Query gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 124
No_of_seqs 127 out of 756
Neff 3.8
Searched_HMMs 23785
Date Tue May 24 09:14:22 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780266.hhm -d /home/congqian_1/database/pdb/pdb70.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2vqe_L 30S ribosomal protein S 100.0 0 0 414.9 10.8 123 1-124 4-126 (135)
2 2zkq_l 40S ribosomal protein S 100.0 4.1E-44 0 278.0 9.4 104 14-117 30-142 (143)
3 3i4o_A Translation initiation 78.2 1.5 6.2E-05 23.1 3.2 45 30-84 15-63 (79)
4 1ah9_A IF1, initiation factor 69.4 2.9 0.00012 21.4 2.9 45 30-84 7-55 (71)
5 1hr0_W Translation initiation 56.0 1.8 7.5E-05 22.7 -0.2 37 45-85 17-57 (71)
6 2oqk_A Putative translation in 51.1 12 0.00049 17.9 3.3 47 29-85 32-81 (117)
7 3lme_A Possible translation in 50.4 5.2 0.00022 19.9 1.5 17 62-78 122-138 (138)
8 1jt8_A EIF-1A, probable transl 40.7 12 0.00048 17.9 2.0 45 30-84 21-68 (102)
9 1d7q_A Translation initiation 40.6 20 0.00085 16.5 4.5 46 30-85 32-80 (143)
10 2e0c_A 409AA long hypothetical 22.9 35 0.0015 15.1 2.0 39 44-84 108-149 (409)
No 1
>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L* 1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O* 1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ...
Probab=100.00 E-value=0 Score=414.85 Aligned_cols=123 Identities=67% Similarity=1.086 Sum_probs=119.5
Q ss_pred CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf 95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r 1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80 (124)
Q Consensus 1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~ 80 (124)
|||||||++++|++.. .+.++++|++|||++|||++|++++|||||||+||||+|+||||++||||||||||||||||+
T Consensus 4 M~T~nQl~r~~R~~~~-~k~k~~aL~~~PqkkGvc~kv~~~tPKKPNSA~RKvarVrLsng~~vtayIPGeGhnlqEHs~ 82 (135)
T 2vqe_L 4 LPTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV 82 (135)
T ss_dssp -CCHHHHHHTCCCCCC-CCCSCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCE
T ss_pred CCCHHHHHCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCCCCCCE
T ss_conf 4768897514888776-567785023797415588997774689965300137899936997999981899867554788
Q ss_pred EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99953783888875478980400144334200121125610789
Q gi|254780266|r 81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124 (124)
Q Consensus 81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk 124 (124)
|||||||++|||||+||+|||+|||+||.+|+++|||||+|+||
T Consensus 83 VLvrGGrv~DLPGVry~vvRG~~D~~gV~~Rk~~RSkYG~Kkpk 126 (135)
T 2vqe_L 83 VLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK 126 (135)
T ss_dssp EEEEECCCTTSTTCCEEECTTSTTSCCCTTCCSSGGGGTCCCCC
T ss_pred EEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99928877889984079964112243346642145546646852
No 2
>2zkq_l 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_L* 1s1h_L*
Probab=100.00 E-value=4.1e-44 Score=278.00 Aligned_cols=104 Identities=29% Similarity=0.592 Sum_probs=93.4
Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEE-CCCCEEEEEECCCC--CCCCCCCEEEE-----EC
Q ss_conf 786466667700068621247875675184567442432889996-69969999807888--75464678999-----53
Q gi|254780266|r 14 GSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL-TSGVEVIAYVPGEG--HNLQEHSVVML-----CG 85 (124)
Q Consensus 14 k~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~L-sng~~v~ayIPGeG--hnlqehs~VLv-----rG 85 (124)
+......|+++|++|||++|||+++++++|||||||+||||+|+| +||++||||||||| |||||||+||| +|
T Consensus 30 ~~~~~~~K~~pl~g~Pq~kGivl~~~~~~pKkPNSA~RK~~rV~L~~ngk~vtA~iPG~G~~h~l~eh~~Vlv~g~G~rG 109 (143)
T 2zkq_l 30 AHLGTALKANPFGGASHAKGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKG 109 (143)
T ss_dssp CCCCCCCCCCCSTTCSCEEEEEEEEEEEECCTTCCCEEEEEEEEESGGGCEEEEECCSSCSSCCCCTTCCEEECSSSSSS
T ss_pred HHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEEEECCCCCCCCCCCCCEEEEEECCCCC
T ss_conf 43033313583458975256899976733579875201699999905990999992798650556648899997357578
Q ss_pred CCCCCCCCCEEEEEECC-CCCCCCCCCCCCCCC
Q ss_conf 78388887547898040-014433420012112
Q gi|254780266|r 86 GRVKDLPGVKYRVIRGV-LDAQGVKNRKQARSR 117 (124)
Q Consensus 86 Grv~DlPGVry~ivRG~-~D~~gv~~Rk~~RSk 117 (124)
|+++|||||+|++|||. +++..+..++..+|+
T Consensus 110 g~~~DlPGVrykvvr~~~~~l~~l~~gkkekpr 142 (143)
T 2zkq_l 110 HAVGDIPGVRFKVVKVANVSLLALYKGKKERPR 142 (143)
T ss_dssp CCBTTBTTCCEECCTTSTTSCSTTTTCCCCC--
T ss_pred CCCCCCCCEEEEEEEECCCCHHHHHCCCCCCCC
T ss_conf 867889971389999648318988636343789
No 3
>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis}
Probab=78.22 E-value=1.5 Score=23.14 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=33.5
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC--C--CCCCCCEEEEE
Q ss_conf 2124787567518456744243288999669969999807888--7--54646789995
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG--H--NLQEHSVVMLC 84 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG--h--nlqehs~VLvr 84 (124)
+..|++++.. ||.- .+|+|.||.++.|||||-= + .+.+.+.|+|.
