Query psy2753
Match_columns 247
No_of_seqs 114 out of 132
Neff 5.0
Searched_HMMs 29240
Date Sat Aug 17 00:20:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2753.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/2753hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3lph_A Protein REV; helix-loop 56.8 4.2 0.00014 29.8 1.4 19 198-216 28-46 (72)
2 2x7l_M HIV REV; nuclear export 55.9 7.1 0.00024 30.9 2.7 19 198-216 25-43 (115)
3 3k4g_A DNA-directed RNA polyme 37.4 22 0.00074 26.6 2.7 48 136-184 5-57 (86)
4 4hyz_A Uncharacterized protein 36.2 40 0.0014 25.6 4.2 29 78-115 85-113 (114)
5 1z3e_B DNA-directed RNA polyme 19.4 77 0.0026 22.7 2.8 43 141-184 7-54 (73)
6 1coo_A RNA polymerase alpha su 16.9 46 0.0016 25.4 1.2 48 136-184 17-69 (98)
7 2fi2_A Zinc finger protein 42; 14.9 71 0.0024 24.3 1.7 24 172-195 15-40 (94)
8 2a15_A Hypothetical protein RV 14.8 3.1E+02 0.011 19.7 5.4 45 11-58 28-75 (139)
9 3gfk_B DNA-directed RNA polyme 13.1 72 0.0025 23.3 1.3 42 140-182 13-59 (79)
10 1nwd_B GAD, glutamate decarbox 12.8 95 0.0033 18.3 1.5 10 4-13 15-24 (28)
No 1
>3lph_A Protein REV; helix-loop-helix, RNA-binding arginine rich motif, protein oligomerization, AIDS, HOST cytoplasm, HOST nucleus; 2.50A {Human immunodeficiency virus type 1}
Probab=56.79 E-value=4.2 Score=29.78 Aligned_cols=19 Identities=37% Similarity=0.740 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCchhhhccc
Q psy2753 198 APPGKRESQRPANKRRKRK 216 (247)
Q Consensus 198 ~p~~~~~~~~p~~k~~~~~ 216 (247)
.|+|.|+.++.+++.|+|+
T Consensus 28 NP~P~p~GTrqaRRNRRRR 46 (72)
T 3lph_A 28 NPPPNPEGTRQARRNRRRR 46 (72)
T ss_dssp CCCCCCCSCHHHHHHHHHH
T ss_pred CCCCCCCCchHHHHHHHHH
Confidence 7888888888888766654
No 2
>2x7l_M HIV REV; nuclear export, immune system, post-transcriptional regulation; 3.17A {Human immunodeficiency virus type 3}
Probab=55.89 E-value=7.1 Score=30.94 Aligned_cols=19 Identities=37% Similarity=0.740 Sum_probs=15.2
Q ss_pred CCCCCCCCCCCchhhhccc
Q psy2753 198 APPGKRESQRPANKRRKRK 216 (247)
Q Consensus 198 ~p~~~~~~~~p~~k~~~~~ 216 (247)
.|+|.|+.+|.++|.|+|+
T Consensus 25 NPyP~peGTRqaRRNRRRR 43 (115)
T 2x7l_M 25 NPPPNPEGTRQARRNRRRR 43 (115)
T ss_dssp SCCCCCCCCTTTHHHHHHH
T ss_pred CCCCCCCCchhhhHhHHHH
Confidence 7888888999888777765
No 3
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D
Probab=37.40 E-value=22 Score=26.61 Aligned_cols=48 Identities=15% Similarity=0.162 Sum_probs=37.5
Q ss_pred hhhHhhccCCCCCCCChhhhhhhhHHHHhhchHHHHHhhhc-----CCCCHHHH
Q psy2753 136 SMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKA-----YALSPRDC 184 (247)
Q Consensus 136 ~~~kql~k~V~~~Gv~~~~~r~LeI~Eil~~Mq~Lm~f~k~-----~~l~P~ea 184 (247)
.+.+.|...|.+.+++.+..|||+=+. |.-..||..++.. .++|+...
