Query 030255
Match_columns 180
No_of_seqs 14 out of 16
Neff 1.6
Searched_HMMs 29240
Date Mon Mar 25 17:41:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030255.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/030255hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3r8s_3 50S ribosomal protein L 97.9 5.8E-06 2E-10 57.0 2.9 34 146-179 2-35 (64)
2 3v2d_8 50S ribosomal protein L 97.8 6.3E-06 2.2E-10 57.1 2.2 34 146-179 3-36 (65)
3 2zjr_3 50S ribosomal protein L 97.7 1.6E-05 5.3E-10 55.4 2.0 34 146-179 3-36 (66)
4 3bbo_5 Ribosomal protein L35; 97.4 5.6E-05 1.9E-09 60.7 2.0 36 144-179 89-124 (159)
5 4gmn_B 60S ribosomal protein L 27.9 7.6 0.00026 26.2 -1.1 25 142-173 4-28 (49)
6 3f14_A Uncharacterized NTF2-li 22.5 28 0.00095 22.7 0.9 10 161-170 100-109 (112)
7 3u5c_f 40S ribosomal protein S 20.9 60 0.002 24.2 2.6 39 130-170 81-119 (152)
8 4aj5_1 SKA3, spindle and kinet 18.8 37 0.0013 25.4 1.0 13 37-49 4-16 (101)
9 3dmc_A NTF2-like protein; stru 17.7 34 0.0012 23.4 0.5 22 148-170 103-125 (134)
10 2xzm_9 RPS31E; ribosome, trans 14.4 90 0.0031 24.6 2.3 38 131-170 77-114 (189)
No 1
>3r8s_3 50S ribosomal protein L35; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ...
Probab=97.90 E-value=5.8e-06 Score=57.03 Aligned_cols=34 Identities=26% Similarity=0.385 Sum_probs=31.8
Q ss_pred eccccccccccceecCCcceeeeccccccccccC
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
|||..++.+.||+.+.+|+|.|+++|++|...-|
T Consensus 2 KmKT~~~a~KRFk~TgsGKikr~~a~k~H~l~kK 35 (64)
T 3r8s_3 2 KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKK 35 (64)
T ss_dssp CCCCCTTTTTTCEECSSSCEEEECSSCSSSCTTS
T ss_pred CCccchhhhheeEEcCCCCEEeccCCCCCCccCC
Confidence 7999999999999999999999999999987654
No 2
>3v2d_8 50S ribosomal protein L35; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ...
Probab=97.83 E-value=6.3e-06 Score=57.08 Aligned_cols=34 Identities=35% Similarity=0.437 Sum_probs=31.9
Q ss_pred eccccccccccceecCCcceeeeccccccccccC
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
|||..++.+.||+.+++|+|.||++|++|...-|
T Consensus 3 KmKT~~ga~KRFk~TgsGKikr~~a~k~H~l~kK 36 (65)
T 3v2d_8 3 KMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQK 36 (65)
T ss_dssp CCCCCHHHHTTEEECTTSCEEEECSSCSSCCTTS
T ss_pred CcccchhhhheeEEcCCCCEEeccCCCCCCccCC
Confidence 7999999999999999999999999999987654
No 3
>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 3pio_3* 3pip_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 ...
Probab=97.66 E-value=1.6e-05 Score=55.35 Aligned_cols=34 Identities=35% Similarity=0.492 Sum_probs=31.7
Q ss_pred eccccccccccceecCCcceeeeccccccccccC
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
|||..++.+.||+.+.+|+|.||++|++|...-|
T Consensus 3 KmKT~~gaaKRFk~TgsGKikr~~a~k~H~l~kK 36 (66)
T 2zjr_3 3 KMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGK 36 (66)
T ss_pred CcccchhhhheeEEcCCCcEEeccCCCccCcccC
Confidence 8999999999999999999999999999987644
No 4
>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=97.38 E-value=5.6e-05 Score=60.72 Aligned_cols=36 Identities=33% Similarity=0.466 Sum_probs=32.1
Q ss_pred eeeccccccccccceecCCcceeeeccccccccccC
Q 030255 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 144 K~KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
..|||..++.+.||+.+.+|+|.||++||+|...-|
T Consensus 89 MPKMKThsgAaKRFKvTgSGKiKR~kAgkrHiLtkK 124 (159)
T 3bbo_5 89 GYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKK 124 (159)
T ss_dssp --CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSC
T ss_pred CcccccchhhhheeEEcCCccEEeccCCCCCCcCcC
Confidence 789999999999999999999999999999987654
No 5
