RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030128
(182 letters)
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_e
Length = 244
Score = 300 bits (771), Expect = e-106
Identities = 11/178 (6%), Positives = 37/178 (20%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFG 60
MASE ++ +++ + E ++ + + ++
Sbjct: 1 MASEAAKVAVPEKVILKRRREEVWAAEKKQKVAAEKIKAAENTKVIYARAEQYAGEYEAQ 60
Query: 61 IRRNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDP 120
+ ++ ++G + L V + T ++ +
Sbjct: 61 DKELVQLKREARMKGGFYVSPEAKPLFVVRIRGINAMHPKTKKILQLLRLRQIFNGVFLK 120
Query: 121 STGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVILNKSQ 178
V Y + + + +
Sbjct: 121 VNKATINMLRRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIPLANNKVIEEGLGKH 178
>2zkr_d 60S ribosomal protein L11; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 178
Score = 296 bits (761), Expect = e-104
Identities = 121/175 (69%), Positives = 147/175 (84%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFG 60
+ + NPMRE++++KL LNI VGESGDRLTRAAKVLEQL+GQTPVFSKARYTVRSFG
Sbjct: 2 AQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFG 61
Query: 61 IRRNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDP 120
IRRNEKIA + TVRG KA ++LE GLKV+EYEL + NFSDTG FGFGIQEHIDLGIKYDP
Sbjct: 62 IRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDP 121
Query: 121 STGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVILN 175
S GIYG+DF+VVL RPG+ + ++R +G +HR++KE+AM+WFQ KY+G+IL
Sbjct: 122 SIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILP 176
>4a17_D L21, RPL11, 60S ribosomal protein L11; eukaryotic ribosome,
ribosome, eukaryotic initiation factor 60S, translation,
large ribosomal subunit; 3.52A {Tetrahymena thermophila}
PDB: 4a1a_D 4a1c_D 4a1e_D
Length = 172
Score = 292 bits (751), Expect = e-103
Identities = 114/173 (65%), Positives = 143/173 (82%), Gaps = 2/173 (1%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFG 60
M +K+ N MRE+K+ KLV+N VGESGD+LT+AAKVL+ LSGQ PVFS+ARYT+RSFG
Sbjct: 1 MTDKKE--NKMREVKIAKLVINCCVGESGDKLTKAAKVLKDLSGQEPVFSRARYTIRSFG 58
Query: 61 IRRNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDP 120
I+RNEK+A +VT+RGDKA +L GLKVKE EL ++NFS+TG FGFGIQEHIDLG+KYDP
Sbjct: 59 IKRNEKMAVHVTIRGDKARDILTRGLKVKEMELRKKNFSNTGNFGFGIQEHIDLGMKYDP 118
Query: 121 STGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVI 173
STGI+GMDF+VVLERPG RV RRRR SRVG ++KE+ + WF+ ++EG +
Sbjct: 119 STGIFGMDFYVVLERPGTRVARRRRATSRVGNNQMISKEECINWFKTEFEGNV 171
>1vq8_D 50S ribosomal protein L5P; 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: d.77.1.1 PDB: 1vq4_D*
1vq5_D* 1vq6_D* 1vq7_D* 1s72_D* 1vq9_D* 1vqk_D* 1vql_D*
1vqm_D* 1vqn_D* 1vqo_D* 1vqp_D* 1yhq_D* 1yi2_D* 1yij_D*
1yit_D* 1yj9_D* 1yjn_D* 1yjw_D* 2otj_D* ...
Length = 177
Score = 261 bits (670), Expect = 9e-91
Identities = 62/175 (35%), Positives = 100/175 (57%), Gaps = 3/175 (1%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFG 60
+ + MRE +++K+V+++ +G G L A +L +++GQ PV +KA+ TV F
Sbjct: 4 ESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGEFD 63
Query: 61 IRRNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDL-GIKYD 119
IR + I VT+R + A + L++ L + EL F DTG F FG++EH + +YD
Sbjct: 64 IREGDPIGAKVTLRDEMAEEFLQTALPLA--ELATSQFDDTGNFSFGVEEHTEFPSQEYD 121
Query: 120 PSTGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVIL 174
PS GIYG+D V L RPGYRV +R + + +HR+ DA+ + + Y+ +
Sbjct: 122 PSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVS 176
>3r8s_F 50S ribosomal protein L5; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3oat_F*
3ofc_F* 3ofz_F* 3ofr_F 3r8t_F 3i1n_F 1vs8_F 1vs6_F
1vt2_F 3i1p_F 3i1r_F 3i1t_F 3i20_F 3i22_F 3iyx_F 3iyy_F
3izt_G* 3izu_G* 3kcr_F 3orb_F* ...
