Query psy3482
Match_columns 279
No_of_seqs 171 out of 402
Neff 4.3
Searched_HMMs 29240
Date Fri Aug 16 17:52:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3482.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/3482hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3r8s_X 50S ribosomal protein L 99.9 3.9E-23 1.3E-27 159.0 5.3 70 82-154 1-70 (77)
2 3bbo_Y Ribosomal protein L28; 99.8 1.2E-21 4E-26 167.1 -1.0 76 76-154 69-144 (151)
3 2zjr_U 50S ribosomal protein L 99.7 9.5E-19 3.2E-23 135.9 -0.2 66 81-152 1-79 (81)
4 2jz6_A 50S ribosomal protein L 99.7 6.8E-17 2.3E-21 124.4 5.9 60 81-143 6-65 (77)
5 2jl6_1 50S ribosomal protein L 99.6 8.7E-17 3E-21 126.8 -1.3 67 81-151 1-79 (89)
6 3v2d_1 50S ribosomal protein L 99.6 8.1E-16 2.8E-20 123.1 3.8 84 81-173 1-96 (98)
7 4fz4_A 0197-18KD, uncharacteri 20.1 30 0.001 29.5 0.8 44 148-192 62-107 (154)
8 2kw0_A CCMH protein; oxidoredu 14.4 2E+02 0.0068 22.2 4.2 38 160-200 38-75 (90)
9 3h7h_A Transcription elongatio 13.2 85 0.0029 25.5 1.9 30 21-56 87-116 (120)
10 2hl7_A Cytochrome C-type bioge 12.2 2.4E+02 0.0084 21.3 4.1 38 160-200 41-78 (84)
No 1
>3r8s_X 50S ribosomal protein L28; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 3j01_X 3j0t_Z* 3j0w_Z* 3j0y_Z* 3j11_Z* 3j12_Z* 3j14_Z* 3j19_X 3oas_X 3oat_X* 2i2t_X* 3ofd_X 3ofc_X 3ofr_X* 3ofz_X* 3og0_X 3ofq_X ...
Probab=99.87 E-value=3.9e-23 Score=159.03 Aligned_cols=70 Identities=17% Similarity=0.345 Sum_probs=67.2
Q ss_pred ccccccccceeecccccCCCCCCCCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhhccChhHHhhcC
Q psy3482 82 QDLGIWGGESVIEGYRRPAHKYETQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHEHYGFDEYLLQT 154 (279)
Q Consensus 82 s~~GL~gGk~i~~Gn~vS~s~~~~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk~GGlD~YLLkT 154 (279)
|+.|...|+++++||+||||+ ++|+|+|.||||++++||+.++++++|+|||+|||+||+. |||+||+..
T Consensus 1 sr~C~itGK~~~~Gn~VShs~--~kTkR~~~PNlq~~r~~~~~~~r~~rlrVst~~LRti~k~-Gld~~l~~~ 70 (77)
T 3r8s_X 1 SRVCQVTGKRPVTGNNRSHAL--NATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKK-GIDTVLAEL 70 (77)
T ss_dssp CCCCTTTCCCCEEEEEECSSC--CEEEEEECCCEEEEEEEEGGGTEEEEEEEEHHHHHHHHHH-CHHHHHHHH
T ss_pred CCEeeeCCCccccCceEeccC--CccCceecCccEEEEEEECCCCEEEEEEEEcceEeeeccc-CHHHHHHHH
Confidence 578999999999999999997 9999999999999999999999999999999999999999 999999753
No 2
>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=99.81 E-value=1.2e-21 Score=167.08 Aligned_cols=76 Identities=11% Similarity=0.207 Sum_probs=67.1
Q ss_pred CCCCccccccccccceeecccccCCCCCCCCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhhccChhHHhhcC
Q psy3482 76 SKYTLEQDLGIWGGESVIEGYRRPAHKYETQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHEHYGFDEYLLQT 154 (279)
Q Consensus 76 ~~~pk~s~~GL~gGk~i~~Gn~vS~s~~~~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk~GGlD~YLLkT 154 (279)
.+++..++.|.++|+++++||+|||++ +||+|+|+||||++++|++.++++++|+||++|||+||+. |||+||++.