T Consensus 5 ~~~~~l~~~I~~L~LSvRa~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl 57 (86)
T 3k4g_A 5 EFDPILLRPVDDLELTVRSANCLXAEA-IHYIGDLVQRTEVELLXTPNLGXXSL 57 (86)
T ss_dssp CCCGGGGSBGGGGCCCHHHHHHHHHTT-CCBHHHHHHSCHHHHHTSTTCCHHHH
T ss_pred chhHHHhCcHHHhCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHhhccccCcccH
Confidence 445567788999999999999999776 6777888888433 78887644
No 4
>4hyz_A Uncharacterized protein; PF13026 family protein, DUF3887, structural genomics, joint for structural genomics, JCSG; 2.25A {Ruminococcus gnavus}
Probab=36.15 E-value=40 Score=25.62 Aligned_cols=29 Identities=17% Similarity=0.363 Sum_probs=23.5
Q ss_pred CcEEEEEecCCcceEEeeeceEEEEEecCccceeeEEE
Q psy2753 78 QCTMVTHHGKPMLTKVCTEGRLILEFTFDDLMRIKSWH 115 (247)
Q Consensus 78 ~a~~v~~y~~~~~~~V~~eG~Lr~~F~~d~~lKIe~we 115 (247)
-+.+.+.|++ |.|...+++|.++||..+-
T Consensus 85 vv~~~~~ye~---------~~~~f~i~Fd~d~kl~G~~ 113 (114)
T 4hyz_A 85 GVIIVVKYEE---------GNVNYSLAYDEDMNLVSFT 113 (114)
T ss_dssp EEEEEEEETT---------EEEEEEEEECTTSCEEEEE
T ss_pred EEEEEEEEec---------cceEEEEEECCCCcEeeeE
Confidence 3456678887 9999999999999998764
No 5
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B
Probab=19.40 E-value=77 Score=22.67 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=34.0
Q ss_pred hccCCCCCCCChhhhhhhhHHHHhhchHHHHHhhhc-----CCCCHHHH
Q psy2753 141 LTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKA-----YALSPRDC 184 (247)
Q Consensus 141 l~k~V~~~Gv~~~~~r~LeI~Eil~~Mq~Lm~f~k~-----~~l~P~ea 184 (247)
+...|.+.+++.+.+|||.=+ =|.-..||..+... .++|+...
T Consensus 7 l~~~Ie~L~LS~Ra~NcLkra-gI~Tv~dL~~~s~~dLlki~n~G~kSl 54 (73)
T 1z3e_B 7 LEMTIEELDLSVRSYNCLKRA-GINTVQELANKTEEDMMKVRNLGRKSL 54 (73)
T ss_dssp HTCBGGGSCCBHHHHHHHHHT-TCCBHHHHHTSCHHHHHTSTTCCHHHH
T ss_pred hcCcHHHhCCCHHHHHHHHHc-CCCcHHHHHcCCHHHHHHcCCCCHHHH
Confidence 446789999999999999965 47888899988443 88888543
No 6
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A
Probab=16.94 E-value=46 Score=25.37 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=36.8
Q ss_pred hhhHhhccCCCCCCCChhhhhhhhHHHHhhchHHHHHhhhc-----CCCCHHHH
Q psy2753 136 SMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKA-----YALSPRDC 184 (247)
Q Consensus 136 ~~~kql~k~V~~~Gv~~~~~r~LeI~Eil~~Mq~Lm~f~k~-----~~l~P~ea 184 (247)
.+.+-+...|.+.+++.+..|||.=+. |.-..||..++.. .|+|+...
