RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15220
(289 letters)
>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein,
nucleotide-binding, protein biosynthesis, translation,
zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB:
3fik_5 3izt_C* 3izu_C* 3j01_5 3j0t_C* 3j0w_C* 3j0y_C*
3j11_C* 3j12_C* 3j14_C* 3kcr_5 2rdo_9 2gya_2 2gyc_2
Length = 234
Score = 196 bits (501), Expect = 1e-62
Identities = 75/148 (50%), Positives = 108/148 (72%)
Query: 140 FDKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIY 199
D K Y + AI L+KE ATAKF ES+D++++L ++ ++SDQ VRG+ VLP TG+ +
Sbjct: 15 VDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVR 74
Query: 200 IAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPK 259
+A F E AK AGA++VGMEDLA +IK E++ D+VIASP++M +V LG++LGP+
Sbjct: 75 VAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAMRVVGQLGQVLGPR 134
Query: 260 GLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GLMPN K GT+ ++ A+KNAK+GQ+R
Sbjct: 135 GLMPNPKVGTVTPNVAEAVKNAKAGQVR 162
>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 352
Score = 194 bits (495), Expect = 2e-60
Identities = 56/148 (37%), Positives = 94/148 (63%)
Query: 140 FDKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIY 199
+ + Y +A++L+K+ ++ KF E+ + LN++ K +DQ +R ++ LP TGK +
Sbjct: 129 REIKQEYDLKTALSLMKQMSSTKFVETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKTVK 188
Query: 200 IAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPK 259
IA +K ++AK AGADIVG E+L ++IK + D +IA+ + M V+SLG+ILGP+
Sbjct: 189 IAVLAQGDKIDEAKAAGADIVGGEELIEQIKGGFMDFDKLIATSDMMAKVASLGRILGPR 248
Query: 260 GLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GLMP K GT+ ++ A++ K G++
Sbjct: 249 GLMPTPKAGTVTPNVAQAVEEFKKGKVE 276
>4f9t_A 50S ribosomal protein L1; rossman fold, RNA; HET: MPD; 1.46A
{Thermus thermophilus} PDB: 3u4m_A 1eg0_N 1vsp_A 2hgj_C
2hgq_C 2hgu_C 1vsa_A 4abs_C 3zvp_C 1zho_A 1ml5_c* 1yl3_C
1giy_C 2hw8_A 2j01_C 2j03_C 2jl6_C 2jl8_C 2om7_K* 2v47_C
...
Length = 229
Score = 189 bits (482), Expect = 7e-60
Identities = 68/149 (45%), Positives = 99/149 (66%), Gaps = 1/149 (0%)
Query: 140 FDKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIY 199
D NKIY+ D A L+KE ATAKFDE++++ L ++ +RSDQ VRG++ LP GK++
Sbjct: 15 VDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVR 74
Query: 200 IAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIV-SSLGKILGP 258
+ A EK ++A+ AGAD VG E++ QKI + D V+A+P+ M V S LG+ILGP
Sbjct: 75 VLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGP 134
Query: 259 KGLMPNIKDGTLNSDILTAIKNAKSGQIR 287
+GL+PN K GT+ +I I+ K+G+I
Sbjct: 135 RGLLPNPKAGTVGFNIGEIIREIKAGRIE 163
>3qoy_A 50S ribosomal protein L1; beta-alpha-beta, structural constituent
of ribosome, rRNA BI regulation of translation,
translation, ribosomal RNA; 2.10A {Aquifex aeolicus}
Length = 242
Score = 183 bits (466), Expect = 2e-57
Identities = 65/152 (42%), Positives = 101/152 (66%), Gaps = 4/152 (2%)
Query: 140 FDKNKIYSFDSAITLIK---EAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGK 196
D+NK Y+ + A+ L+K E +FDE++++++ LNV+ + +DQ+VRGS+VLP GK
