Query psy7983
Match_columns 184
No_of_seqs 119 out of 335
Neff 5.4
Searched_HMMs 29240
Date Fri Aug 16 23:50:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7983.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/7983hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3ei3_A DNA damage-binding prot 100.0 1.6E-30 5.5E-35 258.1 12.1 108 76-184 1051-1158(1158)
2 1dul_A Signal recognition part 75.6 3.7 0.00013 28.1 4.2 29 144-183 34-62 (69)
3 1hq1_A Signal recognition part 66.5 6.3 0.00022 28.9 4.0 28 144-182 68-95 (105)
4 2jqe_A SRP54, signal recogniti 62.5 7.9 0.00027 29.0 3.9 28 144-182 77-104 (119)
5 2fi2_A Zinc finger protein 42; 59.5 16 0.00054 26.5 4.9 43 129-182 47-90 (94)
6 1qb2_A SRP54, human signal rec 56.3 9.8 0.00034 28.0 3.4 28 144-182 74-101 (109)
7 1y7q_A AW-1, zinc finger prote 53.3 17 0.00057 26.5 4.2 43 129-182 49-92 (98)
8 1mfq_C SRP54, signal recogniti 52.6 12 0.00042 28.5 3.5 28 144-182 87-114 (129)
9 3lhr_A Zinc finger protein 24; 52.2 23 0.0008 25.3 4.8 44 128-182 45-89 (93)
10 1jy2_P Fibrinogen gamma-B chai 30.4 15 0.0005 23.6 0.6 38 69-106 4-41 (48)
11 2b9s_A Topoisomerase I-like pr 25.9 37 0.0013 30.8 2.7 70 51-120 296-389 (432)
12 3kl4_A SRP54, signal recogniti 25.2 60 0.0021 28.8 4.0 29 144-183 397-425 (433)
13 3dm5_A SRP54, signal recogniti 23.5 67 0.0023 28.8 3.9 30 143-183 393-422 (443)
14 2ffh_A Protein (FFH); SRP54, s 23.4 67 0.0023 28.4 3.9 29 144-183 381-409 (425)
No 1
>3ei3_A DNA damage-binding protein 1; UV-damage, DDB, nucleotide excision repair, xeroderma pigmentosum, cytoplasm, DNA repair; HET: DNA PG4; 2.30A {Homo sapiens} PDB: 3ei1_A* 3ei2_A* 3ei4_A* 4a0l_A* 3e0c_A* 3i7k_A* 3i7h_A* 3i7l_A* 3i7n_A* 3i7o_A* 3i7p_A* 3i89_A* 3i8c_A* 3i8e_A* 2b5l_A 2b5m_A 2hye_A* 4a11_A* 4a0k_C* 4a0a_A* ...
Probab=99.97 E-value=1.6e-30 Score=258.14 Aligned_cols=108 Identities=55% Similarity=0.892 Sum_probs=93.0
Q ss_pred eeeeEEEEEecChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCCCCCCCcceeehhHHHHHhcCCHHHHHHHHhhc
Q psy7983 76 SFVSTGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLDLNIKDMKSIATGL 155 (184)
Q Consensus 76 s~GsIG~V~pIs~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~r~~p~kgfIDGDLIE~FL~L~~~~q~eV~~~l 155 (184)
.+|+||+++|++++.|+||..||..|++.++++||++|++||+|++.++..|++|||||||||+|++|+.++|++|++++
T Consensus 1051 ~~GsIg~l~pl~~~~~~~L~~Lq~~l~~~~~~~~gl~~~~~Rs~~~~~~~~~~~~~iDGdLle~fl~L~~~~q~~ia~~l 1130 (1158)
T 3ei3_A 1051 VNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANL 1130 (1158)
T ss_dssp TTSCEEEEEEECHHHHHHHHHHHHHHHHHSCCTTSCCHHHHHSEECSSCEECCBSEEEHHHHHGGGGSCHHHHHHHCCCC
T ss_pred cCCEEEEEEEcCHHHHHHHHHHHHHHHhhCCCCcCCCHHHhhCeecccccCCCCccCcHHHHHHHHcCCHHHHHHHHHhh
Confidence 34899999999999999999999999999999999999999999998777889999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhccC
Q psy7983 156 QITPPGSTTKRDATVDDIIKIVEDLTRIH 184 (184)
Q Consensus 156 ~~~~~~~~~~~~~svedI~k~IEeL~rlH 184 (184)
++ +.+++++++.|++||.|+||||+|||
T Consensus 1131 ~~-~~~~~~~~~~t~~ei~k~~e~l~r~h 1158 (1158)