T Consensus 17 ~~~~~l~~~Ie~L~LSvRs~NcLkrag-I~Tv~dL~~~se~dLlki~n~G~KSl 69 (98)
T 1coo_A 17 EFDPILLRPVDDLELTVRSANCLKAEA-IHYIGDLVQRTEVELLKTPNLGKKSL 69 (98)
T ss_dssp -CCHHHHSBGGGGTCCTTTHHHHHTTT-CCBHHHHHTSCHHHHTTSTTCCHHHH
T ss_pred hHHHHhcCcHHHhCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHHhcCCCCHHHH
Confidence 334445577999999999999999554 7888999998544 88888644
No 7
>2fi2_A Zinc finger protein 42; SCAN domain, ZNF-42, MZF-1, homodimer, transcription factor, structural genomics, PSI, protein structure initiative; NMR {Homo sapiens} SCOP: a.28.3.2
Probab=14.88 E-value=71 Score=24.32 Aligned_cols=24 Identities=29% Similarity=0.540 Sum_probs=19.6
Q ss_pred HhhhcCCCCHHHHHH--HHHhhhhhh
Q psy2753 172 SRHKAYALSPRDCLK--TALFQKWQR 195 (247)
Q Consensus 172 ~f~k~~~l~P~eaLk--~~lfq~~q~ 195 (247)
.|+-...-||+|||. .-|+.+|=+
T Consensus 15 ~f~y~e~~gPreaL~rLreLc~qWLr 40 (94)
T 2fi2_A 15 CFHYEEATGPQEALAQLRELCRQWLR 40 (94)
T ss_dssp SCCCCTTTCHHHHHHHHHHHHHHHHC
T ss_pred cCCCCCCCCHHHHHHHHHHHHHHHCC
Confidence 345667889999999 889999965
No 8
>2a15_A Hypothetical protein RV0760C; beta-alpha-barrel, structural genomics, PSI, protein structure initiative; 1.68A {Mycobacterium tuberculosis} SCOP: d.17.4.3 PDB: 2z76_A* 2z77_A* 2z7a_A
Probab=14.80 E-value=3.1e+02 Score=19.74 Aligned_cols=45 Identities=11% Similarity=0.144 Sum_probs=27.0
Q ss_pred HHhhcCCCCceEEEeecCC---CCeeeeecccchhhHHHHhhcccceeeee
Q psy2753 11 ATEFFEDDATLTLTFCLED---GPKRYTIGRTLIPRYFRSIFDGGITELYY 58 (247)
Q Consensus 11 V~eFFsp~a~lr~~~~~~~---~~K~FEI~~~~LPRyF~t~F~sGV~~~~~ 58 (247)
+.++|+|++++.--..... ..+. -.|...|-.||...++.. ++.+
T Consensus 28 ~~~l~a~D~v~~~p~~~~~~~~~g~~-~~G~~ai~~~~~~~~~~~--~~~~ 75 (139)
T 2a15_A 28 WLALMADDVVIEDPIGKSVTNPDGSG-IKGKEAVGAFFDTHIAAN--RLTV 75 (139)
T ss_dssp HHHTEEEEEEEESSSSSBTTBTTSSC-EESHHHHHHHHHHHTTTT--TCEE
T ss_pred HHHhcCCCEEEECCCCCCccCCCCce-eecHHHHHHHHHHhcccc--eeEE
Confidence 4468899987643111100 0111 368899999999988765 4444
No 9
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1
Probab=13.07 E-value=72 Score=23.32 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=32.5
Q ss_pred hhccCCCCCCCChhhhhhhhHHHHhhchHHHHHhhhc-----CCCCHH
Q psy2753 140 QLTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKA-----YALSPR 182 (247)
Q Consensus 140 ql~k~V~~~Gv~~~~~r~LeI~Eil~~Mq~Lm~f~k~-----~~l~P~ 182 (247)
-+...|.+.+++.+..|||.=+. |.-..||..++.. .++|+.
T Consensus 13 ~l~~~Ie~L~LS~Ra~NcLk~ag-I~Tv~dL~~~se~dLlki~n~G~k 59 (79)
T 3gfk_B 13 VLEMTIEELDLSVRSYNCLKRAG-INTVQELANKTEEDMMKVRNLGRK 59 (79)
T ss_dssp GGGCBGGGSCCBHHHHHHHHHTT-CCBHHHHTTCCHHHHTTSTTCHHH
T ss_pred HhcCcHHHhCCCHHHHHHHHHhC-CCCHHHHHhCCHHHHHHcCCCCHh
Confidence 45677999999999999999776 5677788777433 667764
No 10
>1nwd_B GAD, glutamate decarboxylase; calmodulin-peptide complex, calmodulin, dimer, binding protein/hydrolase comple; NMR {Petunia x hybrida}
Probab=12.77 E-value=95 Score=18.27 Aligned_cols=10 Identities=30% Similarity=0.574 Sum_probs=8.4
Q ss_pred hHHHHHHHHh
Q psy2753 4 NLWWDAFATE 13 (247)
Q Consensus 4 i~yW~~FV~e 13 (247)
|.-|.+||.|
T Consensus 15 itawkkfvee 24 (28)
T 1nwd_B 15 ITAWKKFVEE 24 (28)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 5679999987
Done!