Sbjct: 15 VDRNKRYTLEEAVDLLKKMEEVLQRRFDETVELAMRLNVDPRYADQMVRGSVVLPHGLGK 74
Query: 197 KIYIAAFVPKEKYEQAKIAGADIVGMEDLAQKI-KSNEVSCDLVIASPESMHIVSSLGKI 255
I + F E ++A+ AGAD VG ++L KI K D+ IA+PE M V+ LG+I
Sbjct: 75 PIKVVVFAEGEYAKKAEEAGADYVGGDELINKILKEEWTDFDVAIATPEMMPKVAKLGRI 134
Query: 256 LGPKGLMPNIKDGTLNSDILTAIKNAKSGQIR 287
LGP+GLMP+ K GT+ +++ AIK+AK G++
Sbjct: 135 LGPRGLMPSPKTGTVTTNVEQAIKDAKRGRVE 166
>1vq8_I 50S ribosomal protein L11P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: a.4.7.1 PDB: 1vq4_I*
1vq5_I* 1vq6_I* 1vq7_I* 1s72_I* 1vq9_I* 1vqk_I* 1vql_I*
1vqm_I* 1vqn_I* 1vqo_I* 1vqp_I* 1yhq_I* 1yi2_I* 1yij_I*
1yit_I* 1yj9_I* 1yjn_I* 1yjw_I* 2otl_I* ...
Length = 162
Score = 164 bits (416), Expect = 5e-51
Identities = 47/134 (35%), Positives = 75/134 (55%), Gaps = 1/134 (0%)
Query: 5 ITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSD 64
+ G I++ +P G+ANP PP+GP LG +++ + N QT + GT +PV + D
Sbjct: 1 MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFD-GTEVPVTVKYDDD 59
Query: 65 KSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISA 124
SF + V P LIK AG + GS +P D V L+ Q+K+IA K+ DL + ++
Sbjct: 60 GSFEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTN 119
Query: 125 AMRTIAGSARSMGI 138
A + + G+ S+G+
Sbjct: 120 AAKEVVGTCTSLGV 133
>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A
{Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5
1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z
Length = 217
Score = 150 bits (381), Expect = 6e-45
Identities = 34/156 (21%), Positives = 60/156 (38%), Gaps = 11/156 (7%)
Query: 138 IIFDKNKIYSFDSAITLIKEAATAKFDESIDISIHL-NVNIKRSDQIVRGSIVLPFSTGK 196
++ DK + + F +S++I + +++K+ D +R + LP K
Sbjct: 1 MLADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDMKKGDLKLREIVPLPKQPSK 60
Query: 197 KIYIAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEV-------SCDLVIASPESMHIV 249
+ E+ E AK A +V + QK++ + + + + ESM +
Sbjct: 61 AKRVLVVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESMALA 120
Query: 250 -SSLGKILGPKGLMPNIKDGTLNSDILTAIKNAKSG 284
LG LGP+G P T DI I K
Sbjct: 121 GRILGPALGPRGKFPTPLPNTA--DISEYINRFKRS 154
>3bbo_K Ribosomal protein L11; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 224
Score = 144 bits (364), Expect = 2e-42
Identities = 75/138 (54%), Positives = 97/138 (70%), Gaps = 1/138 (0%)
Query: 1 MVKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIIT 60
KK+ G IKL + AGKA P+PP+GPALG +G+NIM FCK++NA+T + G IPV IT
Sbjct: 72 KAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTAD-KPGFVIPVEIT 130
Query: 61 VFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAA 120
VF DKSFTF K P + L+ KA+G +KGS P +KVGK+T Q++ IAT K DL
Sbjct: 131 VFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLPDLNCT 190
Query: 121 SISAAMRTIAGSARSMGI 138
+I +AMR IAG+A +MGI
Sbjct: 191 TIESAMRIIAGTAANMGI 208
>3r8s_I 50S ribosomal protein L11; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_G 1p86_G 2awb_I 2aw4_I 2i2v_I 2j28_I 2i2t_I*
2qao_I* 2qba_I* 2qbc_I* 2qbe_I 2qbg_I 2qbi_I* 2qbk_I*
2qov_I 2qox_I 2qoz_I* 2qp1_I* 2rdo_I 2vhm_I ...