T Consensus 69 ~~~~mMsR~C~itGK~p~~GNnVSHS~--~KTKRrw~PNLQkvri~~~~g~r~vrlrVsTr~LRTikk~-GlD~~l~~~ 144 (151)
T 3bbo_Y 69 SLQPVARRICPFTGKKSNRANKVSHSN--HKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIEKN-GLDAVAKKA 144 (151)
T ss_dssp -------CCCCCSCCTTCCCCCCEECC--SSSCCEECCCCCCCCBCCCTTSSCCCBCCCSSSTTTTTTS-TTTCSCCSS
T ss_pred ccccchhceeeccCcccccCCeeeecC--CccCceeccccEEEEEEECCCCEEEEEEEEchheeehhhh-hHHHHHHHh
Confidence 446668889999999999999999997 9999999999999999999999999999999999999999 999999864
No 3
>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* 3pio_U* 3pip_U*
Probab=99.70 E-value=9.5e-19 Score=135.90 Aligned_cols=66 Identities=6% Similarity=-0.098 Sum_probs=56.5
Q ss_pred cccccccccceeecccccCC-------------CCCCCCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhhccCh
Q psy3482 81 EQDLGIWGGESVIEGYRRPA-------------HKYETQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHEHYGF 147 (279)
Q Consensus 81 ~s~~GL~gGk~i~~Gn~vS~-------------s~~~~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk~GGl 147 (279)
+|+.|...|+++++||+||| ++ ++|+|+|+||||++++| +++++++|+||++|||+||+ ||
T Consensus 1 Msr~C~itGK~~~~Gn~vshrGkak~~Gg~~s~s~--~kTkR~~~PNlq~vr~~--~~g~~~~l~Vst~~LRti~k--Gl 74 (81)
T 2zjr_U 1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTT--GITKRVQRANLHKKAIR--ENGQVKTVWLSANALRTLSK--GP 74 (81)
T ss_dssp -------CCSSSCCCCCCCCCCEESCCCTTTCSCC--EECCCCCCCCCCCCCCC--CSSSCCCCCCCHHHHHHHHS--SC
T ss_pred CCCEeecCCCccccCCeeeeccccccccccchhhC--CccCceecccceEEEEE--ECCEEEEEEEEcceeeeech--hH
Confidence 47789999999999999999 86 99999999999999999 58999999999999999999 99
Q ss_pred hHHhh
Q psy3482 148 DEYLL 152 (279)
Q Consensus 148 D~YLL 152 (279)
|+++.
T Consensus 75 d~~~~ 79 (81)
T 2zjr_U 75 YKGIE 79 (81)
T ss_dssp CSSCC
T ss_pred HHHHh
Confidence 99874
No 4
>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1
Probab=99.66 E-value=6.8e-17 Score=124.45 Aligned_cols=60 Identities=10% Similarity=0.005 Sum_probs=57.3
Q ss_pred cccccccccceeecccccCCCCCCCCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhh
Q psy3482 81 EQDLGIWGGESVIEGYRRPAHKYETQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHE 143 (279)
Q Consensus 81 ~s~~GL~gGk~i~~Gn~vS~s~~~~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk 143 (279)
+|+.|.+.|+++++||+|||++ ++|+|+|+||||++++|++. +++++|+||++|||++.-
T Consensus 6 Msr~C~itGK~~~~Gn~VSHS~--~kTkR~~~PNLq~vr~~~~~-g~~~rl~Vst~~LRtgkv 65 (77)
T 2jz6_A 6 MAKRCEVCGKAPRSGNTVSHSD--KKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKSGKV 65 (77)
T ss_dssp CCCCCTTTCCCCCCCCCCCCSC--CCCSSSCBTTEEEEEEEETT-TEEEEEEEEHHHHHHCCS
T ss_pred eeeeeeecCCccccCCeEeecC--CccCcccccceEEEEEEecC-CcEEEEEEEhHHeeeccE
Confidence 7899999999999999999997 99999999999999999976 999999999999999873
No 5
>2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25; methylation, translation, paromomycin, tRNA-binding, tRNA, zinc, mRNA, ribosome, repressor, RNA-binding; 3.45A {Thermus thermophilus} PDB: 2jl8_1