T Consensus 15 e~~G~V~e~l------~~~~----f~V~l~ng~~~~a~i~GkmRk~ri~i~~GD~V~Ve 63 (79)
T 3i4o_A 15 EVEGRVVEPL------PNAM----FRIELENGHKVLAHISGKMRQHYIRILPEDRVVVE 63 (79)
T ss_dssp EEEEEEEEEE------TTTE----EEEEETTSCEEEEEECHHHHHTTCCCCTTCEEEEE
T ss_pred EEEEEEEEEC------CCCE----EEEEECCCCEEEEEECCHHHHCEEEECCCCEEEEE
T ss_conf 9999999988------9978----99997999999999576364060886699999999
No 4
>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} SCOP: b.40.4.5
Probab=69.44 E-value=2.9 Score=21.42 Aligned_cols=45 Identities=22% Similarity=0.382 Sum_probs=30.6
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC--C--CCCCCCEEEEE
Q ss_conf 2124787567518456744243288999669969999807888--7--54646789995
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG--H--NLQEHSVVMLC 84 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG--h--nlqehs~VLvr 84 (124)
+..|++++.. ||. --+|+|.||.++.|+|||-= + .+.+.+.|+|.
T Consensus 7 e~~G~V~e~l------g~~----~f~V~l~dg~~~la~i~GkmRk~ri~i~~GD~V~Ve 55 (71)
T 1ah9_A 7 EMQGTVLETL------PNT----MFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVE 55 (71)
T ss_dssp ECCEEEEEEC------SSS----EEEEEETTSCEEEEEECSSGGGTTCCCCTTCEECCE
T ss_pred EEEEEEEEEC------CCC----EEEEEECCCCEEEEEECCHHEEEEEEECCCCEEEEE
T ss_conf 9999999988------996----999998899799999373450214997699999999
No 5
>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} SCOP: b.40.4.5 PDB: 1zo1_W
Probab=55.98 E-value=1.8 Score=22.66 Aligned_cols=37 Identities=30% Similarity=0.536 Sum_probs=27.9
Q ss_pred CCCCCCCEEEEEEECCCCEEEEEECCCC--C--CCCCCCEEEEEC
Q ss_conf 6744243288999669969999807888--7--546467899953
Q gi|254780266|r 45 KPNSALRKVIKARLTSGVEVIAYVPGEG--H--NLQEHSVVMLCG 85 (124)
Q Consensus 45 KPNSA~RKvarV~Lsng~~v~ayIPGeG--h--nlqehs~VLvrG 85 (124)
.||.- -+|+|.||.+++|||||-= + .+.+.+.|+|.=
T Consensus 17 lg~~~----f~V~l~ng~~~~a~i~GkmRk~ri~I~~GD~V~Vel 57 (71)
T 1hr0_W 17 LPNAT----FRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEI 57 (71)
T ss_dssp CTTTB----CCCEESSSCBCCCEECHHHHHTCCCCCTTCEEEEEC
T ss_pred CCCCE----EEEEECCCCEEEEECCHHHHEEEEEECCCCEEEEEE
T ss_conf 89989----999988999999987867511058836999999996
No 6
>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II}
Probab=51.08 E-value=12 Score=17.87 Aligned_cols=47 Identities=17% Similarity=0.188 Sum_probs=35.5
Q ss_pred CCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEEC
Q ss_conf 62124787567518456744243288999669969999807888---7546467899953
Q gi|254780266|r 29 PQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLCG 85 (124)
Q Consensus 29 PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvrG 85 (124)
-|.=|++++.+. |+ -+.|.+.+|.+..|+|||-= .-+.+.|.|||.-
T Consensus 32 ~e~ya~V~k~lG------~~----~~~V~~~dg~~~l~~irgkfrkr~~i~~Gd~VlV~~ 81 (117)
T 2oqk_A 32 GQEYGQVQRMLG------NG----RLDAYCFDGQKRLCHIRGKMRKKVWVNPGDIVLVSL 81 (117)
T ss_dssp TEEEEEEEEEEE------TT----EEEEEETTSCEEEEECCHHHHHHSCCCTTCEEEEEE
T ss_pred CEEEEEEEEECC------CC----EEEEEECCCCEEEEEECCHHCCCEEECCCCEEEEEE
T ss_conf 858999999749------97----899997899999999851210752856999999954
No 7
>3lme_A Possible translation initiation inhibitor; structural genomics, RPA2473, PSI-2, protein structure initiative; 2.74A {Rhodopseudomonas palustris}