Length = 177
Score = 65.6 bits (161), Expect = 4e-14
Identities = 44/149 (29%), Positives = 70/149 (46%), Gaps = 24/149 (16%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGESGD---RLTRAAKVLEQLSGQTPVFSKARYTVR 57
+ +E ++ M+ +V+K+ LN+ VGE+ L AA L +SGQ P+ +KAR +V
Sbjct: 15 LMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVA 74
Query: 58 SFGIRRNEKIACYVTVRGDKAMQLLE-------------SGLKVKEYELLRRNFSDTGCF 104
F IR+ I C VT+RG++ + E GL K +F G +
Sbjct: 75 GFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK-------SFDGRGNY 127
Query: 105 GFGIQEHIDLG-IKYDPSTGIYGMDFFVV 132
G++E I I YD + G+D +
Sbjct: 128 SMGVREQIIFPEIDYDKVDRVRGLDITIT 156
>1iq4_A 50S ribosomal protein L5; rRNA-binding, RNP motif, RNA binding
PROT; 1.80A {Geobacillus stearothermophilus} SCOP:
d.77.1.1
Length = 179
Score = 64.9 bits (159), Expect = 9e-14
Identities = 36/142 (25%), Positives = 76/142 (53%), Gaps = 10/142 (7%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVR 57
+ S+ + M+ K++K+V+N+ VG+ + L A + L ++GQ PV ++A+ ++
Sbjct: 16 LMSKFNYKSIMQVPKIEKIVINMGVGDAVQNPKALDSAVEELTLIAGQRPVVTRAKKSIA 75
Query: 58 SFGIRRNEKIACYVTVRGDKAMQLLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEH 111
F +R+ I VT+RG++ + L+ + + +++ + +++F G + GI+E
Sbjct: 76 GFRLRQGMPIGAKVTLRGERMYEFLDKLISVSLPRARDFRGVSKKSFDGRGNYTLGIKEQ 135
Query: 112 IDLG-IKYDPSTGIYGMDFFVV 132
+ I YD + GMD +V
Sbjct: 136 LIFPEIDYDKVNKVRGMDIVIV 157
>1mji_A 50S ribosomal protein L5; ribosomal protein - 5S rRNA complex,
ribosome; 2.50A {Thermus thermophilus} SCOP: d.77.1.1
PDB: 2hgj_G 2hgq_G 2hgu_G 2j01_G 2j03_G 2jl6_G 2jl8_G
2v47_G 2v49_G 2wdi_G 2wdj_G 2wdl_G 2wdn_G 2wh2_G 2wh4_G
2wrj_G 2wrl_G 2wro_G 2wrr_G 2x9s_G ...