T 3ei3_A 1131 QY-DDGSGMKREATADDLIKVVEELTRIH 1158 (1158)
T ss_dssp -------------CCHHHHHHHHHHGGGC
T ss_pred Cc-cccccccCCCCHHHHHHHHHHHhhcC
Confidence 74 45688999999999999999999999
No 2
>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=75.61 E-value=3.7 Score=28.09 Aligned_cols=29 Identities=17% Similarity=0.345 Sum_probs=24.4
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
+++++..||.|.| ++++||.++|.....|
T Consensus 34 ~~SR~~RIA~GSG-----------~~v~eVn~Llkqf~~m 62 (69)
T 1dul_A 34 KGSRKRRIAAGSG-----------MQVQDVNRLLKQFDDM 62 (69)
T ss_dssp CHHHHHHHHHHTT-----------CCHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHccCC-----------CCHHHHHHHHHHHHHH
Confidence 5789999999999 7999998888776543
No 3
>1hq1_A Signal recognition particle protein; protein-RNA complex, double helix, tetraloop, internal loop, SRP, ribonucleoprotein; HET: CCC; 1.52A {Escherichia coli} SCOP: a.36.1.1 PDB: 3lqx_A* 2pxb_A 2pxd_A 2pxe_A 2pxf_A 2pxk_A 2pxl_A 2pxp_A 2pxq_A 2pxt_A 2pxu_A 2pxv_A
Probab=66.51 E-value=6.3 Score=28.93 Aligned_cols=28 Identities=18% Similarity=0.328 Sum_probs=24.1
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
+.+++.+||.|.| ++++||.+.|.....
T Consensus 68 ~~SR~~RIA~GSG-----------~~v~eVn~LLkqf~~ 95 (105)
T 1hq1_A 68 KGSRKRRIAAGSG-----------MQVQDVNRLLKQFDD 95 (105)
T ss_dssp CHHHHHHHHHHHT-----------CCHHHHHHHHHHHHH
T ss_pred CHHHHHHHHccCC-----------CCHHHHHHHHHHHHH
Confidence 6789999999999 799999888876654
No 4
>2jqe_A SRP54, signal recognition 54 kDa protein; AF54, structure, solution, signaling protein; NMR {Archaeoglobus fulgidus}
Probab=62.52 E-value=7.9 Score=29.02 Aligned_cols=28 Identities=11% Similarity=0.278 Sum_probs=24.1
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
+.+++.+||.|.| ++++||.+.|.....
T Consensus 77 ~~SR~~RIA~GSG-----------~~v~eVn~LLkqf~~ 104 (119)
T 2jqe_A 77 DSSRIRRIAIGSG-----------TSPQEVKELLNYYKT 104 (119)
T ss_dssp CHHHHHHHHHHHT-----------SCHHHHHHHHHHHHH
T ss_pred CHHHHHHHHccCC-----------CCHHHHHHHHHHHHH
Confidence 6899999999999 799999888876654
No 5
>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=59.49 E-value=16 Score=26.48 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=35.9
Q ss_pred cceeehhHHHHHhc-CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 129 EGFIDGDLIESFLD-LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 129 kgfIDGDLIE~FL~-L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
.-++|==.+|+||. ||.+.|..|-..-- -|.++.+..+|+|.+
T Consensus 47 EQIlElLVLEQFL~iLP~eiq~wV~~~~P-----------~s~eeav~lvEdl~~ 90 (94)
T 2fi2_A 47 EQMLELLVLEQFLGALPPEIQARVQGQRP-----------GSPEEAAALVDGLRR 90 (94)
T ss_dssp HHHHHHHHHHHHHHHSCHHHHHHHHHHCC-----------CSHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHhCcHHHHHHHHhcCC-----------CcHHHHHHHHHHHHh
Confidence 45788888999996 79999999887653 589999999999975
No 6
>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=56.34 E-value=9.8 Score=28.04 Aligned_cols=28 Identities=14% Similarity=0.338 Sum_probs=23.7
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
+++++.+||.|.| ++++||.+.|.....
