Query psy8034
Match_columns 73
No_of_seqs 44 out of 46
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 16:44:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8034.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8034hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12062 HSNSD: heparan sulfat 100.0 8.8E-39 1.9E-43 254.7 5.1 71 3-73 373-443 (487)
2 KOG3703|consensus 100.0 2.1E-38 4.6E-43 260.5 4.1 70 4-73 393-462 (873)
3 PF13773 DUF4170: Domain of un 37.5 27 0.00059 22.2 1.8 26 34-59 27-52 (69)
4 COG4209 LplB ABC-type polysacc 31.1 32 0.0007 27.3 1.7 22 41-68 196-225 (309)
5 PF13137 DUF3983: Protein of u 30.0 44 0.00096 18.7 1.6 11 43-53 19-29 (34)
6 COG3708 Uncharacterized protei 27.8 44 0.00095 23.3 1.7 25 27-55 94-118 (157)
7 COG0145 HyuA N-methylhydantoin 26.2 46 0.00099 28.4 1.8 48 15-62 142-191 (674)
8 PF09225 Endonuc-PvuII: Restri 26.0 9 0.00019 27.6 -2.0 32 17-54 99-130 (155)
9 COG0108 RibB 3,4-dihydroxy-2-b 25.7 22 0.00048 26.5 -0.1 16 13-28 176-191 (203)
10 PF06445 GyrI-like: GyrI-like 25.2 49 0.0011 19.9 1.4 23 28-54 94-116 (155)
11 cd03521 Link_domain_KIAA0527_l 23.6 53 0.0012 22.1 1.4 10 42-51 33-42 (95)
12 PHA00456 hypothetical protein 22.3 57 0.0012 18.2 1.2 11 42-52 22-32 (34)
13 PF05840 Phage_GPA: Bacterioph 21.4 1.1E+02 0.0023 24.5 2.9 32 6-38 210-248 (371)
14 PF02061 Lambda_CIII: Lambda P 20.7 68 0.0015 18.9 1.3 12 44-55 27-38 (45)
No 1
>PF12062 HSNSD: heparan sulfate-N-deacetylase; InterPro: IPR021930 This family of proteins is are heparan sulphate N-deacetylase enzymes. This protein is found in eukaryotes. This enzyme is often found associated with PF00685 from PFAM. ; GO: 0015016 [heparan sulfate]-glucosamine N-sulfotransferase activity, 0016787 hydrolase activity
Probab=100.00 E-value=8.8e-39 Score=254.66 Aligned_cols=71 Identities=59% Similarity=0.986 Sum_probs=69.2
Q ss_pred CccchhhHHHHHHHHHHhcCCCCCCCceeeccccceecccHHHHHHHHHHhccccccceecCCCCccccCC
Q psy8034 3 PVSGQPAREDLVAQQVLRSAAPVDSGYSIAPHHSGVYPVHEPLYTAWKHIWRVKVTSTEEYPHLRPARLRR 73 (73)
Q Consensus 3 ~~~~l~~~M~lNk~FA~~h~ip~~~~yaVaphhsGvYpvh~~ly~aWk~vw~i~vTsteeyPhlrpa~~rr 73 (73)
-.|.|+++|+|||+||++|+||++++||||||||||||||+|||+|||+||||+||||||||||||||+||
T Consensus 373 n~s~L~~~m~lNk~Fa~~~~ip~~~~yaVaphhsgvypvh~~ly~awk~vw~i~vTstEeYphl~pa~~rr 443 (487)
T PF12062_consen 373 NQSVLAEQMILNKQFAKEHGIPTDMGYAVAPHHSGVYPVHEQLYEAWKKVWNIKVTSTEEYPHLRPARYRR 443 (487)