Length = 141
Score = 140 bits (353), Expect = 7e-42
Identities = 82/136 (60%), Positives = 105/136 (77%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
KK+ ++KLQ+ AG ANPSPP+GPALGQ+G+NIMEFCK FNA+T IE G PIPV+ITV+
Sbjct: 2 KKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVY 61
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASI 122
+D+SFTF K P L+KKAAGI+ GS KP+ DKVGK++ Q++EIA K D+T A I
Sbjct: 62 ADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADI 121
Query: 123 SAAMRTIAGSARSMGI 138
A R+I G+ARSMG+
Sbjct: 122 EAMTRSIEGTARSMGL 137
>3egv_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase;
post-translational modification, multiple
methyltransferase; HET: SAH 4MM; 1.75A {Thermus
thermophilus} SCOP: d.47.1.1 PDB: 2e34_A 2e35_A 2e36_A
2h8w_A 2hgj_L 2hgq_L 2hgu_L 2j01_K 2j03_K 2jl6_K 2jl8_K
2klm_A 2nxn_B 2wh2_K 2wh4_K 2wrj_K 2wrl_K 2x9s_K 2x9u_K
2xtg_K ...
Length = 146
Score = 139 bits (352), Expect = 1e-41
Identities = 73/136 (53%), Positives = 97/136 (71%), Gaps = 1/136 (0%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
KK+ +KLQ+PAG A P+PP+GPALGQ G NIMEF K FNA T + +PV IT++
Sbjct: 1 KKVVAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITIY 59
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASI 122
+D+SFTF K P ++LI+KAAG++KG+ KP +KVG++T+ Q+ EIA K DL +
Sbjct: 60 ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL 119
Query: 123 SAAMRTIAGSARSMGI 138
AA R IAGSARSMG+
Sbjct: 120 EAAARMIAGSARSMGV 135
>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein,
translation repressor, ribosome; 1.85A
{Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB:
1cjs_A 1u63_A 1dwu_A
Length = 219
Score = 141 bits (357), Expect = 2e-41
Identities = 32/151 (21%), Positives = 67/151 (44%), Gaps = 11/151 (7%)
Query: 146 YSFDSAITLIKEAATA-KFDESIDISIHL-NVNIKRSDQIVRGSIVLPFSTGKKIYIAAF 203
+ A+ +E A F +S + L +++++ + ++ +VLP GK+ IA
Sbjct: 4 EALLQAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAVI 63
Query: 204 VPKEKYEQAKIAGADIVGMEDLA------QKIKSNEVSCDLVIASPESMHIVS-SLGKIL 256
+ +QA+ G ++ E++ +K++ + D IA + M ++ +G IL
Sbjct: 64 GTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGRYMGVIL 123
Query: 257 GPKGLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GP+G MP +I ++ K +
Sbjct: 124 GPRGKMPKPVPANA--NIKPLVERLKKTVVI 152
>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 212
Score = 139 bits (352), Expect = 1e-40
Identities = 36/151 (23%), Positives = 71/151 (47%), Gaps = 12/151 (7%)
Query: 146 YSFDSAIT-LIKEAATAKFDESIDISIHL-NVNIKRSDQIVRGSIVLPFSTGKKIYIAAF 203
++A++ +++A F E++D++++L ++++ V S+VLP TG++ I F
Sbjct: 4 QEIENAVSRALEDAPERNFRETVDLAVNLRDLDLNDPSNRVDESVVLPAGTGQETTIVVF 63
Query: 204 VPKEKYEQAKIAGADIVGMEDLAQ------KIKSNEVSCDLVIASPESMHIVS-SLGKIL 256
E +A+ D++ ++L + K D IA M + LG +L
Sbjct: 64 AEGETALRAEEVADDVLDEDELEELGGDDDAAKDLADDTDFFIAEKGLMQDIGRYLGTVL 123
Query: 257 GPKGLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GP+G MP D D++ I+ K ++
Sbjct: 124 GPRGKMPEPLDPDD--DVVEVIERMK-NTVQ 151
>1mms_A Protein (ribosomal protein L11); RNA-protein complex, RNA,