T Consensus 74 ~~SR~~RIA~GSG-----------~~v~eVn~LLkqf~~ 101 (109)
T 1qb2_A 74 QPGRIQRVARGSG-----------VSTRDVQELLTQYTK 101 (109)
T ss_dssp STHHHHHHHHHTT-----------CCHHHHHHHHHHHHH
T ss_pred chHHHHHHHccCC-----------CCHHHHHHHHHHHHH
Confidence 3689999999999 799999988877654
No 7
>1y7q_A AW-1, zinc finger protein 174; SCAN domain, retroviral capsid C-terminal domain, dimer, C2H2 zinc finger associated, transcription; NMR {Homo sapiens} SCOP: a.28.3.2
Probab=53.30 E-value=17 Score=26.52 Aligned_cols=43 Identities=23% Similarity=0.333 Sum_probs=34.8
Q ss_pred cceeehhHHHHHhc-CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 129 EGFIDGDLIESFLD-LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 129 kgfIDGDLIE~FL~-L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
.-++|==.+|+||. ||.+.|..|-..- .-|.++.+..+|+|.+
T Consensus 49 EQIlElLVLEQFL~iLP~eiq~wV~~~~-----------P~s~eeav~lvEdl~~ 92 (98)
T 1y7q_A 49 EQILELLVMEQFLTILPEEIQARVRHRC-----------LMSSKEIVTLVEDFHR 92 (98)
T ss_dssp HHHHHHHHHHHHHHHSCTHHHHHHHTSC-----------CCCHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHhccC-----------CCcHHHHHHHHHHHHH
Confidence 45778888999996 7989988876644 2589999999999876
No 8
>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=52.58 E-value=12 Score=28.45 Aligned_cols=28 Identities=14% Similarity=0.338 Sum_probs=23.9
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
+++++.+||.|.| ++++||.+.|.....
T Consensus 87 ~~SRk~RIA~GSG-----------~~v~eVn~LLkqf~q 114 (129)
T 1mfq_C 87 QPGRIQRVARGSG-----------VSTRDVQELLTQYTK 114 (129)
T ss_dssp CTHHHHHHHHHTT-----------CCHHHHHHHHHHHHH
T ss_pred ChHHHHHHHccCC-----------CCHHHHHHHHHHHHH
Confidence 5789999999999 799999888877654
No 9
>3lhr_A Zinc finger protein 24; SCAN domain, protein structure initiative, center for eukary structural genomics, PSI-2, CESG, nucleus, phosphoprotein; 1.90A {Homo sapiens} SCOP: a.28.3.0
Probab=52.20 E-value=23 Score=25.31 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=34.0
Q ss_pred CcceeehhHHHHHhc-CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 128 CEGFIDGDLIESFLD-LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 128 ~kgfIDGDLIE~FL~-L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
..-+++==.+|+||. ||.+.|..|-..- .-|-++....+|+|.+
T Consensus 45 KEQileLLVLEQFL~ilP~e~q~wv~~~~-----------p~s~~eav~l~E~l~~ 89 (93)
T 3lhr_A 45 KEQILELVVLEQFVAILPKELQTWVRDHH-----------PENGEEAVTVLEDLES 89 (93)
T ss_dssp HHHHHHHHHHHHHHHTSCHHHHHHHHHTC-----------CSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHhC-----------CCCHHHHHHHHHHHHh
Confidence 356778888999988 6877777776644 2488899999999875
No 10
>1jy2_P Fibrinogen gamma-B chain; fragment E, disulfide bonds, asymmetry, coiled- coil, beta-sheet, blood clotting; 1.40A {Bos taurus} SCOP: h.1.8.1 PDB: 1jy3_P 2a45_I*
Probab=30.37 E-value=15 Score=23.55 Aligned_cols=38 Identities=16% Similarity=0.111 Sum_probs=31.0
Q ss_pred ccCcccceeeeEEEEEecChHHHHHHHHHHHHHHhhcC
Q psy7983 69 EADASLNSFVSTGLVTQISPELYSFLFDLQERLAQTIR 106 (184)
Q Consensus 69 ~~~~~~Ts~GsIG~V~pIs~~~y~~L~~LQ~~L~~~v~ 106 (184)
..++||..+.++|..+|-.=-.-+||+..|..+.+.+.
