RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029665
(190 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 = 298 bits (766), Expect = e-105
Identities = 8/176 (4%), Positives = 35/176 (19%)
Query: 11 SDKKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIR 70
S+ ++ +++ + E ++ + + ++ +
Sbjct: 3 SEAAKVAVPEKVILKRRREEVWAAEKKQKVAAEKIKAAENTKVIYARAEQYAGEYEAQDK 62
Query: 71 RNEKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPST 130
++ ++G + L V + T ++ +
Sbjct: 63 ELVQLKREARMKGGFYVSPEAKPLFVVRIRGINAMHPKTKKILQLLRLRQIFNGVFLKVN 122
Query: 131 GIYGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVILNKSQ 186
V Y + + + +
Sbjct: 123 KATINMLRRVEPYVTYGYPNLKSVRELIYKRGYGKLNKQRIPLANNKVIEEGLGKH 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 (759), Expect = e-104
Identities = 121/170 (71%), Positives = 146/170 (85%)
Query: 14 KLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNE 73
+ NPMRE++++KL LNI VGESGDRLTRAAKVLEQL+GQTPVFSKARYTVRSFGIRRNE
Sbjct: 7 EKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNE 66
Query: 74 KIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPSTGIY 133
KIA + TVRG KA ++LE GLKV+EYEL + NFSDTG FGFGIQEHIDLGIKYDPS GIY
Sbjct: 67 KIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIY 126
Query: 134 GMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVILN 183
G+DF+VVL RPG+ + ++R +G +HR++KE+AM+WFQ KY+G+IL
Sbjct: 127 GLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILP 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 = 293 bits (752), Expect = e-103
Identities = 113/169 (66%), Positives = 140/169 (82%)
Query: 13 KKLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRN 72
K N MRE+K+ KLV+N VGESGD+LT+AAKVL+ LSGQ PVFS+ARYT+RSFGI+RN
Sbjct: 3 DKKENKMREVKIAKLVINCCVGESGDKLTKAAKVLKDLSGQEPVFSRARYTIRSFGIKRN 62
Query: 73 EKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDLGIKYDPSTGI 132
EK+A +VT+RGDKA +L GLKVKE EL ++NFS+TG FGFGIQEHIDLG+KYDPSTGI
Sbjct: 63 EKMAVHVTIRGDKARDILTRGLKVKEMELRKKNFSNTGNFGFGIQEHIDLGMKYDPSTGI 122
Query: 133 YGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVI 181
+GMDF+VVLERPG RV RRRR SRVG ++KE+ + WF+ ++EG +
Sbjct: 123 FGMDFYVVLERPGTRVARRRRATSRVGNNQMISKEECINWFKTEFEGNV 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 (668), Expect = 2e-90
Identities = 62/170 (36%), Positives = 99/170 (58%), Gaps = 3/170 (1%)
Query: 14 KLSNPMREIKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRNE 73
+ MRE +++K+V+++ +G G L A +L +++GQ PV +KA+ TV F IR +
Sbjct: 9 GDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGEFDIREGD 68
Query: 74 KIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHIDL-GIKYDPSTGI 132
I VT+R + A + L++ L + EL F DTG F FG++EH + +YDPS GI
Sbjct: 69 PIGAKVTLRDEMAEEFLQTALPLA--ELATSQFDDTGNFSFGVEEHTEFPSQEYDPSIGI 126
Query: 133 YGMDFFVVLERPGYRVGRRRRCKSRVGIQHRVTKEDAMKWFQVKYEGVIL 182
YG+D V L RPGYRV +R + + +HR+ DA+ + + Y+ +
Sbjct: 127 YGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVS 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 = 6e-14
Identities = 43/144 (29%), Positives = 67/144 (46%), Gaps = 24/144 (16%)
Query: 14 KLSNPMREIKVQKLVLNISVGESGD---RLTRAAKVLEQLSGQTPVFSKARYTVRSFGIR 70
++ M+ +V+K+ LN+ VGE+ L AA L +SGQ P+ +KAR +V F IR
Sbjct: 20 NYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIR 79
Query: 71 RNEKIACYVTVRGDKAMQLLE-------------SGLKVKEYELLRRNFSDTGCFGFGIQ 117
+ I C VT+RG++ + E GL K +F G + G++
Sbjct: 80 QGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK-------SFDGRGNYSMGVR 132
Query: 118 EHIDLG-IKYDPSTGIYGMDFFVV 140
E I I YD + G+D +
Sbjct: 133 EQIIFPEIDYDKVDRVRGLDITIT 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 = 1e-13
Identities = 35/135 (25%), Positives = 73/135 (54%), Gaps = 10/135 (7%)
Query: 16 SNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRN 72
+ M+ K++K+V+N+ VG+ + L A + L ++GQ PV ++A+ ++ F +R+
Sbjct: 23 KSIMQVPKIEKIVINMGVGDAVQNPKALDSAVEELTLIAGQRPVVTRAKKSIAGFRLRQG 82
Query: 73 EKIACYVTVRGDKAMQLLESGL-----KVKEYE-LLRRNFSDTGCFGFGIQEHIDLG-IK 125
