Query 032407
Match_columns 141
No_of_seqs 112 out of 126
Neff 3.1
Searched_HMMs 29240
Date Mon Mar 25 22:28:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032407.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/032407hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1bh9_B TAFII28; histone fold, 99.2 3E-12 1E-16 91.4 3.5 30 112-141 1-30 (89)
2 3nrw_A Phage integrase/site-sp 48.5 23 0.0008 23.1 4.0 32 109-140 51-83 (117)
3 2beq_D E2 glycoprotein; viral 44.1 20 0.00067 23.1 2.9 24 100-123 17-45 (48)
4 1mfq_C SRP54, signal recogniti 39.8 39 0.0013 25.1 4.4 26 98-123 56-84 (129)
5 2key_A Putative phage integras 38.3 35 0.0012 21.4 3.5 31 109-139 49-81 (112)
6 2qxf_A Exodeoxyribonuclease I; 34.5 31 0.0011 30.0 3.6 31 110-140 417-447 (482)
7 2kiw_A INT protein; alpha, str 33.4 58 0.002 20.3 3.9 31 109-139 41-71 (111)
8 1qb2_A SRP54, human signal rec 30.8 91 0.0031 22.3 5.0 27 98-124 43-72 (109)
9 2oxo_A Integrase; DNA-binding 30.3 70 0.0024 18.8 3.8 30 109-138 43-72 (103)
10 2khq_A Integrase; all-alpha, s 29.6 56 0.0019 20.2 3.4 30 109-138 44-73 (110)
11 1n1j_B NF-YC; histone-like PAI 27.9 23 0.00079 24.4 1.4 20 120-139 12-31 (97)
12 1dul_A Signal recognition part 27.7 44 0.0015 22.3 2.7 33 100-137 10-42 (69)
13 1ojh_A NBLA; degradation prote 25.5 91 0.0031 21.0 3.9 37 103-139 16-54 (65)
No 1
>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B*
Probab=99.24 E-value=3e-12 Score=91.43 Aligned_cols=30 Identities=47% Similarity=0.843 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032407 112 FTEDQMNRYESFRRSALQKSNMRRLLLEWL 141 (141)
Q Consensus 112 FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL 141 (141)
||+|||+|||+||||+|+|+.||||||+++
T Consensus 1 ft~eQ~~Rye~~Rrs~f~k~~vKrl~~~~~ 30 (89)
T 1bh9_B 1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSIT 30 (89)
T ss_dssp CCHHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhcCCHHHHHHHHHHHc
Confidence 899999999999999999999999999874
No 2
>3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain, structural genomics, PSI-2, protein ST initiative; 1.70A {Haloarcula marismortui}
Probab=48.49 E-value=23 Score=23.12 Aligned_cols=32 Identities=19% Similarity=0.442 Sum_probs=26.4
Q ss_pred HhcCCHHHHHHHHHHHhc-cCChHHHHHHHHhh
Q 032407 109 LNQFTEDQMNRYESFRRS-ALQKSNMRRLLLEW 140 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRRS-~f~Ka~VKKLinsv 140 (141)
+..+++..+.+|-.|++. ++..++|++.+..+
T Consensus 51 l~~it~~~i~~y~~~l~~~~~s~~Ti~~~ls~l 83 (117)
T 3nrw_A 51 MRELTGWKLDEYETFRRGSDVSPATLNGEMQTL 83 (117)
T ss_dssp GGGCCHHHHHHHHHHHHTSSCCHHHHHHHHHHH
T ss_pred hHHCCHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 457889999999999874 69999999887653
No 3
>2beq_D E2 glycoprotein; viral protein, coiled coil, membrane fusion, viral entry, envelope protein, signal, transmembrane, virulence; 1.6A {Sars coronavirus PUMC03} SCOP: h.3.3.1 PDB: 1zv7_A
Probab=44.13 E-value=20 Score=23.07 Aligned_cols=24 Identities=8% Similarity=0.522 Sum_probs=19.9
Q ss_pred HHHHHHHHHHhcCC-----HHHHHHHHHH
Q 032407 100 AKMAKMQAILNQFT-----EDQMNRYESF 123 (141)
Q Consensus 100 ee~~km~~Ll~~FS-----eEQmdRYE~f 123 (141)
.+..+++.+|.++. =++++|||.|
T Consensus 17 ~Ei~~Lq~~I~~LN~slIDLe~Ln~~E~y 45 (48)
T 2beq_D 17 KEIDRLNEVAKNLNESLIDLQELGKYEQY 45 (48)