T ss_pred cHHHHHHHHHHHHHhhhhccCCCCCcceEecccCceechhHHHHHHHHHHHccccccceeccccccchhhc
Confidence 36899999999999999999999999999999999999999999999999999999999999999999987
No 2
>KOG3703|consensus
Probab=100.00 E-value=2.1e-38 Score=260.53 Aligned_cols=70 Identities=60% Similarity=1.044 Sum_probs=68.5
Q ss_pred ccchhhHHHHHHHHHHhcCCCCCCCceeeccccceecccHHHHHHHHHHhccccccceecCCCCccccCC
Q psy8034 4 VSGQPAREDLVAQQVLRSAAPVDSGYSIAPHHSGVYPVHEPLYTAWKHIWRVKVTSTEEYPHLRPARLRR 73 (73)
Q Consensus 4 ~~~l~~~M~lNk~FA~~h~ip~~~~yaVaphhsGvYpvh~~ly~aWk~vw~i~vTsteeyPhlrpa~~rr 73 (73)
.|.|++||.|||+||.+||||+|+|||||||||||||||+|||+|||+||||+||||||||||||||.||
T Consensus 393 ~s~L~~qM~lNk~FA~ehgiPtd~gYavaPhHsGVyPvH~qLy~AWkkVWni~VTsTEEYPHlkPAr~Rr 462 (873)
T KOG3703|consen 393 ESVLAAQMALNKKFALEHGIPTDMGYAVAPHHSGVYPVHEQLYEAWKKVWNIKVTSTEEYPHLKPARYRR 462 (873)
T ss_pred HHHHHHHHHHhHHHHHhcCCCcCcccccccccCCcchHHHHHHHHHHHHcCeEeeecccCCccChhhhhc
Confidence 4789999999999999999999999999999999999999999999999999999999999999999997
No 3
>PF13773 DUF4170: Domain of unknown function (DUF4170)
Probab=37.50 E-value=27 Score=22.22 Aligned_cols=26 Identities=23% Similarity=0.498 Sum_probs=21.7
Q ss_pred cccceecccHHHHHHHHHHhcccccc
Q psy8034 34 HHSGVYPVHEPLYTAWKHIWRVKVTS 59 (73)
Q Consensus 34 hhsGvYpvh~~ly~aWk~vw~i~vTs 59 (73)
+--|+||-++.-+.|||..=+.+|-+
T Consensus 27 diVG~fp~y~~A~~aWrakAq~TVDn 52 (69)
T PF13773_consen 27 DIVGIFPDYASAYAAWRAKAQRTVDN 52 (69)
T ss_pred eEEecCCChHHHHHHHHHHHhCchhc
Confidence 45699999999999999887766644
No 4
>COG4209 LplB ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]
Probab=31.07 E-value=32 Score=27.27 Aligned_cols=22 Identities=41% Similarity=1.207 Sum_probs=16.9
Q ss_pred ccHHHHHH--------HHHHhccccccceecCCCCc
Q psy8034 41 VHEPLYTA--------WKHIWRVKVTSTEEYPHLRP 68 (73)
Q Consensus 41 vh~~ly~a--------Wk~vw~i~vTsteeyPhlrp 68 (73)
|..++||| |+.+|+|++ |.++|
T Consensus 196 Idpt~YEAA~vDGA~rwqqiwhITl------P~i~P 225 (309)
T COG4209 196 IDPTLYEAAMVDGASRWQQIWHITL------PAIRP 225 (309)
T ss_pred CCHHHHHHHHcccHHHHHHHHhcch------hhhhh
Confidence 56778886 999999865 66665
No 5
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=30.02 E-value=44 Score=18.71 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=9.0
Q ss_pred HHHHHHHHHHh
Q psy8034 43 EPLYTAWKHIW 53 (73)
Q Consensus 43 ~~ly~aWk~vw 53 (73)
+++..||+++.