I VT+RG++ + L+ + + +++ + +++F G + GI+E + I
Sbjct: 83 MPIGAKVTLRGERMYEFLDKLISVSLPRARDFRGVSKKSFDGRGNYTLGIKEQLIFPEID 142
Query: 126 YDPSTGIYGMDFFVV 140
YD + GMD +V
Sbjct: 143 YDKVNKVRGMDIVIV 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 = 2e-13
Identities = 38/142 (26%), Positives = 64/142 (45%), Gaps = 24/142 (16%)
Query: 16 SNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRN 72
N +++K+V+N +GE D L +AA+ L ++GQ P ++A+ ++ +F +R+
Sbjct: 26 QNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKG 85
Query: 73 EKIACYVTVRGDKAMQLLE-------------SGLKVKEYELLRRNFSDTGCFGFGIQEH 119
I VT+R D+ LE GL +F G + G++E
Sbjct: 86 MPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPN-------SFDGRGNYNLGLREQ 138
Query: 120 IDLG-IKYDPSTGIYGMDFFVV 140
+ I YD + GMD VV
Sbjct: 139 LIFPEITYDMVDALRGMDIAVV 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 = 64.6 bits (158), Expect = 3e-13
Identities = 36/136 (26%), Positives = 65/136 (47%), Gaps = 12/136 (8%)
Query: 16 SNPMREIKVQKLVLNISVGE-SGDR--LTRAAKVLEQLSGQTPVFSKARYTVRSFGIRRN 72
SN + KV K+V+N +G+ S + L A L ++GQ PV +KA+ ++ F +R
Sbjct: 38 SNILEVPKVVKIVVNCGIGDASQNAKGLDAAINELALITGQRPVKTKAKTSIAGFKVREG 97
Query: 73 EKIACYVTVRGDKAM-----QLLESGL-KVKEYE-LLRRNFSDTGCFGFGIQEHIDLG-I 124
+ VT+RG+ M +L+ L + ++++ + +F G + G +E I
Sbjct: 98 MTLGIAVTLRGNL-MYSFLDRLINLALPRTRDFQGVNPNSFDGHGNYSVGFREQSVFPEI 156
Query: 125 KYDPSTGIYGMDFFVV 140
K + GMD +
Sbjct: 157 KPEIVGKARGMDVCIT 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 = 34.8 bits (79), Expect = 0.014
Identities = 31/205 (15%), Positives = 51/205 (24%), Gaps = 72/205 (35%)
Query: 2 VWLFMVNQASDKKLSNPMREIKVQKLVL--NISVGESGDRLTRAAKVLEQLS-GQTP--- 55
V + K N + + L+ V + T L+ S TP
Sbjct: 253 VQ--------NAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 56 --VFSKARYTVRSFGIRRNE--KIAC-----------------------YVTVRGDKAMQ 88
+ K R + + + V DK
Sbjct: 304 KSLLLKY------LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 89 LLESGLKVKEYELLRRNFSDTGCFGFGIQEHID-----LGI------KYDPSTGIYGMDF 137
++ES L V E R+ F F L + K D M
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVF----PPSAHIPTILLSLIWFDVIKSDV------MVV 407
Query: 138 FVVLERPGYRVGRRRRCKSRVGIQH 162
L + Y + ++ +S + I
Sbjct: 408 VNKLHK--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 = 28.8 bits (63), Expect = 0.72
Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 19/49 (38%)
Query: 73 EKIACYVTVRGDKAMQLLESGLKVKEYELLRRNFSDTGCFGFGIQEHID 121
EK +A++ L++ LK+ Y D+ I+ ++
Sbjct: 18 EK----------QALKKLQASLKL--YA------DDSAP-ALAIKATME 47
>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 = 1.6
Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 21/129 (16%)
Query: 23 KVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVF----SKARYTVRSFG-IRRNEKIAC 77
+ I+ E+ + L + V+ TP + ++A+Y V R I
Sbjct: 10 QEVGEHREITAEETAELLKNSHSVI-----ITPGYGMAVAQAQYPVAEITEKLRARGINV 64
Query: 78 YVTV-------RGDKAMQLLESGL---KVKEYELLRRNFSDT-GCFGFGIQEHIDLGIKY 126
+ G + L E+ + V E + + +F+DT G + ++ +
Sbjct: 65 RFGIHPVAGRLPGHMNVLLAEAKVPYDIVLEMDEINDDFADTDTVLVIGANDTVNPAAQD 124
Query: 127 DPSTGIYGM 135
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 = 8.6
Identities = 23/130 (17%), Positives = 51/130 (39%), Gaps = 21/130 (16%)
Query: 22 IKVQKLVLNISVGESGDRLTRAAKVLEQLSGQTPVF----SKARYTVRSFG-IRRNEKIA 76
+++ I++ + D + A ++ TP + +KA+Y + + +
Sbjct: 1 MEISGTHTEINLDNAIDMIREANSII-----ITPGYGLCAAKAQYPIADLVKMLSEQGKK 55
Query: 77 CYVTV-------RGDKAMQLLESGL---KVKEYELLRRNFSDT-GCFGFGIQEHIDLGIK 125
+ G + L E+G+ V E + + +F DT G + ++ +
Sbjct: 56 VRFGIHPVAGRMPGQLNVLLAEAGVPYDIVLEMDEINHDFPDTDLVLVIGANDTVNSAAQ 115
Query: 126 YDPSTGIYGM 135
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
0.323 0.139 0.406
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: 2,942,979
Number of extensions: 176392
Number of successful extensions: 378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 14
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
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)