T ss_dssp HHHHHHHHHHTTGGGGEECHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhHccHHHhchhhee
Confidence 56778888898875 4899999998
No 4
>1mfq_C SRP54, signal recognition particle 54KDA protein; RNA-protein complex, A-minor motif, 3-helix junction, signaling protein/RNA complex; HET: CCC; 3.10A {Homo sapiens} SCOP: a.36.1.1
Probab=39.81 E-value=39 Score=25.13 Aligned_cols=26 Identities=15% Similarity=0.483 Sum_probs=21.9
Q ss_pred cHHHHHHHHHHHhcCCHHHHHH---HHHH
Q 032407 98 DPAKMAKMQAILNQFTEDQMNR---YESF 123 (141)
Q Consensus 98 dEee~~km~~Ll~~FSeEQmdR---YE~f 123 (141)
++.+..++.++|++||++.++. -+.+
T Consensus 56 ~e~~lkr~eaII~SMT~~Er~n~~~P~ii 84 (129)
T 1mfq_C 56 SMARLKKLMTIMDSMNDQELDSTDGAKVF 84 (129)
T ss_dssp HHHHHHHHHHHHTTSCHHHHTCTTHHHHH
T ss_pred hHHHHHHHHHHHHccCHHHHhcCCCcccc
Confidence 3556688899999999999998 7877
No 5
>2key_A Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown F protein structure initiative; NMR {Bacteroides fragilis}
Probab=38.31 E-value=35 Score=21.42 Aligned_cols=31 Identities=23% Similarity=0.323 Sum_probs=23.5
Q ss_pred HhcCCHHHHHHHHHHHh--ccCChHHHHHHHHh
Q 032407 109 LNQFTEDQMNRYESFRR--SALQKSNMRRLLLE 139 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRR--S~f~Ka~VKKLins 139 (141)
+..+++..+.+|-.|-+ .++..++|++.+..
T Consensus 49 l~~it~~~i~~~~~~l~~~~~~s~~Ti~~~~~~ 81 (112)
T 2key_A 49 FHELTEDFLRDYLIYMKKTLCNADSTAQRNLST 81 (112)
T ss_dssp TTTCCHHHHHHHHHHHHHTSCCCHHHHHHHHHH
T ss_pred HHHcCHHHHHHHHHHHHHccCcchhhHHHHHHH
Confidence 45678888888888865 46888888887654
No 6
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A*
Probab=34.54 E-value=31 Score=29.97 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=26.0
Q ss_pred hcCCHHHHHHHHHHHhccCChHHHHHHHHhh
Q 032407 110 NQFTEDQMNRYESFRRSALQKSNMRRLLLEW 140 (141)
Q Consensus 110 ~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsv 140 (141)
+.||++++.|+..||+..|...++....+.+
T Consensus 417 ~~l~~~e~~~w~~~~~~~l~~~~~~~~~~~~ 447 (482)
T 2qxf_A 417 GTLDYAEQQRWLEHRRQVFTPEFLQGYADEL 447 (482)
T ss_dssp GGCCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHHhhhhhHHHHHHHH
Confidence 4589999999999999999988777766543
No 7
>2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435}
Probab=33.43 E-value=58 Score=20.26 Aligned_cols=31 Identities=6% Similarity=0.189 Sum_probs=24.4
Q ss_pred HhcCCHHHHHHHHHHHhccCChHHHHHHHHh
Q 032407 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLLE 139 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRRS~f~Ka~VKKLins 139 (141)
|+.++...+.+|-.+...++..+++++++..
T Consensus 41 l~~It~~~i~~~~~~l~~~~s~~t~~~~~~~ 71 (111)
T 2kiw_A 41 IQTIKKHDYQRFVDDISAQYSKNYVDSIVAS 71 (111)
T ss_dssp GGGCCHHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred HHHcCHHHHHHHHHHHHhhhCHHHHHHHHHH
Confidence 5678888899998887777888888877653
No 8
>1qb2_A SRP54, human signal recognition particle 54 KD protein; alpha-helix, helix-turn-helix, signaling protein; 2.10A {Homo sapiens} SCOP: a.36.1.1 PDB: 1ry1_W* 2go5_W
Probab=30.75 E-value=91 Score=22.28 Aligned_cols=27 Identities=15% Similarity=0.463 Sum_probs=22.1
Q ss_pred cHHHHHHHHHHHhcCCHHHHHH---HHHHH
Q 032407 98 DPAKMAKMQAILNQFTEDQMNR---YESFR 124 (141)
Q Consensus 98 dEee~~km~~Ll~~FSeEQmdR---YE~fR 124 (141)
++.+..++.++|++||++.++. -+.+.