T Consensus 19 ~rv~kAWRNiF 29 (34)
T PF13137_consen 19 YRVDKAWRNIF 29 (34)
T ss_pred HHHHHHHHHHH
Confidence 57889999875
No 6
>COG3708 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.76 E-value=44 Score=23.28 Aligned_cols=25 Identities=36% Similarity=1.006 Sum_probs=18.0
Q ss_pred CCceeeccccceecccHHHHHHHHHHhcc
Q psy8034 27 SGYSIAPHHSGVYPVHEPLYTAWKHIWRV 55 (73)
Q Consensus 27 ~~yaVaphhsGvYpvh~~ly~aWk~vw~i 55 (73)
.-|||..|. | |+.+ +.++|.+||+-
T Consensus 94 ~~YavFt~~-G--~~~~-i~etw~~I~~~ 118 (157)
T COG3708 94 STYAVFTHK-G--PIEE-IQETWQEIWKE 118 (157)
T ss_pred ceEEEEEec-C--CHHH-HHHHHHHHHHh
Confidence 348886533 3 4445 99999999995
No 7
>COG0145 HyuA N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=26.22 E-value=46 Score=28.42 Aligned_cols=48 Identities=17% Similarity=0.108 Sum_probs=34.8
Q ss_pred HHHHHhcCCCCCCCceeeccccceecccHH-HHHHHHHHh-cccccccee
Q psy8034 15 AQQVLRSAAPVDSGYSIAPHHSGVYPVHEP-LYTAWKHIW-RVKVTSTEE 62 (73)
Q Consensus 15 k~FA~~h~ip~~~~yaVaphhsGvYpvh~~-ly~aWk~vw-~i~vTstee 62 (73)
++|+..-.-.=-..+|||--||-.+|.||. .-+.-++++ ++.|++..|
T Consensus 142 ~~~~~~l~~~gv~siAVs~~~S~~NP~HE~~v~eiire~~~~i~V~~she 191 (674)
T COG0145 142 REAAAALKAAGVEAIAVSSLFSYRNPEHELRVAEIIREIGPDIPVSLSHE 191 (674)
T ss_pred HHHHHHHHhCCCcEEEEEEecccCCcHHHHHHHHHHHHhcCCceEEechh
Confidence 344444332223579999999999999996 567888899 898887543
No 8
>PF09225 Endonuc-PvuII: Restriction endonuclease PvuII; InterPro: IPR015306 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 type II restriction endonuclease PvuII, which recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3 []. ; PDB: 1H56_B 1EYU_A 3KSK_B 1F0O_A 1PVI_B 1PVU_B 3PVI_A 1K0Z_B 1NI0_A 2PVI_A ....
Probab=26.03 E-value=9 Score=27.63 Aligned_cols=32 Identities=22% Similarity=0.621 Sum_probs=24.7
Q ss_pred HHHhcCCCCCCCceeeccccceecccHHHHHHHHHHhc
Q psy8034 17 QVLRSAAPVDSGYSIAPHHSGVYPVHEPLYTAWKHIWR 54 (73)
Q Consensus 17 FA~~h~ip~~~~yaVaphhsGvYpvh~~ly~aWk~vw~ 54 (73)
||.=.+|.+...|...|-+- |.+|..|-+.|.
T Consensus 99 FAiy~~I~l~~iY~l~p~~l------E~~y~~WE~kw~ 130 (155)
T PF09225_consen 99 FAIYRNIELQEIYKLTPEDL------EPFYDKWERKWY 130 (155)
T ss_dssp EEEEETTEEEEEEEE-HHHH------HHHHHHHHHHHH
T ss_pred eeeecCcchhhhhhcCHHHh------HHHHHHHHHHHH
Confidence 67777788888887777664 778999999996
No 9
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=25.69 E-value=22 Score=26.50 Aligned_cols=16 Identities=13% Similarity=-0.002 Sum_probs=12.8
Q ss_pred HHHHHHHhcCCCCCCC
Q psy8034 13 LVAQQVLRSAAPVDSG 28 (73)
Q Consensus 13 lNk~FA~~h~ip~~~~ 28 (73)
.-.+||++|++|+-.+
T Consensus 176 ~~~~fa~~h~l~~iti 191 (203)
T COG0108 176 ELEEFAKEHGLPVITI 191 (203)
T ss_pred HHHHHHHHcCCcEEEH
Confidence 4679999999997544
No 10
>PF06445 GyrI-like: GyrI-like small molecule binding domain; InterPro: IPR010499 This domain is found in the probable effector binding domain of a number of different bacterial transcription activators [] and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.; PDB: 1JYH_A 1D5Y_B 3B49_A 3E0H_A 2KCU_A 3LUR_B 1EXI_A 3Q3D_A 1EXJ_A 3Q5S_A ....