Probab=99.58 E-value=8.7e-17 Score=126.79 Aligned_cols=67 Identities=10% Similarity=-0.029 Sum_probs=59.5
Q ss_pred cccccccccceeecccccCCCCCC------------CCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhhccChh
Q psy3482 81 EQDLGIWGGESVIEGYRRPAHKYE------------TQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHEHYGFD 148 (279)
Q Consensus 81 ~s~~GL~gGk~i~~Gn~vS~s~~~------------~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk~GGlD 148 (279)
+|+.|...|+++++||+|||++ + ++|+|+|+||||++++|+ .+++++|+||+++||+||+. |++
T Consensus 1 Msr~C~itGK~~~~Gn~VShs~-~ak~~GGvG~k~t~kTkR~f~PNLqkvr~~~--~g~~~rl~Vstk~LRtI~k~-g~~ 76 (89)
T 2jl6_1 1 MSKVCEISGKRPIVANSIQRRG-KAKREGGVGKKTTGISKRRQYPNLQKVRVRV--AGQEITFRVAASHIPKVYEL-VER 76 (89)
T ss_dssp --CCCSSSCCCCEEEEEEEEES-CCTTTSSSCCEEEEEEEEEECCCBCCBCCEE--TTEECCBCCBGGGHHHHHHH-HSC
T ss_pred CCCEeecCCCccccCceEeecC-ccccccccccccCCccceEEccccEEEEEEE--CCEEEEEEEEChhheEcccc-chh
Confidence 4789999999999999999996 2 499999999999999999 49999999999999999999 766
Q ss_pred HHh
Q psy3482 149 EYL 151 (279)
Q Consensus 149 ~YL 151 (279)
..+
T Consensus 77 a~~ 79 (89)
T 2jl6_1 77 AAA 79 (89)
T ss_dssp CCC
T ss_pred HHH
Confidence 543
No 6
>3v2d_1 50S ribosomal protein L28; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 2wrj_1 2wrl_1 2wro_1 2wrr_1 2x9s_1 2x9u_1 2xqe_1 2xtg_1 2xux_1 2y0v_1 2y0x_1 ...
Probab=99.57 E-value=8.1e-16 Score=123.07 Aligned_cols=84 Identities=14% Similarity=0.122 Sum_probs=71.7
Q ss_pred cccccccccceeecccccCCCCCC------------CCCCcccccceeEEEEeEeccCcEeEEeeehhHHhhhhhccChh
Q psy3482 81 EQDLGIWGGESVIEGYRRPAHKYE------------TQPPEYWVPHLLDHIVYSEILDKYLNVPVTQRTVDLIHEHYGFD 148 (279)
Q Consensus 81 ~s~~GL~gGk~i~~Gn~vS~s~~~------------~KtrR~w~PNL~~k~lySeiLdk~i~l~VTtraLrtIdk~GGlD 148 (279)
+|+.|...|+++++||+|||++ + ++|+|+|.||||++++|+ .+++++++||++|||+||+.
T Consensus 1 Msr~C~itGK~p~~Gn~VShs~-~Ak~~GGvG~k~t~kTkR~f~PNLqkvr~~~--~G~~~rlrVst~~LRtI~~~---- 73 (98)
T 3v2d_1 1 MSKVCEISGKRPIVANSIQRRG-KAKREGGVGKKTTGISKRRQYPNLQKVRVRV--AGQEITFRVAASHIPKVYEL---- 73 (98)
T ss_dssp -CCCCTTTCCCCEEEEEEEEEE-ECGGGTSSEEEEEEEEEEEECCCEEEEEEEE--TTEEEEEEEEGGGHHHHHHH----
T ss_pred CCCeeecCCCccccCccEeccC-ccccccccccccCCcccceeccceEEEEEEE--CCEEEEEEEEchhheehhhh----
Confidence 4789999999999999999996 2 499999999999999999 49999999999999999853
Q ss_pred HHhhcCCccccCCHHHHHHHHHHHH
Q psy3482 149 EYLLQTRACNLNSLIACKIKRKMLL 173 (279)
Q Consensus 149 ~YLLkT~~~~L~S~~g~~LKr~Il~ 173 (279)
+-..+.-+|.+...-++|.++|+
T Consensus 74 --verakg~~~~~l~~k~~~~~~~~ 96 (98)
T 3v2d_1 74 --VERAKGLKLEGLSPKEIKKELLK 96 (98)
T ss_dssp --HHHGGGSCCSSCCHHHHHHHHHH
T ss_pred --hhhhhcccccCCCHHHHHHHHHh
Confidence 44455667778888888887765
No 7
>4fz4_A 0197-18KD, uncharacterized protein conserved in bacteria; surface antigen, immune system; 2.44A {Streptococcus suis}
Probab=20.11 E-value=30 Score=29.49 Aligned_cols=44 Identities=20% Similarity=0.280 Sum_probs=32.8