ribosome, translocation, thiostrep; 2.57A {Thermotoga
maritima} SCOP: a.4.7.1 d.47.1.1 PDB: 1mvr_L 1oln_A*
1giy_L 1mj1_L* 1ml5_l* 1yl3_L 2b66_K 2b9n_K 2b9p_K
2jq7_A* 2k3f_A 1eg0_K 1jqm_A 1jqs_A 1jqt_A 1r2w_A 1r2x_A
487d_L 1pn8_L 1pn7_L
Length = 140
Score = 133 bits (335), Expect = 3e-39
Identities = 82/136 (60%), Positives = 103/136 (75%), Gaps = 1/136 (0%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
KK+ IKLQ+PAGKA P+PP+GPALGQ G+NIMEFCK FNA+T + G +PV+ITV+
Sbjct: 2 KKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETA-DKAGMILPVVITVY 60
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASI 122
DKSFTF K P +FL+KKAAGI+KGS++P VGK+T QI+EIA K DL A S+
Sbjct: 61 EDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSL 120
Query: 123 SAAMRTIAGSARSMGI 138
AAM+ I G+A+SMGI
Sbjct: 121 EAAMKIIEGTAKSMGI 136
>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus}
Length = 189
Score = 132 bits (335), Expect = 2e-38
Identities = 29/121 (23%), Positives = 56/121 (46%), Gaps = 4/121 (3%)
Query: 167 IDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPK--EKYEQAKIAGADIVGMED 224
+D+++ + + K++ + + LP+ +I A + + + A+ GA G
Sbjct: 1 LDLTLDMALGKKKNVEPFTSVLSLPYPFASEINKVAVFTENASEVKIAEENGAAFAGGTS 60
Query: 225 LAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPKGLMPNIKDGTLNSDILTAIKNAKSG 284
L QKI +E+ D +A PE M ++ L K L K P + ++ DI ++ K+G
Sbjct: 61 LIQKIWDDEIVADFYVAVPEIMPELNRLRKKLNKK--YPKLSRNSIGRDIPKMLELFKNG 118
Query: 285 Q 285
Sbjct: 119 H 119
>3o58_A L10A, 60S ribosomal protein L1; ribosomal RNA and proteins,
ribosome; 4.00A {Saccharomyces cerevisiae} PDB: 3izc_A
3izs_A 1s1i_A 3o5h_A 2noq_G 3j0l_B 3j0o_B 3j0p_B 3j0q_B
3jyw_A
Length = 217
Score = 131 bits (332), Expect = 1e-37
Identities = 31/155 (20%), Positives = 56/155 (36%), Gaps = 9/155 (5%)
Query: 136 MGIIFDKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTG 195
M I + E F E++++ + L + D+ GS+ LP
Sbjct: 1 MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPR 60
Query: 196 KKIYIAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEV------SCDLVIASPESMHIV 249
+ I F ++AK G D + ++DL + K+ ++ + IAS + V
Sbjct: 61 PNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQV 120
Query: 250 S-SLGKILGPKGLMPNIKDGTLNSDILTAIKNAKS 283
LG L G P D+ + + +S
Sbjct: 121 PRLLGPQLSKAGKFPTPVSHN--DDLYGKVTDVRS 153
>2ftc_G L11MT, MRP-L11, 39S ribosomal protein L11, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_G
Length = 145
Score = 124 bits (311), Expect = 1e-35
Identities = 58/140 (41%), Positives = 86/140 (61%), Gaps = 4/140 (2%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
++ G I+ + AG A P PP+GP LGQRG++I +FCK FN +T+ I+ G P+P I V
Sbjct: 2 PEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVK 61
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVD----LT 118
D++F K V++ +K AAGI+KG+ + + G +T + EIA IK D L
Sbjct: 62 PDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQ 121
Query: 119 AASISAAMRTIAGSARSMGI 138
+S+ +R+I GSARS+GI
Sbjct: 122 DVPLSSVVRSIIGSARSLGI 141