Probab=25.21 E-value=49 Score=19.86 Aligned_cols=23 Identities=26% Similarity=0.691 Sum_probs=17.7
Q ss_pred CceeeccccceecccHHHHHHHHHHhc
Q psy8034 28 GYSIAPHHSGVYPVHEPLYTAWKHIWR 54 (73)
Q Consensus 28 ~yaVaphhsGvYpvh~~ly~aWk~vw~ 54 (73)
.|||. .|-|-| +.+.++|..+++
T Consensus 94 ~ya~~-~~~G~~---~~l~~~~~~l~~ 116 (155)
T PF06445_consen 94 KYAVF-EHKGPY---DDLQEAYQKLYN 116 (155)
T ss_dssp EEEEE-EEESCG---HGHHHHHHHHHH
T ss_pred EEEEE-EEEccH---HHHHHHHHHHHh
Confidence 57776 555666 888899998888
No 11
>cd03521 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.
Probab=23.55 E-value=53 Score=22.05 Aligned_cols=10 Identities=20% Similarity=-0.024 Sum_probs=8.7
Q ss_pred cHHHHHHHHH
Q psy8034 42 HEPLYTAWKH 51 (73)
Q Consensus 42 h~~ly~aWk~ 51 (73)
-+|||.||+.
T Consensus 33 ~~QL~~AW~~ 42 (95)
T cd03521 33 AAELRRAVVE 42 (95)
T ss_pred HHHHHHHHHH
Confidence 4799999996
No 12
>PHA00456 hypothetical protein
Probab=22.32 E-value=57 Score=18.21 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=8.8
Q ss_pred cHHHHHHHHHH
Q psy8034 42 HEPLYTAWKHI 52 (73)
Q Consensus 42 h~~ly~aWk~v 52 (73)
..+||+.||..
T Consensus 22 Y~ely~lWk~R 32 (34)
T PHA00456 22 YQELYNLWKRR 32 (34)
T ss_pred HHHHHHHHHHc
Confidence 47899999964
No 13
>PF05840 Phage_GPA: Bacteriophage replication gene A protein (GPA); InterPro: IPR008766 Replication gene A proteins (also known as GpA) are found in bacteriophages and in bacteria as part of a suspected prophage. These proteins function as endonucleases during DNA replication [,,].; GO: 0006260 DNA replication
Probab=21.35 E-value=1.1e+02 Score=24.53 Aligned_cols=32 Identities=28% Similarity=0.429 Sum_probs=21.0
Q ss_pred chhhHHHHHHHHH------HhcCCCCCCCceee-ccccce
Q psy8034 6 GQPAREDLVAQQV------LRSAAPVDSGYSIA-PHHSGV 38 (73)
Q Consensus 6 ~l~~~M~lNk~FA------~~h~ip~~~~yaVa-phhsGv 38 (73)
.-.+|=-||+.+| ...+|++ .|..|+ |||+|.
T Consensus 210 P~daq~yL~~~W~~~Ra~l~r~~i~~-yG~RV~EPHhDGT 248 (371)
T PF05840_consen 210 PRDAQRYLNKVWARIRAALKRRGIRF-YGFRVAEPHHDGT 248 (371)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCe-eeEEeecccCCCC
Confidence 3355556666663 3567876 566665 999997
No 14
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.65 E-value=68 Score=18.91 Aligned_cols=12 Identities=33% Similarity=1.107 Sum_probs=9.6
Q ss_pred HHHHHHHHHhcc
Q psy8034 44 PLYTAWKHIWRV 55 (73)
Q Consensus 44 ~ly~aWk~vw~i 55 (73)
.|-..||++|.|
T Consensus 27 klr~gwKRl~~i 38 (45)
T PF02061_consen 27 KLRDGWKRLWDI 38 (45)
T ss_pred HHHHHHHHHHHH
Confidence 456689999986
Done!