Q ss_pred hHHhhcCCccccCCHHHHHHHHHHHHHHhcc--CCCCCChHhHHHHH
Q psy3482 148 DEYLLQTRACNLNSLIACKIKRKMLLALYDK--TLYPDDETKRETIY 192 (279)
Q Consensus 148 D~YLLkT~~~~L~S~~g~~LKr~Il~~la~~--~l~p~d~~k~~~i~ 192 (279)
|.+..+.-..+| -.+|..++..+|.+.... .-||+|++-...+-
T Consensus 62 d~~~~kk~~~dL-~dFg~h~k~E~~tRqVa~YrkKYp~n~eIe~eyk 107 (154)
T 4fz4_A 62 DDKFFHKVKGDL-NDFKYQIKVENYIRQVAELRKKYPGDNTIEEEYN 107 (154)
T ss_dssp TCTTHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHSCSCHHHHHHHH
T ss_pred hHHHHHHHHhHH-HHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHH
Confidence 444444445566 678999999999998887 78999997775553
No 8
>2kw0_A CCMH protein; oxidoreductase, cytochrome C maturation; NMR {Escherichia coli}
Probab=14.41 E-value=2e+02 Score=22.19 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHHhccCCCCCChHhHHHHHHHhhhhcc
Q psy3482 160 NSLIACKIKRKMLLALYDKTLYPDDETKRETIYNKYKHYLE 200 (279)
Q Consensus 160 ~S~~g~~LKr~Il~~la~~~l~p~d~~k~~~i~~kyk~f~~ 200 (279)
.+.++.+||.+|...++.+. +|.+-.+.+.+.|-+|+.
T Consensus 38 nA~iA~dlR~~Vre~l~~G~---Sd~eI~~~mv~RYGdfVl 75 (90)
T 2kw0_A 38 NSMIATDLRQKVYELMQEGK---SKKEIVDYMVARYGNFVT 75 (90)
T ss_dssp CCHHHHHHHHHHHHHHHHTC---CHHHHHHHHHHHHTTTCB
T ss_pred CcHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHhcCCeEE
Confidence 36899999999999998883 366777777899999886
No 9
>3h7h_A Transcription elongation factor SPT4; helices surrounding beta sheet, activator, ME binding, nucleus, repressor, transcription regulation; 1.55A {Homo sapiens}
Probab=13.20 E-value=85 Score=25.51 Aligned_cols=30 Identities=13% Similarity=0.336 Sum_probs=23.2
Q ss_pred ccchhhhhcCcHHHHHHHHHHhhcCCCCcccccCCc
Q psy3482 21 AFDTEIASKLPESYRKFYAEWKMEKPKPVHYVEEPG 56 (279)
Q Consensus 21 ~~~~gi~~rLP~~Y~k~~~ew~~~~p~~Vhy~p~~~ 56 (279)
.+---|..+||++....+++ . -|+|+|..+
T Consensus 87 ~YAlkV~g~lp~~i~~~le~-~-----gi~y~prd~ 116 (120)
T 3h7h_A 87 VYAVSVTGRLPQGIVRELKS-R-----GVAYKSRDT 116 (120)
T ss_dssp EEEEEECCCCCHHHHHHHHH-T-----TCCCCCCCC
T ss_pred eEEEEecCcCCHHHHHHHHH-c-----CCeeeCCCC
Confidence 33335667999999999988 3 789999854
No 10
>2hl7_A Cytochrome C-type biogenesis protein CCMH; three-helices bundle, oxidoreductase; HET: PG4; 1.70A {Pseudomonas aeruginosa}
Probab=12.23 E-value=2.4e+02 Score=21.29 Aligned_cols=38 Identities=16% Similarity=0.343 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHHHhccCCCCCChHhHHHHHHHhhhhcc
Q psy3482 160 NSLIACKIKRKMLLALYDKTLYPDDETKRETIYNKYKHYLE 200 (279)
Q Consensus 160 ~S~~g~~LKr~Il~~la~~~l~p~d~~k~~~i~~kyk~f~~ 200 (279)
.+.++.+||.+|...++.+. +|.+-.+.+.+.|-+|+.
T Consensus 41 na~iA~dlR~~V~~~l~~G~---sd~eI~~~~v~RYG~fVl 78 (84)
T 2hl7_A 41 NAPIAADLRKQIYGQLQQGK---SDGEIVDYMVARYGDFVR 78 (84)
T ss_dssp CSHHHHHHHHHHHHHHHHTC---CHHHHHHHHHHHHTTTCE
T ss_pred CcHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHhcCCeee
Confidence 36899999999999998873 366667777789998875
Done!