>2zkr_i 60S ribosomal protein L12; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 3izc_J 3izs_J 3j16_H* 3o5h_L 3jyw_K
1s1i_K
Length = 165
Score = 121 bits (305), Expect = 2e-34
Identities = 23/131 (17%), Positives = 51/131 (38%), Gaps = 1/131 (0%)
Query: 8 FIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSDKSF 67
+ L+ G+ + + P +G GL+ + + T + G I V +T+ + ++
Sbjct: 12 VVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTIQNRQAQ 70
Query: 68 TFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMR 127
+ + + + G +T+ +I IA A +S ++
Sbjct: 71 IEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIK 130
Query: 128 TIAGSARSMGI 138
I G+A+S+G
Sbjct: 131 EILGTAQSVGC 141
>3iz5_J 60S ribosomal protein L12 (L11P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_J
Length = 166
Score = 120 bits (303), Expect = 4e-34
Identities = 25/140 (17%), Positives = 52/140 (37%), Gaps = 4/140 (2%)
Query: 1 MVKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIIT 60
+ + +++ G+ + + P +G GL+ + ++ +T G + V +T
Sbjct: 5 LDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLT 64
Query: 61 VFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHS--DKVGKLTYLQIKEIATIKNVDLT 118
V V L+ KA + K G ++ + EIA I
Sbjct: 65 V--QNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHSGNISLDDVIEIARIMRNRSM 122
Query: 119 AASISAAMRTIAGSARSMGI 138
A ++ ++ I G+ S+G
Sbjct: 123 AKEMAGTVKEILGTCVSVGC 142
>3iz5_A 60S ribosomal protein L1 (L1P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_A
Length = 216
Score = 121 bits (305), Expect = 1e-33
Identities = 38/155 (24%), Positives = 65/155 (41%), Gaps = 9/155 (5%)
Query: 141 DKNKIYSFDSAITLIKEAAT---AKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKK 197
K + + AIT I A KF E++++ I L + D+ GS+ LP K
Sbjct: 2 SKLQSDAVKDAITQIVGEAREKKRKFTETVELQIGLKNYDPQKDKRFSGSVKLPHIPRPK 61
Query: 198 IYIAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESM---HIVSSLGK 254
+ + + +QA+ G D + +E L + K+ ++ L + I+ + +
Sbjct: 62 MRVCMLGDAQHVDQAEKMGLDYMDVESLKKMNKNKKLVKKLAKKYHAFLASEAIIKQIPR 121
Query: 255 ILGPKGLMPNIKDGTLNSDI--LTAIKNAKSGQIR 287
+LGP GL K TL S L A N ++
Sbjct: 122 LLGP-GLNKAGKFPTLVSHQESLEAKVNETKATVK 155
>3cjs_B 50S ribosomal protein L11, ribosomal protein L11
methyltransferase; S-adenosyl-L-methionine dependent
methyltransferase; 1.37A {Thermus thermophilus} SCOP:
d.47.1.1 PDB: 3cju_B* 2bcw_A
Length = 72
Score = 90.4 bits (224), Expect = 1e-23
Identities = 42/74 (56%), Positives = 54/74 (72%), Gaps = 2/74 (2%)
Query: 2 VKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITV 61
+KK+ +KLQ+PAGKA P+PP+GPALGQ G NIMEF K FNA T + +PV IT+
Sbjct: 1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMG-DAIVPVEITI 59
Query: 62 FSDKSFTFKKKVTP 75
++D+SFTF K TP
Sbjct: 60 YADRSFTFVTK-TP 72
>1hc8_A Ribosomal protein L11; ribosome, ribosomal RNA, tertiary structure,
RNA-protein; HET: GTP; 2.8A {Bacillus
stearothermophilus} SCOP: a.4.7.1 PDB: 1y39_A* 1aci_A
1fow_A 1fox_A 1foy_A 2fow_A
Length = 76
Score = 85.3 bits (211), Expect = 1e-21
Identities = 39/72 (54%), Positives = 50/72 (69%)
