Query 031725
Match_columns 154
No_of_seqs 143 out of 968
Neff 3.8
Searched_HMMs 29240
Date Mon Mar 25 06:41:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031725.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/031725hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3bbo_Y Ribosomal protein L28; 100.0 2E-46 6.7E-51 295.5 -3.4 148 1-154 1-151 (151)
2 3r8s_X 50S ribosomal protein L 100.0 9.1E-34 3.1E-38 201.5 4.9 76 78-153 1-76 (77)
3 2jz6_A 50S ribosomal protein L 99.9 1.5E-28 5.1E-33 175.3 5.9 64 74-138 3-66 (77)
4 2zjr_U 50S ribosomal protein L 99.9 6.6E-30 2.2E-34 183.6 -5.4 67 77-146 1-80 (81)
5 2jl6_1 50S ribosomal protein L 99.9 2.6E-28 9E-33 178.3 -4.1 67 77-145 1-80 (89)
6 3v2d_1 50S ribosomal protein L 99.9 9.9E-26 3.4E-30 167.1 5.0 69 77-152 1-83 (98)
7 1zfo_A LAsp-1; LIM domain, zin 56.3 4.5 0.00015 23.0 1.2 22 77-98 2-23 (31)
8 1znf_A 31ST zinc finger from X 20.1 32 0.0011 16.1 0.6 9 80-88 3-11 (27)
9 1ard_A Yeast transcription fac 17.9 37 0.0013 16.0 0.6 9 80-88 4-12 (29)
10 2lvu_A Zinc finger and BTB dom 22.2 28 0.00096 16.4 0.0 10 80-89 4-13 (26)
No 1
>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=100.00 E-value=2e-46 Score=295.52 Aligned_cols=148 Identities=65% Similarity=0.902 Sum_probs=74.8
Q ss_pred CcccccCCc--eEeeccCCCCcccCcCCCccccccccCCcceeeeeeeecceEEEecCC-CCCCCccCCCCCCCCCcccc
Q 031725 1 MATMATPGG--VLLGNTSNLPFRRPRLSPKSMVKAVSSSEELGFVTSQLSGIKISYSLP-DVATPISSRPFAPGLQPIVA 77 (154)
Q Consensus 1 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~g~~l~~~~~-~~~~~~~~~~~~~~~~~~~M 77 (154)
||||+++|+ +++|.+. ...+.+..+..++ .--+++|||+||||+|++|+++.+ ..+++ ..+|..+++++ +|
T Consensus 1 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~ts~~~g~~~~~~~~~~~~~~-~~~p~~~~~~~-mM 74 (151)
T 3bbo_Y 1 MATMVAGISLRGPVMSSH-RTFSVTKRASLPQ---SKLSSELSFVTSQLSGLKISSTHFISSSAP-LSVPFKPSLQP-VA 74 (151)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Cceeeeccccccceeecc-ccccccccccccc---ccccchhhhhhhhccCcccccccccccccc-cccCCCCcccc-ch
Confidence 899999876 5555322 2222232222221 112789999999999999999986 22233 35677788888 79
Q ss_pred cccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHHHHHcccccccC
Q 031725 78 RRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAVAKKAGIDLRKE 154 (154)
Q Consensus 78 SR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~yl~k~~~~l~k~ 154 (154)
+|+|+||||++++||+||||++||||+|+||||++++|+++++++++|||||+|||+|++.|||+||+++|+||+||
T Consensus 75 sR~C~itGK~p~~GNnVSHS~~KTKRrw~PNLQkvri~~~~g~r~vrlrVsTr~LRTikk~GlD~~l~~~g~~l~k~ 151 (151)
T 3bbo_Y 75 RRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIEKNGLDAVAKKAGIDLSKK 151 (151)
T ss_dssp -CCCCCSCCTTCCCCCCEECCSSSCCEECCCCCCCCBCCCTTSSCCCBCCCSSSTTTTTTSTTTCSCCSSSSCSSCC
T ss_pred hceeeccCcccccCCeeeecCCccCceeccccEEEEEEECCCCEEEEEEEEchheeehhhhhHHHHHHHhchhhcCC
Confidence 99999999999999999999999999999999999999998889999999999999999999999999999999987
No 2
>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=99.98 E-value=9.1e-34 Score=201.53 Aligned_cols=76 Identities=36% Similarity=0.587 Sum_probs=72.3
Q ss_pred cccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHHHHHccccccc
Q 031725 78 RRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAVAKKAGIDLRK 153 (154)
