdDFnn 22 (75)
T PHA02844 1 MDKLYTAIFGVFLSSENEDFNN 22 (75)
T ss_pred ChhHHHHHHhhhcCCchHHHHH
Confidence 3678999999999999877654
No 10
>PHA02819 hypothetical protein; Provisional
Probab=43.78 E-value=6 Score=25.92 Aligned_cols=22 Identities=45% Similarity=0.792 Sum_probs=18.4
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MDKLYaaiFGvFmsS~DdDFnn 22 (71)
T PHA02819 1 MDKLYSAIFGVFMSSSDDDFNN 22 (71)
T ss_pred ChhHHHHHHHhhhCCchhHHHH
Confidence 3678999999999999877653
No 11
>PHA03054 IMV membrane protein; Provisional
Probab=43.51 E-value=6 Score=25.98 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=18.1
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MdkLya~ifGvF~ss~d~Df~~ 22 (72)
T PHA03054 1 MDKLYAAIFGVFMGSPEDDLTD 22 (72)
T ss_pred ChhHHHHHHHHhhCCchHHHHH
Confidence 3678999999999999876543
No 12
>PHA02650 hypothetical protein; Provisional
Probab=42.29 E-value=7.5 Score=26.07 Aligned_cols=22 Identities=36% Similarity=0.765 Sum_probs=18.4
Q ss_pred HHHhccccccccCcCCHHHHHH
Q psy1508 36 LDHLYSCRFGTFLFNSDRERNQ 57 (119)
Q Consensus 36 ~d~~~s~~fgtFl~n~e~eR~~ 57 (119)
+|-+|++.||.|+-+++.+=..
T Consensus 1 MDKLYaaiFGVFmsS~DdDFnn 22 (81)
T PHA02650 1 MDKLYAAIFGVFMSSTDDDFNN 22 (81)
T ss_pred ChhHHHHHHhhhcCCcHHHHHH
Confidence 3778999999999999877654
No 13
>PF04661 Pox_I3: Poxvirus I3 ssDNA-binding protein; InterPro: IPR006754 The 34kDa protein encoded by the I3 gene of vaccinia virus is expressed at early and intermediate times post-infection and is phosphorylated on serine residues. I3 protein demonstrates a striking affinity for single-stranded, but not for double-stranded, DNA which suggests a role in DNA replication and/or repair. Electrophoretic mobility shift assays indicate that numerous I3 molecules can bind to a template, reflecting the stoichiometric interaction of I3 with DNA. Sequence analysis reveals that a pattern of aromatic and charged amino acids common to many replicative single-stranded DNA binding proteins (SSBs) is conserved in I3 [].; GO: 0003697 single-stranded DNA binding
Probab=37.53 E-value=21 Score=28.79 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=13.1
Q ss_pred cCchHHHHHHHHHHH
Q psy1508 3 GSPVFLQLIDAVWQV 17 (119)
Q Consensus 3 ~SPiFlqFLDcV~Ql 17 (119)
-||+..|+|||||-=
T Consensus 97 ASPmLYQlle~IY~n 111 (262)
T PF04661_consen 97 ASPMLYQLLECIYTN 111 (262)
T ss_pred cCHHHHHHHHHHHhh
Confidence 489999999999854
No 14
>PHA03068 DNA-binding phosphoprotein; Provisional
Probab=37.53 E-value=21 Score=28.89 Aligned_cols=16 Identities=25% Similarity=0.625 Sum_probs=13.5
Q ss_pred cCchHHHHHHHHHHHH
Q psy1508 3 GSPVFLQLIDAVWQVT 18 (119)
Q Consensus 3 ~SPiFlqFLDcV~Ql~ 18 (119)
-||+..|+|||||-=+
T Consensus 107 aSPmLYQllE~IY~nI 122 (270)
T PHA03068 107 ASPMLYQLLECIYGNI 122 (270)
T ss_pred cCHHHHHHHHHHHhhh
Confidence 4899999999999543
No 15
>PF09569 RE_ScaI: ScaI restriction endonuclease; InterPro: IPR019069 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 the restriction endonuclease ScaI, which recognises and cleaves the double-stranded sequence AGT^ACT.
Probab=28.32 E-value=65 Score=24.81 Aligned_cols=39 Identities=13% Similarity=0.226 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcCCCCccCHHHHHHHHHHhcccccccc
Q psy1508 9 QLIDAVWQVTTMFRHAFEFNEHFLITILDHLYSCRFGTF 47 (119)
Q Consensus 9 qFLDcV~Ql~~q~P~~FEFn~~~L~~L~d~~~s~~fgtF 47 (119)
.|+.-.-||+.++|.+-|+=-...+.-++.+++.++||+
T Consensus 10 ~W~siT~~LIe~hPLs~e~Iv~iVL~SW~~If~s~~g~~ 48 (191)
T PF09569_consen 10 EWSSITQQLIEEHPLSMETIVSIVLKSWNDIFSSSIGSF 48 (191)
T ss_pred HHHHHHHHHHHhCCccHHHHHHHHHHHHHHHHhhhcCcc
Confidence 467778899999999988888888888999999999994
Done!