Query: 67 FTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAM 126
FTF K P L+KKAAGI+ GS +P+ +KV + +++EIA +K DL AASI AAM
Sbjct: 1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAM 60
Query: 127 RTIAGSARSMGI 138
R I G+ARSMGI
Sbjct: 61 RMIEGTARSMGI 72
>1qa6_A Ribosomal protein L11; ribosomal RNA, tertiary structur,E
RNA-protein interaction, minor groove binding,
antibiotic binding; 2.80A {Geobacillus
stearothermophilus} SCOP: a.4.7.1 PDB: 1c04_C
Length = 67
Score = 82.1 bits (203), Expect = 2e-20
Identities = 36/67 (53%), Positives = 47/67 (70%)
Query: 72 KVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMRTIAG 131
K P L+KKAAGI+ GS +P+ +KV + +++EIA +K DL AASI AAMR I G
Sbjct: 1 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEG 60
Query: 132 SARSMGI 138
+ARSMGI
Sbjct: 61 TARSMGI 67
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A
2vpl_A
Length = 137
Score = 67.7 bits (166), Expect = 2e-14
Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 4/55 (7%)
Query: 237 DLVIASPESMHIVSSLGKILGPKGLMPNIKDGTLNS----DILTAIKNAKSGQIR 287
+ + E+ H+V L + + + K G ++ + G+I
Sbjct: 17 NKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGGRIE 71
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 58.1 bits (140), Expect = 1e-09
Identities = 58/322 (18%), Positives = 95/322 (29%), Gaps = 111/322 (34%)
Query: 22 PPIGPALGQRGLNIMEFCK-------NFNAQTQGIELGTPIPVIITVF-----SDKSFT- 68
P IG + Q + + K + +G G ++ V S +SF
Sbjct: 239 PLIG--VIQLA-HYVVTAKLLGFTPGELRSYLKGA-TGHSQGLVTAVAIAETDSWESFFV 294
Query: 69 -FKKKVTPVTFLI----KKAAGIQKGSAKPHSDKV----GK---------LTYLQIKEIA 110
+K +T V F I +A D + G LT Q+++
Sbjct: 295 SVRKAIT-VLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
Query: 111 TIKNVDLTAA---SIS----AAMRTIAGSARSMGIIFDKNKIYSFDSAITLIKEAATAKF 163
N L A IS A ++G +S+ Y + L K A +
Sbjct: 354 NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSL---------YGLNLT--LRKAKAPSGL 402
Query: 164 DESIDISIHLNVNIKRSDQIVRGS-----IVLPF------STGKKIYIAAFVPKEKYEQA 212
D+S I S++ ++ S + PF I +
Sbjct: 403 DQS---------RIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAK 453
Query: 213 KIA--------GADIVGMEDLAQKIKSNEVS--CDLVIASP---------ESMHIVSSLG 253
I G+D+ + + + D +I P ++ HI+
Sbjct: 454 DIQIPVYDTFDGSDL-------RVLSGSISERIVDCIIRLPVKWETTTQFKATHILD--- 503
Query: 254 KILGPKG------LMPNIKDGT 269
GP G L KDGT
Sbjct: 504 --FGPGGASGLGVLTHRNKDGT 523
>1wib_A 60S ribosomal protein L12; N-terminal domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, ribosome; NMR {Mus musculus} SCOP:
d.47.1.1
Length = 92
Score = 44.9 bits (106), Expect = 1e-06
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)
Query: 8 FIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSDKSF 67
+ L+ G+ + + P +G GL+ + + T + G I V +T+ ++
Sbjct: 18 VVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTI-QNRQA 75
Query: 68 TFKKKVTPVTFLIKKAAG 85
+ V + L ++G
Sbjct: 76 QI-EVVPSASALSGPSSG 92
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.0 bits (74), Expect = 0.056
Identities = 10/49 (20%), Positives = 14/49 (28%), Gaps = 23/49 (46%)
