Query 028473
Match_columns 208
No_of_seqs 162 out of 912
Neff 2.8
Searched_HMMs 29240
Date Mon Mar 25 20:03:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028473.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/028473hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3v2d_8 50S ribosomal protein L 99.9 5.7E-25 2E-29 158.3 5.0 61 144-204 1-61 (65)
2 2zjr_3 50S ribosomal protein L 99.9 6.8E-25 2.3E-29 158.5 5.3 61 144-204 1-61 (66)
3 3r8s_3 50S ribosomal protein L 99.9 4.4E-24 1.5E-28 153.1 5.8 60 145-204 1-60 (64)
4 3bbo_5 Ribosomal protein L35; 99.8 1.4E-22 4.7E-27 167.4 0.4 61 144-204 89-149 (159)
5 2xzm_9 RPS31E; ribosome, trans 64.4 5 0.00017 33.3 3.4 48 117-168 65-112 (189)
6 3u5c_f 40S ribosomal protein S 61.8 6 0.0002 31.2 3.2 50 116-169 69-118 (152)
7 1ofu_X SULA, hypothetical prot 16.3 1.1E+02 0.0036 23.1 3.0 37 28-66 8-45 (119)
8 4aj5_1 SKA3, spindle and kinet 13.3 78 0.0027 24.4 1.6 13 37-49 4-16 (101)
9 1mli_A Muconolactone isomerase 12.5 72 0.0024 24.1 1.1 22 23-44 50-71 (96)
10 2ekk_A UBA domain from E3 ubiq 7.5 1.6E+02 0.0055 18.4 1.2 18 190-207 5-22 (47)
No 1
>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=99.90 E-value=5.7e-25 Score=158.30 Aligned_cols=61 Identities=30% Similarity=0.292 Sum_probs=59.1
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
|||||||+||+|||++||+|||+|++||++|++++||.+++|+|++..+|+++|++.|++|
T Consensus 1 MPKmKT~~ga~KRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~vk~l 61 (65)
T 3v2d_8 1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLL 61 (65)
T ss_dssp -CCCCCCHHHHTTEEECTTSCEEEECSSCSSCCTTSCHHHHHHTTSEEECCHHHHHHHHHT
T ss_pred CCCcccchhhhheeEEcCCCCEEeccCCCCCCccCCCHHHHHhcCCCEEECHHHHHHHHHh
Confidence 7999999999999999999999999999999999999999999999999999999999886
No 2
>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=99.90 E-value=6.8e-25 Score=158.47 Aligned_cols=61 Identities=28% Similarity=0.262 Sum_probs=59.8
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
|||||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|+++|++|
T Consensus 1 MPKmKT~~gaaKRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~ik~l 61 (66)
T 2zjr_3 1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLM 61 (66)
T ss_pred CCCcccchhhhheeEEcCCCcEEeccCCCccCcccCCHHHHHhcCCCeeECHHHHHHHHHh
Confidence 7999999999999999999999999999999999999999999999999999999999885
No 3
>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=99.89 E-value=4.4e-24 Score=153.14 Aligned_cols=60 Identities=27% Similarity=0.328 Sum_probs=58.8
Q ss_pred cCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 145 IKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 145 pKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
||||||+||+|||++||+|||+|++||++|++++||.+++|+|++..+|+++|++.|++|
T Consensus 1 PKmKT~~~a~KRFk~TgsGKikr~~a~k~H~l~kKs~krkR~Lr~~~~v~~~d~k~vk~l 60 (64)
T 3r8s_3 1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIAC 60 (64)
T ss_dssp CCCCCCTTTTTTCEECSSSCEEEECSSCSSSCTTSCHHHHHHTSSEEECCTTTHHHHHHH
T ss_pred CCCccchhhhheeEEcCCCCEEeccCCCCCCccCCCHHHHHhcCCCEEECHHHHHHHHHH
Confidence 799999999999999999999999999999999999999999999999999999999886
No 4
>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=99.84 E-value=1.4e-22 Score=167.44 Aligned_cols=61 Identities=28% Similarity=0.303 Sum_probs=58.1
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
|||||||+||+||||+||+|||+|++||++|++++|+.++||+||++.+|+++|+++|++|
T Consensus 89 MPKMKThsgAaKRFKvTgSGKiKR~kAgkrHiLtkKS~KrKR~LRk~~~V~~aD~k~IKrl 149 (159)
T 3bbo_5 89 GYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGA 149 (159)
T ss_dssp --CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTTT
T ss_pred CcccccchhhhheeEEcCCccEEeccCCCCCCcCcCCHHHHHhcCCCeeECHHHHHHHHHh
Confidence 8999999999999999999999999999999999999999999999999999999999885
No 5