Length = 182
Score = 64.5 bits (158), Expect = 1e-13
Identities = 38/149 (25%), Positives = 65/149 (43%), Gaps = 24/149 (16%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVR 57
+ N +++K+V+N +GE D L +AA+ L ++GQ P ++A+ ++
Sbjct: 19 LIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSIS 78
Query: 58 SFGIRRNEKIACYVTVRGDKAMQLLE-------------SGLKVKEYELLRRNFSDTGCF 104
+F +R+ I VT+R D+ LE GL +F G +
Sbjct: 79 NFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPN-------SFDGRGNY 131
Query: 105 GFGIQEHIDLG-IKYDPSTGIYGMDFFVV 132
G++E + I YD + GMD VV
Sbjct: 132 NLGLREQLIFPEITYDMVDALRGMDIAVV 160
>3bbo_H Ribosomal protein L5; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 220
Score = 64.2 bits (157), Expect = 3e-13
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 12/143 (8%)
Query: 1 MASEKKLSNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVR 57
+ E SN + KV K+V+N +G+ S + L A L ++GQ PV +KA+ ++
Sbjct: 31 LKEEFSYSNILEVPKVVKIVVNCGIGDASQNAKGLDAAINELALITGQRPVKTKAKTSIA 90
Query: 58 SFGIRRNEKIACYVTVRGDKAM-----QLLESGL-KVKEYE-LLRRNFSDTGCFGFGIQE 110
F +R + VT+RG+ M +L+ L + ++++ + +F G + G +E
Sbjct: 91 GFKVREGMTLGIAVTLRGNL-MYSFLDRLINLALPRTRDFQGVNPNSFDGHGNYSVGFRE 149
Query: 111 HIDLG-IKYDPSTGIYGMDFFVV 132
IK + GMD +
Sbjct: 150 QSVFPEIKPEIVGKARGMDVCIT 172
>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 = 32.1 bits (72), Expect = 0.11
Identities = 27/162 (16%), Positives = 47/162 (29%), Gaps = 49/162 (30%)
Query: 22 NISVGESGDRLTRA------AKVLEQLSGQTP------------VFSKARYTVRSFGIRR 63
+IS+ LT K L+ P + +++ +R
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES---IRDGLATW 344
Query: 64 NEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHID-----LGI-- 116
+ + V DK ++ES L V E R+ F F L +
Sbjct: 345 DN----WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF----PPSAHIPTILLSLIW 396
Query: 117 ----KYDPSTGIYGMDFFVVLERPGYRVGRRRRCKSRVGIQH 154
K D M L + Y + ++ +S + I
Sbjct: 397 FDVIKSDV------MVVVNKLHK--YSLVEKQPKESTISI-P 429
>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 = 28.4 bits (62), Expect = 0.92
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 12/28 (42%)
Query: 65 EKIACYVTVRGDKAMQLLESGLKVKEYE 92
EK +A++ L++ LK+ Y
Sbjct: 18 EK----------QALKKLQASLKL--YA 33
>2bru_C NAD(P) transhydrogenase subunit beta; paramagnetic
transhydrogenase, inner membrane, membrane,
oxidoreductase, transmembrane; HET: NAD NAP; NMR
{Escherichia coli}
Length = 186
Score = 27.9 bits (62), Expect = 1.5
Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 21/129 (16%)
Query: 15 KVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVF----SKARYTVRSFG-IRRNEKIAC 69
+ I+ E+ + L + V+ TP + ++A+Y V R I
Sbjct: 10 QEVGEHREITAEETAELLKNSHSVI-----ITPGYGMAVAQAQYPVAEITEKLRARGINV 64
Query: 70 YVTV-------RGDKAMQLLESGL---KVKEYELLRRNFSDT-GCFGFGIQEHIDLGIKY 118
+ G + L E+ + V E + + +F+DT G + ++ +
Sbjct: 65 RFGIHPVAGRLPGHMNVLLAEAKVPYDIVLEMDEINDDFADTDTVLVIGANDTVNPAAQD 124
Query: 119 DPSTGIYGM 127
DP + I GM
Sbjct: 125 DPKSPIAGM 133
>1d4o_A NADP(H) transhydrogenase; nucleotide-binding fold, protein-NADP(H)
complex, inverted binding of NADP(H), oxidoreductase;
HET: NAP; 1.21A {Bos taurus} SCOP: c.31.1.4
Length = 184
Score = 25.6 bits (56), Expect = 7.8
Identities = 23/130 (17%), Positives = 51/130 (39%), Gaps = 21/130 (16%)
Query: 14 IKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVF----SKARYTVRSFG-IRRNEKIA 68
+++ I++ + D + A ++ TP + +KA+Y + + +
Sbjct: 1 MEISGTHTEINLDNAIDMIREANSII-----ITPGYGLCAAKAQYPIADLVKMLSEQGKK 55
Query: 69 CYVTV-------RGDKAMQLLESGL---KVKEYELLRRNFSDT-GCFGFGIQEHIDLGIK 117
+ G + L E+G+ V E + + +F DT G + ++ +
Sbjct: 56 VRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQ 115
Query: 118 YDPSTGIYGM 127
DP++ I GM
Sbjct: 116 EDPNSIIAGM 125
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
0.321 0.138 0.398
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,833,644
Number of extensions: 171608
Number of successful extensions: 377
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 15
Length of query: 182
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 94
Effective length of database: 4,244,745
Effective search space: 399006030
Effective search space used: 399006030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)