Query: 2 VKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIE 50
+KK+ +KL A PAL A +E
Sbjct: 22 LKKLQASLKLYAD-DSA-------PALA------------IKAT---ME 47
Score = 29.1 bits (64), Expect = 1.1
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 144 KIYSFDSAITL-IKEAAT 160
K+Y+ DSA L IK AT
Sbjct: 30 KLYADDSAPALAIK--AT 45
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 31.0 bits (69), Expect = 0.53
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 209 YEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPKG--LMPNIK 266
+E A + D ++D+ + I S E D +I S +++ L L K ++
Sbjct: 25 FEDAFVDNFDCKDVQDMPKSILSKEE-IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFV 83
Query: 267 DGTLNSD---ILTAIKN 280
+ L + +++ IK
Sbjct: 84 EEVLRINYKFLMSPIKT 100
>2pbe_A AAD6, aminoglycoside 6-adenylyltransferase; NYSGXRC, aminoglycoside
6-adenyltransferase, PSI-2, structural genomics; 2.65A
{Bacillus subtilis} SCOP: a.160.1.5 d.218.1.13
Length = 294
Score = 27.6 bits (61), Expect = 4.4
Identities = 25/146 (17%), Positives = 57/146 (39%), Gaps = 32/146 (21%)
Query: 96 DKVGKLTYLQIKEIATIKNVDLTAASISAAMRTIAGSARSMGIIFDK----NKIYSFDSA 151
+ +Y+ + E +DLT I A A + + ++ DK N + +
Sbjct: 85 ELGNWFSYIILFEDGN--KLDLTLIPIREAEDYFANNDGLVKVLLDKDSFINYKVTPNDR 142
Query: 152 ITLIKEAATAKFDESID----ISIHLNVNIKRS---------DQIVRGSIVLP------- 191
IK +FD+ + +S ++ + R+ ++IVR +++
Sbjct: 143 QYWIKRPTAREFDDCCNEFWMVSTYVVKGLARNEILFAIDHLNEIVRPNLLRMMAWHIAS 202
Query: 192 -----FSTGKKI-YIAAFVPKEKYEQ 211
FS GK ++ ++ +++E+
Sbjct: 203 QKGYSFSMGKNYKFMKRYLSNKEWEE 228
>2hkt_A Putative transcriptional regulator; structural genomics, APC27974,
YGGD, mannitol operon repressor, MTLR, shigella flexneri
2A 2457T, PSI-2; 2.50A {Shigella flexneri} PDB: 3c8g_D*
3c8g_A* 3c8g_B*
Length = 172
Score = 26.4 bits (58), Expect = 9.1
Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 140 FDKNKIYSFDSAITLIKEAATA-KFDESIDISIHLNVNIKRSDQIVRGSIVL 190
F + + F S + I AT +++ + + R +V+ ++ L
Sbjct: 110 FADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTL 161
>2qlt_A (DL)-glycerol-3-phosphatase 1; APC7326, RHR2P, saccharom
cerevisiae, structural genomics, PSI-2, protein
structure initiative; 1.60A {Saccharomyces cerevisiae}
Length = 275
Score = 26.6 bits (59), Expect = 9.5
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 212 AKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKI 255
K AG IVG+ E CD+++ + ES+ + +
Sbjct: 210 GKAAGCKIVGIATTFDLDFLKEKGCDIIVKNHESIRVGEYNAET 253
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.133 0.365
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,297,639
Number of extensions: 265027
Number of successful extensions: 678
Number of sequences better than 10.0: 1
Number of HSP's gapped: 647
Number of HSP's successfully gapped: 32
Length of query: 289
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 196
Effective length of database: 4,105,140
Effective search space: 804607440
Effective search space used: 804607440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.7 bits)