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9
Probab=64.36 E-value=5 Score=33.31 Aligned_cols=48 Identities=15% Similarity=0.203 Sum_probs=30.7
Q ss_pred hhhhhcchhhhhhcccCcCCcccccccccCcccCcccccceEeccCccEEee
Q 028473 117 FIQVRHVSSRDRKKRRKPVTPVTSKVKKIKMKSYSSYKSRFRTMNDGQVRRW 168 (208)
Q Consensus 117 ~~QvRh~~~~~r~~~r~p~tp~~skmkmpKMKThKgAkKRFKVTgSGKIKRk 168 (208)
++-+|+-..+ |+ +..+.+|.+.+..+.|.|+ ++-|-|+|..+|+|.|-
T Consensus 65 vlRLrGG~~k-rk-K~~~~tPK~~k~~kKkvkl--~~Lk~y~Vd~~Gkv~~~ 112 (189)
T 2xzm_9 65 SLKLLGGKKK-KK-KKSYTTKKKTKHRHVHTKL--GALAFYKLENNGKVSLQ 112 (189)
T ss_dssp -------CCC-CC-CCCCCSSSCCCCCCCCCCC--SCCCCEEEETTTEEEEC
T ss_pred EEecCCCccc-cc-ccccCCCccccccccccCC--ceeeEEEECCCceEEEc
Confidence 3444544332 33 6788899888776666666 77888999999998754
No 6
>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=61.77 E-value=6 Score=31.20 Aligned_cols=50 Identities=10% Similarity=0.158 Sum_probs=27.2
Q ss_pred hhhhhhcchhhhhhcccCcCCcccccccccCcccCcccccceEeccCccEEeec
Q 028473 116 SFIQVRHVSSRDRKKRRKPVTPVTSKVKKIKMKSYSSYKSRFRTMNDGQVRRWH 169 (208)
Q Consensus 116 ~~~QvRh~~~~~r~~~r~p~tp~~skmkmpKMKThKgAkKRFKVTgSGKIKRkr 169 (208)
+++.+|+- .+.++|..+.+|.+.+-+..| .+=++-|-|+|.++|||.|-+
T Consensus 69 Lvlrl~GG--gKkrkKk~~t~Pkk~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 118 (152)
T 3u5c_f 69 LVLRLRGG--GKKRKXXXXXXXXXXXXXXXX--XXXXVLSYYKVDAEGKVTKLR 118 (152)
T ss_dssp ---------------CCCCCCCSCCCCCCCC--CCCCCCCCSEECSSSCEECCS
T ss_pred EEeeccCC--CcCcccccccccccccccccc--cccceeeEEEEccCCeEEECc
Confidence 34444554 233345778888876554333 344888999999999998654
No 7
>1ofu_X SULA, hypothetical protein PA3008; bacterial cell division inhibitor, SULA protein; HET: GDP; 2.1A {Pseudomonas aeruginosa} SCOP: c.37.1.22
Probab=16.26 E-value=1.1e+02 Score=23.14 Aligned_cols=37 Identities=19% Similarity=0.168 Sum_probs=29.0
Q ss_pred cccCchHHHHHHHHHHhhhhhh-ccccccccccCCCCCCC
Q 028473 28 LFDAPSAVEMQRLCNKLRTLTL-SSSRRLLFQSHAPIHRP 66 (208)
Q Consensus 28 ~~~~~~~~~m~~~~~klr~~~~-~s~r~~~~~~~~~~~~~ 66 (208)
|.+.+...|+.-|++-|+.++- |..|.++++. +++.|
T Consensus 8 l~~~~g~~e~~lLlp~L~~l~~~~~~r~ilwi~--pp~~~ 45 (119)
T 1ofu_X 8 SLSGLPGHCLTLLAPILRELSEEQDARWLTLIA--PPASL 45 (119)
T ss_dssp EEESCHHHHHHHHHHHHHHHTTCSSSSEEEEES--CCTTS
T ss_pred eecCCCccHHHHHHHHHHHhcccccCccEEEEC--CCCCC
Confidence 5677889999999999998874 4778899987 65544
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=13.31 E-value=78 Score=24.45 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=10.9
Q ss_pred HHHHHHHhhhhhh
Q 028473 37 MQRLCNKLRTLTL 49 (208)
Q Consensus 37 m~~~~~klr~~~~ 49 (208)
...||-|||+||+
T Consensus 4 ~~~Ff~KLR~La~ 16 (101)
T 4aj5_1 4 IRSFCGKLRSLAS 16 (101)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4689999999974
No 9
>1mli_A Muconolactone isomerase; intramolecular oxidoreductase; 3.30A {Pseudomonas putida} SCOP: d.58.4.1
Probab=12.51 E-value=72 Score=24.14 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=17.8
Q ss_pred ccccccccCchHHHHHHHHHHh
Q 028473 23 FNNKALFDAPSAVEMQRLCNKL 44 (208)
Q Consensus 23 ~~~~~~~~~~~~~~m~~~~~kl 44 (208)
+.|-++||+.|..|+..++..|
T Consensus 50 y~nisIfdv~s~~eLh~iL~~L 71 (96)
T 1mli_A 50 YANYSVFDVPSVEALHDTLMQL 71 (96)
T ss_pred ccEEEEEEcCCHHHHHHHHHhC
Confidence 4577899999999998876544
No 10
>2ekk_A UBA domain from E3 ubiquitin-protein ligase HUWE1; ubiquitin associated domain, compact three helix bundle, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=7.48 E-value=1.6e+02 Score=18.38 Aligned_cols=18 Identities=11% Similarity=0.122 Sum_probs=14.5
Q ss_pred CeeeChhcHHHHHhcccC
Q 028473 190 PALVPLAYAKVMKKLNFC 207 (208)
Q Consensus 190 ~~~VskaD~KrIKkm~F~ 207 (208)
...++...+..+-.|||.
T Consensus 5 ~~~~~~~~v~~L~~MGF~ 22 (47)
T 2ekk_A 5 SSGVNQQQLQQLMDMGFT 22 (47)
T ss_dssp CCSSCHHHHHHHHHHHCC
T ss_pred CCCCCHHHHHHHHHcCCC
Confidence 456778889999999994
Done!