Q Consensus 78 SR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~yl~k~~~~l~k 153 (154)
||+|++|||++++||+||||+++|+|+|+||||++++|+++++++++|+|||+|||||||.|||+||+++...+.+
T Consensus 1 sr~C~itGK~~~~Gn~VShs~~kTkR~~~PNlq~~r~~~~~~~r~~rlrVst~~LRti~k~Gld~~l~~~~~~g~~ 76 (77)
T 3r8s_X 1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEK 76 (77)
T ss_dssp CCCCTTTCCCCEEEEEECSSCCEEEEEECCCEEEEEEEEGGGTEEEEEEEEHHHHHHHHHHCHHHHHHHHHHTTCC
T ss_pred CCEeeeCCCccccCceEeccCCccCceecCccEEEEEEECCCCEEEEEEEEcceEeeecccCHHHHHHHHHHccCc
Confidence 6899999999999999999999999999999999999999999999999999999999999999999988776543
No 3
>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=99.95 E-value=1.5e-28 Score=175.27 Aligned_cols=64 Identities=25% Similarity=0.326 Sum_probs=60.2
Q ss_pred cccccccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhccccc
Q 031725 74 PIVARRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKN 138 (154)
Q Consensus 74 ~~~MSR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~ 138 (154)
.++|||+|+||||++++||+||||+++|||+|+||||++++|+|+ |++++|+|||+|||+++..
T Consensus 3 ~~~Msr~C~itGK~~~~Gn~VSHS~~kTkR~~~PNLq~vr~~~~~-g~~~rl~Vst~~LRtgkv~ 66 (77)
T 2jz6_A 3 HMIMAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKSGKVK 66 (77)
T ss_dssp CCCCCCCCTTTCCCCCCCCCCCCSCCCCSSSCBTTEEEEEEEETT-TEEEEEEEEHHHHHHCCSC
T ss_pred CCceeeeeeecCCccccCCeEeecCCccCcccccceEEEEEEecC-CcEEEEEEEhHHeeeccEE
Confidence 356999999999999999999999999999999999999999976 8999999999999998754
No 4
>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=99.94 E-value=6.6e-30 Score=183.57 Aligned_cols=67 Identities=30% Similarity=0.273 Sum_probs=56.6
Q ss_pred ccccccccCccccccccccc-------------ccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHH
Q 031725 77 ARRVCPFTGKKSNKANKVSF-------------SNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAV 143 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVSh-------------S~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~y 143 (154)
|||+|++|||++.+||+||| |+++|||+|+||||++++|+ +|++++|+|||+|||+||| |||++
T Consensus 1 Msr~C~itGK~~~~Gn~vshrGkak~~Gg~~s~s~~kTkR~~~PNlq~vr~~~--~g~~~~l~Vst~~LRti~k-Gld~~ 77 (81)
T 2zjr_U 1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRE--NGQVKTVWLSANALRTLSK-GPYKG 77 (81)
T ss_dssp -------CCSSSCCCCCCCCCCEESCCCTTTCSCCEECCCCCCCCCCCCCCCC--SSSCCCCCCCHHHHHHHHS-SCCSS
T ss_pred CCCEeecCCCccccCCeeeeccccccccccchhhCCccCceecccceEEEEEE--CCEEEEEEEEcceeeeech-hHHHH
Confidence 89999999999999999999 99999999999999999995 5899999999999999999 99988
Q ss_pred HHH
Q 031725 144 AKK 146 (154)
Q Consensus 144 l~k 146 (154)
+..
T Consensus 78 ~~~ 80 (81)
T 2zjr_U 78 IEL 80 (81)
T ss_dssp CC-
T ss_pred Hhh
Confidence 754
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=99.93 E-value=2.6e-28 Score=178.26 Aligned_cols=67 Identities=22% Similarity=0.326 Sum_probs=60.8
Q ss_pred ccccccccCcccccccccccccC-------------cccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHH
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNH-------------KTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAV 143 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~-------------KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~y 143 (154)
|||+|++|||++++||+||||++ +|||+|+||||++++|++ |++++|+|||+|||+|+|.|+++.