T Consensus 43 ~~~~lkr~~aII~SMT~~Er~~~~~P~ii~ 72 (109)
T 1qb2_A 43 SMARLKKLMTIMDSMNDQELDSTDGAKVFS 72 (109)
T ss_dssp HHHHHHHHHHHHTTSCHHHHHSTTTHHHHH
T ss_pred hHHHHHHHHHHHHcCCHHHHhcCCCccccc
Confidence 3455688899999999999998 77774
No 9
>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage}
Probab=30.27 E-value=70 Score=18.85 Aligned_cols=30 Identities=7% Similarity=-0.009 Sum_probs=21.3
Q ss_pred HhcCCHHHHHHHHHHHhccCChHHHHHHHH
Q 032407 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLL 138 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRRS~f~Ka~VKKLin 138 (141)
|+.++...+.+|-.+.......+++++++.
T Consensus 43 l~~it~~~i~~~~~~l~~~~~~~t~~~~~~ 72 (103)
T 2oxo_A 43 LEDITTKEIAAMLNGYIDEGKAASAKLIRS 72 (103)
T ss_dssp GGGCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred hhhCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence 456788888888887765556677776654
No 10
>2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp}
Probab=29.56 E-value=56 Score=20.19 Aligned_cols=30 Identities=10% Similarity=0.144 Sum_probs=22.2
Q ss_pred HhcCCHHHHHHHHHHHhccCChHHHHHHHH
Q 032407 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLL 138 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRRS~f~Ka~VKKLin 138 (141)
|+.++...+.+|-.+...++..+++++++.
T Consensus 44 l~~it~~~i~~~~~~l~~~~s~~t~~~~~~ 73 (110)
T 2khq_A 44 LKDIKRTEYQKFLNEYGLTHSYETIRKLNS 73 (110)
T ss_dssp GGGCCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred HhhCCHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 556788888888877766677777777654
No 11
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3
Probab=27.92 E-value=23 Score=24.35 Aligned_cols=20 Identities=15% Similarity=0.371 Sum_probs=11.1
Q ss_pred HHHHHhccCChHHHHHHHHh
Q 032407 120 YESFRRSALQKSNMRRLLLE 139 (141)
Q Consensus 120 YE~fRRS~f~Ka~VKKLins 139 (141)
-..|+...||-+.|||||+.
T Consensus 12 ~~~~~~~~lP~arIkrImK~ 31 (97)
T 1n1j_B 12 VKDFRVQELPLARIKKIMKL 31 (97)
T ss_dssp --------CCHHHHHHHHTT
T ss_pred cCCcCCCcCCHHHHHHHHcc
Confidence 45689999999999999975
No 12
>1dul_A Signal recognition particle protein (fifty-four homolog); protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.80A {Escherichia coli} SCOP: a.36.1.1 PDB: 2xkv_C
Probab=27.69 E-value=44 Score=22.32 Aligned_cols=33 Identities=27% Similarity=0.404 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHH
Q 032407 100 AKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137 (141)
Q Consensus 100 ee~~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLi 137 (141)
.+..++.++|++||++.++.-+.+ +.+.++||.
T Consensus 10 ~~lkr~~aII~SMT~~Er~nP~ii-----~~SR~~RIA 42 (69)
T 1dul_A 10 KVLVRMEAIINSMTMKERAKPEII-----KGSRKRRIA 42 (69)
T ss_dssp CHHHHHHHHHHTSCHHHHHCGGGC-----CHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHhCcccc-----CHHHHHHHH
Confidence 345788899999999999864443 444555554
No 13
>1ojh_A NBLA; degradation protein, phycobilisome degradation, protein BIND; HET: MSE; 1.80A {Anabaena SP} SCOP: a.214.1.1
Probab=25.49 E-value=91 Score=20.96 Aligned_cols=37 Identities=11% Similarity=0.339 Sum_probs=32.6
Q ss_pred HHHHHHHhcCCHHHHHHH--HHHHhccCChHHHHHHHHh
Q 032407 103 AKMQAILNQFTEDQMNRY--ESFRRSALQKSNMRRLLLE 139 (141)
Q Consensus 103 ~km~~Ll~~FSeEQmdRY--E~fRRS~f~Ka~VKKLins 139 (141)
+.++--|.+||.||...| +.||..=+..+.||.||..
T Consensus 16 ~~~~~qv~~ls~EQaqe~Lve~~rQmMikeN~~k~liK~ 54 (65)
T 1ojh_A 16 RSFATQVQNMSHDQAKDFLVKLYEQMVVREATYQELLKH 54 (65)
T ss_dssp HHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 666779999999999998 7899999999999999865
Done!