T Consensus 4 t~~~~Ci~d~rFGsYCPTTCGiadfL~~Yq~~vd~dL~ 41 (48)
T 1jy2_P 4 TRDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLR 41 (48)
T ss_dssp -CCSSCCSBTTTBCEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccCcCCccccHHHHhcccccchhhHHH
Confidence 34569999999999999988889999999987766543
No 11
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA complex; HET: DNA; 2.27A {Leishmania donovani}
Probab=25.90 E-value=37 Score=30.75 Aligned_cols=70 Identities=20% Similarity=0.353 Sum_probs=43.7
Q ss_pred cccccceeEEEeeeeccc--ccCc-----ccceee-eEEEEEecChHHHHHHHHHHHH---------------HHhhcCC
Q psy7983 51 YQESSQTFGVITTRIDIQ--EADA-----SLNSFV-STGLVTQISPELYSFLFDLQER---------------LAQTIRS 107 (184)
Q Consensus 51 ~~~qs~tfa~~s~~~~v~--~~~~-----~~Ts~G-sIG~V~pIs~~~y~~L~~LQ~~---------------L~~~v~~ 107 (184)
|-++.+|+|.||++..=+ .++. |.--+| .--.-+.+++..|+.|..++.. +.++++.
T Consensus 296 Ya~endTvGl~TLR~eHV~l~~~~~V~FdF~GKdgir~~~~V~vD~~l~k~L~~~~~~K~Pg~~LF~~l~s~~lN~yL~e 375 (432)
T 2b9s_A 296 GEDEADTVGCCSLRVEHIQLMPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTRRKSPGMDIFDQLNPTQLNDHLKS 375 (432)
T ss_dssp CTTSCCCCCGGGCBGGGEEECTTSEEEEEEECGGGCEEEEEEECCHHHHHHHHHHHTTCCTTSBTTTTCCHHHHHHHHTT
T ss_pred ccccCCCEeecccccccEEEcCCCeEEEEEecCCceEEEEEEecCHHHHHHHHHHHhCCCChhHhcccCCHHHHHHHHHH
Confidence 446899999999997732 2211 211111 2223356688999999888754 3444433
Q ss_pred -CcCCCCcccceee
Q psy7983 108 -VGRIEHSFWRSFN 120 (184)
Q Consensus 108 -vGGl~h~~yRs~~ 120 (184)
.||++-+.||.|.
T Consensus 376 lmgg~TAKdFRTw~ 389 (432)
T 2b9s_A 376 FMDGLSAKVFRTYN 389 (432)
T ss_dssp TSTTCCTTHHHHHH
T ss_pred HhCCCceeeeccCc
Confidence 3688888888764
No 12
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Probab=25.18 E-value=60 Score=28.85 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=24.5
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
+.+++++|+.|-| ++++||.+.|.....|
T Consensus 397 ~~sr~~ria~gsg-----------~~~~~v~~ll~~~~~~ 425 (433)
T 3kl4_A 397 DKSRMRRIAEGSG-----------LEVEEVRELLEWYNNM 425 (433)
T ss_dssp CHHHHHHHHHHHT-----------CCHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHccCC-----------CCHHHHHHHHHHHHHH
Confidence 7899999999999 7999998888766543
No 13
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}
Probab=23.48 E-value=67 Score=28.76 Aligned_cols=30 Identities=20% Similarity=0.472 Sum_probs=24.9
Q ss_pred CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 143 LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 143 L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
++.+++++|+.|-| ++++||.+.|.....|
T Consensus 393 ~~~sr~~ria~gsg-----------~~~~~v~~ll~~~~~~ 422 (443)
T 3dm5_A 393 INYSRIKRIARGSG-----------TSTKDVKELLDQYRQM 422 (443)
T ss_dssp CCHHHHHHHHHHHT-----------SCHHHHHHHHHHHHHH
T ss_pred cChHHHHHHHccCC-----------CCHHHHHHHHHHHHHH
Confidence 47899999999999 7999998888766543
No 14
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A
Probab=23.41 E-value=67 Score=28.43 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=24.0
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
+.+++++|+.|-| ++++||.+.|.....|
T Consensus 381 ~~sr~~ria~gsg-----------~~~~~v~~ll~~~~~~ 409 (425)
T 2ffh_A 381 NGSRRKRIAKGSG-----------TSVQEVNRFIKAFEEM 409 (425)
T ss_dssp CHHHHHHHHHHHT-----------SCHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHccCC-----------CCHHHHHHHHHHHHHH
Confidence 6789999999999 7999998888766543
Done!