Probab=50.39 E-value=5.2 Score=19.94 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=12.7
Q ss_pred CEEEEEECCCCCCCCCC
Q ss_conf 69999807888754646
Q gi|254780266|r 62 VEVIAYVPGEGHNLQEH 78 (124)
Q Consensus 62 ~~v~ayIPGeGhnlqeh 78 (124)
-+++||+|++||.-..|
T Consensus 122 Ie~iA~~P~~g~~~~~~ 138 (138)
T 3lme_A 122 IDGTFYAPAEGHHHHHH 138 (138)
T ss_dssp EEEEEECCC--------
T ss_pred EEEEEEECCCCCCCCCC
T ss_conf 99999956887666679
No 8
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} SCOP: b.40.4.5
Probab=40.68 E-value=12 Score=17.92 Aligned_cols=45 Identities=20% Similarity=0.294 Sum_probs=33.6
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEE
Q ss_conf 2124787567518456744243288999669969999807888---754646789995
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLC 84 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvr 84 (124)
|.=|+|++.+. |+ -..|.+.+|.+.+|+|||-- -.+...|.|||.
T Consensus 21 e~y~~V~k~lG------~~----~~~V~c~dg~~rl~~irGK~Rk~~~I~~Gd~VlV~ 68 (102)
T 1jt8_A 21 EILGIIEQMLG------AS----RVRVRCLDGKTRLGRIPGRLKNRIWVREGDVVIVK 68 (102)
T ss_dssp CEEEEEECSSC------SS----EEEEEEETTEEEEEECCHHHHHHHCCCSCEEEEEC
T ss_pred EEEEEEEEECC------CC----EEEEEECCCCEEEEEECCCCCCCEEECCCCEEEEE
T ss_conf 89999999839------98----89999799999999986661112496499999999
No 9
>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein, gene regulation; NMR {Homo sapiens} SCOP: b.40.4.5
Probab=40.63 E-value=20 Score=16.48 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=32.6
Q ss_pred CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEEC
Q ss_conf 2124787567518456744243288999669969999807888---7546467899953
Q gi|254780266|r 30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLCG 85 (124)
Q Consensus 30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvrG 85 (124)
|.-|+|++.+. | --+.|.+.+|.+.+|.|||-= .-+...+.|||.-
T Consensus 32 e~y~~V~k~lG------~----~~~~V~~~dg~~rl~~irgk~rkr~~i~~Gd~VlV~~ 80 (143)
T 1d7q_A 32 QEYAQVIKMLG------N----GRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGL 80 (143)
T ss_dssp EEEEEEEEECS------S----SEEEEEETTTEEEEEECCSGGGGSCCCCTTCEEEEEC
T ss_pred EEEEEEEEECC------C----CEEEEEECCCCEEEEEECCCCEEEEEECCCCEEEEEC
T ss_conf 18999999749------9----7799997899999999655220013753899999943
No 10
>2e0c_A 409AA long hypothetical NADP-dependent isocitrate dehydrogenase; homedimer, oxidoreductase; 2.00A {Sulfolobus tokodaii str} PDB: 2dht_A 2e5m_A*
Probab=22.94 E-value=35 Score=15.08 Aligned_cols=39 Identities=21% Similarity=0.385 Sum_probs=16.7
Q ss_pred CCCCCCCCEEEEEEECCCCEEEEEECCCCCCC---CCCCEEEEE
Q ss_conf 56744243288999669969999807888754---646789995
Q gi|254780266|r 44 KKPNSALRKVIKARLTSGVEVIAYVPGEGHNL---QEHSVVMLC 84 (124)
Q Consensus 44 KKPNSA~RKvarV~Lsng~~v~ayIPGeGhnl---qehs~VLvr 84 (124)
+-+|.++|+- ..|.-...-.-++||.-..+ ++-+.|.||
T Consensus 108 ~~~~~~lR~~--ldlyanvRP~r~~~gl~s~~~~~~~iDivIvR 149 (409)
T 2e0c_A 108 KSVNVAIRLM--LDLYANIRPVKYIEGLESPLKHPEKVDMIIFR 149 (409)
T ss_dssp -CHHHHHHHH--TTCCEEEEEEECCTTCCCSBSCCTTCEEEEEE
T ss_pred CCCCHHHHHH--CCCCEECCCEECCCCCCCCCCCCCCCCEEEEC
T ss_conf 6513567886--49845413033146887876786667679971
Done!