T Consensus 1 Msr~C~itGK~~~~Gn~VShs~~ak~~GGvG~k~t~kTkR~f~PNLqkvr~~~~--g~~~rl~Vstk~LRtI~k~g~~a~ 78 (89)
T 2jl6_1 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYELVERAA 78 (89)
T ss_dssp --CCCSSSCCCCEEEEEEEEESCCTTTSSSCCEEEEEEEEEECCCBCCBCCEET--TEECCBCCBGGGHHHHHHHHSCCC
T ss_pred CCCEeecCCCccccCceEeecCccccccccccccCCccceEEccccEEEEEEEC--CEEEEEEEEChhheEccccchhHH
Confidence 89999999999999999999995 999999999999999993 899999999999999999998755
Q ss_pred HH
Q 031725 144 AK 145 (154)
Q Consensus 144 l~ 145 (154)
+.
T Consensus 79 ~~ 80 (89)
T 2jl6_1 79 AA 80 (89)
T ss_dssp CH
T ss_pred HH
Confidence 43
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=99.92 E-value=9.9e-26 Score=167.10 Aligned_cols=69 Identities=23% Similarity=0.448 Sum_probs=60.3
Q ss_pred ccccccccCcccccccccccccC-------------cccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHH
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNH-------------KTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAV 143 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~-------------KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~y 143 (154)
|||+|++|||++.+||+||||++ +|||+|+||||++++|++ |++++++|||+|||||++ .
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 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYE-----L 73 (98)
T ss_dssp -CCCCTTTCCCCEEEEEEEEEEECGGGTSSEEEEEEEEEEEECCCEEEEEEEET--TEEEEEEEEGGGHHHHHH-----H
T ss_pred CCCeeecCCCccccCccEeccCccccccccccccCCcccceeccceEEEEEEEC--CEEEEEEEEchhheehhh-----h
Confidence 89999999999999999999995 999999999999999994 899999999999999974 2
Q ss_pred HHHc-ccccc
Q 031725 144 AKKA-GIDLR 152 (154)
Q Consensus 144 l~k~-~~~l~ 152 (154)
+.++ |+||+
T Consensus 74 verakg~~~~ 83 (98)
T 3v2d_1 74 VERAKGLKLE 83 (98)
T ss_dssp HHHGGGSCCS
T ss_pred hhhhhccccc
Confidence 3344 56654
No 7
>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4
Probab=56.25 E-value=4.5 Score=22.97 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=18.1
Q ss_pred ccccccccCccccccccccccc
Q 031725 77 ARRVCPFTGKKSNKANKVSFSN 98 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~ 98 (154)
|+.+|..|||....+.++.-..
T Consensus 2 m~~~C~~C~k~Vy~~Ek~~~~g 23 (31)
T 1zfo_A 2 MNPNCARCGKIVYPTEKVNCLD 23 (31)
T ss_dssp CCCBCSSSCSBCCGGGCCCSSS
T ss_pred CCCcCCccCCEEecceeEEECC
Confidence 7778999999998888877543
No 8
>1znf_A 31ST zinc finger from XFIN; zinc finger DNA binding domain; NMR {Xenopus laevis} SCOP: g.37.1.1
Probab=20.05 E-value=32 Score=16.13 Aligned_cols=9 Identities=11% Similarity=0.331 Sum_probs=7.0
Q ss_pred cccccCccc
Q 031725 80 VCPFTGKKS 88 (154)
Q Consensus 80 ~C~ltGKk~ 88 (154)
.|.+|||.-
T Consensus 3 ~C~~C~k~f 11 (27)
T 1znf_A 3 KCGLCERSF 11 (27)
T ss_dssp BCSSSCCBC
T ss_pred cCCCCCCcC
Confidence 589999864
No 9
>1ard_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 PDB: 1arf_A 1are_A
Probab=17.87 E-value=37 Score=16.00 Aligned_cols=9 Identities=22% Similarity=0.460 Sum_probs=7.1
Q ss_pred cccccCccc
Q 031725 80 VCPFTGKKS 88 (154)
Q Consensus 80 ~C~ltGKk~ 88 (154)
.|.+||+.-
T Consensus 4 ~C~~C~~~f 12 (29)
T 1ard_A 4 VCEVCTRAF 12 (29)
T ss_dssp BCTTTCCBC
T ss_pred ECCCCCccc
Confidence 599999864
No 10
>2lvu_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}
Probab=22.15 E-value=28 Score=16.40 Aligned_cols=10 Identities=40% Similarity=0.607 Sum_probs=7.4
Q ss_pred cccccCcccc
Q 031725 80 VCPFTGKKSN 89 (154)
Q Consensus 80 ~C~ltGKk~~ 89 (154)
.|.+|||.-.
T Consensus 4 ~C~~C~k~f~ 13 (26)
T 2lvu_A 4 VCERCGKRFV 13 (26)
Confidence 5899998643
Done!