>4gmn_B 60S ribosomal protein L5-like protein; ARM, heat, solenoid, linear motif, nuclear transport, chaper ribosome assembly, RPL11, KAP104; 2.95A {Chaetomium thermophilum}
Probab=27.94 E-value=7.6 Score=26.23 Aligned_cols=25 Identities=40% Similarity=0.634 Sum_probs=16.5
Q ss_pred ceeeeccccccccccceecCCcceeeeccccc
Q 030255 142 VKKIKMKSYSSYKSRFRTMNDGQVRRWHEGKR 173 (180)
Q Consensus 142 vKK~KiK~ySSyK~RFR~m~dG~irRwr~GKr 173 (180)
||-+|-|+|. .||++ ++||-||||-
T Consensus 4 vKvvKnkaYf---kRyQv----kfRRRREGKT 28 (49)
T 4gmn_B 4 HKLVKNSAYY---SRFQT----KFKRRRQGKT 28 (49)
T ss_pred eeeehhHHHH---HHHhh----HHhhhhcccc
Confidence 4556666664 47764 5788888874
No 6
>3f14_A Uncharacterized NTF2-like protein; YP_680363.1, NTF2-like protein of unknown function, structur genomics; HET: MSE TRS PGE; 1.45A {Cytophaga hutchinsonii atcc 33406}
Probab=22.50 E-value=28 Score=22.71 Aligned_cols=10 Identities=0% Similarity=0.232 Sum_probs=8.4
Q ss_pred CCcceeeecc
Q 030255 161 NDGQVRRWHE 170 (180)
Q Consensus 161 ~dG~irRwr~ 170 (180)
.||+|.+|++
T Consensus 100 ~dGkI~e~~~ 109 (112)
T 3f14_A 100 ENDTIKTITS 109 (112)
T ss_dssp ETTEEEEEEE
T ss_pred eCCEEEEEEE
Confidence 3899999985
No 7
>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f
Probab=20.88 E-value=60 Score=24.16 Aligned_cols=39 Identities=10% Similarity=0.097 Sum_probs=25.6
Q ss_pred cccCCCCCccccceeeeccccccccccceecCCcceeeecc
Q 030255 130 KRRKPVTPVTSKVKKIKMKSYSSYKSRFRTMNDGQVRRWHE 170 (180)
Q Consensus 130 K~rkP~TP~~SKvKK~KiK~ySSyK~RFR~m~dG~irRwr~ 170 (180)
|+.--.||-..|-++.|+|. ..-.-|.+..||+|.|-|+
T Consensus 81 kKk~~t~Pkk~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 119 (152)
T 3u5c_f 81 KXXXXXXXXXXXXXXXXXXX--XVLSYYKVDAEGKVTKLRR 119 (152)
T ss_dssp -CCCCCCCSCCCCCCCCCCC--CCCCCSEECSSSCEECCSC
T ss_pred cccccccccccccccccccc--ceeeEEEEccCCeEEECcC
Confidence 34456778777776666665 3334577888999987654
No 8
>4aj5_1 SKA3, spindle and kinetochore-associated protein 3; cell cycle, SKA complex, mitosis, cell division, kinetochore microtubule attachment; 3.32A {Homo sapiens}
Probab=18.76 E-value=37 Score=25.44 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=11.3
Q ss_pred HHHHHHhhhhccc
Q 030255 37 MQRLCNKLRTLTL 49 (180)
Q Consensus 37 MqrlctKLRs~a~ 49 (180)
...+|-|||+||+
T Consensus 4 ~~~Ff~KLR~La~ 16 (101)
T 4aj5_1 4 IRSFCGKLRSLAS 16 (101)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4689999999986
No 9
>3dmc_A NTF2-like protein; structural genomics, joint center for STR genomics, JCSG, protein structure initiative, PSI-2, unknow function; 1.65A {Anabaena variabilis atcc 29413} SCOP: d.17.4.10
Probab=17.72 E-value=34 Score=23.43 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=15.2
Q ss_pred cccc-cccccceecCCcceeeecc
Q 030255 148 KSYS-SYKSRFRTMNDGQVRRWHE 170 (180)
Q Consensus 148 K~yS-SyK~RFR~m~dG~irRwr~ 170 (180)
++|. .|-.-|+ +.||+|.+||+
T Consensus 103 ~~y~~~~~~~f~-v~dGkI~~~r~ 125 (134)
T 3dmc_A 103 KPYKNRVAVSFD-VRGDKICSYRE 125 (134)
T ss_dssp EEEEEEEEEEEE-EETTEEEEEEE
T ss_pred cEeeccEEEEEE-EECCEEEEEEE
Confidence 4454 4556664 46999999986
No 10
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9
Probab=14.40 E-value=90 Score=24.57 Aligned_cols=38 Identities=16% Similarity=0.269 Sum_probs=27.1
Q ss_pred ccCCCCCccccceeeeccccccccccceecCCcceeeecc
Q 030255 131 RRKPVTPVTSKVKKIKMKSYSSYKSRFRTMNDGQVRRWHE 170 (180)
Q Consensus 131 ~rkP~TP~~SKvKK~KiK~ySSyK~RFR~m~dG~irRwr~ 170 (180)
+..-.||-..|-++.|+|. .-+|. |++..||+|.|-+.
T Consensus 77 K~~~~tPK~~k~~kKkvkl-~~Lk~-y~Vd~~Gkv~~~~~ 114 (189)
T 2xzm_9 77 KKSYTTKKKTKHRHVHTKL-GALAF-YKLENNGKVSLQQK 114 (189)
T ss_dssp CCCCCSSSCCCCCCCCCCC-SCCCC-EEEETTTEEEECSE
T ss_pred ccccCCCccccccccccCC-ceeeE-EEECCCceEEEccc
Confidence 5667788888887777765 23333 78888999987654
Done!